@article{Kinlan2003, abstract = {Studies in terrestrial systems suggest that long-distance propagule dispersal is. important for landscape pattern and dynamics, but largely inconsequential for local demography. By contrast, in marine systems, dispersal at regional scales may drive local dynamics, because many species may have large mean dispersal distances. To assess variation in marine dispersal scales, we estimated mean dispersal distances from genetic isolation-by-distance slopes. Estimates ranged widely, from a few meters to hundreds of kilometers. Dispersal differed among taxonomic groups (macroalgae, invertebrates, and fish) and among species in different functional groups (e.g., producers and herbivores). Differences in dispersal scale have important implications for marine community dynamics, reserve design, responses to large-scale perturbations, and evolution of interacting species.To place genetic estimates of marine dispersal in context, we compared them to other measures of dispersal in the ocean and to estimates of dispersal on land. Maximum scales of dispersal by sedentary marine species exceeded maximum estimates of terrestrial plant dispersal by at least one to two orders of magnitude. Direct and genetic estimates of terrestrial plant dispersal were comparable to estimates of marine plant dispersal. Rates of marine macroalgal range expansion, however, far exceeded spread rates of terrestrial plants. Terrestrial plant spread rates were more similar to those of short-dispersing marine organisms that lack secondary dispersal by drifting adults. Genetic estimates of dispersal by different functional groups suggest that herbivores typically disperse much farther than their plant resources both on land and in the sea, although the timing, frequency, and consequences of dispersal may differ in the two systems. Terrestrial herbivores have more flexible dispersal behavior than marine organisms that disperse each generation by planktonic transport of larvae.Our results validate some long-standing views about the greater dispersal potential of species in the ocean, but also highlight the extreme heterogeneity in dispersal scale among marine species. As a result, development of a community perspective on marine connectivity will require consideration of multiple dispersal mechanisms and scales.}, author = {Kinlan, Brian P. and Gaines, Steven D.}, doi = {10.1890/01-0622}, file = {:Users/eastonwhite/Desktop/Research/mpa-disturbances/literature/2003 Kinlan and Gaines - propagule dispersal in marine and terrestrial environments.pdf:pdf}, issn = {0012-9658}, journal = {Ecology}, keywords = {benthic invertebrates,connectivity,demersal fish,design,dispersal scale,functional groups,genetic structure,invasion,isolation distance,long distance dispersal,macroalgae,marine reserve,marine terrestrial comparisons}, number = {8}, pages = {2007--2020}, title = {{Propagule dispersal in marine and terrestrial environments: a community perspective}}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed{\&}cmd=Retrieve{\&}dopt=AbstractPlus{\&}list{\_}uids=000185073100008}, volume = {84}, year = {2003} } @article{Barnett2014, abstract = {{\textcopyright} 2015, National Research Council of Canada. All rights reserved. Climate change has caused shifts in seasonal timing of climatic events such as the onset of spring upwelling, which can lead to temporal mismatches between fish spawning and production of zoopklankton prey. Fishing may exacerbate mismatches through age truncation, particularly when offspring survival is dependent on maternal age, but no-take reserves or harvest reductions might buffer this effect. To quantify the potential for management to buffer synergistic interactions between fishing and climate, we developed a dynamic population model of a harvested species where larval survival depended on spring transition timing and maternal age. We applied this model to rockfishes (Sebastes spp.) after verifying empirically that spring transition timing affects their recruitment success. We found that yield and persistence changed more with maternal-agedependent larval provisioning than maternal-age-dependent spawning timing across a range of spring transition timings, especially with environmental stochasticity. Either implementing reserves or reducing fishing can mitigate impacts on larval survival, but reserves convey the added benefit of decreased sensitivity of yield and persistence to fishing. However, reserve buffering effects decreased with the inclusion of environmental stochasticity.}, author = {Barnett, Lewis A.K. and Baskett, Marissa L. and Botsford, Louis W.}, doi = {10.1139/cjfas-2014-0243}, file = {:Users/eastonwhite/Desktop/Research/mpa-disturbances/literature/2015 Barnett - reserves and temporal variability.pdf:pdf}, issn = {0706-652X}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, number = {3}, pages = {376--389}, title = {{Quantifying the potential for marine reserves or harvest reductions to buffer temporal mismatches caused by climate change}}, volume = {72}, year = {2014} } @article{Cabral2017a, abstract = {{\textcopyright} 2016 by the Ecological Society of America. Marine spatial planning (MSP) is increasingly utilized to sustainably manage ocean uses. Marine protected areas (MPAs), a form of spatial management in which parts of the ocean are regulated to fishing, are now a common tool in MSP for conserving marine biodiversity and managing fisheries. However, the use of MPAs in MSP often neglects, or simplifies, the redistribution of fishing and non-fishing activities inside and outside of MPAs following their implementation. This redistribution of effort can have important implications for effective MSP. Using long-term (14 yr) aerial surveys of boats at the California Channel Islands, we examined the spatial redistribution of fishing and non-fishing activities and their drivers following MPA establishment. Our data represent 6 yr of information before the implementation of an MPA network and 8 yr after implementation. Different types of boats responded in different ways to the closures, ranging from behaviors by commercial dive boats that support the hypothesis of fishing-the-line, to behaviors by urchin, sport fishing, and recreational boats that support the theory of ideal free distribution. Additionally, we found that boats engaged in recreational activities targeted areas that are sheltered from large waves and located near their home ports, while boats engaged in fishing activities also avoided high wave areas but were not constrained by the distance to their home ports. We did not observe the expected pattern of effort concentration near MPA borders for some boat types; this can be explained by the habitat preference of certain activities (for some activities, the desired habitat attributes are not inside the MPAs), species' biology (species such as urchins where the MPA benefit would likely come from larval export rather than adult spillover), or policy-infraction avoidance. The diversity of boat responses reveals variance from the usual simplified assumption that all extractive boats respond similarly to MPA establishment. Our work is the first empirical study to analyze the response of both commercial and recreational boats to closure. Our results will inform MSP in better accounting for effort redistribution by ocean users in response to the implementation of MPAs and other closures.}, author = {Cabral, Reniel B. and Gaines, Steven D. and Johnson, Brett A. and Bell, Tom W. and White, Crow}, doi = {10.1002/eap.1446}, file = {:Users/eastonwhite/Desktop/Research/mpa-disturbances/literature/2017 Cabral et al - redistributino of fishing effort after MPA.pdf:pdf}, issn = {19395582}, journal = {Ecological Applications}, keywords = {California Channel Islands,ecosystem-based management,fisheries management,fishing behavior,fishing strategy,fishing-the-line,ideal free distribution,marine protected area,marine protected area network,marine reserve,marine spatial planning}, number = {2}, pages = {416--428}, title = {{Drivers of redistribution of fishing and non-fishing effort after the implementation of a marine protected area network:}}, volume = {27}, year = {2017} } @article{Shchepetkin2005, abstract = {The purpose of this study is to find a combination of optimal numerical algorithms for time-stepping and mode-splitting suitable for a high-resolution, free-surface, terrain-following coordinate oceanic model. Due to mathematical feedback between the baroclinic momentum and tracer equations and, similarly, between the barotropic momentum and continuity equations, it is advantageous to treat both modes so that, after a time step for the momentum equation, the computed velocities participate immediately in the computation of tracers and continuity, and vice versa, rather than advancing all equations for one time step simultaneously. This leads to a new family of time-stepping algorithms that combine forward-backward feedback with the best known synchronous algorithms, allowing an increased time step due to the enhanced internal stability without sacrificing its accuracy. Based on these algorithms we design a split-explicit hydrodynamic kernel for a realistic oceanic model, which addresses multiple numerical issues associated with mode splitting. This kernel utilizes consistent temporal averaging of the barotropic mode via a specially designed filter function to guarantee both exact conservation and constancy preservation properties for tracers and yields more accurate (up to second-order), resolved barotropic processes, while preventing aliasing of unresolved barotropic signals into the slow baroclinic motions. It has a more accurate mode-splitting due to redefined barotropic pressure-gradient terms to account for the local variations in density field, while maintaining the computational efficiency of a split model. It is naturally compatible with a variety of centered and upstream-biased high-order advection algorithms, and helps to mitigate computational cost of expensive physical parameterization of mixing processes and submodels. {\textcopyright} 2004 Elsevier Ltd. All rights reserved.}, author = {Shchepetkin, Alexander F. and McWilliams, James C.}, doi = {10.1016/j.ocemod.2004.08.002}, file = {:Users/eastonwhite/Desktop/Research/mpa-disturbances/literature/2005 Shchepetkin - regional oceanic modeling systems.pdf:pdf}, issn = {14635003}, journal = {Ocean Modelling}, number = {4}, pages = {347--404}, title = {{The regional oceanic modeling system (ROMS): A split-explicit, free-surface, topography-following-coordinate oceanic model}}, volume = {9}, year = {2005} } @article{Botsford2015, author = {Botsford, Louis W. and Holland, Matthew D. and Field, John C. and Hastings, Alan}, doi = {10.1093/icesjms/fst176}, file = {:Users/eastonwhite/Desktop/Research/mpa-disturbances/literature/2014 Botsford et al - cohort resonance.pdf:pdf}, isbn = {1206616369}, issn = {1206616369}, journal = {Marine science}, keywords = {fisheries management,marine science,plankton dynamics,turbulence}, pages = {1--7}, title = {{Cohort resonance: a significant component of fluctuations in recruitment, egg production, and catch of fished populations}}, volume = {no hay}, year = {2015} } @article{White2018b, abstract = {Seasonality is an important feature of essentially all natural systems but the consequences of seasonality have been vastly underappreciated. Early work emphasized the role of seasonality in driving cyclic population dynamics, but the consequences of seasonality for ecological processes are far broader. In ecological systems, seasonality may include variations in temperature, precipitation, or other processes. Seasonality is typically not explicitly included in either empirical or theoretical studies. However, many aspects of ecological dynamics can only be understood when seasonality is included, ranging from the oscillations in the incidence of childhood diseases to the coexistence of species. Further, studies of phenology and global climate change only make sense in the context of seasonal dynamics. Our goal is to outline what is now known about seasonality and to set the stage for future efforts. We review the effects of seasonality on ecological systems in both laboratory and field settings. We then discuss approaches for incorporating seasonality in mathematical models, including Floquet theory. We argue, however, that these tools are still limited in scope and more approaches need to be developed. We demonstrate the range of impacts of seasonality on ecological systems and show the necessity of incorporating seasonality to understand ecological dynamics.}, author = {White, Easton R and Hastings, Alan}, doi = {10.7287/peerj.preprints.27235v1}, file = {:Users/eastonwhite/Desktop/Research/mpa-disturbances/literature/2018 White Hastings - seasonality ecology review.pdf:pdf}, issn = {2167-9843}, journal = {PeerJ Preprints}, keywords = {annual cycle,phenology,seasonal forcing,seasonal variability,temporal variability,timescales}, number = {Preprint}, pages = {e27235v1}, title = {{Seasonality in ecology: Progress and prospects in theory}}, url = {https://doi.org/10.7287/peerj.preprints.27235v1}, volume = {6}, year = {2018} } @article{Oliver2018, abstract = {{\textcopyright} 2018 The Author(s). Heatwaves are important climatic extremes in atmospheric and oceanic systems that can have devastating and long-term impacts on ecosystems, with subsequent socioeconomic consequences. Recent prominent marine heatwaves have attracted considerable scientific and public interest. Despite this, a comprehensive assessment of how these ocean temperature extremes have been changing globally is missing. Using a range of ocean temperature data including global records of daily satellite observations, daily in situ measurements and gridded monthly in situ-based data sets, we identify significant increases in marine heatwaves over the past century. We find that from 1925 to 2016, global average marine heatwave frequency and duration increased by 34{\%} and 17{\%}, respectively, resulting in a 54{\%} increase in annual marine heatwave days globally. Importantly, these trends can largely be explained by increases in mean ocean temperatures, suggesting that we can expect further increases in marine heatwave days under continued global warming.}, author = {Oliver, Eric C.J. and Donat, Markus G. and Burrows, Michael T. and Moore, Pippa J. and Smale, Dan A. and Alexander, Lisa V. and Benthuysen, Jessica A. and Feng, Ming and {Sen Gupta}, Alex and Hobday, Alistair J. and Holbrook, Neil J. and Perkins-Kirkpatrick, Sarah E. and Scannell, Hillary A. and Straub, Sandra C. and Wernberg, Thomas}, doi = {10.1038/s41467-018-03732-9}, file = {:Users/eastonwhite/Desktop/Research/mpa-disturbances/literature/2015 Oliver et al - longer and more frequent marine heatwaves.pdf:pdf}, issn = {20411723}, journal = {Nature Communications}, number = {1}, pages = {1--12}, publisher = {Springer US}, title = {{Longer and more frequent marine heatwaves over the past century}}, url = {http://dx.doi.org/10.1038/s41467-018-03732-9}, volume = {9}, year = {2018} } @article{Baker-Medard2019, author = {Baker-M{\'{e}}dard, Merrill and Allnutt, Thomas F. and Baskett, Marissa L. and Watson, Reg A. and Lagabrielle, Erwinn and Kremen, Claire}, doi = {10.1016/j.ocecoaman.2019.104824}, file = {:Users/eastonwhite/Desktop/1-s2.0-S0964569118309840-main.pdf:pdf}, issn = {09645691}, journal = {Ocean {\&} Coastal Management}, keywords = {Fisheries,Madagascar,Marine conservation,Marine reserves,Marxan,Spatial planning}, number = {April}, pages = {104824}, publisher = {Elsevier}, title = {{Rethinking spatial costs and benefits of fisheries in marine conservation}}, url = {https://linkinghub.elsevier.com/retrieve/pii/S0964569118309840}, volume = {178}, year = {2019} } @article{Leslie2015, abstract = {Environmental governance is more effective when the scales of ecological processes are well matched with the human institutions charged with managing human-environment interactions. The social-ecological systems (SESs) framework provides guidance on how to assess the social and ecological dimensions that contribute to sustainable resource use and management, but rarely if ever has been operationalized for multiple localities in a spatially explicit, quantitative manner. Here, we use the case of small-scale fisheries in Baja California Sur, Mexico, to identify distinct SES regions and test key aspects of coupled SESs theory. Regions that exhibit greater potential for social-ecological sustainability in one dimension do not necessarily exhibit it in others, highlighting the importance of integrative, coupled system analyses when implementing spatial planning and other ecosystem-based strategies.}, author = {Leslie, Heather M and Basurto, Xavier and Nenadovic, Mateja and Sievanen, Leila and Cavanaugh, Kyle C and Cota-Nieto, Juan Jos{\'{e}} and Erisman, Brad E and Finkbeiner, Elena and Hinojosa-Arango, Gustavo and Moreno-B{\'{a}}ez, Marcia and Nagavarapu, Sriniketh and Reddy, Sheila M W and S{\'{a}}nchez-Rodr{\'{i}}guez, Alexandra and Siegel, Katherine and Ulibarria-Valenzuela, Jos{\'{e}} Juan and Weaver, Amy Hudson and Aburto-Oropeza, Octavio}, doi = {10.1073/pnas.1414640112}, file = {:Users/eastonwhite/Desktop/heather{\_}leslie{\_}work/pnas.1414640112.sapp.pdf:pdf;:Users/eastonwhite/Desktop/heather{\_}leslie{\_}work/2015 Leslie et al - operationalizing social-ecological systems framework.pdf:pdf}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {19}, pages = {5979--84}, pmid = {25918372}, title = {{Operationalizing the social-ecological systems framework to assess sustainability.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25918372{\%}0Ahttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC4434725}, volume = {112}, year = {2015} } @article{Leslie2009, abstract = {Key elements of the rapidly expanding field of ecosystem-based management include: (a) understanding connections among social and ecological systems and (b) developing analytical approaches to inform the necessary trade-offs among ecosystemservices and human activities in coastal and marine areas. To address these needs, we investigate the impacts of multiple economic sectors on the marine ecosystem and dependent human community in the Gulf of California with an ecological-economic model. We focus on the spotted rose snapper (Lutjanus guttatus), an economically important species targeted concurrently by the nearshore artisanal fleet, the sportfishing fleet, and by the industrial shrimp fleet as bycatch. Economic returns to the local community are driven by the artisanal fishery catch and the number of tourists who engage in the sportsfishery, and these variables are in turn impacted by fish abundance. We find that the coexistence of the two sectors (and production of both seafood and tourism services) creates stability in key elements of the coupled systems. When the coupled systems are perturbed by changes in exploitation and climate variability, the artisanal fishery responds more rapidly and to a greater degree than the sportsfishery to shifts in the fish population. Our results suggest that vital components of coupled systems may well respond differently to climate variability or other perturbations, and that management strategies should be developed with this in mind. Models like ours can facilitate the development and testing of hypotheses about the form and strength of interactions between ecosystems, services, and the human communities that rely on them.}, annote = {- study how El NIno events affect fish reproductivve output and then ultimately the entire system}, author = {Leslie, Heather M. and Schl{\"{u}}ter, Maja and Cudney-Bueno, Richard and Levin, Simon A.}, doi = {10.1007/s11284-009-0603-8}, file = {:Users/eastonwhite/Desktop/heather{\_}leslie{\_}work/2009 Leslie - Baja coupled systems and perturbations.pdf:pdf}, issn = {09123814}, journal = {Ecological Research}, keywords = {Ecological-economics,Ecosystem-based management,Fisheries,Marine ecosystem services,Modeling,Social-ecological system,Trade-offs}, number = {3}, pages = {505--519}, title = {{Modeling responses of coupled social-ecological systems of the Gulf of California to anthropogenic and natural perturbations}}, volume = {24}, year = {2009} } @article{., author = {.}, journal = {Materials and methods are available as supplementary materials at the Science website}, title = {.} } @article{Epanchin-Niell2010, abstract = {We review studies that address economically optimal control of established invasive species. We describe three important components for determining optimal invasion management: invasion dynamics, costs of control efforts and a monetary measure of invasion damages. We find that a management objective that explicitly considers both costs and damages is most appropriate for determining economically optimal strategies, but also leads to large challenges due to uncertainty in components of the management problem. To address uncertainty, some studies have included stochasticity in their models; others have quantified the value of information or focused on decision-making with limited information. Our synthesis shows how invasion characteristics, such as costs, damages, pattern of spread and invasion and landscape size, affect optimal control strategies and goals in systematic ways. We find that even for simple questions, such as whether control should be applied at the centre of an invasion or to satellite patches, the answer depends on the details of a particular invasion. Future work should seek to better quantify key components of this problem, determine best management in the face of limited information, improve understanding of spatial aspects of invasion control and design approaches to improve the feasibility of achieving regional control goals.}, author = {Epanchin-Niell, Rebecca S. and Hastings, Alan}, doi = {10.1111/j.1461-0248.2010.01440.x}, file = {:Users/eastonwhite/Desktop/Epanchin-Niell{\_}et{\_}al-2010-Ecology{\_}Letters.pdf:pdf}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Alien species,Bioeconomics,Biological invasions,Noxious species,Optimal control,Spatial spread,Spatial-dynamics}, number = {4}, pages = {528--541}, title = {{Controlling established invaders: Integrating economics and spread dynamics to determine optimal management}}, volume = {13}, year = {2010} } @article{Rauschert2017, abstract = {{\textcopyright} 2017, The Society of Population Ecology and Springer Japan. As the number of biological invasions increases, interactions between different invasive species will become increasingly important. Several studies have examined facilitative invader–invader interactions, potentially leading to invasional meltdown. However, if invader interactions are negative, invasional interference may lead to lower invader abundance and spread. To explore this possibility, we develop models of two competing invaders. A landscape simulation model examines the patterns created by two such species invading into the same region. We then apply the model to a case study of Carduus nutans L. and C. acanthoides L., two economically important invasive weeds that exhibit a spatially segregated distribution in central Pennsylvania, USA. The results of these spatially-explicit models are generally consistent with the results of classic Lotka–Volterra competition models, with widespread coexistence predicted if interspecific effects are weaker than intraspecific effects for both species. However, spatial segregation of the two species (with lower net densities and no further spread) may arise, particularly when interspecific competition is stronger than intraspecific competition. A moving area of overlap may result when one species is a superior competitor. In the Carduus system, our model suggests that invasional interference will lead to lower levels of each species when together, but a similar net level of thistle invasion due to the similarity of intra- and interspecific competition. Thus, invasional interference may have important implications for the distribution and management of invasive species.}, author = {Rauschert, Emily Sofia Jalics and Shea, Katriona}, doi = {10.1007/s10144-016-0569-7}, file = {:Users/eastonwhite/Desktop/Rauschert-Shea2017{\_}Article{\_}CompetitionBetweenSimilarInvas.pdf:pdf}, isbn = {0123456789}, issn = {14383896}, journal = {Population Ecology}, keywords = {Carduus,Invader interactions,Plant competition,Plant invasion,Spatial segregation}, number = {1}, pages = {79--88}, publisher = {Springer Japan}, title = {{Competition between similar invasive species: modeling invasional interference across a landscape}}, volume = {59}, year = {2017} } @article{Faillace2017, abstract = {Evolution has the capacity to alter the course of biological invasions, although such changes remain mostly unexplored by experiments. Integrating evolution into studies of invasions is important, because species traits can potentially evolve in ways that either moderate or exacerbate the impacts of invasions. We have assessed whether species evolved during experimental invasions by comparing the performance of founder populations and their potentially evolved descendants in communities of ciliates and rotifers. Residents (analogous to native species) that have previous experience with invaders consistently reduced the performance of naive invaders, supporting the emergence of increased biotic resistance as one consequence of evolution during invasions. Experienced invaders exhibited both increased and decreased performance depending on the invader species considered. Through its influence on performance and species abundance, evolution also changed community composition during the course of invasions. The idiosyncratic patterns of evolutionary changes in invading and resident species complicate predictions about the long-term consequences of invasions from initial post-invasion dynamics.}, author = {Faillace, Cara A. and Morin, Peter J.}, doi = {10.1038/s41559-017-0117}, journal = {Nature Ecology {\&} Evolution}, title = {{Evolution alters the consequences of invasions in experimental communities}}, year = {2017} } @article{Buckley2014, author = {Buckley, By Yvonne M and Han, Yi}, file = {:Users/eastonwhite/Desktop/975.full.pdf:pdf}, journal = {Science}, number = {6187}, pages = {975--977}, title = {{Managing the side effects of invasion control}}, volume = {344}, year = {2014} } @article{Vahsen2018, author = {Vahsen, Megan L and Shea, Katriona and Hovis, Ciara L and Teller, Brittany J and Hufbauer, Ruth A}, doi = {10.1007/s10530-018-1713-4}, file = {:Users/eastonwhite/Desktop/Vahsen2018{\_}Article{\_}PriorAdaptationDiversityAndInt.pdf:pdf}, isbn = {0123456789}, issn = {1573-1464}, journal = {Biological Invasions}, keywords = {Adaptation,Colonization,Genetic diversity,Invasive species,Propagule pressure,department of biology,genetic diversity {\'{a}} invasive,hovis {\'{a}} b,j,k,l,propagule pressure {\'{a}} colonization,shea {\'{a}} c,species {\'{a}} adaptation,teller,the pennsylvania state,{\'{a}}}, number = {9}, pages = {2451--2459}, publisher = {Springer International Publishing}, title = {{Prior adaptation, diversity, and introduction frequency mediate the positive relationship between propagule pressure and the initial success of founding populations}}, url = {https://doi.org/10.1007/s10530-018-1713-4}, volume = {20}, year = {2018} } @article{Buckley2017, author = {Buckley, Yvonne M}, doi = {10.1073/pnas.1703510114}, file = {:Users/eastonwhite/Desktop/2017 Buckley and Csergo - predicting invasion winners and losers under climate change.pdf:pdf}, journal = {Proceedings of the National Academy of Sciences}, number = {16}, pages = {4040--4041}, title = {{Predicting invasion winners and losers under climate change}}, volume = {114}, year = {2017} } @article{Firn2015, author = {Firn, Jennifer and Maggini, Ramona and Chades, Iadine and Nicol, Sam and Walters, Belinda and Reeson, Andy and Martin, Tara G. and Possingham, Hugh P. and Pichancourt, Jen-Baptiste and Ponce-Reyes, Rocio and Carwardine, Josie}, doi = {10.1111/gcb.13034}, file = {:Users/eastonwhite/Desktop/2015 Firn et al - priority threat management of invasive species.pdf:pdf}, journal = {Global Change Biology}, keywords = {adaptive management,benefit analyses,climate adaptation,climate variability,complementarity,decision theory,ecological cost-,epbc act 1999,ipcc rcp6 scenario,iucn red list,maxent,multi-objective optimization,synergistic threats}, pages = {3917--3930}, title = {{Priority threat management of invasive animals to protect biodiversity under climate change}}, volume = {21}, year = {2015} } @article{Urban2016, author = {Urban, M. C. and Bocedi, G. and Hendry, A. P. and Mihoub, J.-B. and Pe'er, G. and Singer, A. and Bridle, J. R. and Crozier, L. G. and Meester, L. De and Godsoe, W. and Gonzalez, A. and Hellmann, J. J. and Holt, R. D. and Huth, A. and Johst, K. and Krug, C. B. and Leadley, P. W. and Palmer, S. C. F. and Pantel, J. H. and Schmitz, A. and Zollner, P. A. and Travis, J. M. J.}, doi = {10.1126/science.aad8466}, file = {:Users/eastonwhite/Desktop/2016 Urban et al - improving the forecast for biodiversity under climate change.pdf:pdf}, journal = {Science}, number = {6304}, pages = {1113}, title = {{Improving the forecast for biodiversity under climate change}}, volume = {353}, year = {2016} } @article{Solow1998, abstract = {Species in community food webs are commonly aggregated or lumped on the basis of overlap in predators and prey. This note reports an unexpected result of lumping species in observed food webs and simulated food webs. The main result is that it is much easier to lump species in observed webs than in simulated webs. The reason is that there is much more overlap in predators and prey for species in observed webs than in simulated webs. This points to a fundamental deficiency in web assembly models that assume a random distribution of links.}, author = {Solow, Andrew R. and Beet, Andrew R.}, doi = {10.1890/0012-9658(1998)079[2013:OLSIFW]2.0.CO;2}, file = {:Users/eastonwhite/Desktop/Research/lumping{\_}species{\_}and{\_}conservation/literature/1998{\_}Solow{\_}and{\_}Beet{\_}lumping{\_}species{\_}food{\_}webs.pdf:pdf}, issn = {00129658}, journal = {Ecology}, keywords = {Cascade model,Constant connectance model}, number = {6}, pages = {2013--2018}, title = {{On lumping species in food webs}}, volume = {79}, year = {1998} } @article{Senn2014, abstract = {Managers of threatened species often face the dilemma of whether to keep populations separate to conserve local adaptations and minimize the risk of outbreeding, or whether to manage populations jointly to reduce loss of genetic diversity and minimise inbreeding. In this study we examine genetic relatedness and diversity in three of the five last remaining wild populations of dama gazelle and a number of captive populations, using mtDNA control region and cytochrome b data. Despite the sampled populations belonging to the three putative subspecies, which are delineated according to phenotypes and geographical location, we find limited evidence for phylogeographical structure within the data and no genetic support for the putative subspecies. In the light of these data we discuss the relevance of inbreeding depression, outbreeding depression, adaptive variation, genetic drift, and phenotypic variation to the conservation of the dama gazelle and make some recommendations for its future conservation management. The genetic data suggest that the best conservation approach is to view the dama gazelle as a single species without subspecific divisions.}, annote = {Papers focuses on whether you should lump or split populations for management purposes - different than my original question. Instead, the thought is that individual populations have local adaptation, but you also want to prevent inbreeding (or outbreeding too much)}, author = {Senn, Helen and Banfield, Lisa and Wacher, Tim and Newby, John and Rabeil, Thomas and Kaden, Jennifer and Kitchener, Andrew C. and Abaigar, Teresa and Silva, Teresa Lu{\'{i}}sa and Maunder, Mike and Ogden, Rob}, doi = {10.1371/journal.pone.0098693}, file = {:Users/eastonwhite/Desktop/Research/lumping{\_}species{\_}and{\_}conservation/literature/2014{\_}Senn{\_}et{\_}al{\_}splitting{\_}or{\_}lumping{\_}for{\_}gazelle{\_}conservation.PDF:PDF}, issn = {19326203}, journal = {PLoS ONE}, number = {6}, title = {{Splitting or lumping? A conservation dilemma exemplified by the critically endangered dama gazelle (Nanger dama)}}, volume = {9}, year = {2014} } @article{Frankham2012, abstract = {The ∼26 definitions of species often yield different numbers of species and disparate groupings, with financial, legal, biological and conservation implications. Using conservation genetic considerations, we demonstrate that different species concepts have a critical bearing on our ability to conserve species. Many species of animals and plants persist as small isolated populations suffering inbreeding depression, loss of genetic diversity, and elevated extinction risks. Such small populations usually can be rescued by restoring gene flow, but substantial genetic drift effects can lead them to be classified as distinct species under the diagnostic phylogenetic species concept. Minimum harm to fitness is done and maximum potential fitness and evolutionary potential benefits accrue when reproductive isolation (pre- and/or post-zygotic) is used as the criterion to define distinct species. For sympatric populations, distinct species are diagnosed by very limited gene flow. For allopatric populations, both minimal gene flow and evidence of reduced reproductive fitness in crosses (or effects predicted from adaptive differentiation among populations and/or fixed chromosomal differences) are required to satisfy conservation issues. Species delineations based upon the biological and differential fitness species concepts meet the above requirements. Conversely, if species are delineated using the diagnostic phylogenetic species concept, genetic rescue of small genetically isolated populations may require crosses between species, with consequent legal and regulatory ramifications that could preclude actions to prevent extinction. Consequently, we conclude that the diagnostic phylogenetic species concept is unsuitable for use in conservation contexts, especially for classifying allopatric populations. {\textcopyright} 2012 Elsevier Ltd.}, annote = {They look at the implications of using differnt species concepts on conservation, with an emphasis on a balance between local adaptation and reducing outbreeding... They conclude that reproducive isolation be the key metric used for conservation genetics puposes... -- THey really don't like the taxonomic species concept or the phylogogentic species concept as this does not explicelty denote what species concept is actually being used under the hood}, author = {Frankham, Richard and Ballou, Jonathan D. and Dudash, Michele R. and Eldridge, Mark D B and Fenster, Charles B. and Lacy, Robert C. and Mendelson, Joseph R. and Porton, Ingrid J. and Ralls, Katherine and Ryder, Oliver A.}, doi = {10.1016/j.biocon.2012.04.034}, file = {:Users/eastonwhite/Desktop/Research/lumping{\_}species{\_}and{\_}conservation/literature/2012{\_}Frankham{\_}et{\_}al{\_}different{\_}species{\_}concepts{\_}and{\_}biodiversity.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {Fragmented populations,Genetic rescue,Inbreeding depression,Loss of genetic diversity,Outbreeding depression,Species concepts}, pages = {25--31}, publisher = {Elsevier Ltd}, title = {{Implications of different species concepts for conserving biodiversity}}, url = {http://dx.doi.org/10.1016/j.biocon.2012.04.034}, volume = {153}, year = {2012} } @article{DominguezLozano2007, abstract = {Abstract Concern has been raised regarding the continually changing nature of biotic taxonomies and how these changes alter perceptions of extinction risk and conservation priority setting. Within this realm, we can identify two distinct problems. First, there is a perception that the activity of a new, fine-scale taxonomy may have an effect in the taxonomy structure producing a taxonomic bias because larger groups may become disproportionably large as a result of new described variation is principally allocated into them. Second, there is an information gap where conservation planning occasionally neglects the most recent taxonomic information derived from fine-scale taxonomy. But, if not, this taxonomic bias has also the potential to alter the proportion of large to small lineages in conservation lists, because most newly described taxa are narrowly distributed and not common, therefore targeted for conservation lists. We use data sources from Iberian vascular flora in 1984 and 2000 to analyze these issues. Results show that rare species description in Iberia has proceeded continuously through time, has been dominated by descriptions in large genera, and shows a sharp increase in description rate since the 1970s. Further, the distribution of newly described taxa reflects proportional representation among groups of differing initial diversity. Finally, change through circumscription (lumping and splitting of former taxa) form part of the description process, but they do not dominate new rare plant taxa. Categorizations of endangered plants appear fairly stable in Spain with 76 {\%} of the most endangered taxa maintaining their species identities through this 16-years period. We conclude that the work of fine scale taxonomy, while representing the bulk of new taxonomic descriptions in Spain, is not biased toward any group size. Although conservation listing can be affected by this taxonomic pattern, we consider the conservation-taxonomy gap to be narrow in Spain.}, author = {{Dom{\'{i}}nguez Lozano}, Felipe and {Moreno Saiz}, Juan Carlos and {Sainz Ollero}, Helios and Schwartz, Mark W.}, doi = {10.1007/s10531-007-9206-2}, file = {:Users/eastonwhite/Desktop/Research/lumping{\_}species{\_}and{\_}conservation/literature/2007{\_}Lozano{\_}et{\_}al{\_}dynamic{\_}taxonomy{\_}and{\_}conservation.pdf:pdf}, issn = {09603115}, journal = {Biodiversity and Conservation}, keywords = {Conservation,Genus size,IUCN categories,Plants,Rarity,Spain,Taxonomic inflation}, number = {14}, pages = {4039--4050}, title = {{Effects of dynamic taxonomy on rare species and conservation listing: Insights from the Iberian vascular flora}}, volume = {16}, year = {2007} } @article{Mace2004, abstract = {Taxonomy and species conservation are often assumed to be completely interdependent activities. However, a shortage of taxonomic information and skills, and confusion over where the limits to 'species' should be set, both cause problems for conservationists. There is no simple solution because species lists used for conservation planning (e.g. threatened species, species richness estimates, species covered by legislation) are often also used to determine which units should be the focus of conservation actions; this despite the fact that the two processes have such different goals and information needs. Species conservation needs two kinds of taxonomic solution: (i) a set of practical rules to standardize the species units included on lists; and (ii) an approach to the units chosen for conservation recovery planning which recognizes the dynamic nature of natural systems and the differences from the units in listing processes that result. These solutions are well within our grasp but require a new kind of collaboration among conservation biologists, taxonomists and legislators, as well as an increased resource of taxonomists with relevant and high-quality skills.}, annote = {Key too my next two papers: Specific context determines if you shuld examine status of single population, or a group of species organized by locatlity or higher taxnoic grouping... What is the effect of listing a species under various legal mechanisms? Comparisons of extinction risks across groups of species is very sensitive to how species are lumped... 27{\%} of threatened list of bird species came about because of taxonomy differences instead of actual conservation status IUCN focuses on global levels threat WE MONINOTR AND MAKE ACTIONS ON SMALL SCALES, but we do regional assessments for particular species...}, author = {Mace, Georgina M.}, doi = {10.1098/rstb.2003.1454}, file = {:Users/eastonwhite/Desktop/Research/lumping{\_}species{\_}and{\_}conservation/literature/2014{\_}Mace{\_}taxonomy{\_}in{\_}species{\_}conservation.pdf:pdf}, issn = {09628436}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {Conservation planning,Phylogeny,Species,Taxonomy}, number = {1444}, pages = {711--719}, title = {{The role of taxonomy in species conservation}}, volume = {359}, year = {2004} } @article{Isaac2004, abstract = {Species numbers are increasing rapidly. This is due mostly to taxonomic inflation, where known subspecies are raised to species as a result in a change in species concept, rather than to new discoveries. Yet macroecologists and conservation biologists depend heavily on species lists, treating them as accurate and stable measures of biodiversity. Deciding on a standardized, universal species list might ameliorate the mismatch between taxonomy and the uses to which it is put. However, taxonomic uncertainty is ultimately due to the evolutionary nature of species, and is unlikely to be solved completely by standardization. For the moment, at least, users must acknowledge the limitations of taxonomic species and avoid unrealistic expectations of species lists.}, author = {Isaac, Nick J.B. and Mallet, James and Mace, Georgina M.}, doi = {10.1016/j.tree.2004.06.004}, file = {:Users/eastonwhite/Desktop/Research/lumping{\_}species{\_}and{\_}conservation/literature/2004{\_}Issac{\_}et{\_}al{\_}taxonomic{\_}inflation{\_}and{\_}conservation.pdf:pdf}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {9}, pages = {464--469}, title = {{Taxonomic inflation: Its influence on macroecology and conservation}}, volume = {19}, year = {2004} } @article{Pielou1981, author = {Pielou, E.C.}, file = {:Users/eastonwhite/Desktop/School/UVM/QuantReasoning/readings/1981{\_}Pielou{\_}useful{\_}of{\_}ecological{\_}models.pdf:pdf}, journal = {The Quarterly Review of Biology}, number = {1}, pages = {17--31}, title = {{The usefulness of ecological models: a stock-taking}}, url = {10.1086/394673}, volume = {56}, year = {1981} } @misc{Kean2019, annote = {Kean, J., Suckling, D., Sullivan, N., PC, T., Stringer, L., Smith, G., {\ldots} et al. (2019). Global eradication and response database. http://b3.net.nz/gerda.}, author = {Kean, JM and Suckling, DM and Sullivan, NJ and PC, Tobin and Stringer, LD and Smith, GR and Kimber, B and Lee, DC and Flores, Vargas R and Fletcher, J and Macbeth, F and McCullough, DG and Herms, DA and Et al}, title = {{Global eradication and response database. http://b3.net.nz/gerda}}, year = {2019} } @article{Serrouya2019, abstract = {Adaptive management is a powerful means of learning about complex ecosystems, but is rarely used for recovering endangered species. Here, we demonstrate how it can benefit woodland caribou, which became the first large mammal extirpated from the contiguous United States in recent history. The continental scale of forest alteration and extended time needed for forest recovery means that relying only on habitat protection and restoration will likely fail. Therefore, population management is also needed as an emergency measure to avoid further extirpation. Reductions of predators and overabundant prey, translocations, and creating safe havens have been applied in a design covering {\textgreater}90,000 km 2 . Combinations of treatments that increased multiple vital rates produced the highest population growth. Moreover, the degree of ecosystem alteration did not influence this pattern. By coordinating recovery involving scientists, governments, and First Nations, treatments were applied across vast scales to benefit this iconic species.}, annote = {- able to look at different management strategies empirically to make suggestions for further improvements via adaptive management - show that in order to be effective, management needs to be intense, and it works better when couple with other strategies... - there was variability within management replicates... - wolf removal increased growth in 5 of 6 sites. Moose removal worked in 2 of 4 sites.}, author = {Serrouya, Robert and Seip, Dale R. and Hervieux, Dave and McLellan, Bruce N. and McNay, R. Scott and Steenweg, Robin and Heard, Doug C. and Hebblewhite, Mark and Gillingham, Michael and Boutin, Stan}, doi = {10.1073/pnas.1816923116}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/2019 Serrouya et al - saving endagered species using adaptive management.pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {13}, pages = {6181--6186}, title = {{Saving endangered species using adaptive management}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1816923116}, volume = {116}, year = {2019} } @article{Walters1990, annote = {This paper explores the general ideas of adaptive management and how we both manage, and learn, from large management experiments. The authors point to important issues about uncertainty, lack of replication, short time series, value of information, and the difficulty in seperating out causes of dynamics retrospectively. I also like that they talk about two kinds of science: 1) the science of parts focused on small experiments that determine things like survival and 2) the science of the integration of parts --- it thinks about the whole system and uses results from the first type of science... THey point out that more work needs to look at the explicit costs and benefits of monitoring....THey hypothesize that larger experiments (and more crude monitoring) would be favored by ecological researchers... Is this true?!?! - given a fixed dollar amount. SHould you monitor more or do more experiments... Tara Martin has work related to this}, author = {Walters, Carl J and Holling, C.S.}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/1990 Walter and Holling - learning by doing.pdf:pdf}, journal = {Ecology}, number = {6}, pages = {2060--2068}, title = {{Large-scale management experiments and learning by doing}}, volume = {71}, year = {1990} } @article{Liebhold2016, abstract = {Eradication is the deliberate elimination of a species from an area. Given that international quarantine measures can never be 100{\%} effective, surveillance for newly arrived populations of nonnative species coupled with their eradication represents an important strategy for excluding potentially damaging insect species. Historically, eradication efforts have not always been successful and have sometimes been met with public opposition. But new developments in our understanding of the dynamics of low-density populations, the availability of highly effective treatment tactics, and bioeconomic analyses of eradication strategies offer new opportunities for developing more effective surveillance and eradication programs. A key component that connects these new developments is the harnessing of Allee effects, which naturally promote localized species extinction. Here we review these developments and suggest how research might enhance eradication strategies. Expected final online publication date for the Annual Review of Entomology Volume 61 is January 07, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.}, author = {Liebhold, Andrew M. and Berec, Ludek and Brockerhoff, Eckehard G. and Epanchin-Niell, Rebecca S. and Hastings, Alan and Herms, Daniel A. and Kean, John M. and McCullough, Deborah G. and Suckling, David M. and Tobin, Patrick C. and Yamanaka, Takehiko}, doi = {10.1146/annurev-ento-010715-023809}, file = {:Users/eastonwhite/Downloads/289. liebhold et al. annurev-ento-010715-023809-1.pdf:pdf}, issn = {0066-4170}, journal = {Annual Review of Entomology}, keywords = {Allee effect,biological invasions,biosecurity,early detection rapid response,surveillance}, number = {1}, pages = {335--352}, title = {{Eradication of invading insect populations: From concepts to applications}}, volume = {61}, year = {2016} } @article{Johnson2017, abstract = {Biodiversity is essential to human well-being, but people have been reducing biodiversity throughout human history. Loss of species and degradation of ecosystems are likely to further accelerate in the coming years. Our understanding of this crisis is now clear, and world leaders have pledged to avert it. Nonetheless, global goals to reduce the rate of biodiversity loss have mostly not been achieved. However, many examples of conservation success show that losses can be halted and even reversed. Building on these lessons to turn the tide of biodiversity loss will require bold and innovative action to transform historical relationships between human populations and nature.}, author = {Johnson, Christopher N. and Balmford, Andrew and Brook, Barry W. and Buettel, Jessie C. and Galetti, Mauro and Guangchun, Lei and Wilmshurst, Janet M.}, doi = {10.1126/science.aam9317}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/2017 Johnson et al - biodiversity losses and conservation in the Anthropocene.pdf:pdf}, issn = {0036-8075}, journal = {Science}, number = {6335}, pages = {270--275}, title = {{Biodiversity losses and conservation responses in the Anthropocene}}, url = {http://www.sciencemag.org/lookup/doi/10.1126/science.aam9317}, volume = {356}, year = {2017} } @article{Westgate2013, abstract = {Adaptive Management (AM) is widely considered to be the best available approach for managing biological systems in the presence of uncertainty. But AM has arguably only rarely succeeded in improving biodiversity outcomes. There is therefore an urgent need for reflection regarding how practitioners might overcome key problems hindering greater implementation of AM. In this paper, we present the first structured review of the AM literature that relates to biodiversity and ecosystem management, with the aim of quantifying how rare AM projects actually are. We also investigated whether AM practitioners in terrestrial and aquatic systems described the same problems; the degree of consistency in how the term 'adaptive management' was applied; the extent to which AM projects were sustained over time; and whether articles describing AM projects were more highly cited than comparable non-AM articles. We found that despite the large number of articles identified through the ISI web of knowledge (n= 1336), only 61 articles ({\textless}5{\%}) explicitly claimed to enact AM. These 61 articles cumulatively described 54 separate projects, but only 13 projects were supported by published monitoring data. The extent to which these 13 projects applied key aspects of the AM philosophy - such as referring to an underlying conceptual model, enacting ongoing monitoring, and comparing alternative management actions - varied enormously. Further, most AM projects were of short duration; terrestrial studies discussed biodiversity conservation significantly more frequently than aquatic studies; and empirical studies were no more highly cited than qualitative articles. Our review highlights that excessive use of the term 'adaptive management' is rife in the peer-reviewed literature. However, a small but increasing number of projects have been able to effectively apply AM to complex problems. We suggest that attempts to apply AM may be improved by: (1) Better collaboration between scientists and representatives from resource-extracting industries. (2) Better communication of the risks of not doing AM. (3) Ensuring AM projects " pass the test of management relevance" {\textcopyright} 2012 Elsevier Ltd.}, annote = {THey note 6 different criteria for adaptive management 1) identification of management goals 2) specification of more than 2 management options 3) process for interpreting if systems responds to management interventions 4) number of management actions implementd 5) regular monitoring of system and 6) adjust management practice in response to monitoring... Why is AM so hard to do?}, author = {Westgate, Martin J. and Likens, Gene E. and Lindenmayer, David B.}, doi = {10.1016/j.biocon.2012.08.016}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/2013 Westgate et al - review of adaptive management.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {Conservation,Evidence-based ecosystem management,Uncertainty}, pages = {128--139}, title = {{Adaptive management of biological systems: A review}}, url = {http://dx.doi.org/10.1016/j.biocon.2012.08.016}, volume = {158}, year = {2013} } @article{Sutherland2004, abstract = {Much of current conservation practice is based upon anecdote and myth rather than upon the systematic appraisal of the evidence, including experience of others who have tackled the same problem. We suggest that this is a major problem for conservationists and requires a rethinking of the manner in which conservation operates. There is an urgent need for mechanisms that review available information and make recommendations to practitioners. We suggest a format for web-based databases that could provide the required information in accessible form.}, author = {Sutherland, William J. and Pullin, Andrew S. and Dolman, Paul M. and Knight, Teri M.}, doi = {10.1016/j.tree.2004.03.018}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/2004 Sutherland et al - the need for evidence based conservation.pdf:pdf}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {6}, pages = {305--308}, title = {{The need for evidence-based conservation}}, volume = {19}, year = {2004} } @article{Dainese2019, abstract = {Human land use threatens global biodiversity and compromises multiple ecosystem functions critical to food production. Whether crop yield-related ecosystem services can be maintained by few abundant species or rely on high richness remains unclear. Using a global database from 89 crop systems, we partition the relative importance of abundance and species richness for pollination, biological pest control and final yields in the context of on-going land-use change. Pollinator and enemy richness directly supported ecosystem services independent of abundance. Up to 50{\%} of the negative effects of landscape simplification on ecosystem services was due to richness losses of service-providing organisms, with negative consequences for crop yields. Maintaining the biodiversity of ecosystem service providers is therefore vital to sustain the flow of key agroecosystem benefits to society.}, annote = {- how does biodiversity (abundance or richness) affect ecosystem services - pollinator richness, pest enemy richness Where do we think this paper will be submitted to? Are preprints useful? Is there qeuestion interesting? Are their methods approrpriate? Do findings support their hypotheses? What should they do next?}, author = {Dainese, Matteo and Martin, Emily A and Aizen, Marcelo A and Albrecht, Matthias and Bommarco, Riccardo and Carvalheiro, Luisa G and Chaplin-kramer, Rebecca and Garibaldi, Lucas A and Ghazoul, Jaboury and Grab, Heather and Jonsson, Mattias and Daniel, S and Andersson, Georg K S and Badenhausser, Isabelle and Baensch, Svenja and Ekroos, Johan and Fijen, Thijs and Franck, Pierre and Freitas, Breno M and Michael, P D and Jha, Shalene and Keasar, Tamar and Kim, Tania N and Kishinevsky, Miriam and Bj{\"{o}}rn, K}, doi = {10.1101/554170}, file = {:Users/eastonwhite/Downloads/A-global-synthesis-reveals-biodiversity-mediated-benefits-for-crop-production.pdf:pdf}, journal = {bioRxiv}, number = {February}, pages = {1--19}, title = {{A global synthesis reveals biodiversity-mediated benefits for crop production}}, year = {2019} } @article{Lodge2016a, abstract = {Risk analysis of species invasions links biology and economics, is increasingly mandated by international and national policies, and enables improved management of invasive species. Biological invasions proceed through a series of transition probabilities (i.e., introduction, establishment, spread, and impact), and each of these presents opportunities for management. Recent research advances have improved estimates of probability and associated uncertainty. Improvements have come from species-specific trait-based risk assessments (of estimates of introduction, establishment, spread, and impact probabilities, especially from pathways of commerce in living organisms), spatially explicit dispersal models (introduction and spread, especially from transportation pathways), and species distribution models (establishment, spread, and impact). Results of these forecasting models combined with improved and cheaper surveillance technologies and practices [e.g., environmental DNA (eDNA), drones, citizen science] enable more efficient management by focusing surveillance, prevention, eradication, and control efforts on the highest-risk species and locations. Bioeconomic models account for the interacting dynamics within and between ecological and economic systems, and allow decision makers to better understand the financial consequences of alternative management strategies. In general, recent research advances demonstrate that prevention is the policy with the greatest long-term net benefit.}, author = {Lodge, David and Simonin, Paul W. and Burgiel, Stanley W. and Keller, Reuben and Bossenbroek, Jonathan M. and Jerde, Christopher and Kramer, Andrew and Rutherford, Edward and Barnes, Matthew and Wittmann, Marion and Chadderton, W. and Apriesnig, Jenny and Beletsky, Dmitry and Cooke, Roger M. and Drake, John and Egan, Scott and Finnoff, David and Gantz, Crysta and Grey, Erin and Hoff, Michael and Howeth, Jennifer and Jensen, Richard A. and Larson, Eric and Mandrak, Nicholas and Mason, Doran and Martinez, Felix and Newcomb, Tammy and Rothlisberger, John and Tucker, Andrew and Warziniack, Travis and Zhang, Hongyan}, doi = {10.1146/annurev-environ-110615-085532}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/2016 Lodge et al - risk analysis and bioeconomics of invasive species.pdf:pdf}, journal = {Annual Review Environmental Resources}, pages = {453--488}, title = {{Risk Analysis and Bioeconomics of Invasive Species to Inform Policy and Management}}, volume = {41}, year = {2016} } @article{Game2013, abstract = {A vast number of prioritization schemes have been developed to help conservation navigate tough decisions about the allocation of finite resources. However, the application of quantitative approaches to setting priorities in conservation frequently includes mistakes that can undermine their authors' intention to be more rigorous and scientific in the way priorities are established and resources allocated. Drawing on well-established principles of decision science, we highlight 6 mistakes commonly associated with setting priorities for conservation: not acknowledging conservation plans are prioritizations; trying to solve an ill-defined problem; not prioritizing actions; arbitrariness; hidden value judgments; and not acknowledging risk of failure. We explain these mistakes and offer a path to help conservation planners avoid making the same mistakes in future prioritizations.}, author = {Game, Edward T. and Kareiva, Peter and Possingham, Hugh P.}, doi = {10.1111/cobi.12051}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/2013 Game et al - six common mitakes in conservation priority setting.pdf:pdf}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Conservation Action Planning,Conservation planning,Decision science,Measurement theory,Operations research,Prioritization}, number = {3}, pages = {480--485}, title = {{Six common mistakes in conservation priority setting}}, volume = {27}, year = {2013} } @article{Lampert2019, abstract = {Ecosystems worldwide have become degraded due to global change, and therefore, restoration of these ecosystems is critical for the prolonged provision of ecosystem services. Specifically, major restora- tion efforts are directed toward the restoration of key species that provide important services and functions. There are often several alternative methods to restore a species population, such as the reintroduction of its individuals, improvement of its habitat quality, and removal of competing invasive species. However, these methods can be expensive, and hence, it is important to determine how to cost effectively combine them over time. In this paper, we use optimal control theory and we find a general rule of thumb for combining two restoration methods. The general rule, which applies to a wide variety of ecosystems, is that cost-effective restoration entails one of the following two strategies: (1) using a single method until the system approaches a “restoration threshold” or (2) combining both methods to approach an “investment benchmark,” which is a certain configuration of the system that does not depend on the system's initial state. After either the restoration threshold or the investment benchmark has been approached, investment should stop and the system should be left to recover naturally. Therefore, finding the restoration threshold and the investment benchmark is key for guiding effective restoration, and we demonstrate a simple method for finding them.}, author = {Lampert, Adam and Hastings, Alan}, doi = {10.1002/ecs2.2552}, file = {:Users/eastonwhite/Desktop/Research/BeetleLab/beetle{\_}project{\_}papers/2019 Lampert and Hastings - combining two methods for restoration.pdf:pdf}, issn = {21508925}, journal = {Ecosphere}, keywords = {Stochastic Programming,bioeconomics,conservation,ecosystem services,optimal control,restoration}, number = {1}, title = {{How to combine two methods to restore populations cost effectively}}, volume = {10}, year = {2019} } @article{May1974, author = {May, Robert M.}, file = {:Users/eastonwhite/Desktop/School/UVM/QuantReasoning/readings/1974{\_}May{\_}complex{\_}dynamics{\_}in{\_}nonoverlapping{\_}generations.pdf:pdf}, journal = {Science}, pages = {645--647}, title = {{Biological populations with nonoverlapping generations: Stable points, stable cycles, and chaos}}, volume = {186}, year = {1974} } @article{May1976, author = {May, Robert M.}, file = {:Users/eastonwhite/Desktop/School/UVM/QuantReasoning/readings/1976{\_}May{\_}simple{\_}models{\_}very{\_}complicated{\_}dynamics.pdf:pdf}, journal = {Nature}, number = {June}, pages = {459--467}, title = {{Simple mathematical models with very complicated dynamics}}, volume = {261}, year = {1976} } @article{Cuddington2013a, author = {Cuddington, K. and Fortin, M.-J. and Gerber, L. R. and Hastings, A. and Liebhold, A. and O'Connor, M. and Ray, C.}, doi = {10.1890/es12-00178.1}, file = {:Users/eastonwhite/Desktop/School/UVM/QuantReasoning/readings/2013{\_}Cuddington{\_}et{\_}al{\_}process{\_}based{\_}models{\_}in{\_}changing{\_}world.pdf:pdf}, issn = {2150-8925}, journal = {Ecosphere}, keywords = {accepted 2 january 2013,al,article distributed under the,c,climate change,commons,copyright,corresponding,d,editor,expert opinion,extrapolation,p,peters,published 8 february 2013,received 19 june 2012,revised 31 december 2012,simulation model,terms of the creative,this is an open-access,{\'{o}} 2013 cuddington et}, number = {2}, pages = {art20}, title = {{Process-based models are required to manage ecological systems in a changing world}}, volume = {4}, year = {2013} } @article{Drake2006, abstract = {Genomesize has been suggested as one of the traits associated with invasiveness of plant species.To provide a quantitative insight into the role of this trait,we estimated nuclearDNAcontent in 93 alien species naturalized in the Czech Republic, belonging to 32 families, by using flow cytometry, and compared it with the values reported for non-invading congeneric and confamilial species from the PlantDNAC-values database. Species naturalized in the Czech Republic have significantly smaller genomes than their congeners not known to be naturalized or invasive in any part of theworld. This trend is supported at the family level: alien species naturalized in the Czech flora have on average a smaller genome than is the mean value for non-invading confamilials. Moreover, naturalized and non-invading species clearly differed in the frequency of five genome size categories; this difference was mainly due to very small genomes prevailing and intermediate to very large genomes under- represented in the former group. Our results provide the first quantitative support for association of genome size with invasiveness, based on a large set of alien species across a number of plant fami- lies. However, there was no difference in the genome size of invasive species compared to natural- ized but non-invasive. This suggests that small genome size provides alien plants with an advantage already at the stage of naturalization and need not be necessarily associated with the final stage of the process, i.e. invasion.}, author = {Drake, John M. and Lodge, David M.}, doi = {10.1007/s10530-004-8122-6}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Drake, Lodge - 2006 - Allee effects, propagule pressure and the probability of establishment risk analysis for biological invasions.pdf:pdf}, isbn = {0032-7786}, issn = {00327786}, journal = {Biological Invasions}, keywords = {Alien plants,C-value,Confamilials,Congeners,Flow cytometry,Genome size,Invasive species,Large genome constraint hypothesis,Nuclear DNA content,Plant invasions}, pages = {365--375}, pmid = {25189347}, title = {{Allee effects, propagule pressure and the probability of establishment: risk analysis for biological invasions}}, volume = {8}, year = {2006} } @article{Kettenring2011, abstract = {1. Invasive plants can reduce biodiversity, alter ecosystem functions and have considerable eco- nomic impacts. Invasive plant control is therefore the focus of restoration research in invader-domi- nated ecosystems. Increasing the success of restoration practice requires analysis and synthesis of research findings and assessment of howexperiments can be improved. 2. In a systematic review and meta-analysis of invasive plant control research papers, we asked: (i) what control efforts have been most successful; and (ii) what invasive plant control research best translates into successful restoration application? 3. The literature evaluated typically described experiments that were limited in scope. Most plot sizes were small ({\textless}1 m2), time frames were brief (51{\%}evaluated control for one growing season or less) and few species and ecosystems (predominantly grasslands) were studied throughout much of the literature. The scale at which most experiments were conducted potentially limits relevance to the large scales atwhich restorations typically occur. 4. Most studies focused on invasive species removal and lacked an evaluation of native revegetation following removal. Fewstudies (33{\%}) included active revegetation even though native species prop- agule limitation was common. Restoration success was frequently complicated by re-invasion or establishment of a novel invader. 5. Few studies (29{\%}) evaluated the costs of invasive species control. Additionally, control some- times had undesirable effects, including negative impacts to native species. 6. Synthesis and applications. Despite a sizeable literature on invasive plant control experiments, many large-scale invasive plant management efforts have had only moderate restoration success. We identified several limitations to successful invasive species control including: minimal focus on revegetation with natives after invasive removal, limited spatial and temporal scope of invasive plant control research, and incomplete evaluation of costs and benefits associated with invasive species management actions. We suggest that information needed to inform invasive plant man- agement can be better provided if researchers specifically address these limitations. Many limita- tions can be addressed by involving managers in research, particularly through adaptive management.}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Kettenring, Karin M. and Adams, Carrie Reinhardt}, doi = {10.1111/j.1365-2664.2011.01979.x}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kettenring, Adams - 2011 - Lessons learned from invasive plant control experiments A systematic review and meta-analysis.pdf:pdf}, isbn = {0021-8901}, issn = {00218901}, journal = {Journal of Applied Ecology}, keywords = {Alien species,Control,Herbicide,Novel invader,Propagule limitation,Restoration,Revegetation,Weed}, number = {4}, pages = {970--979}, pmid = {16417727}, title = {{Lessons learned from invasive plant control experiments: A systematic review and meta-analysis}}, volume = {48}, year = {2011} } @article{Park2012, author = {Park, Andrew W}, doi = {10.1002/ece3.257}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Park - 2012 - Infectious disease in animal metapopulations the importance of environmental transmission.pdf:pdf}, keywords = {animal movement,endangered species,epidemiology,free-living pathogen,model}, title = {{Infectious disease in animal metapopulations : the importance of environmental transmission}}, year = {2012} } @article{Sample2018, author = {Sample, Christine and Fryxell, John M and Bieri, Joanna A and Federico, Paula and Earl, Julia E and Nicol, Sam and Wiederholt, Ruscena and Mattsson, Brady J and Flockhart, D T Tyler and Wayne, E Diffendorfer and Richard, E Thogmartin and Ryan, A Erickson D}, doi = {10.1002/ece3.3685}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sample et al. - 2018 - A general modeling framework for describing spatially structured population dynamics.pdf:pdf}, journal = {Ecology and Evolution}, number = {November 2017}, pages = {493--508}, title = {{A general modeling framework for describing spatially structured population dynamics}}, year = {2018} } @article{Lodge2016, author = {Lodge, David M and Simonin, Paul W and Burgiel, Stanley W and Keller, Reuben P and Bossenbroek, Jonathan M and Jerde, Christopher L and Kramer, Andrew M and Rutherford, Edward S and Barnes, Matthew A and Wittmann, Marion E and Chadderton, W Lindsay and Apriesnig, Jenny L and Beletsky, Dmitry and Cooke, Roger M and Drake, John M and Egan, Scott P and Finnoff, David C and Gantz, Crysta A and Grey, Erin K and Hoff, Michael H and Howeth, Jennifer G and Jensen, Richard A and Larson, Eric R and Mandrak, Nicholas E and Mason, Doran M and Martinez, Felix A and Newcomb, Tammy J and Rothlisberger, John D and Tucker, Andrew J and Warziniack, Travis W and Zhang, Hongyan}, doi = {10.1146/annurev-environ-110615-085532}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lodge et al. - 2016 - Risk Analysis and Bioeconomics of Invasive Species to Inform Policy and Management.pdf:pdf}, journal = {Annu. Rev. Environ. Resour.}, keywords = {control,damage,dispersal,early detection,eradication,forecasting,prevention,species distribution modeling,surveillance}, pages = {453--488}, title = {{Risk analysis and bioeconomics of invasive species to inform policy and management}}, volume = {41}, year = {2016} } @article{Nalesso2019, abstract = {Many species of sharks form aggregations around oceanic islands, yet their levels of residency and their site specificity around these islands may vary. In some cases, the waters around oceanic islands have been designated as marine protected areas, yet the conservation value for threatened shark species will depend greatly on how much time they spend within these protected waters. Eighty-four scalloped hammerhead sharks (Sphyrna lewini Griffith {\&} Smith), were tagged with acoustic transmitters at Cocos Island between 2005–2013. The average residence index, expressed as a proportion of days present in our receiver array at the island over the entire monitoring period, was 0.52±0.31, implying that overall the sharks are strongly associated with the island. Residency was significantly greater at Alcyone, a shallow seamount located 3.6 km offshore from the main island, than at the other sites. Timing of presence at the receiver locations was mostly during daytime hours. Although only a single individual from Cocos was detected on a region-wide array, nine hammerheads tagged at Galapagos and Malpelo travelled to Cocos. The hammerheads tagged at Cocos were more resident than those visiting from elsewhere, suggesting that the Galapagos and Malpelo populations may use Cocos as a navigational waypoint or stopover during seasonal migrations to the coastal Central and South America. Our study demonstrates the importance of oceanic islands for this species, and shows that they may form a network of hotspots in the Eastern Tropical Pacific.}, author = {Nalesso, Elena and Hearn, Alex and Sosa-Nishizaki, Oscar and Steiner, Todd and Antoniou, Alex and Reid, Andrew and Bessudo, Sandra and Soler, Germ{\'{a}}n and Klimley, A. Peter and Lara, Frida and Ketchum, James T. and Arauz, Randall}, doi = {10.1371/journal.pone.0213741}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nalesso et al. - 2019 - Movements of scalloped hammerhead sharks (Sphyrna lewini) at Cocos Island, Costa Rica and between oceanic island.pdf:pdf}, isbn = {1111111111}, journal = {Plos One}, number = {3}, pages = {e0213741}, title = {{Movements of scalloped hammerhead sharks (Sphyrna lewini) at Cocos Island, Costa Rica and between oceanic islands in the Eastern Tropical Pacific}}, url = {http://dx.plos.org/10.1371/journal.pone.0213741}, volume = {14}, year = {2019} } @article{Fryxell2005, author = {Fryxell, J M and Smith, I M and Lynn, D H}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fryxell, Smith, Lynn - 2005 - Evaluation of Alternate Harvesting Strategies Using Experimental Microcosms Evaluation of alternate harves.pdf:pdf}, journal = {Oikos}, number = {February}, pages = {143--149}, title = {{Evaluation of alternate harvesting strategies using experimental microcosms}}, volume = {111}, year = {2005} } @article{Albins2013, abstract = {The Pacific red lionfish has recently invaded Western Atlantic and Caribbean coral reefs, and may become one of the most ecologically harmful marine fish introductions to date. Lionfish possess a broad suite of traits that makes them particularly successful invaders and strong negative interactors with native fauna, including defensive venomous spines, cryptic form, color and behavior, habitat generality, high competitive ability, low parasite load, efficient predation, rapid growth, and high reproductive rates. With an eye on the future, we describe a possible “worst case scenario” in which the direct and indirect effects of lionfish could combine with the impacts of preexisting stressors—especially overfishing—and cause substantial deleterious changes in coral-reef communities. We also discuss management actions that could be taken to minimize these potential effects by, first, developing targeted lionfish fisheries and local removals, and second, enhancing native biotic resistance, particularly via marine reserves that could conserve and foster potential natural enemies of this invader. Ultimately, the lionfish invasion will be limited either by the lionfish starving—the worst end to the worst case scenario—or by some combination of native pathogens, parasites, predators, and competitors controlling the abundance of lionfish.}, author = {Albins, Mark A. and Hixon, Mark A.}, doi = {10.1007/s10641-011-9795-1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Albins, Hixon - 2013 - Worst case scenario Potential long-term effects of invasive predatory lionfish (Pterois volitans) on Atlantic and.pdf:pdf}, isbn = {0378-1909}, issn = {03781909}, journal = {Environmental Biology of Fishes}, keywords = {Biological invasions,Biotic resistance,Coral-reef fishes,Ecological release,Invasive species}, number = {10-11}, pages = {1151--1157}, pmid = {24356753}, title = {{Worst case scenario: Potential long-term effects of invasive predatory lionfish (Pterois volitans) on Atlantic and Caribbean coral-reef communities}}, volume = {96}, year = {2013} } @article{Smith2007, abstract = {{\textless}abstract xml:lang="en"{\textgreater} Year to year variation in yield is an inherent risk associated with crop production and many growers rely on intensive mechanical or chemical inputs to preserve crop yield in the face of fluctuating environmental conditions. However, as interest grows in alternative crop management systems which depend less on external inputs, determining the degree to which management systems can impact the temporal yield variability will help the development of sustainable agroecosystems. This study assessed average crop yields and temporal yield variability over a 12-yr period in four agricultural management systems that are part of a long-term cropping systems experiment at the W.K. Kellogg Biological Station (KBS) Long Term Ecological Research (LTER) site in southwestern Michigan. The four systems follow a corn (Zea mays L.), soybean [Glycine max (L.) Merr.], and winter wheat (Triticum aestivum L.) 3-yr rotation under conventional (CT), no-till (NT), low-input (LI), or organic (ORG) management, and each crop phase was present in the rotation four times from 1993 to 2004. Yields were measured each year and crop yield variability was estimated using the coefficient of variation calculated separately for each crop phase. Averaged over the study period, yields in the CT and NT systems were similar across all crop phases of the rotation and of higher magnitude than the LI system only in the winter wheat phase of the rotation. Compared to the other three management systems, yields in the ORG system were lower in the corn and winter wheat phases of the rotation. Yields in the soybean phase were similar across the four management systems. Temporal yield variability differed among management systems and rotation phases and was highest in the ORG system during the soybean (CV = 48{\%}) and winter wheat (CV = 33{\%}) phases of the rotation. Compared to the CT system, yield variability was 40{\%} lower in the LI (corn phase), 33{\%} lower in the NT (soybean phase) and similar in the NT (corn and winter wheat phases) systems. Results of this study suggest that yield and temporal yield variability under alternative management systems such as no-till and low-input can be comparable to that in conventional systems. However, temporal yield variability can be as high or higher in organic cropping systems without external inputs of manure or compost.}, author = {Smith, Richard G. and Menalled, Fabian D. and Robertson, G. P.}, doi = {10.2134/agronj2007.0096}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Menalled, Robertson - 2007 - Temporal yield variability under conventional and alternative management systems.pdf:pdf}, isbn = {0002-1962}, issn = {00021962}, journal = {Agronomy Journal}, number = {6}, pages = {1629--1634}, title = {{Temporal yield variability under conventional and alternative management systems}}, volume = {99}, year = {2007} } @article{Palamara2016, abstract = {Invasive species are a serious threat to biodiversity worldwide and predicting whether an introduced species will first establish and then become invasive can be useful to preserve ecosystem services. Establishment is influenced by multiple factors, such as the interactions between the introduced individuals and the resident community, and demographic and environmental stochasticity. Field observations are often incomplete or biased. This, together with an imperfect knowledge of the ecological traits of the introduced species, makes the prediction of establishment challenging. Methods that consider the combined effects of these factors on our ability to predict the establishment of an introduced species are currently lacking. We develop an inference framework to assess the combined effects of demographic stochasticity and parameter uncertainty on our ability to predict the probability of establishment following the introduction of a small number of individuals. We find that even moderate levels of demographic stochasticity influence both the probability of establishment, and, crucially, our ability to correctly predict that probability. We also find that estimation of the demographic parameters of an introduced species is fundamental to obtain precise estimates of the interaction parameters. For typical values of demographic stochasticity, the drop in our ability to predict an establishment can be 30{\%} when having priors on the demographic parameters compared to having their accurate values. The results from our study illustrate how demographic stochasticity may bias the prediction of the probability of establishment. Our method can be applied to estimate probability of establishment of introduced species in field scenarios, where time series data and prior information on the demographic traits of the introduced species are available. }, author = {Palamara, Gian Marco and Carrara, Francesco and Smith, Matthew J. and Petchey, Owen L.}, doi = {10.1002/ece3.2495}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Palamara et al. - 2016 - The effects of demographic stochasticity and parameter uncertainty on predicting the establishment of introduce.pdf:pdf}, issn = {20457758}, journal = {Ecology and Evolution}, keywords = {Bayesian inference,Lotka–Volterra equations,birth and death process,demographic stochasticity,establishment probability,invasion dynamics}, number = {23}, pages = {8440--8451}, title = {{The effects of demographic stochasticity and parameter uncertainty on predicting the establishment of introduced species}}, volume = {6}, year = {2016} } @article{Ben-Ari2014, abstract = {Recent food crises have highlighted the need to better understand the between-year variability of agricultural production. Although increasing future production seems necessary, the globalization of commodity markets suggests that the food system would also benefit from enhanced supplies stability through a reduction in the year-to-year variability. Here, we develop an analytical expression decomposing global crop yield interannual variability into three informative components that quantify how evenly are croplands distributed in the world, the proportion of cultivated areas allocated to regions of above or below average variability and the covariation between yields in distinct world regions. This decomposition is used to identify drivers of interannual yield variations for four major crops (i.e., maize, rice, soybean and wheat) over the period 1961–2012. We show that maize production is fairly spread but marked by one prominent region with high levels of crop yield interannual variability (which encompasses the North American corn belt in the USA, and Canada). In contrast, global rice yields have a small variability because, although spatially concentrated, much of the production is located in regions of below-average variability (i.e., South, Eastern and South Eastern Asia). Because of these contrasted land use allocations, an even cultivated land distribution across regions would reduce global maize yield variance, but increase the variance of global yield rice. Intermediate results are obtained for soybean and wheat for which croplands are mainly located in regions with close-to-average variability. At the scale of large world regions, we find that covariances of regional yields have a negligible contribution to global yield variance. The proposed decomposition could be applied at any spatial and time scales, including the yearly time step. By addressing global crop production stability (or lack thereof) our results contribute to the understanding of a key aspect of global food availability.}, author = {Ben-Ari, Tamara and Makowski, David}, doi = {10.1088/1748-9326/9/11/114011}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ben-Ari, Makowski - 2014 - Decomposing global crop yield variability.pdf:pdf}, isbn = {1748-9326}, issn = {17489326}, journal = {Environmental Research Letters}, keywords = {Simpson index,food security,land use,yield variance}, number = {11}, pmid = {20219969}, publisher = {IOP Publishing}, title = {{Decomposing global crop yield variability}}, volume = {9}, year = {2014} } @article{Koricheva2014, abstract = {* The number of published meta-analyses in plant ecology has increased greatly over the last two decades. Meta-analysis has made a significant contribution to the field, allowing review of evidence for various ecological hypotheses and theories, estimation of effects of major environmental drivers (climate change, habitat fragmentation, invasive species, air pollution), assessment of management and conservation strategies, and comparison of effects across different temporal and spatial scales, taxa and ecosystems, as well as research gap identification.$\backslash$n$\backslash$n$\backslash$n* We identified 322 meta-analyses published in the field of plant ecology between 1996 and 2013 in 95 different journals and assessed their methodological and reporting quality according to standard criteria. Despite significant recent developments in the methodology of meta-analysis, the quality of published meta-analyses was uneven and showed little improvement over time.$\backslash$n$\backslash$n$\backslash$n* We found many cases of imprecise and inaccurate usage of the term ‘meta-analysis' in plant ecology, particularly confusion between meta-analysis and vote counting and incorrect application of statistical techniques designed for primary studies to meta-analytical data, without recognition of the violation of statistical assumptions of the analyses.$\backslash$n$\backslash$n$\backslash$n* Methodological issues for meta-analyses in plant ecology include incomplete reporting of search strategy used to retrieve primary studies, failure to test for possible publication bias and to conduct sensitivity analysis to test the robustness of the results, as well as lack of availability of the data set used for the analyses.$\backslash$n$\backslash$n$\backslash$n* The use of meta-analysis is particularly common in community ecology, ecophysiology and ecosystem ecology, but meta-analyses in ecophysiology are more likely not to meet standard quality criteria than papers in other subdisciplines. Fewer meta-analyses have been conducted in plant population ecology.$\backslash$n$\backslash$n$\backslash$n* Synthesis. Over the past two decades, plant ecologists have embraced meta-analysis as a statistical tool to combine results across studies, and much has been learned as a result. However, as the popularity and usage of meta-analysis in the field of plant ecology has grown, establishment of quality standards, as has been done in other disciplines, becomes increasingly important. In order to improve the quality of future meta-analyses in plant ecology, we suggest adoption of a checklist of quality criteria for meta-analysis for use by research synthesists, peer reviewers and journal editors.}, author = {Koricheva, Julia and Gurevitch, Jessica}, doi = {10.1111/1365-2745.12224}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Koricheva, Gurevitch - 2014 - Uses and misuses of meta-analysis in plant ecology.pdf:pdf}, isbn = {1365-2745}, issn = {13652745}, journal = {Journal of Ecology}, keywords = {Ecophysiology,Meta-analysis,Methodological quality,Plant ecology,Research synthesis,Systematic review,Vote counting}, number = {4}, pages = {828--844}, title = {{Uses and misuses of meta-analysis in plant ecology}}, volume = {102}, year = {2014} } @article{Eisenlord2016a, author = {Eisenlord, Morgan E and Groner, Maya L and Yoshioka, Reyn M and Elliott, Joel and Maynard, Jeffrey and Fradkin, Steven and Turner, Margaret and Pyne, Katie and Rivlin, Natalie and Hooidonk, Ruben Van and Harvell, C Drew and Eisenlord, Morgan E}, journal = {Phil}, keywords = {ecology,epidemiology,health and disease and}, number = {20150212}, title = {{Ochre star mortality during the 2014 wasting disease epizootic : role of population size structure and temperature}}, volume = {361}, year = {2016} } @article{Menge2016, author = {Menge, Bruce A and Cerny-chipman, Elizabeth B and Johnson, Angela and Sullivan, Jenna and Gravem, Sarah and Chan, Francis}, doi = {10.6085/AA/publication}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Menge et al. - 2016 - Sea Star Wasting Disease in the Keystone Predator Pisaster ochraceus in Oregon Insights into Differential Populati.pdf:pdf}, journal = {PLoSONE}, number = {5}, pages = {e0153994}, title = {{Sea Star Wasting Disease in the Keystone Predator Pisaster ochraceus in Oregon: Insights into Differential Population Impacts, Recovery, Predation Rate, and Temperature Effects from Long-Term Research}}, volume = {11}, year = {2016} } @article{, title = {{No Title}} } @article{Harvell2019, abstract = {{\textless}p{\textgreater} Multihost infectious disease outbreaks have endangered wildlife, causing extinction of frogs and endemic birds, and widespread declines of bats, corals, and abalone. Since 2013, a sea star wasting disease has affected {\textgreater}20 sea star species from Mexico to Alaska. The common, predatory sunflower star ( {\textless}italic{\textgreater}Pycnopodia helianthoides{\textless}/italic{\textgreater} ), shown to be highly susceptible to sea star wasting disease, has been extirpated across most of its range. Diver surveys conducted in shallow nearshore waters ( {\textless}italic{\textgreater}n{\textless}/italic{\textgreater} = 10,956; 2006–2017) from California to Alaska and deep offshore (55 to 1280 m) trawl surveys from California to Washington ( {\textless}italic{\textgreater}n{\textless}/italic{\textgreater} = 8968; 2004–2016) reveal 80 to 100{\%} declines across a {\~{}}3000-km range. Furthermore, timing of peak declines in nearshore waters coincided with anomalously warm sea surface temperatures. The rapid, widespread decline of this pivotal subtidal predator threatens its persistence and may have large ecosystem-level consequences. {\textless}/p{\textgreater}}, annote = {- the novelty relys on the fact that this is a subtidal species as opposed to the classic story with Pisaster spp. and SSWD}, author = {Harvell, C. D. and Montecino-Latorre, D. and Caldwell, J. M. and Burt, J. M. and Bosley, K. and Keller, A. and Heron, S. F. and Salomon, A. K. and Lee, L. and Pontier, O. and Pattengill-Semmens, C. and Gaydos, J. K.}, doi = {10.1126/sciadv.aau7042}, issn = {2375-2548}, journal = {Science Advances}, number = {1}, pages = {eaau7042}, title = {{Disease epidemic and a marine heat wave are associated with the continental-scale collapse of a pivotal predator ( {\textless}i{\textgreater}Pycnopodia helianthoides{\textless}/i{\textgreater} )}}, url = {http://advances.sciencemag.org/lookup/doi/10.1126/sciadv.aau7042}, volume = {5}, year = {2019} } @article{Daly1992, annote = {-argues that economists have recongnized importance of allocation and distribution, but few have thought about scale Do these three things require 3 different solutions? - allocation - what products are created with some input (this is the only thing a market should deal with) - distribution - which people receive these end products - scale is the amount of product produced in absolute terms, only matters if nate is finite e.g. tradeable pollution scheme - I have also thought about the need to fix prices (implicently saying scale can be part of allocation) - discussion of "just price" doctrine which is now rejectly by economists (though it is still used)}, author = {Daly, E}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Daly - 1992 - Allocation, distribution, and scale towards an economics that is efficient, just, and sustainable.pdf:pdf}, journal = {Ecological Economics}, pages = {185--193}, title = {{Allocation, distribution, and scale: towards an economics that is efficient, just, and sustainable}}, volume = {6}, year = {1992} } @article{Funtowicz1994, annote = {- we have similar discussions about uncertainty in ecology, but with different terminollogy - how do we communicate uncertainty appropriately? - people tend to belive things, without evidence, if something has been quantified... - discussino about burdens of proof, type I and II errors}, author = {Funtowicz, Silvio and Ravetz, Jerome R}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Funtowicz, Ravetz - 1994 - The worth of a songbird ecological economics as a post-normal science.pdf:pdf}, journal = {Ecological Economics}, keywords = {ecological}, number = {93}, title = {{The worth of a songbird: ecological economics as a post-normal science}}, volume = {8009}, year = {1994} } @article{Chmura2018, abstract = {{\textless}section class="article-section article-section{\_}{\_}abstract" lang="en" data-lang="en" id="section-1-en"{\textgreater} {\textless}h3 class="article-section{\_}{\_}header main main"{\textgreater}Abstract{\textless}/h3{\textgreater} {\textless}div class="article-section{\_}{\_}content en main"{\textgreater} {\textless}p{\textgreater}Species across a wide‐range of taxa and habitats are shifting phenological events in response to climate change. While advances are common, shifts vary in magnitude and direction within and among species, and the basis for this variation is relatively unknown. We examine previously suggested patterns of variation in phenological shifts in order to understand the cue‐response mechanisms that underlie phenological change. Here, we review what is known about the mechanistic basis for nine factors proposed to predict phenological change (latitude, elevation, habitat type, trophic level, migratory strategy, ecological specialization, species' seasonality, thermoregulatory mode, and generation time). We find that many studies either do not identify a specific underlying mechanism or do not evaluate alternative mechanistic hypotheses, limiting the ability of scientists to predict future responses to global change with accuracy. We present a conceptual framework that emphasizes a critical distinction between environmental (cue‐driven) and organismal (response‐driven) mechanisms causing variation in phenological shifts and discuss how this distinction can reduce confusion in the field and improve predictions of future phenological change.{\textless}/p{\textgreater} {\textless}p{\textgreater}This article is protected by copyright. All rights reserved.{\textless}/p{\textgreater}}, author = {Chmura, Helen E. and Kharouba, Heather M. and Ashander, Jaime and Ehlman, Sean M. and Rivest, Emily B. and Yang, Louie H.}, doi = {10.1002/ecm.1337}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chmura et al. - 2018 - The mechanisms of phenology the patterns and processes of phenological shifts.pdf:pdf}, isbn = {0000000292375}, issn = {15577015}, journal = {Ecological Monographs}, keywords = {altitude,climate change,cue,generation time,latitude,mechanism,migration,phenology,trophic mismatch}, number = {0}, pages = {1--20}, pmid = {7189}, title = {{The mechanisms of phenology: the patterns and processes of phenological shifts}}, volume = {0}, year = {2018} } @article{Day2015, abstract = {Ongoing climate change threatens to cause mismatches between the phenology of many organisms and their resources. Populations of migratory birds may need to undergo ‘evolutionary rescue' if resource availability moves to earlier dates in the year, as shifted arrival dates at the breeding grounds may be required for persistence under new environmental schedules. Here we show a counterintuitive process that can reduce the strength of selection for early arrival when the resource peaks earlier. This happens when two processes combine to determine selection for early arrival: breeding success is higher if a bird does not miss the resource peak, but this occurs together with a ‘zero-sum game' where birds acquire good territories ahead of their competitors if they arrive early. The latter process can relax if the population has experienced a recent decline. Therefore, climate change can have two opposing effects: its direct effect on breeding success strengthens selection for early arrival, but this combines with an indirect effect of relaxed selection due to population declines, if territoriality is a significant determinant of population dynamics and fitness. We show that the latter process can predominate, and this can cause a failure for a population to adapt to a new schedule under changing environmental conditions.}, author = {Day, Emma and Kokko, Hanna}, doi = {10.1111/oik.01340}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Day, Kokko - 2015 - Relaxed selection when you least expect it Why declining bird populations might fail to respond to phenological mism.pdf:pdf}, isbn = {1600-0706}, issn = {16000706}, journal = {Oikos}, number = {1}, pages = {62--68}, pmid = {16008674}, title = {{Relaxed selection when you least expect it: Why declining bird populations might fail to respond to phenological mismatches}}, volume = {124}, year = {2015} } @article{Poethke2016, abstract = {Proper timing of activities is one of the principal challenges faced by most organisms. Organisms need to account for various aspects in decision making like avoiding inordinate risks, synchronizing with resource availability, or finding mates. We provide analytical and simulation models to investigate the influence of life expectancy, resource competition and unpredictable environmental conditions (environmental uncertainty) on the evolutionarily stable distribution of emergence times in organisms depending on seasonally available resources. We focus on the partitioning of total phenotypic variance in emergence times into 1) genetic variance in mean emergence times between lineages and 2) environmental trait variance that determines the intra-lineage variance in the timing of emergence. Both, life expectancy of organisms and intensity of competition severely influence the evolutionary response to environmental uncertainty. Our main findings can be summarized as follows: 1) in general diversifying bet hedging (environmental trait variance) is the adequate mechanism to reduce the risk arising from environmental uncertainty while conservative bet hedging, i.e. delaying emergence into 'safe' phases of the season is restricted to short lived organisms and to situations with vanishing competition. 2) Environmental trait variance increases with increasing environmental uncertainty whereas 3) significant genetic variance evolves only under severe resource competition; it is driven by selection for an ideal free distribution of emergence times. 4) The level of genetic variance evolving declines with increasing life expectancy of organisms. 5) With sufficiently short life expectancy evolutionary branching and coexistence of distinctly different emergence strategies occurs; the number of co-occurring strategies is determined by the level of environmental uncertainty. Our model provides cues for understanding how different ecological factors contribute and interact to shape the evolution of emergence strategies.}, author = {Poethke, Hans Joachim and Hovestadt, Thomas and Mitesser, Oliver}, doi = {10.1111/oik.03213}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Poethke, Hovestadt, Mitesser - 2016 - The evolution of optimal emergence times bet hedging and the quest for an ideal free temporal dist.pdf:pdf}, isbn = {1600-0706}, issn = {16000706}, journal = {Oikos}, number = {11}, pages = {1647--1656}, title = {{The evolution of optimal emergence times: bet hedging and the quest for an ideal free temporal distribution of individuals}}, volume = {125}, year = {2016} } @article{Reed2015, abstract = {Life cycle events in plants and animals are typically adaptively tuned to anticipate predictable seasonal changes in environmental conditions or resources. Climate change is expected to affect the temporal component of species' interactions, e.g. by creating a mismatch between a predator's breeding time (when ample food supply is critical) and the time when prey abundance is high. The demographic implications of such a mismatch remain unclear, however. Here we focussed on changes in the phenology of consumers relative to that of their food. We developed a model where reproductive output of the consumer up to offspring independence depended on mismatch and recruitment of the offspring to breeders depended on offspring density according to a Beverton–Holt function. Using a deterministic version of the model, we clarified how the effects of (constant) mismatch on equilibrium population size depended on the emergent strength of negative density dependence (DD). Using a stochastic, individual-based version, we showed that when the environment changed abruptly, the rate of population recovery was faster when heritability of seasonal timing was higher and DD was stronger. When the environment shifted continuously, the rate of decline in population size was inversely proportional to the rate of microevolution, but stronger DD slowed the rate of decline for a given heritability and thus effectively ‘bought time' for evolutionary rescue. These results highlight the importance of negative DD, which interacts with the effects of trait heritability and stabilizing selection strength, in influencing the fate of populations experiencing environmental change. We emphasize, however, that outcomes in nature will depend crucially on the exact nature of DD, in particular whether population growth rate differences are greatest at low or high densities, highlighting the need for empirical comparisons of compensatory processes in different populations or species.}, author = {Reed, Thomas E. and Gienapp, Phillip and Visser, Marcel E.}, doi = {10.1111/oik.01398}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reed, Gienapp, Visser - 2015 - Density dependence and microevolution interactively determine effects of phenology mismatch on population.pdf:pdf}, isbn = {1600-0706}, issn = {16000706}, journal = {Oikos}, number = {1}, pages = {81--91}, title = {{Density dependence and microevolution interactively determine effects of phenology mismatch on population dynamics}}, volume = {124}, year = {2015} } @article{Harts2016, abstract = {For migratory species, the timing of arrival at breeding grounds is an important determinant of fitness. Too early arrival at the breeding ground is associated with various costs, and we focus on one understudied cost: that migrants can experience a higher risk of predation if arriving earlier than the bulk of the breeding population. We show, using both a semi-analytic and simulation model, that predation can select for later arrival. This is because of safety in numbers: predation risk becomes diluted if many other individuals, either con- or heterospecific, are already residing in the area. Predation risk dilution can also select for more synchronous arrival because deviating from the current population-wide norm to earlier or later dates leads to higher predation risk or to failures in territory acquisition, respectively. The fact that selection for high arrival synchrony can in some cases be more important than selection for a specific date (early or late) within the season is an example of an ‘evolutionary priority effect': whichever strategy – in this case a particular arrival time – becomes established in a population can remain stable over long periods of time; there are many possible equilibria (multiple stable states) which the population can remain at. Mixed arrival strategies are also possible under some circumstances.}, author = {Harts, Anna M.F. and Kristensen, Nadiah P. and Kokko, Hanna}, doi = {10.1111/oik.02973}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Harts, Kristensen, Kokko - 2016 - Predation can select for later and more synchronous arrival times in migrating species.pdf:pdf}, issn = {16000706}, journal = {Oikos}, number = {10}, pages = {1528--1538}, title = {{Predation can select for later and more synchronous arrival times in migrating species}}, volume = {125}, year = {2016} } @article{Gill2017, abstract = {Marine protected areas are proliferating quickly in the hope of safeguarding marine resources. Here David Gill and colleagues show that inadequate staffing capacity is compromising the efficacy of marine protected areas globally. They analyse fish biomass and management data for marine protected areas around the world and find that, although 71 of these protected areas are benefiting fish populations, the effects are highly variable. Staff capacity was identified as the most important explanatory variable, accounting for around 19 of the variation in the benefits of marine protection. They suggest that continued expansion of marine protected areas around the globe without adequate investment in human and financial capacity could limit marine conservation outcomes.}, archivePrefix = {arXiv}, arxivId = {NIHMS150003}, author = {Gill, David A. and Mascia, Michael B. and Ahmadia, Gabby N. and Glew, Louise and Lester, Sarah E. and Barnes, Megan and Craigie, Ian and Darling, Emily S. and Free, Christopher M. and Geldmann, Jonas and Holst, Susie and Jensen, Olaf P. and White, Alan T. and Basurto, Xavier and Coad, Lauren and Gates, Ruth D. and Guannel, Greg and Mumby, Peter J. and Thomas, Hannah and Whitmee, Sarah and Woodley, Stephen and Fox, Helen E.}, doi = {10.1038/nature21708}, eprint = {NIHMS150003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gill et al. - 2017 - Capacity shortfalls hinder the performance of marine protected areas globally.pdf:pdf}, isbn = {1476-4687 (Electronic) 0028-0836 (Linking)}, issn = {14764687}, journal = {Nature}, number = {7647}, pages = {665--669}, pmid = {28329771}, publisher = {Nature Publishing Group}, title = {{Capacity shortfalls hinder the performance of marine protected areas globally}}, url = {http://dx.doi.org/10.1038/nature21708}, volume = {543}, year = {2017} } @article{Niles2017, abstract = {Given that smallholder farmers are frequently food insecure and rely significantly on rain-fed agriculture, it is critical to examine climate variability and food insecurity. We utilize data from smallholder farmer surveys from 12 countries with 30 years of rainfall data to examine how rainfall variability and household resources are correlated with food security. We find that on average, households that experienced a drier than average year are 3.81 months food insecure, while households within a normal range of rainfall were 3.67 months food insecure, and wetter than average households were 2.86 months food insecure. Reduced odds of food insecurity is associated with agricultural inputs, ownership of livestock, water use efficiency, financial services, and participation in a group. However, in drier than average households, financial services as compared to agricultural inputs and agroecological practices have a greater prevalence of reduced instances of food insecurity, while agricultural inputs are more common for reduced food insecurity in wetter than average households. Only the use of fertilizer consistently results in reduced odds of food insecurity across all households regardless of rainfall, demonstrating that one-size fits all approaches to food security interventions are likely ineffective, and place-specific interventions considering climatic factors are critically important.}, author = {Niles, Meredith T. and Brown, Molly E.}, doi = {10.1038/s41598-017-16282-9}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Niles, Brown - 2017 - A multi-country assessment of factors related to smallholder food security in varying rainfall conditions.pdf:pdf}, isbn = {2045-2322}, issn = {20452322}, journal = {Scientific Reports}, number = {1}, pages = {1--11}, publisher = {Springer US}, title = {{A multi-country assessment of factors related to smallholder food security in varying rainfall conditions}}, url = {http://dx.doi.org/10.1038/s41598-017-16282-9}, volume = {7}, year = {2017} } @article{WhiteHastings2018, author = {White, Easton R. and Hastings, Alan}, journal = {PeerJ Preprints}, number = {e27235v1}, title = {{Seasonality in ecology: Progress and prospects in theory}}, volume = {6}, year = {2018} } @article{White2018a, author = {White, Easton R}, journal = {PeerJ Preprints}, number = {e3168v4}, title = {{Minimum time required to detect population trends: the need for long-term monitoring programs}}, volume = {6}, year = {2018} } @article{White2018, author = {White, Easton R. and Smith, Andrew T.}, doi = {https://doi.org/10.1002/ecy.2546}, journal = {Ecology}, title = {{The role of spatial structure in the collapse of regional metapopulations}}, year = {2018} } @article{Rosa2008, abstract = {By the end of this century, anthropogenic carbon dioxide (CO(2)) emissions are expected to decrease the surface ocean pH by as much as 0.3 unit. At the same time, the ocean is expected to warm with an associated expansion of the oxygen minimum layer (OML). Thus, there is a growing demand to understand the response of the marine biota to these global changes. We show that ocean acidification will substantially depress metabolic rates (31{\%}) and activity levels (45{\%}) in the jumbo squid, Dosidicus gigas, a top predator in the Eastern Pacific. This effect is exacerbated by high temperature. Reduced aerobic and locomotory scope in warm, high-CO(2) surface waters will presumably impair predator-prey interactions with cascading consequences for growth, reproduction, and survival. Moreover, as the OML shoals, squids will have to retreat to these shallower, less hospitable, waters at night to feed and repay any oxygen debt that accumulates during their diel vertical migration into the OML. Thus, we demonstrate that, in the absence of adaptation or horizontal migration, the synergism between ocean acidification, global warming, and expanding hypoxia will compress the habitable depth range of the species. These interactions may ultimately define the long-term fate of this commercially and ecologically important predator.}, author = {Rosa, R. and Seibel, B. A.}, doi = {10.1073/pnas.0806886105}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rosa, Seibel - 2008 - Synergistic effects of climate-related variables suggest future physiological impairment in a top oceanic predator.pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {52}, pages = {20776--20780}, pmid = {19075232}, title = {{Synergistic effects of climate-related variables suggest future physiological impairment in a top oceanic predator}}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0806886105}, volume = {105}, year = {2008} } @article{Moreno-b2018, author = {Moreno-b, Marcia and Johnson, Andrew Frederick and Erisman, Brad and Jim, Victoria}, doi = {10.1111/conl.12358}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moreno-b et al. - 2018 - Endangered Species , Ecosystem Integrity , and Human.pdf:pdf}, keywords = {bycatch,california,conservation,economics,extinction,fisheries,shrimp,trawling,upper gulf of,vaquita marina}, number = {February}, pages = {1--8}, title = {{Endangered Species , Ecosystem Integrity , and Human}}, volume = {11}, year = {2018} } @article{Lluch-Cota2007, annote = {- lots of good background in formation on environmental drivers and non-exploited species Fisheries: - shrimp is one of the most important fisheries. There is also a lot of shrimp farming. Destructive trawling gear - small pelgaic fishes (Pacific sardine is most important, also herring and anchovy) - squid - large pelagic fishes - tuna, billfish, sailfish, dorado, 40 species of shark Artisinal fisheries - still a large part. A diverse set of species and fishing practices that are used Sport fishing - brings in a lot of tourism and money}, author = {Lluch-Cota, Salvador E and Arago, Eugenio A and Aurioles-Gamboa, David and Arreguı, Francisco and Brusca, Richard C and Cervantes-Duarte, Rafael and Corte, Roberto and Del-Monte-Luna, Pablo and Esquivel-herrera, Alfonso and Ferna, Guillermo and Herrera-Cervantes, Hugo and Hendrickx, Michel E and Herna, Sergio and Lluch-Belda, Daniel and Lluch-Cota, Daniel B and Kahru, Mati and Lavı, Miguel and Lo, Juana and Palacios-Castro, Eduardo and Pare, Alejandro and Ortega-Garcı, Sofia and Schwartzlose, Richard A and Sierra-Beltra, Arturo P}, doi = {10.1016/j.pocean.2007.01.013}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lluch-Cota et al. - 2007 - The Gulf of California Review of ecosystem status and sustainability challenges.pdf:pdf}, journal = {Progress in Oceanography}, pages = {1--26}, title = {{The Gulf of California: Review of ecosystem status and sustainability challenges}}, volume = {73}, year = {2007} } @article{Cisneros-Montemayor2016, abstract = {Socio-political issues are important in environmental policy outcomes but are often overlooked in conservation planning. We analyze the effects of historical social, political, and ecological contexts on conservation policy outcomes as applied to the Upper Gulf of California and Colorado River Delta Biosphere Reserve. A rushed implementation, perhaps necessary for the protection of endangered totoaba (Totoaba macdonaldi) and vaquita (Phocoena sinus), occurred with little community consultation, resulting in enduring disgruntlement among stakeholders that undermined its effectiveness. Overfishing and habitat degradation continue both inside and outside the reserve, and totoaba and vaquita remain Critically Endangered, with the latter's population estimated at approximately 90 individuals. Marine reserves can be useful, but when top-down enforcement is unfeasible, effective environmental policy requires full recognition and integration of political history and social structures and needs, and open discussion on trade-offs when win-win situations are not possible.}, author = {Cisneros-Montemayor, Andr{\'{e}}s M. and Vincent, Amanda C.J.}, doi = {10.5751/ES-08255-210209}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cisneros-Montemayor, Vincent - 2016 - Science, society, and flagship species Social and political history as keys to conservation outcom.pdf:pdf}, isbn = {17083087}, issn = {17083087}, journal = {Ecology and Society}, keywords = {Biosphere reserve,Flagship species,Gulf of California,Social-ecological dynamics,Totoaba,Vaquita}, number = {2}, title = {{Science, society, and flagship species: Social and political history as keys to conservation outcomes in the gulf of California}}, volume = {21}, year = {2016} } @article{Sagarin2008, abstract = {One of the most storied biological expeditions is the 1940 trip to the Sea of Cortez (Gulf of California) by author John Steinbeck and his close friend Edward F Ricketts, a professional biologist. Steinbeck and Ricketts visited intertidal sites around the Gulf and made extensive collections, taking notes on fauna and natural his- tory. In 2004, we retraced the Steinbeck and Ricketts' voyage, visiting the same intertidal sites during the same season and using the authors' extensive natural history notes as a baseline for comparison. Although we found many of the same species as they did, populations were, in many cases, not as geographically widespread, and individuals were fewer in number and smaller in size. In particular, echinoderms and large gastropods showed declines, as did most large pelagic vertebrate species. One of the most remarkable changes in the pelagic com- munity is the present abundance of jumbo squid, Dosidicus gigas, a species not reported in 1940. Although Steinbeck and Ricketts, by their own admission, “could not yet relate the microcosm of the Gulf with the ont Ecol Enviro macrocosm of the sea”, the changes we observed with historical perspective are in agreement with docu- mented changes in ocean and coastal ecosystems around the world.}, annote = {Nice paper where they reexamined the plots of the famous Steinbeck and Ricketts expedition of 1940. They show that in most places, and for most taxa, the number of species has declining. The lowest declines seemed to occur in more remote places...}, author = {Sagarin, Raphael D. and Gilly, William F. and Baxter, Charles H. and Burnett, Nancy and Christensen, Jon}, doi = {10.1890/070067}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sagarin et al. - 2008 - Remembering the Gulf Changes to the marine communities of the Sea of Cortez since the Steinbeck and Ricketts exp.pdf:pdf}, isbn = {1540-9295}, issn = {15409295}, journal = {Frontiers in Ecology and the Environment}, number = {7}, pages = {372--379}, title = {{Remembering the Gulf: Changes to the marine communities of the Sea of Cortez since the Steinbeck and Ricketts expedition of 1940}}, volume = {6}, year = {2008} } @article{Blowes2012, author = {Blowes, Shane A and Connolly, Sean R}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Blowes, Connolly - 2012 - Risk spreading, connectivity, and optimal reserve spacing.pdf:pdf}, journal = {Ecological Applications}, keywords = {connectivity,environmental covariance,population synchrony,reserve design,risk,spatial population ecology,spreading}, number = {1}, pages = {311--321}, title = {{Risk spreading, connectivity, and optimal reserve spacing}}, volume = {22}, year = {2012} } @article{Gouhier2013, annote = {Is there a trophic cascade occuring at Cocos? Tiger sharks have been able to reduce other species perhaps? --Basket et al 2007 show that incresaing the size and decreasing spacing between reservs descresas these trophic and competitve effects Show that increased connectivity can actually decrease persistence in a nonequilbrium world because it sycronizes the dynamics between populations... Getting at the Moran effect... Instead they argue that models should study extent of species patchiness instead of extent of dispersal... They point out that all these results depend if the variability in population size is driven by endogenous or exogenous forces. If exogeneous, then the classic results from equilbrium models still apply (which I think they show in the Appendix)}, author = {Gouhier, Tarik C and Guichard, Fr{\'{e}}d{\'{e}}ric and Menge, Bruce A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gouhier, Guichard, Menge - 2013 - Designing effective reserve networks for nonequilibrium metacommunities.pdf:pdf}, journal = {Ecological Applications}, number = {6}, pages = {1488--1503}, title = {{Designing effective reserve networks for nonequilibrium metacommunities}}, volume = {23}, year = {2013} } @article{Hutchings2013, author = {Hutchings, Jeffrey A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hutchings - 2013 - Renaissance of a caveat Allee effects in marine fish.pdf:pdf}, journal = {ICES Journal of Marine Science}, keywords = {a scientific legacy predicated,academy of,by uncommon breadth,depensation,in 1947,it was,johan hjort delivered a,lecture to the danish,natural sciences entitled,population growth rate,rebuilding,recovery,reference point,renaissance of the individual,threshold}, pages = {1--6}, title = {{Renaissance of a caveat: Allee effects in marine fish}}, year = {2013} } @article{Pellowe2017, author = {Pellowe, Kara E and Leslie, Heather M}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pellowe, Leslie - 2017 - Seasonal variability shapes resilience of small- scale fisheries in Baja California Sur, Mexico.pdf:pdf}, isbn = {1111111111}, journal = {PLoSONE}, pages = {1--15}, title = {{Seasonal variability shapes resilience of small- scale fisheries in Baja California Sur, Mexico}}, year = {2017} } @article{Lubchenco2013, annote = {this review lays out the entire special issue. Here they define marine reserves and MPAs for what seems like the first time in the literature They point to the current state of knowledge for MPAs, including expected ecological effects and how their design affects both fisheries and conservatoin. They point to several key issues that are not well-addressed yet: multi-species situations and socio-economic questions. I don't think that either of theese questions has been partircrauy well-addressed, especially not in tandem.}, author = {Lubchenco, Jane and Palumbi, Stephen R and Gaines, Steven D and Andelman, Sandy and Applications, Source Ecological and The, Supplement and Reserves, Marine}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lubchenco et al. - 2013 - Plugging a hole in the ccean The emerging science of marine reserves.pdf:pdf}, journal = {Ecological Applications}, number = {1}, pages = {3--7}, title = {{Plugging a hole in the ccean: The emerging science of marine reserves}}, volume = {13}, year = {2013} } @article{Sala2011, author = {Sala, Enric and Aburto-Oropeza, Octavio and Reza, Miriam and Paredes, Gustavo and L{\'{o}}pez-Lemus, Luis G.}, doi = {10.1577/1548-8446(2004)29}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sala et al. - 2011 - Fishing Down Coastal Food Webs in the Gulf of California.pdf:pdf}, journal = {Fisheries}, number = {2004}, title = {{Fishing Down Coastal Food Webs in the Gulf of California}}, volume = {2415}, year = {2011} } @article{Sala2011a, author = {Sala, Enric}, doi = {10.1371/journal.pone.0023601}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sala - 2011 - Large Recovery of Fish Biomass in a No-Take Marine Reserve.pdf:pdf}, number = {8}, title = {{Large Recovery of Fish Biomass in a No-Take Marine Reserve}}, volume = {6}, year = {2011} } @article{Alvarez-romero2018, author = {Alvarez-romero, Jorge G and Beger, Maria and Robert, Georgina G Gurney and Su, Mar Mancha-cisneros Alvin N and Leah, L Pressey and Hem, R Gerber and Adams, Vanessa M and Kolb, Melanie and Graham, Erin M and Vanderwal, Jeremy and Castillo-l, Alejandro and Petat, David and Torre, Jorge}, doi = {10.1111/gcb.13989}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Alvarez-romero et al. - 2018 - Designing connected marine reserves in the face of global warming.pdf:pdf}, number = {September 2017}, title = {{Designing connected marine reserves in the face of global warming}}, year = {2018} } @article{Bizzarro, author = {Bizzarro, Joseph J and Smith, Wade D and Hueter, Robert E and Carlos, J and Garayzar, Villavicencio}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bizzarro et al. - Unknown - Activities and Catch Composition of Artisanal Elasmobranch Fishing Sites on the Eastern Coast of Baja Califo.pdf:pdf}, title = {{Activities and Catch Composition of Artisanal Elasmobranch Fishing Sites on the Eastern Coast of Baja California Sur , Mexico Activities and Catch Composition of Artisanal Elasmobranch}} } @article{Sievanen2014, annote = {Interesting paper that discusses how fishers in Baja deal with environmental change and perturbations. There is usually a lot of movement, spatially, by fishers to deal with this... In patchily-disturbed environmental, people can move (just like fish but probably to a greater extent) to low disturbance areas temporairly}, author = {Sievanen, Leila}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sievanen - 2014 - How do small-scale fishers adapt to environmental variability Lessons from Baja California , Sur , Mexico.pdf:pdf}, journal = {Maritime Studies}, keywords = {adaptation,as in many parts,environmental variability,fisheries,fishers in mexico face,for people living in,livelihoods,major source of livelihood,many challenges like competition,nevertheless,of the world,other,small-scale,small-scale fisheries are a,state of baja california,sur,the mexican,vulnerability,with coastal tourism and}, number = {9}, pages = {1--19}, title = {{How do small-scale fishers adapt to environmental variability ? Lessons from Baja California , Sur , Mexico}}, volume = {13}, year = {2014} } @article{Erisman2010, author = {Erisman, Brad and Mascarenas, Ismael and Paredes, Gustavo and Sadovy, Yvonne and Mitcheson, De and Aburto-oropeza, Octavio and Hastings, Philip}, doi = {10.1016/j.fishres.2010.08.007}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Erisman et al. - 2010 - Seasonal , annual , and long-term trends in commercial fisheries for aggregating reef fishes in the Gulf of Cali.pdf:pdf}, issn = {0165-7836}, journal = {Fisheries Research}, keywords = {fish spawning aggregations}, number = {3}, pages = {279--288}, publisher = {Elsevier B.V.}, title = {{Seasonal , annual , and long-term trends in commercial fisheries for aggregating reef fishes in the Gulf of California , Mexico}}, url = {http://dx.doi.org/10.1016/j.fishres.2010.08.007}, volume = {106}, year = {2010} } @article{Williams2017, abstract = {Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging. Here, we have identified four important research questions with the goal of advancing our understanding of evolutionary impacts of seasonality. First, we ask how characteristics of environments and species will determine which adaptive response occurs. Relevant characteristics include costs and limits of plasticity, predictability, and reliability of cues, and grain of environmental variation relative to generation time. A second important question is how phenological shifts will amplify or ameliorate selection on physiological hardiness. Shifts in phenology can preserve the thermal niche despite shifts in climate, but may fail to completely conserve the niche or may even expose life stages to conditions that cause mortality. Considering distinct environmental sensitivities of life history stages will be key to refining models that forecast susceptibility to climate change. Third, we must identify critical physiological phenotypes that underlie seasonal adaptation and work toward understanding the genetic architectures of these responses. These architectures are key for predicting evolutionary responses. Pleiotropic genes that regulate multiple responses to changing seasons may facilitate coordination among functionally related traits, or conversely may constrain the expression of optimal phenotypes. Finally, we must advance our understanding of how changes in seasonal fluctuations are impacting ecological interaction networks. We should move beyond simple dyadic interactions, such as predator prey dynamics, and understand how these interactions scale up to affect ecological interaction networks. As global climate change alters many aspects of seasonal variability, including extreme events and changes in mean conditions, organisms must respond appropriately or go extinct. The outcome of adaptation to seasonality will determine responses to climate change.}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Williams, Caroline M. and Ragland, Gregory J. and Betini, Gustavo and Buckley, Lauren B. and Cheviron, Zachary A. and Donohue, Kathleen and Hereford, Joe and Humphries, Murray M. and Lisovski, Simeon and Marshall, Katie E. and Schmidt, Paul S. and Sheldon, Kimberly S. and Varpe, {\O}ystein and Visser, Marcel E.}, doi = {10.1093/icb/icx122}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Williams et al. - 2017 - Understanding Evolutionary Impacts of Seasonality An Introduction to the Symposium.pdf:pdf}, isbn = {9781455748013}, issn = {15577023}, journal = {Integrative and comparative biology}, number = {5}, pages = {921--933}, pmid = {29045649}, title = {{Understanding Evolutionary Impacts of Seasonality: An Introduction to the Symposium}}, volume = {57}, year = {2017} } @article{Kennett2012, author = {Kennett, Douglas J and Breitenbach, Sebastian F M and Aquino, Valorie V and Asmerom, Yemane and Awe, Jaime and Baldini, James U L and Bartlein, Patrick and Culleton, Brendan J and Ebert, Claire and Jazwa, Christopher and Macri, Martha J and Marwan, Norbert and Polyak, Victor and Prufer, Keith M and Ridley, Harriet E and Sodemann, Harald and Winterhalder, Bruce and Haug, Gerald H}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kennett et al. - 2012 - Development and Disintegration of Maya Political Systems in Response to Climate Change.pdf:pdf}, journal = {Science}, number = {November}, pages = {788--792}, title = {{Development and Disintegration of Maya Political Systems in Response to Climate Change}}, volume = {338}, year = {2012} } @article{Dennis2016, author = {Dennis, Brian and Assas, Laila and Elaydi, Saber and Kwessi, Eddy and Livadiotis, George and Dennis, Brian}, doi = {10.1007/s12080-015-0288-2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dennis et al. - 2016 - Allee effects and resilience in stochastic populations.pdf:pdf}, issn = {1874-1738}, journal = {Theoretical Ecology}, keywords = {Allee effect,Alternative stable states,Diffusion process,Ecological resilience,First passage time,Logistic model,Positive density dependence,Potential function,Stationary distribution,Stochastic population model,Volterra model,allee effect,diffusion process,ecological resilience,firstpassage time,logistic model,populationmodel,positive density dependence,potential function,stationarydistribution,stochastic,volterra model}, pages = {323--335}, publisher = {Theoretical Ecology}, title = {{Allee effects and resilience in stochastic populations}}, url = {http://dx.doi.org/10.1007/s12080-015-0288-2}, volume = {9}, year = {2016} } @article{Garavelli2018, author = {Garavelli, Lysel and White, J. Wilson and Chollett, Iliana and Ch{\'{e}}rubin, Laurent Marcel}, doi = {10.1111/conl.12567}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Garavelli et al. - 2018 - Population models reveal unexpected patterns of local persistence despite widespread larval dispersal in a hig.pdf:pdf}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {fisheries,larval connectivity,panulirus argus,persistence,population models,transboundary management}, number = {April}, pages = {e12567}, title = {{Population models reveal unexpected patterns of local persistence despite widespread larval dispersal in a highly exploited species}}, url = {http://doi.wiley.com/10.1111/conl.12567}, year = {2018} } @article{Mailleret2009, abstract = {Semi-discrete models are a particular class of hybrid dynamical systems that undergo continuous dynamics most of the time but repeatedly experience discrete changes at some given moments. In the life sciences, since the first semi-discrete model was derived to describe population dynamics by Beverton {\&} Holt (Beverton {\&} Holt 1957 In Fisheries investigations, series 2, vol. 19), a large body of literature has been concerned with such modelling approaches. The aim of the present contribution is twofold. On the one hand, it provides a comprehensive introduction to semi-discrete modelling through two illustrative examples: the classical work by Beverton and Holt is recalled and an original example on immigration in a population model affected by a strong Allee effect is worked out. On the other hand, a short overview of the different applications of semi-discrete models in the life sciences is proposed.}, author = {Mailleret, Ludovic and Lemesle, Val{\'{e}}rie}, doi = {10.1098/rsta.2009.0153}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mailleret, Lemesle - 2009 - A note on semi-discrete modelling in the life sciences.pdf:pdf}, isbn = {1364-503X}, issn = {1364503X}, journal = {Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences}, keywords = {Allee effect model,Beverton-Holt model,Epidemiology,Impulsive differential equations,Medicine,Population dynamics}, number = {1908}, pages = {4779--4799}, pmid = {19884180}, title = {{A note on semi-discrete modelling in the life sciences}}, volume = {367}, year = {2009} } @article{Quinn1987, annote = {This paper examines a very simple model of two patches that are not connected to one another. They show that it is always better to have more than one patch if their is environmental stochastcity. The replication of patches simply serves as an insurance factor}, author = {Quinn, James F and Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Quinn, Hastings - 1987 - Society for Conservation Biology Extinction in Subdivided Habitats Extinction in Subdivided Habitat.pdf:pdf}, journal = {Conservation Biology}, number = {3}, pages = {198--208}, title = {{Society for Conservation Biology Extinction in Subdivided Habitats Extinction in Subdivided Habitat}}, volume = {1}, year = {1987} } @article{Hiddink2007, author = {Hiddink, J G and Jennings, S and Kaiser, M J}, doi = {10.1111/j.1365-2664.2007.01274.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hiddink, Jennings, Kaiser - 2007 - Assessing and predicting the relative ecological impacts of disturbance on habitats with different se.pdf:pdf}, journal = {Journal of Applied Ecology}, pages = {405--413}, title = {{Assessing and predicting the relative ecological impacts of disturbance on habitats with different sensitivities}}, volume = {44}, year = {2007} } @article{Moeller2013, annote = {Can implemented MPAs then increase tourist pressures in the area? Negated potential benefits.... "Crop rotation" of tourist areas.. THey provide reason why you might want to set aside small, numerous areas. For them it is not about replication here. This is probably because they are trying to maximize yield as well....}, author = {Moeller, Holly V and Neubert, Michael G}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moeller, Neubert - 2013 - Habitat damage, marine reserves, and the value of spatial management.pdf:pdf}, journal = {Ecological Applications}, keywords = {areas,bioeconomics,destructive fishing practices,fisheries,habitat damage,marine protected,marine reserves,optimal control,optimal harvesting,spatial management}, number = {5}, pages = {959--971}, title = {{Habitat damage, marine reserves, and the value of spatial management}}, volume = {23}, year = {2013} } @article{Claudet2010b, annote = {How would life history traits affect your ability to detect positive effects of a marine reserve? -{\textgreater} Fundamentally a question about statistical power... Surprising that highly mobile species also benefited from marine reserves - Noncommerical bycatch and unexploitated species rarely benefited from protection}, author = {Claudet, J. and Osenberg, C.W. and Domenici, P. and Badalamenti, F. and Milazzo, M. and Falc{\'{o}}n, J.M. and Bertocci, I. and Benedetti-Cecchi, L and Garc{\'{i}}a-Charton, J.A. and Go{\~{n}}i, R. and Borg, J.A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Claudet et al. - 2010 - Marine reserves Fish life history and ecological traits matter(2).pdf:pdf}, journal = {Ecological Applications}, keywords = {body size,bycatch,habitat,home range,life history traits,marine,marine protected area,marine reserve design,reserve age,schooling behavior,species mobility,territoriality,weighted meta-}, number = {3}, pages = {830--839}, title = {{Marine reserves: Fish life history and ecological traits matter}}, volume = {20}, year = {2010} } @article{LaRiviere2018, abstract = {Environmental and resource economists often use models that include uncertainty and ways to reduce that uncertainty through learning. Using a standard environmental and resource economics framework, this article parses several different forms of uncertainty and learning that are commonly considered in the literature. We then review the applied theory literature using that framework to assess whether there is support for four hypotheses associated with uncertainty and learning in environmental management that have been raised in policy circles. We find that these hypotheses are often true for one type of uncertainty or learning but not another, highlighting how a lack of clarity can lead to confusion among researchers and policymakers.}, author = {LaRiviere, Jacob and Kling, David and Sanchirico, James N. and Sims, Charles and Springborn, Michael}, doi = {10.1093/reep/rex021}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/LaRiviere et al. - 2018 - The treatment of uncertainty and learning in the economics of natural resource and environmental management.pdf:pdf}, issn = {17506824}, journal = {Review of Environmental Economics and Policy}, number = {1}, pages = {92--112}, title = {{The treatment of uncertainty and learning in the economics of natural resource and environmental management}}, volume = {12}, year = {2018} } @article{Thomas1997a, author = {Thomas, L and Krebs, C}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thomas, Krebs - 1997 - A review of statistical power analysis software.pdf:pdf}, issn = {0012-9623}, journal = {Bulletin of the Ecological Society of America}, number = {2}, pages = {128--139}, title = {{A review of statistical power analysis software}}, url = {http://scholar.google.com/scholar?q=intitle:A+REVIEW+OF+STATISTICAL+POWER+ANALYSIS+SOFTWARE{\#}0}, volume = {78}, year = {1997} } @article{Thomas1996, annote = {uses simulations to test different types of population trend analysis methods... focuses on breeding bird survey}, author = {Thomas, Len}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thomas - 1996 - Monitoring long-term population change why are there so many analysis methods.pdf:pdf}, journal = {Ecology}, keywords = {annual indices of abundance,change,comparison of analysis methods,monitoring population,monte carlo simulation,neotropical migrants,north american breeding bird,pop-,survey,ulation trend estimate}, number = {1}, pages = {49--58}, title = {{Monitoring long-term population change: why are there so many analysis methods?}}, volume = {77}, year = {1996} } @article{Sole2002, abstract = {Why are some ecosystems so rich, yet contain so many rare species? High species diversity, together with $\backslash$nrarity, is a general trend in neotropical forests and coral reefs. However, the origin of such diversity and $\backslash$nthe consequences of food web complexity in both species abundances and temporal fluctuations are not $\backslash$nwell understood. Several regularities are observed in complex, multispecies ecosystems that suggest that $\backslash$nthese ecologies might be organized close to points of instability. We explore, in greater depth, a recent $\backslash$nstochastic model of population dynamics that is shown to reproduce: (i) the scaling law linking species $\backslash$nnumber and connectivity; (ii) the observed distributions of species abundance reported from field studies $\backslash$n(showing long tails and thus a predominance of rare species); (iii) the complex fluctuations displayed by $\backslash$nnatural communities (including chaotic dynamics); and (iv) the species–area relations displayed by rainfor- $\backslash$nest plots. It is conjectured that the conflict between the natural tendency towards higher diversity due to $\backslash$nimmigration, and the ecosystem level constraints derived from an increasing number of links, leaves the $\backslash$nsystem poised at a critical boundary separating stable from unstable communities, where large fluctuations $\backslash$nare expected to occur. We suggest that the patterns displayed by species-rich communities, including $\backslash$nrarity, would result from such a spontaneous tendency towards instability.}, author = {Sol{\'{e}}, Ricard V. and Alonso, David and McKane, Alan}, doi = {10.1098/rstb.2001.0992}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sol{\'{e}}, Alonso, McKane - 2002 - Self-organized instability in complex ecosystems.pdf:pdf}, isbn = {0962-8436}, issn = {09628436}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {Rarity,Scaling,Spatial dynamics,Species-abundance distributions,Species-area relations}, number = {1421}, pages = {667--681}, pmid = {12079528}, title = {{Self-organized instability in complex ecosystems}}, volume = {357}, year = {2002} } @article{Thomas1997, abstract = {Many papers have appeared in the recent biological literature encouraging us to incorporate statistical power analysis into our hypothesis testing protocol (Peterman 1990; Fairweather 1991; Muller {\&} Benignus 1992; Taylor {\&} Gerrodette 1993; SearcyBernal 1994; Thomas {\&} Juanes 1996). The importance of doing a power analysis before beginning a study (prospective power analysis) is universally accepted: such analyses help us to decide how many samples are required to have a good chance of getting unambiguous results. In contrast, the role of power analysis after the data are collected and analyzed (retrospective power analysis) is controversial, as is evidenced by the papers of Reed and Blaustein (1995) and Hayes and Steidl (1997). The controversy is over the use of information from the sample data in retrospective power calculations. As I will show, the type of information used has fundamental implications for the value of such analyses. I compare the approaches to calculating retrospective power, noting the strengths and weaknesses of each, and make general recommendations as to how and when retrospective power analyses should be conducted.}, author = {Thomas, Len}, doi = {10.1046/j.1523-1739.1997.96102.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thomas - 1997 - Retrospective Power Analysis.pdf:pdf}, isbn = {0888-8892}, issn = {0888-8892}, journal = {Conservation Biology}, number = {1}, pages = {276--280}, pmid = {16244281}, title = {{Retrospective Power Analysis}}, url = {http://doi.wiley.com/10.1046/j.1523-1739.1997.96102.x}, volume = {11}, year = {1997} } @article{Paradis2004, author = {Paradis, E. and Claude, J. and Strimmer, K.}, journal = {Bioinformatics}, pages = {289--290}, title = {{APE: analyses of phylogenetics and evolution in R language}}, volume = {20}, year = {2004} } @misc{Bennett2018, author = {Bennett, D.J.}, title = {treeman: phylogenetic tree manipulation class and methods}, year = {2018} } @article{Felsenstein2008, abstract = {Comparative methods analyses have usually assumed that the species phenotypes are the true means for those species. In most analyses, the actual values used are means of samples of modest size. The covariances of contrasts then involve both the covariance of evolutionary changes and a fraction of the within-species phenotypic covariance, the fraction depending on the sample size for that species. Ives et al. have shown how to analyze data in this case when the within-species phenotypic covariances are known. The present model allows them to be unknown and to be estimated from the data. A multivariate normal statistical model is used for multiple characters in samples of finite size from species related by a known phylogeny, under the usual Brownian motion model of change and with equal within-species phenotypic covariances. Contrasts in each character can be obtained both between individuals within a species and between species. Each contrast can be taken for all of the characters. These sets of contrasts, each the same contrast taken for different characters, are independent. The within-set covariances are unequal and depend on the unknown true covariance matrices. An expectation-maximization algorithm is derived for making a reduced maximum likelihood estimate of the covariances of evolutionary change and the within-species phenotypic covariances. It is available in the Contrast program of the PHYLIP package. Computer simulations show that the covariances are biased when the finiteness of sample size is not taken into account and that using the present model corrects the bias. Sampling variation reduces the power of inference of covariation in evolution of different characters. An extension of this method to incorporate estimates of additive genetic covariances from a simple genetic experiment is also discussed.}, author = {Felsenstein, Joseph}, doi = {10.1086/587525}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Felsenstein - 2008 - Comparative Methods with Sampling Error and Within-Species Variation Contrasts Revisited and Revised.pdf:pdf}, isbn = {1537-5323 (Electronic)$\backslash$r0003-0147 (Linking)}, issn = {0003-0147}, journal = {The American Naturalist}, keywords = {comparative method,contrasts,contrasts has been widely,felsenstein 1985,phenotypic variance,phylogeny,pling error,sam-,since its introduction,statistics,the method of,used to correct comparative}, number = {6}, pages = {713--725}, pmid = {18419518}, title = {{Comparative Methods with Sampling Error and Within-Species Variation: Contrasts Revisited and Revised}}, url = {http://www.journals.uchicago.edu/doi/10.1086/587525}, volume = {171}, year = {2008} } @incollection{Ball2009, author = {Ball, Ian R and Possingham, Hugh P and Watts, Matthew E}, booktitle = {Spatial Conservation Prioritization: Quantitative Methods and Computational Tools}, editor = {Moilanen, Atte and Wilson, Kerrie A. and Possingham, Hugh P.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ball, Possingham, Watts - 2009 - Marxan and Relatives Software for Spatial Conservation Prioritization.pdf:pdf}, pages = {185--195}, publisher = {Oxford University Press}, title = {{Marxan and Relatives : Software for Spatial Conservation Prioritization}}, year = {2009} } @article{Lampert2014, abstract = {Resolving conflicting ecosystem management goals-such as maintaining fisheries while conserving marine species or harvesting timber while preserving habitat-is a widely recognized challenge. Even more challenging may be conflicts between two conservation goals that are typically considered complementary. Here, we model a case where eradication of an invasive plant, hybrid Spartina, threatens the recovery of an endangered bird that uses Spartina for nesting. Achieving both goals requires restoration of native Spartina. We show that the optimal management entails less intensive treatment over longer time scales to fit with the time scale of natural processes. In contrast, both eradication and restoration, when considered separately, would optimally proceed as fast as possible. Thus, managers should simultaneously consider multiple, potentially conflicting goals, which may require flexibility in the timing of expenditures.}, author = {Lampert, Adam and Hastings, Alan and Grosholz, Edwin D. and Jardine, Sunny L. and Sanchirico, James N.}, doi = {10.1126/science.1250763}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lampert et al. - 2014 - Optimal approaches for balancing invasive species eradication and endangered species management.pdf:pdf}, isbn = {1095-9203 (Electronic)$\backslash$n0036-8075 (Linking)}, issn = {10959203}, journal = {Science}, number = {6187}, pages = {1028--1031}, pmid = {24876497}, title = {{Optimal approaches for balancing invasive species eradication and endangered species management}}, volume = {344}, year = {2014} } @article{Sharov1998, author = {Sharov, Alexei A and Liebhold, Andrew M}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sharov, Liebhold - 1998 - Model of Slowing the Spread of Gypsy Moth (Lepidoptera Lymantriidae) with a Barrier Zone.pdf:pdf}, journal = {Ecological Applications}, keywords = {barrier zone,biological invasion,gypsy moth,lymantria dispar,model,population}, number = {4}, pages = {1170--1179}, title = {{Model of Slowing the Spread of Gypsy Moth (Lepidoptera: Lymantriidae) with a Barrier Zone}}, volume = {8}, year = {1998} } @article{DAloia2017, abstract = {A major objective of marine protected area (MPA) network design is to ensure the persistence of species with diverse life histories and functional traits. Considering how species differ in their propensity to move within and between MPAs is therefore a key consideration for multi-species MPA network design. Here, we propose a conceptual framework to incorporate ecological processes that affect movement at multiple life stages into the MPA network design process. We illustrate how our framework can be implemented using a set of hypothetical species that represent regional trait diversity in coastal British Columbia, Canada. We focused on two ecological processes: (1) dispersal during the larval phase and (2) daily home range movement during the adult phase. To identify functional connectivity patterns, we used a biophysical model to simulate larval dispersal, and then prioritized highly-connected patches using a reserve selection algorithm. To ensure that individual reserves were commensurate with home ranges, we also imposed reserve size constraints. Candidate areas for protection were identified based on multi-species connectivity patterns and home range size constraints. Collectively, this conceptual framework offers a flexible approach to multi-species, cross-life stage conservation planning, which can be further adapted to address complex life histories. As marine conservation efforts around the globe aim to design ecologically connected networks of protected areas, the integration of movement and connectivity data throughout ontogeny will be a key component of effective multi-species MPA network design.}, author = {D'Aloia, Cassidy C. and Daigle, R{\'{e}}mi M. and C{\^{o}}t{\'{e}}, Isabelle M. and Curtis, Janelle M.R. and Guichard, Fr{\'{e}}d{\'{e}}ric and Fortin, Marie Jos{\'{e}}e}, doi = {10.1016/j.biocon.2017.10.012}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/D'Aloia et al. - 2017 - A multiple-species framework for integrating movement processes across life stages into the design of marine pro.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {Home range,Larval dispersal,MPA,Marxan,Movement,Pelagic larval duration}, number = {October}, pages = {93--100}, publisher = {Elsevier}, title = {{A multiple-species framework for integrating movement processes across life stages into the design of marine protected areas}}, url = {http://dx.doi.org/10.1016/j.biocon.2017.10.012}, volume = {216}, year = {2017} } @article{Hastings2005a, abstract = {We review and synthesize recent developments in the study of the spread of invasive species, emphasizing both empirical and theoretical approaches. Recent theoretical work has shown that invasive species spread is a much more complex process than the classical models suggested, as long range dispersal events can have a large influence on the rate of range expansion through time. Empirical work goes even further, emphasizing the role of spatial heterogeneity, temporal variability, other species, and evolution. As in some of the classic work on spread, the study of range expansion of invasive species provides unique opportunities to use differences between theory and data to determine the important underlying processes that control spread rates. The spatial spread of invasive species has been a subject of empirical and theoretical study for many decades (Fisher 1937; Skellam 1951). The earliest work seemed to point to a simple and robust prediction of a linear rate of spread, perhaps after some initial phase where spread was not linear (reviewed by Hengeveld 1989; Andow et al. 1990; Okubo {\&} Levin 2002). The problem of spread has, however, turned out to be much richer and more interesting than was supposed 20 years ago. Some recent theoretical develop-ments have called basic results into question, while others have clarified just when the earlier results should hold (Kot et al. 1996; Weinberger et al. 2002). Much more data are becoming available, and new statistical techniques are being developed to match data with theory. While the early models included only a single non-evolving species in a homogen-eous habitat with random short range dispersal, newer theory is beginning to include the effects of changing all these assumptions. The initial models of Fisher (1937) were phrased as partial differential equations that could be used to predict an asymptotic rate of spread. In the simplest form in one spatial dimension, with p(x,t) a density function for the population level as a function of spatial location x at time t, f [ p(x,t)] the per capita rate of increase of the population at spatial location x and D a measure of the mean squared displacement of individuals per unit time, the model can be written as}, author = {Hastings, Alan and Cuddington, Kim and Davies, Kendi F. and Dugaw, Christopher J. and Elmendorf, Sarah and Freestone, Amy and Harrison, Susan and Holland, Matthew and Lambrinos, John and Malvadkar, Urmila and Melbourne, Brett A. and Moore, Kara and Taylor, Caz and Thomson, Diane}, doi = {10.1111/j.1461-0248.2004.00687.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings et al. - 2005 - The spatial spread of invasions New developments in theory and evidence.pdf:pdf}, isbn = {1461-023X}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Diffusion,Dispersal,Integro-difference equations,Invasions,Reaction-diffusion,Spatial spread}, number = {1}, pages = {91--101}, pmid = {2089}, title = {{The spatial spread of invasions: New developments in theory and evidence}}, volume = {8}, year = {2005} } @article{Rout2014, abstract = {Savanna rangelands worldwide are threatened by shrub encroachment, i.e. the increase of woody plant species at the cost of perennial grasses, causing a strong decline in the productivity of domestic livestock production. Although recent studies indicate that fire might be of great importance for semi-arid and arid savanna dynamics, it is largely not applied in the management of semi-arid rangelands especially with regard to woody plant control. We used the eco-hydrological savanna model EcoHyD to simulate the effects of different fire management strategies on semi-arid savanna vegetation and to assess their long-term suitability for semi-arid rangeland management. Simulation results show that prescribed fires, timed to kill tree seedlings prevented shrub encroachment for a broad range of livestock densities while the possible maximum long-term cattle densities on the simulated semi-arid rangeland in Namibia increased by more than 30{\%}. However, when grazing intensity was too high, fire management failed in preventing shrub encroachment. Our findings indicate that with regard to fire management a clear distinction between mesic and more arid savannas is necessary: While the frequency of fires is of relevance for mesic savannas, we recommend a fire management focussing on the timing of fire for semi-arid and arid savannas.}, author = {Rout, Tracy M. and Moore, Joslin L. and Mccarthy, Michael A.}, doi = {10.1111/1365-2664.12234}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rout, Moore, Mccarthy - 2014 - Prevent, search or destroy A partially observable model for invasive species management.pdf:pdf}, isbn = {1365-2664}, issn = {13652664}, journal = {Journal of Applied Ecology}, keywords = {Control,Cost-effectiveness,Detection,Eradication,Markov decision process,Monitoring,Quarantine,Surveillance,Survey}, number = {3}, pages = {804--813}, title = {{Prevent, search or destroy? A partially observable model for invasive species management}}, volume = {51}, year = {2014} } @article{Merrill2017, abstract = {BACKGROUND: Models describing the effects of climate change on arthropod pest ecology are needed to help mitigate and adapt to forthcoming changes. Challenges arise because climate data are at resolutions that do not readily synchronize with arthropod biology. Here we explain how multiple sources of climate and weather data can be synthesized to quantify the effects of climate change on pest phenology. RESULTS: Predictions of phenological events differ substantially between models that incorporate scale-appropriate temperature variability and models that do not. As an illustrative example, we predicted adult emergence of a pest of sunflower, the sunflower stem weevil Cylindrocopturus adspersus (LeConte). Predictions of the timing of phenological events differed by an average of 11 days between models with different temperature variability inputs. Moreover, as temperature variability increases, developmental rates accelerate. CONCLUSION: Our work details a phenological modeling approach intended to help develop tools to plan for and mitigate the effects of climate change. Results show that selection of scale-appropriate temperature data is of more importance than selecting a climate change emission scenario. Predictions derived without appropriate temperature variability inputs will likely result in substantial phenological event miscalculations. Additionally, results suggest that increased temperature instability will lead to accelerated pest development. {\textcopyright} 2016 Society of Chemical Industry. {\textcopyright} 2016 Society of Chemical Industry}, author = {Merrill, Scott C. and Peairs, Frank B.}, doi = {10.1002/ps.4320}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Merrill, Peairs - 2017 - Temperature variability is a key component in accurately forecasting the effects of climate change on pest phen.pdf:pdf}, issn = {15264998}, journal = {Pest Management Science}, keywords = {Cylindrocopturus adspersus,Kaufmann effect,non-linear modeling,spatiotemporal model,sunflower stem weevil,variance signal}, number = {2}, pages = {380--388}, title = {{Temperature variability is a key component in accurately forecasting the effects of climate change on pest phenology}}, volume = {73}, year = {2017} } @article{Boettiger2016, author = {Boettiger, Carl and Bode, Michael and Sanchirico, James N. and LaRiviere, Jacob and Hastings, Alan and Armsworth, Paul R.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Boettiger et al. - 2016 - Optimal management of a stochastically varying population when policy adjustment is costly.pdf:pdf}, journal = {Ecological Applications}, keywords = {adjustment costs,ecological management,fisheries,optimal control}, number = {3}, pages = {808--817}, title = {{Optimal management of a stochastically varying population when policy adjustment is costly}}, volume = {26}, year = {2016} } @article{Memarzadeh2018, author = {Memarzadeh, Milad and Boettiger, Carl}, doi = {10.1016/j.biocon.2018.05.009}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Memarzadeh, Boettiger - 2018 - Adaptive management of ecological systems under partial observability.pdf:pdf}, issn = {0006-3207}, journal = {Biological Conservation}, keywords = {Adaptive management,Conservation,Decision making under uncertainty,Fisheries}, number = {May}, pages = {9--15}, publisher = {Elsevier}, title = {{Adaptive management of ecological systems under partial observability}}, url = {https://doi.org/10.1016/j.biocon.2018.05.009}, volume = {224}, year = {2018} } @article{Chollett2017, author = {Chollett, Iliana and Garavelli, Lysel and Farrell, Shay O and Cherubin, Laurent and Matthews, Thomas R and Mumby, Peter J and Box, Stephen J}, doi = {10.1111/conl.12318}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chollett et al. - 2017 - A Genuine Win-Win Resolving the “Conserve or Catch” Conflict in Marine Reserve Network Design.pdf:pdf}, journal = {Conservation Letters}, keywords = {argus,fisheries,home range,larval dispersal,no-takes,ontogenetic migration,panulirus,population persistence,spatial planning}, number = {October}, pages = {555--563}, title = {{A Genuine Win-Win : Resolving the “Conserve or Catch” Conflict in Marine Reserve Network Design}}, volume = {10}, year = {2017} } @article{Mestre2017, abstract = {Forecasting future species distributions under climate change scenarios using Ecological Niche Models (ENM) is common practice. Typically, these projections do not account for landscape connectivity and species dispersal abilities. When they do account for these factors, they are based on either rather simplistic or overly complex and data-hungry approaches. Here we apply a new approach for predicting species range shifts under different climate change and landscape connectivity scenarios that balances data requirements and output quality. The approach builds on the metapopulation concept to produce a dispersal model based on repeated simulations of stochastic extinction-colonization dynamics across multiple landscapes of variable connectivity. The model is then combined with an ENM to produce more realistic predictions of species range shifts under environmental change. Using the near-threatened Cabrera vole (Microtus cabrerae) as a model species and considering two contrasting climate change scenarios (B2 and A1b) and three scenarios of increasing landscape connectivity, we confirmed that model predictions based solely on ENM overestimated future range sizes (2050 and 2080) in relation to predictions incorporating both future climates and landscape connectivity constraints. This supports the idea that landscape change critically affects species range shifts in addition to climate change, and that models disregarding landscape connectivity tend to produce overly optimistic predictions, particularly for species with low dispersal abilities. We suggest that our empirically-based simulation modelling approach provides a useful framework to improve range shift predictions for a broad range of species, which is essential for the conservation planning of metapopulations under climate and landscape change.}, author = {Mestre, Frederico and Risk, Benjamin B. and Mira, Ant{\'{o}}nio and Beja, Pedro and Pita, Ricardo}, doi = {10.1016/j.ecolmodel.2017.06.013}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mestre et al. - 2017 - A metapopulation approach to predict species range shifts under different climate change and landscape connectivi.pdf:pdf}, isbn = {0304-3800}, issn = {03043800}, journal = {Ecological Modelling}, keywords = {Climate change,Dispersal,Ecological niche modelling,Landscape change,Metapopulation}, pages = {406--414}, publisher = {Elsevier B.V.}, title = {{A metapopulation approach to predict species range shifts under different climate change and landscape connectivity scenarios}}, url = {http://dx.doi.org/10.1016/j.ecolmodel.2017.06.013}, volume = {359}, year = {2017} } @article{Broms2016, abstract = {The dynamic, multi-season occupancy model framework has become a popular tool for modeling open populations with occupancies that change over time through local colonizations and extinctions. However, few versions of the model relate these probabilities to the occupancies of neighboring sites or patches. We present a modeling framework that incorporates this information and is capable of describing a wide variety of spatio-temporal colonization and extinction processes. A key feature of the model is that it is based on a simple set of small-scale rules describing how the process evolves. The result is a dynamic process that can account for complicated large-scale features. In our model, a site is more likely to be colonized if more of its neighbors were previously occupied and if it provides more appealing environmental characteristics than its neighboring sites. Additionally, a site without occupied neighbors may also become colonized through the inclusion of a long-distance dispersal process. While simi...}, author = {Broms, Kristin M. and Hooten, Mevin B. and Johnson, Devin S. and Altwegg, Res and Conquest, Loveday L.}, doi = {10.1890/15-0416.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Broms et al. - 2016 - Dynamic occupancy models for explicit colonization processes.pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {Acridotheres tristis,Citizen science,Colonization,Common Myna,Dynamic occupancy model,Extinction,Invasive species,Multi-season model,Southern African Bird Atlas Project,Spatiotemporal processes,Species distribution maps}, number = {1}, pages = {194--204}, title = {{Dynamic occupancy models for explicit colonization processes}}, volume = {97}, year = {2016} } @article{Penczykowski2015a, abstract = {Pathogens are considered to drive ecological and evolutionary dynamics of plant populations, but we lack data measuring the population-level consequences of infection in wild plant-pathogen interactions. Moreover, while it is often assumed that offseason environmental conditions drive seasonal declines in pathogen population size, little is known about how offseason environmental conditions impact the survival of pathogen resting stages, and how critical the offseason is for the next season's epidemic. The fungal pathogen Podosphaera plantaginis persists as a dynamic metapopulation in the large network of Plantago lanceolata host populations. Here, we analyze long-term data to measure the spatial synchrony of epidemics and consequences of infection for over 4000 host populations. Using a theoretical model, we study whether large-scale environmental change could synchronize disease occurrence across the metapopulation. During 2001-2013 exposure to freezing decreased, while pathogen extinction-colonization-persistence rates became more synchronized. Simulations of a theoretical model suggest that increasingly favorable winter conditions for pathogen survival could drive such synchronization. Our data also show that infection decreases host population growth. These results confirm that mild winter conditions increase pathogen overwintering success and thus increase disease prevalence across the metapopulation. Further, we conclude that the pathogen can drive host population growth in the Plantago-Podosphaera system.}, author = {Penczykowski, Rachel M. and Walker, Emily and Soubeyrand, Samuel and Laine, Anna Liisa}, doi = {10.1111/nph.13145}, isbn = {1469-8137}, issn = {14698137}, journal = {New Phytologist}, keywords = {Epidemiology,Host-parasite interactions,Overwintering,Plant-pathogen,Plantago-Podosphaera system,Powdery mildew,Resting structure,Spatial synchrony}, number = {3}, pages = {1142--1152}, pmid = {25382661}, title = {{Linking winter conditions to regional disease dynamics in a wild plant-pathogen metapopulation}}, volume = {205}, year = {2015} } @article{Penczykowski2015, abstract = {Pathogens are considered to drive ecological and evolutionary dynamics of plant populations, but we lack data measuring the population-level consequences of infection in wild plant-pathogen interactions. Moreover, while it is often assumed that offseason environmental conditions drive seasonal declines in pathogen population size, little is known about how offseason environmental conditions impact the survival of pathogen resting stages, and how critical the offseason is for the next season's epidemic. The fungal pathogen Podosphaera plantaginis persists as a dynamic metapopulation in the large network of Plantago lanceolata host populations. Here, we analyze long-term data to measure the spatial synchrony of epidemics and consequences of infection for over 4000 host populations. Using a theoretical model, we study whether large-scale environmental change could synchronize disease occurrence across the metapopulation. During 2001-2013 exposure to freezing decreased, while pathogen extinction-colonization-persistence rates became more synchronized. Simulations of a theoretical model suggest that increasingly favorable winter conditions for pathogen survival could drive such synchronization. Our data also show that infection decreases host population growth. These results confirm that mild winter conditions increase pathogen overwintering success and thus increase disease prevalence across the metapopulation. Further, we conclude that the pathogen can drive host population growth in the Plantago-Podosphaera system.}, author = {Penczykowski, Rachel M. and Walker, Emily and Soubeyrand, Samuel and Laine, Anna Liisa}, doi = {10.1111/nph.13145}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Penczykowski et al. - 2015 - Linking winter conditions to regional disease dynamics in a wild plant-pathogen metapopulation.pdf:pdf}, isbn = {1469-8137}, issn = {14698137}, journal = {New Phytologist}, keywords = {Epidemiology,Host-parasite interactions,Overwintering,Plant-pathogen,Plantago-Podosphaera system,Powdery mildew,Resting structure,Spatial synchrony}, number = {3}, pages = {1142--1152}, pmid = {25382661}, title = {{Linking winter conditions to regional disease dynamics in a wild plant-pathogen metapopulation}}, volume = {205}, year = {2015} } @article{Metcalf2015, author = {Metcalf, C J E and Birger, R B and Funk, S and Kouyos, R D and Lloyd-smith, J O and Jansen, V A A}, doi = {10.1016/j.epidem.2014.12.003}, issn = {1755-4365}, journal = {Epidemics}, pages = {40--44}, publisher = {Elsevier B.V.}, title = {{Five challenges in evolution and infectious diseases}}, url = {http://dx.doi.org/10.1016/j.epidem.2014.12.003}, volume = {10}, year = {2015} } @article{Colautti2017, author = {Colautti, Robert I and Alexander, Jake M and Dlugosch, Katrina M and Keller, Stephen R and Sultan, Sonia E}, journal = {Phil. Trans. R. Soc. B}, number = {20160031}, title = {{Invasions and extinctions through the looking glass of evolutionary ecology}}, volume = {372}, year = {2017} } @article{Zurell2010, abstract = {Ecologists carry a well-stocked toolbox with a great variety of sampling methods, statistical analyses and modelling tools, and new methods are constantly appearing. Evaluation and optimisation of these methods is crucial to guide methodological choices. Simulating error-free data or taking high-quality data to qualify methods is common practice. Here, we emphasise the methodology of the 'virtual ecologist' (VE) approach where simulated data and observer models are used to mimic real species and how they are 'virtually' observed. This virtual data is then subjected to statistical analyses and modelling, and the results are evaluated against the 'true' simulated data. The VE approach is an intuitive and powerful evaluation framework that allows a quality assessment of sampling protocols, analyses and modelling tools. It works under controlled conditions as well as under consideration of confounding factors such as animal movement and biased observer behaviour. In this review, we promote the approach as a rigorous research tool, and demonstrate its capabilities and practical relevance. We explore past uses of VE in different ecological research fields, where it mainly has been used to test and improve sampling regimes as well as for testing and comparing models, for example species distribution models. We discuss its benefits as well as potential limitations, and provide some practical considerations for designing VE studies. Finally, research fields are identified for which the approach could be useful in the future. We conclude that VE could foster the integration of theoretical and empirical work and stimulate work that goes far beyond sampling methods, leading to new questions, theories, and better mechanistic understanding of ecological systems.}, author = {Zurell, Damaris and Berger, Uta and Cabral, Juliano S. and Jeltsch, Florian and Meynard, Christine N. and M{\"{u}}nkem{\"{u}}ller, Tamara and Nehrbass, Nana and Pagel, J{\"{o}}rn and Reineking, Bj{\"{o}}rn and Schr{\"{o}}der, Boris and Grimm, Volker}, doi = {10.1111/j.1600-0706.2009.18284.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Zurell et al. - 2010 - The virtual ecologist approach Simulating data and observers.pdf:pdf}, isbn = {0030-1299}, issn = {00301299}, journal = {Oikos}, number = {4}, pages = {622--635}, title = {{The virtual ecologist approach: Simulating data and observers}}, volume = {119}, year = {2010} } @incollection{Harrison1994, abstract = {Metapopulation approach in style for conservation, but few organisms in nature appear to be organized as classic Levin's metatpopulations."Mainland-island", "patchy populations", and "non-equilibrium metapopulation" type organizations appear more common than classic metapopulations.If habitat patchiness is fine-grained relative to vagility of organism then this produces patchy distributions of individuals, not of populations, and it is inappropriate to look at effects of fragmentation on extinction and recolonization.A usefully realistic spatial model must have an enormous amount of species-specific info.Metapopulation theory is useful for thought, but should not be used to conclude that single populations are doomed, or that linked populations are necessary for conservation. Conservation biology is an essentially empiricle science,}, address = {Blackwell, Oxford}, author = {Harrison, S}, booktitle = {Large Scale Ecology and Conservation Biology}, editor = {Edwards, P.J. and May, R.M. and Webb, N.R.}, isbn = {0068-1954$\backslash$r0-632-03832-2 (cloth); 0-86542-801-8 (paper)}, pages = {111--128}, pmid = {1646}, publisher = {British Ecological Society}, title = {{Metapopulations and conservation}}, year = {1994} } @article{Hanski2001, abstract = {Much of spatial ecology since the late 1960s has been dominated by two theories, the dynamic theory of island biogeography and the classical metapopulation theory. The latter theory largely replaced the former one in the 1980s, especially in conservation applications. It is only recently that ecologists have fully realized that a relatively simple general theory can be readily constructed that makes some of the simplifying assumptions of the two earlier theories unnecessary. The spatially realistic metapopulation theory thereby provides a more unified framework for spatial ecology than the island theory or the classical metapopulation theory. This article describes the application of the spatially realistic metapopulation theory to real metapopulations living in highly fragmented landscapes. I discuss the principal messages for population ecology and conservation biology, and I also place this theory into a broader context of other approaches to spatial ecology.}, author = {Hanski, Ilkka}, doi = {10.1007/s001140100246}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hanski - 2001 - Spatially realistic theory of metapopulation ecology.pdf:pdf}, isbn = {0028-1042}, issn = {00281042}, journal = {Naturwissenschaften}, number = {9}, pages = {372--381}, pmid = {11688412}, title = {{Spatially realistic theory of metapopulation ecology}}, volume = {88}, year = {2001} } @misc{Hanski2003, abstract = {We review recent developments in spatially realistic metapopulation theory, which leads to quantitative models of the dynamics of species inhabiting highly fragmented landscapes. Our emphasis is in stochastic patch occupancy models, which describe the presence or absence of the focal species in habitat patches. We discuss a number of ecologically important quantities that can be derived from the full stochastic models and their deterministic approximations, with a particular aim of characterizing the respective roles of the structure of the landscape and the properties of the species. These quantities include the threshold condition for persistence, the contributions that individual habitat patches make to metapopulation dynamics and persistence, the time to metapopulation extinction, and the effective size of a metapopulation living in a heterogeneous patch network. {\textcopyright} 2003 Elsevier Science (USA). All rights reserved.}, author = {Hanski, Ilkka and Ovaskainen, Otso}, booktitle = {Theoretical Population Biology}, doi = {10.1016/S0040-5809(03)00022-4}, isbn = {0040-5809}, issn = {00405809}, keywords = {Extinction threshold,Extinction-colonization dynamics,Landscape ecology,Landscape structure,Levins model,SPOM,Stochastic metapopulation model,Stochastic patch occupancy model}, number = {1}, pages = {119--127}, pmid = {12804876}, title = {{Metapopulation theory for fragmented landscapes}}, volume = {64}, year = {2003} } @article{Metz1992, abstract = {adaptive dynamics, fitness, evolution}, author = {Metz, J.A.J. and Nisbet, R.M. and Geritz, S.A.H.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Metz, Nisbet, Geritz - 1992 - How should we define 'fitness' for general ecological scenarios.pdf:pdf}, journal = {Trends in Ecology {\&} Evolution}, keywords = {adaptive dyanmics}, mendeley-tags = {adaptive dyanmics}, number = {6}, pages = {198--202}, title = {{How should we define 'fitness' for general ecological scenarios?}}, volume = {7}, year = {1992} } @article{Geritz1998, abstract = {We present a general framework for modelling adaptive trait dynamics in which we integrate various concepts and techniques from modern ESS-theory. The concept of evolutionarily singular strategies is introduced as a generalization of the ESS-concept. We give a full classification of the singular strategies in terms of ESS-stability, convergence stability, the ability of the singular strategy to invade other populations if initially rare itself, and the possibility of protected dimorphisms occurring within the singular strategy's neighbourhood. Of particular interest is a type of singular strategy that is an evolutionary attractor from a great distance, but once in its neighbourhood a population becomes dimorphic and undergoes disruptive selection leading to evolutionary branching. Modelling the adaptive growth and branching of the evolutionary tree can thus be considered as a major application of the framework. A haploid version of Levene's `soft selection' model is developed as a specific example to demonstrate evolutionary dynamics and branching in monomorphic and polymorphic populations.}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Geritz, S. A.H. and Kisdi, {\'{E}} and Mesz{\'{e}}na, G. and Metz, J. A.J.}, doi = {10.1023/A:1006554906681}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Geritz et al. - 1998 - Evolutionarily singular strategies and the adaptive growth and branching of the evolutionary tree.pdf:pdf}, isbn = {0269-7653}, issn = {02697653}, journal = {Evolutionary Ecology}, keywords = {Adaptive dynamics,Evolutionarily singular strategy,Evolutionary branching,Evolutionary modelling}, number = {1}, pages = {35--57}, title = {{Evolutionarily singular strategies and the adaptive growth and branching of the evolutionary tree}}, volume = {12}, year = {1998} } @article{Metz1996, abstract = {We set out to explore a class of stochastic processes called, 'adaptive dynamics', which supposedly capture some of the essentials of the long-term biological evolution. These processes have a strong deterministic component. This allows a classification of their qualitative features which in many aspects is similar to classifications from the theory of deterministic dynamical systems. But, they also display a good number of clear-cut novel dynamical phenomena. The sample functions of an adaptive dynamics are piece-wise constant function from R+ to the finite subsets of some 'trait' space X in R k. Those subsets we call 'adaptive conditions'. Both the range and the jumps of a sample function are governed by a function s, called 'fitness', mapping the present adaptive condition and the trait value of a potential 'mutant' to R. Sign(s) tell us which subsets of X qualify as adaptive conditions, which mutants can potentially 'invade', leading to a jump in the sample function, and which adaptive condition(s) can result from such invasion. Fitness supposedly satisfy certain constraints derived from their population/ community dynamical origin, such as the fact that all mutants which are equal to some 'residents', i.e., element of the present adaptive condition, have zero fitness. Apart from that, we suppose that s is as smooth as can be possibly condoned by its community dynamical origin. Moreover, we assume that a mutant can differ but little from its resident 'progenitor'. In Sections 1 and 2, we describe the biological background of our mathematical framework. In Section 1, we deal with the position of our framework relative to present and past evolutionary research. In Section 2, we discuss the community dynamical origin of s, and the reason for making a number of specific simplifications relative to the full complexity seen in nature. In Sections 3 and 4, we consider some general, mathematical, as well as biological conclusions that can be drawn from our frame work in its simplest guise, that is, when we assume that X is 1-dimensional, and that the cardinality of the adaptive conditions stays low. The main result is a classification of the adaptively singular points. These points comprise both the adaptive point attractors, as well as the points where the adaptive trajectory can branch; thus, attaining its characteristic tree-like shape. In Section 5, we discuss how adaptive dynamics relate through a limiting argument to stochastic models in which individual organisms are represented as separate entities. It is only through such a limiting procedure that any class of population or evolutionary models can eventually be justified. Our basic assumptions are : (i) clonal reproduction, i.e., the resident individuals reproduce faithfully without any of the complications of sex or Mendelian genetics, except for the occasional occurrence of a mutant, (ii) a large system size and an even rarer occurrence of mutations per birth event, (iii) uniqueness and global attractiveness of any interior attractor of the community dynamics in the limit of the infinite system size. In Section 6, we try to delineate, by a tentative listing of 'axioms', the largest possible class of processes that can result from the kind of limiting considerations spelled out in Section 5. And in Section 7, we heuristically derive some very general predictions about macro-evolutionary patterns, based on those weak assumptions only. In the final Section 8, we discuss (i) how the results from the preceding sections may fit into a more encompassing view of biological evolution, and (ii) some directions for further research.}, author = {Metz, Johan a J and Geritz, Stefan a H and Meszena, Geza and Jacobs, F J a and van Heerwaarden, J S}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Metz et al. - 1996 - Adaptive dynamics, a geometrical study of the consequences of nearly faithful reproduction.pdf:pdf}, isbn = {9789251081518}, journal = {Stochastic and Spatial Structures of Dynamical Systems. Proceedings of the Royal Dutch Academy of Science}, number = {September}, pages = {183--231}, title = {{Adaptive dynamics, a geometrical study of the consequences of nearly faithful reproduction}}, year = {1996} } @article{Eagan2018, annote = {Males underestimate academic performance of their female peers in undergrad bio classrooms I should examine how COPUS works.... I could use it when observing classroooms on my own --inter-obsever reliability is also important WOuld more resources promote student-centered classrooms? How much does department culture support pedgological training? - might explain differences between groups}, author = {Eagan, M K and Esson, J M and Plank, K M and Rodela, T M and Schimpf, N G and Schulte, P M and Smith, K and Stetzer, M and Valkenburgh, B Van and Vinson, E and Weir, L K and Wendel, P J and Young, A M}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eagan et al. - 2018 - Anatomy of STEM teaching in North American universities.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eagan et al. - 2018 - Anatomy of STEM teaching in North American universities(2).pdf:pdf}, journal = {Science}, title = {{Anatomy of STEM teaching in North American universities}}, year = {2018} } @article{Risk2011, annote = {- use a combination of IFMs and SPOMs to think about issues related to missing data and imperfect detection}, author = {Risk, Benjamin B and Valpine, Perry De and Beissinger, Steven R}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Risk, Valpine, Beissinger - 2011 - A robust-design formulation of the incidence function model of metapopulation dynamics applied to two.pdf:pdf}, journal = {Ecology}, keywords = {area,connectivity,false absences,hierarchical bayesian model,incidence function model,laterallus jamaicensis coturniculus and,metapopulation,missing data,rallus limicola,robust design,stochastic patch occupancy models}, number = {2}, pages = {462--474}, title = {{A robust-design formulation of the incidence function model of metapopulation dynamics applied to two species of rails}}, volume = {92}, year = {2011} } @article{Sutherland2012, author = {Sutherland, Chris S and Elston, David A. and Lambin, Xavier}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sutherland, Elston, Lambin - 2012 - Multi-scale processes in metapopulations contributions of stage structure, rescue effect, and correl.pdf:pdf}, journal = {Ecology}, keywords = {arvicola amphibius,bayesian models,colonization,dispersal,effect,metapopulation,rescue,scale,spatially correlated extinction,spom,stage structure,stochastic patch occupancy model}, number = {11}, pages = {2465--2473}, title = {{Multi-scale processes in metapopulations: contributions of stage structure, rescue effect, and correlated extinctions}}, volume = {93}, year = {2012} } @article{Hanski1995, annote = {- desacribe the four conditions neccessary for metapopulation persistence}, author = {Hanski, Ilkka and Pakkala, Timo and Kuussaari, Mikko and Lei, Guangchun}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hanski et al. - 1995 - Metapopulation persistence of an endangered butterfly in a fragmented landscape.pdf:pdf}, journal = {Oikos}, number = {1}, pages = {21--28}, title = {{Metapopulation persistence of an endangered butterfly in a fragmented landscape}}, volume = {72}, year = {1995} } @article{Howell2018, annote = {- vary patches (amount of pond water) over time to add realism -{\textgreater} this is not the same as examing the effect of having different types of patches - they are studying how the matix affects coonnectivity}, author = {Howell, Paige E. and Muths, Erin and Hossack, Blake R. and Sigafus, Brent H. and Chandler, Richard B.}, doi = {10.1002/ecy.2189}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Howell et al. - 2018 - Increasing connectivity between metapopulation ecology and landscape ecology.pdf:pdf}, journal = {Ecology}, keywords = {and a term that,between two ecological disciplines,carlo,chiricahua leopard frog,connectivity is a concept,conservation,is shared,landscape ecol-,landscape resistance,least-cost path,markov chain monte,occupancy,spatially explicit,spatially realistic metapopulation theory}, number = {0}, pages = {1--10}, title = {{Increasing connectivity between metapopulation ecology and landscape ecology}}, volume = {0}, year = {2018} } @article{Chandler2015, author = {Chandler, Richard B and Muths, Erin and Sigafus, Brent H and Schwalbe, Cecil R and Jarchow, Christopher J and Hossack, Blake R}, doi = {10.1111/1365-2664.12481}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chandler et al. - 2015 - Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction.pdf:pdf}, journal = {Journal of Animal Ecology}, pages = {1325--1333}, title = {{Spatial occupancy models for predicting metapopulation dynamics and viability following reintroduction}}, volume = {52}, year = {2015} } @article{Lane2018, author = {Lane, Jeffrey and McAdam, Andrew G. and McFarlane, Eryn and Williams, Cory and Humphries, Murray M and Coltman, David and Gorrell, Jamieson and Boutin, Stan}, doi = {10.1111/jeb.13263}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lane et al. - 2018 - Phenological shifts in North American red squirrels disentangling the roles of phenotypic plasticity and microevolu.pdf:pdf}, issn = {1010061X}, journal = {Journal of Evolutionary Biology}, pages = {0--3}, title = {{Phenological shifts in North American red squirrels: disentangling the roles of phenotypic plasticity and microevolution}}, url = {http://doi.wiley.com/10.1111/jeb.13263}, year = {2018} } @article{Heard2015, author = {Heard, Geoffrey W and Chris, D and Scroggie, Michael P and David, S L}, doi = {10.1111/ele.12463}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Heard et al. - 2015 - Refugia and connectivity sustain amphibian metapopulations afflicted by disease.pdf:pdf}, keywords = {18,2015,853,863,amphibian,chytrid,colonisation,conservation,ecology letters,extinction,litoria raniformis,microclimate,pathogen,reservoir host}, pages = {853--863}, title = {{Refugia and connectivity sustain amphibian metapopulations afflicted by disease}}, volume = {18}, year = {2015} } @article{Mcnamara2011, abstract = {Organisms time activities by using environmental cues to forecast the future availability of important resources. Presently, there is limited understanding of the relationships between cues and optimal timing, and especially about how this relationship will be affected by environmental changes. We develop a general model to explore the relation between a cue and the optimal timing of an important life history activity. The model quantifies the fitness loss for organisms failing to time behaviours optimally. We decompose the immediate change in fitness resulting from environmental changes into a component that is due to changes in the predictive power of the cue and a component that derives from the mismatch of the old response to the cue to the new environmental conditions. Our results show that consequences may range from negative, neutral to positive and are highly dependent on how cue and optimal timing and their relation are specifically affected by environmental changes.}, author = {Mcnamara, John M. and Barta, Zoltan and Klaassen, Marcel and Bauer, Silke}, doi = {10.1111/j.1461-0248.2011.01686.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mcnamara et al. - 2011 - Cues and the optimal timing of activities under environmental changes.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Cue-response,Evolutionary trap,Fitness loss,Life history activity,Migration,Mistiming,Phenology,Photoperiod,Reaction norm,Reproduction}, number = {12}, pages = {1183--1190}, pmid = {22017534}, title = {{Cues and the optimal timing of activities under environmental changes}}, volume = {14}, year = {2011} } @article{, title = {{No Title}}, year = {2018} } @article{Edmunds2014, abstract = {The reduction in coral cover on many contemporary tropical reefs suggests a different set of coral community assemblages will dominate future reefs. To evaluate the capacity of reef corals to persist over various time scales, we examined coral community dynamics in contemporary, fossil, and simulated future coral reef ecosystems. Based on studies between 1987 and 2012 at two locations in the Caribbean, and between 1981 and 2013 at five locations in the Indo-Pacific, we show that many coral genera declined in abundance, some showed no change in abundance, and a few coral genera increased in abundance. Whether the abundance of a genus declined, increased, or was conserved, was independent of coral family. An analysis of fossil-reef communities in the Caribbean revealed changes in numerical dominance and relative abundances of coral genera, and demonstrated that neither dominance nor taxon was associated with persistence. As coral family was a poor predictor of performance on contemporary reefs, a trait-based, dynamic, multi-patch model was developed to explore the phenotypic basis of ecological performance in a warmer future. Sensitivity analyses revealed that upon exposure to thermal stress, thermal tolerance, growth rate, and longevity were the most important predictors of coral persistence. Together, our results underscore the high variation in the rates and direction of change in coral abundances on contemporary and fossil reefs. Given this variation, it remains possible that coral reefs will be populated by a subset of the present coral fauna in a future that is warmer than the recent past.}, author = {Edmunds, Peter J. and Adjeroud, Mehdi and Baskett, Marissa L. and Baums, Iliana B. and Budd, Ann F. and Carpenter, Robert C. and Fabina, Nicholas S. and Fan, Tung Yung and Franklin, Erik C. and Gross, Kevin and Han, Xueying and Jacobson, Lianne and Klaus, James S. and McClanahan, Tim R. and O'Leary, Jennifer K. and {Van Oppen}, Madeleine J.H. and Pochon, Xavier and Putnam, Hollie M. and Smith, Tyler B. and Stat, Michael and Sweatman, Hugh and {Van Woesik}, Robert and Gates, Ruth D.}, doi = {10.1371/journal.pone.0107525}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Edmunds et al. - 2014 - Persistence and change in community composition of reef corals through present, past, and future climates.pdf:pdf}, isbn = {1932-6203 (Electronic)$\backslash$r1932-6203 (Linking)}, issn = {19326203}, journal = {PLoS ONE}, number = {10}, pmid = {25272143}, title = {{Persistence and change in community composition of reef corals through present, past, and future climates}}, volume = {9}, year = {2014} } @article{Paine1998, abstract = {All species have evolved in the presence of distur- bance, and thus are in a sense matched to the recurrence pattern of the perturbations. Conse- quently, disturbances within the typical range, even at the extreme of that range as defined by large, infrequent disturbances (LIDs), usually result in little long-term change to the system's fundamental character. We argue that more serious ecological consequences result from compounded perturba- tions within the normative recovery time of the community in question. We consider both physi- cally based disturbance (for example, storm, volca- nic eruption, and forest fire) and biologically based disturbance of populations, such as overharvesting, invasion, and disease, and their interactions. Dis- persal capability and measures of generation time or age to first reproduction of the species of interest seem to be the important metrics for scaling the size and frequency of disturbances among different types of ecosystems. We develop six scenarios that de- scribe communities that have been subjected to multiple perturbations, either simultaneously or at a rate faster than the rate of recovery, and appear to have entered new domains or ‘‘ecological surprises.'' In some cases, three or more disturbances seem to have been required to initiate the changed state.We argue that in a world of ever-more-pervasive anthro- pogenic impacts on natural communities coupled with the increasing certainty of global change, compounded perturbations and ecological surprises will become more common. Understanding these ecological synergisms will be basic to environmental management decisions of the 21st century. Key}, author = {Paine, Robert T and Tegner, Mia J and Johnson, Edward a}, doi = {10.1007/s100219900049}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Paine, Tegner, Johnson - 1998 - Compounded perturbations yield ecological surprises.pdf:pdf}, isbn = {1432-9840}, issn = {1432-9840}, journal = {Ecosystems}, keywords = {altered community states,dispersal,multiple disturbances,recovery intervals,scaling}, number = {July}, pages = {535--545}, pmid = {11717134209414142489}, title = {{Compounded perturbations yield ecological surprises}}, volume = {1}, year = {1998} } @article{Cuddington2013, abstract = {Several modeling approaches can be used to guide management decisions. However, some approaches are better fitted than others to address the problem of prediction under global change. Process-based models, which are based on a theoretical understanding of relevant ecological processes, provide a useful framework to incorporate specific responses to altered environmental conditions. As a result, these models can offer significant advantages in predicting the effects of global change as compared to purely statistical or rule-based models based on previously collected data. Process-based models also offer more explicitly stated assumptions and easier interpretation than detailed simulation models. We provide guidelines for identifying the appropriate type of model and level of complexity for management decisions. Finally we outline some of those factors that make modeling for local and regional management under global change a particular challenge: changes to relevant scales and processes, additional sources of uncertainty, legacy effects, threshold dynamics, and socio-economic impacts.}, author = {Cuddington, K. and Fortin, M. J. and Gerber, L. R. and Hastings, A. and Liebhold, A. and O'connor, M. and Ray, C.}, doi = {10.1890/ES12-00178.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cuddington et al. - 2013 - Process-based models are required to manage ecological systems in a changing world.pdf:pdf}, isbn = {2150-8925}, issn = {21508925}, journal = {Ecosphere}, keywords = {Climate change,Expert opinion,Extrapolation,Simulation model}, number = {2}, pages = {1--12}, pmid = {20083067642}, title = {{Process-based models are required to manage ecological systems in a changing world}}, volume = {4}, year = {2013} } @article{Chades2014, abstract = {Stochastic dynamic programming (SDP) or Markov decision processes (MDP) are increasingly being used in ecology to find the best decisions over time and under uncertainty so that the chance of achieving an objective is maximised. To date, few programs are available to solve SDP/MDP. We present MDPtoolbox, a multi-platform set of functions to solve Markov decision problems (MATLAB, GNU Octave, Scilab and R). MDPtoolbox provides state-of-the-art and ready to use algorithms to solve a wide range of MDPs. MDPtoolbox is easy to use, freely available and has been continuously improved since 2004. We illustrate how to use MDPtoolbox on a dynamic reserve design problem.}, author = {Chad{\`{e}}s, Iadine and Chapron, Guillaume and Cros, Marie Jos{\'{e}}e and Garcia, Fr{\'{e}}d{\'{e}}rick and Sabbadin, R{\'{e}}gis}, doi = {10.1111/ecog.00888}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chad{\`{e}}s et al. - 2014 - MDPtoolbox A multi-platform toolbox to solve stochastic dynamic programming problems.pdf:pdf}, isbn = {1600-0587}, issn = {16000587}, journal = {Ecography}, number = {9}, pages = {916--920}, title = {{MDPtoolbox: A multi-platform toolbox to solve stochastic dynamic programming problems}}, volume = {37}, year = {2014} } @article{Cabral2017, abstract = {{\textcopyright} 2016 Wiley Periodicals, Inc.Resource management and conservation increasingly focus on ecosystem service provisioning and potential tradeoffs among services under different management actions. Application of bioeconomic approaches to tradeoffs assessment is touted as a way to find win-win outcomes or avoid unnecessary stakeholder conflict. Yet, nearly all assessments to date have ignored inherent uncertainties in the provision and valuation of services. We incorporate uncertainty into the ecosystem services analytical framework and show how such inclusion improves optimal decision making. In particular, we show: (1) "suboptimal" solutions can become optimal when uncertainties are accounted for; (2) uncertainty paradoxically makes stakeholders value conservation despite their lack of preference for it; and (3) substantial losses or missed gains in ecosystem service provisioning can be incurred when uncertainty is ignored. Our results highlight the urgency of accounting for uncertainties in ecosystem services in tradeoff assessments given the widespread use of this approach by government agencies and conservation organizations.}, author = {Cabral, Reniel B. and Halpern, Benjamin S. and Costello, Christopher and Gaines, Steven D.}, doi = {10.1111/conl.12303}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cabral et al. - 2017 - Unexpected management choices when accounting for uncertainty in ecosystem service tradeoff analyses.pdf:pdf}, isbn = {1044071060}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Bioeconomic model,decision making,ecosystem services,ecosystem-based management,multisector planning,second best theory,spatial planning,tradeoff analysis,uncertainty}, number = {4}, pages = {421--429}, title = {{Unexpected management choices when accounting for uncertainty in ecosystem service tradeoff analyses}}, volume = {10}, year = {2017} } @article{Gibbs1998, abstract = {Computerized monitoring programs have been developed to keep track of changes in plants and animal populations. Tests on the validity of these programs seek to verify if the sampling methods used were unbiased and statistically powerful.}, annote = {- focus on how temporal variability affects the ability to detect trends - look at time series of more than 5 years... - reduce the 512 populations down into 24 taxa---ignoring variability within taxa, which is large - they study sampling intensity required for 10 years of monitoring... - they don't deal with autocorrelation either...}, author = {Gibbs, James P and Droege, Sam and Eagle, Paige}, doi = {10.2307/1313297}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gibbs, Droege, Eagle - 1998 - Monitoring populations of plants and animals.pdf:pdf}, isbn = {9780632044429}, issn = {00063568}, journal = {BioScience}, number = {11}, pages = {935--940.}, title = {{Monitoring populations of plants and animals}}, url = {census}, volume = {48}, year = {1998} } @article{Peters2010, abstract = {Large volumes of data have been collected to document the many ways that ecological systems are responding to changing environmental drivers. A general buy-in on solutions to these problems can be reached only if these and future data are made easily accessible to and understood by a broad audience that includes the public, decision-makers, and other scientists. A developing framework for synthesis is reviewed that integrates three main strategies of ecological research (long-term studies; short-term, process-based studies; and broad-scale observations) with derived data products and additional sources of knowledge. This framework focuses on making data from multiple sources and disciplines easily understood by many, a prerequisite for finding synthetic solutions and predicting future dynamics in a changing world. {\textcopyright} 2010.}, annote = {This article compares and contasts different types of commonly collected ecological data. The author than points to the importance of integrating these different data sources.}, author = {Peters, Debra P.C.}, doi = {10.1016/j.tree.2010.07.005}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Peters - 2010 - Accessible ecology Synthesis of the long, deep, and broad.pdf:pdf}, isbn = {0169-5347}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {10}, pages = {592--601}, pmid = {20728958}, title = {{Accessible ecology: Synthesis of the long, deep, and broad}}, volume = {25}, year = {2010} } @article{Olivier2009, abstract = {ABSTRACT * 1The metapopulation metaphor is increasingly used to explain the spatial dynamics of animal populations. However, metapopulation structure is difficult to identify in long-lived species that are widely distributed in stochastic environments, where they can resist extinctions. The literature on mammals may not provide supporting evidence for classic metapopulation dynamics, which call for the availability of discrete habitat patches, asynchrony in local population dynamics, evidence for extinction and colonization processes, and dispersal between local populations. * 2Empirical evidence for metapopulation structure among mammals may exist when applying more lenient criteria. To meet these criteria, mammals should live in landscapes as discrete local breeding populations, and their demography should be asynchronous. * 3We examined the literature for empirical evidence in support of the classical criteria set by Hanski (1999), and for the more lenient subset of criteria proposed by Elmhagen {\&} Angerbj{\"{o}}rn (2001). We suggest circumstances where metapopulation theory could be important in understanding population processes in mammals of different body sizes. * 4The patchy distribution of large ({\textgreater}100 kg) mammals and dispersal often motivate inferences in support of a metapopulation structure. Published studies seldom address the full suite of classical criteria. However, studies on small mammals are more likely to record classic metapopulation criteria than those on large mammals. The slow turnover rate that is typical for medium-sized and large mammals apparently makes it difficult to identify a metapopulation structure during studies of short duration. * 5To identify a metapopulation structure, studies should combine the criteria set by Hanski (1999) and Elmhagen {\&} Angerbj{\"{o}}rn (2001). Mammals frequently live in fragmented landscapes, and processes involved in the maintenance of a metapopulation structure should be considered in conservation planning and management.}, author = {Olivier, Pieter I. and {Van Aarde}, Rudi J. and Ferreira, Sam M.}, doi = {10.1111/j.1365-2907.2009.00143.x}, isbn = {0305-1838}, issn = {03051838}, journal = {Mammal Review}, keywords = {Asynchrony,Conservation,Discrete local populations,Dispersal,Population turnover,Vacant habitats}, number = {3}, pages = {178--192}, title = {{Support for a metapopulation structure among mammals}}, volume = {39}, year = {2009} } @article{Schuur2008, abstract = {ABSTRACT Thawing permafrost and the resulting microbial decomposition of previously frozen organic carbon (C) is one of the most significant potential feedbacks from terrestrial ecosystems to the atmosphere in a changing climate. In this article we present an overview of the global permafrost C pool and of the processes that might transfer this C into the atmosphere, as well as the associated ecosystem changes that occur with thawing. We show that accounting for C stored deep in the permafrost more than doubles previous high-latitude inventory estimates, with this new estimate equivalent to twice the atmospheric C pool. The thawing of permafrost with warming occurs both gradually and catastrophically, exposing organic C to microbial decomposition. Other aspects of ecosystem dynamics can be altered by climate change along with thawing permafrost, such as growing season length, plant growth rates and species composition, and ecosystem energy exchange. However, these processes do not appear to be able to com...}, author = {Schuur, Edward A. G. and Bockheim, James and Canadell, Josep G. and Euskirchen, Eugenie and Field, Christopher B. and Goryachkin, Sergey V. and Hagemann, Stefan and Kuhry, Peter and Lafleur, Peter M. and Lee, Hanna and Mazhitova, Galina and Nelson, Frederick E. and Rinke, Annette and Romanovsky, Vladimir E. and Shiklomanov, Nikolay and Tarnocai, Charles and Venevsky, Sergey and Vogel, Jason G. and Zimov, Sergei A.}, doi = {10.1641/B580807}, isbn = {0006-3568}, issn = {1525-3244}, journal = {BioScience}, number = {8}, pages = {701--714}, title = {{Vulnerability of Permafrost Carbon to Climate Change: Implications for the Global Carbon Cycle}}, url = {http://academic.oup.com/bioscience/article/58/8/701/380621/Vulnerability-of-Permafrost-Carbon-to-Climate}, volume = {58}, year = {2008} } @article{Yang2004, abstract = {Resource pulses are occasional events of ephemeral resource superabundance that occur in many ecosystems. Aboveground consumers in diverse communities often respond strongly to resource pulses, but few studies have investigated the belowground consequences of resource pulses in natural ecosystems. This study shows that resource pulses of 17-year periodical cicadas (Magicicada spp.) directly increase microbial biomass and nitrogen availability in forest soils, with indirect effects on growth and reproduction in forest plants. These findings suggest that pulses of periodical cicadas create "bottom-up cascades," resulting in strong and reciprocal links between the aboveground and belowground components of a North American forest ecosystem.}, author = {Yang, Louie H.}, doi = {10.1126/science.1103114}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yang - 2004 - Periodical cicadas as resource pulses in North American forests.pdf:pdf}, isbn = {0036-8075}, issn = {00368075}, journal = {Science}, number = {5701}, pages = {1565--1567}, pmid = {15567865}, title = {{Periodical cicadas as resource pulses in North American forests}}, volume = {306}, year = {2004} } @article{Bullock2000, author = {Bullock, James M and Clarke, Ralph T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bullock, Clarke - 2000 - Long distance seed dispersal by wind Measuring and modelling the tail of the curve.pdf:pdf}, journal = {Oecologia}, number = {4}, pages = {506--521}, title = {{Long distance seed dispersal by wind: Measuring and modelling the tail of the curve}}, volume = {124}, year = {2000} } @article{Straile2015, author = {Straile, Dietmar and Kerimoglu, Onur and Peeters, Frank}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Straile, Kerimoglu, Peeters - 2015 - Trophic mismatch requires seasonal heterogeneity of warming.pdf:pdf}, journal = {Ecology}, keywords = {climate warming,daphnia,fish,food webs,germany,lake constance,mismatch,phenology,plankton,whitefish}, number = {10}, pages = {2794--2805}, title = {{Trophic mismatch requires seasonal heterogeneity of warming}}, volume = {96}, year = {2015} } @article{Vaidyanathan1978, abstract = {... II. Series. Qa351.B66 574.4'01'84 78-15923 AMS Subject Classifications (1970): 41 A05, 41 A 15,41 A63, 50-02, 62 PlO, 65S05, 73P05, 92A05 ISBN-13: 978-3-540-08912-4 DOl: 10.1007 / 978 - 3 - 642 - 93093 - 5 e-ISBN-13: 978-3-642-93093-5 This work is subject to copyright. ... $\backslash$n}, author = {Vaidyanathan, V.S.}, doi = {10.1016/0302-4598(87)85058-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vaidyanathan - 1978 - Lecture Notes in Biomathematics.pdf:pdf}, isbn = {9783540525714}, issn = {03024598}, journal = {Bioelectrochemistry and Bioenergetics}, number = {3}, pages = {597--598}, title = {{Lecture Notes in Biomathematics}}, url = {http://linkinghub.elsevier.com/retrieve/pii/0302459887850584}, volume = {5}, year = {1978} } @article{Griesemer2013, abstract = {Exact sciences are described as sciences whose theories are formalized. These are contrasted to inexact sciences, whose theories are not formalized. Formalization is described as a broader category than mathematization, involving any form/content distinction allowing forms, e.g., as represented in theoretical models, to be studied independently of the empirical content of a subject-matter domain. Exactness is a practice depending on the use of theories to control subject-matter domains and to align theoretical with empirical models and not merely a state of a science. Inexact biological sciences tolerate a degree of “mismatch” between theoretical and empirical models and concepts. Three illustrations from biological sciences are discussed in which formalization is achieved by various means: Mendelism, Weismannism, and Darwinism. Frege's idea of a “conceptual notation” is used to further characterize the notion of a form/content distinction.}, author = {Griesemer, James}, doi = {10.1007/s13752-012-0065-z}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Griesemer - 2013 - Formalization and the Meaning of “Theory” in the Inexact Biological Sciences.pdf:pdf}, issn = {1555-5542}, journal = {Biological Theory}, keywords = {cation of models in,darwin {\'{a}} exact and,formalization {\'{a}} mendel,i do not want,inexact science {\'{a}},mainly,model {\'{a}} theory {\'{a}},that the appli-,the empirical sciences is,to give the impression,weismann}, number = {4}, pages = {298--310}, title = {{Formalization and the Meaning of “Theory” in the Inexact Biological Sciences}}, url = {http://link.springer.com/10.1007/s13752-012-0065-z}, volume = {7}, year = {2013} } @article{Teitelbaum2015, abstract = {Animal migration is a global phenomenon, but few studies have examined the substantial within- and between-species variation in migration distances. We built a global database of 94 land migra- tions of large mammalian herbivore populations ranging from 10 to 1638 km. We examined how resource availability, spatial scale of resource variability and body size affect migration distance among populations. Resource availability measured as normalised difference vegetation index had a strong negative effect, predicting a tenfold difference in migration distances between low- and high-resource areas and explaining 23{\%} of the variation in migration distances. We found a weak, positive effect of the spatial scale of resource variability but no effect of body size. Resource-poor environments are known to increase the size of mammalian home ranges and territories. Here, we demonstrate that for migratory populations as well, animals living in resource-poor environments travel farther to fulfil their resource needs.}, author = {Teitelbaum, Claire S. and Fagan, William F. and Fleming, Chris H. and Dressler, Gunnar and Calabrese, Justin M. and Leimgruber, Peter and Mueller, Thomas}, doi = {10.1111/ele.12435}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Teitelbaum et al. - 2015 - How far to go Determinants of migration distance in land mammals.pdf:pdf}, isbn = {1461-0248 (Electronic)$\backslash$r1461-023X (Linking)}, issn = {14610248}, journal = {Ecology Letters}, keywords = {Foraging resources,Land migrations,Mammalian herbivores,Migration distance,Normalised difference vegetation index,Scaling relationships,Ungulates}, number = {6}, pages = {545--552}, pmid = {25865946}, title = {{How far to go? Determinants of migration distance in land mammals}}, volume = {18}, year = {2015} } @book{Gause1934, address = {Baltimore}, author = {Gause, G F}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gause - 1934 - The Struggle for Existence.htm:htm}, keywords = {Existence,struggle}, pages = {163}, publisher = {Williams and Wilkins}, title = {{The Struggle for Existence}}, year = {1934} } @article{Passarge2006, author = {Passarge, Jutta and Hol, Suzanne and Escher, Marieke and Huisman, Jef}, doi = {10.1890/04-1824}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Passarge et al. - 2006 - Competition for nuntrients and light stable coexistence, alternative stable states, or competitive exclusion.pdf:pdf}, isbn = {0012-9615}, issn = {0012-9615}, journal = {Ecological Monographs}, keywords = {all competition experiments led,aquatic ecosystems,biodiversity,coexistence nor alternative stable,competition model,continuous culture,cyanobac,for light as well,green algae,hence,neutral coexistence,phosphate,phosphorus were strong competitors,photosynthesis,productivity gradient,resource,states,teria,to competitive,we found neither stable}, number = {1}, pages = {57--72}, title = {{Competition for nuntrients and light: stable coexistence, alternative stable states, or competitive exclusion?}}, volume = {76}, year = {2006} } @article{Rosenzweig1963, author = {Rosenzweig, M.L. and MacArthur, R.H.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rosenzweig, MacArthur - 1963 - Graphical representation and stability conditions of predator-prey interactions.pdf:pdf}, journal = {The}, number = {895}, pages = {209--223}, title = {{Graphical representation and stability conditions of predator-prey interactions}}, volume = {97}, year = {1963} } @article{Chesson1994, author = {Chesson, Peter}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chesson - 1994 - Multispecies competition in variable environments.pdf:pdf}, journal = {Theoretical Population Biology}, pages = {227--276}, title = {{Multispecies competition in variable environments}}, volume = {45}, year = {1994} } @article{Kendall1999, author = {Kendall, Bruce E and Briggs, Cheryl J and Murdoch, William W and Turchin, Peter and P, Stephen and Mccauley, Edward and Nisbet, Roger M and Wood, Simon N}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kendall et al. - 1999 - Why do populations cycle A synthesis of statistical and mechanistic modeling approaches.pdf:pdf}, journal = {Ecology}, number = {6}, pages = {1789--1805}, title = {{Why do populations cycle? A synthesis of statistical and mechanistic modeling approaches}}, volume = {80}, year = {1999} } @book{Tilman1982, abstract = {In a detailed analysis of the Park Grass Experiments at the Rothamsted Experimental Station in England, the author demonstrates that the dramatic results of these 120 years of experimentation are consistent with his theory, as are observations in many other natural communities.}, author = {Tilman, David}, booktitle = {Monographs in Population Biology}, doi = {10.7861/clinmedicine.14-3-000}, isbn = {0691083010$\backslash$n0691083029 (pbk.)}, issn = {0077-0930}, pages = {1--296}, pmid = {7162524}, title = {{Resource competition and community structure.}}, url = {http://books.google.fr/books?hl=fr{\&}lr={\&}id=-nx11-ExBd0C{\&}oi=fnd{\&}pg=PP10{\&}dq=tilman+1982{\&}ots=bQZk96hFgd{\&}sig=EOZCjOUM9Zxu843mE9BUHZFVP2U}, volume = {17}, year = {1982} } @article{Tylianakis2008, abstract = {Abstract The main drivers of global environmental change (CO2 enrichment, nitrogen deposition, climate, biotic invasions and land use) cause extinctions and alter species distributions, and recent evidence shows that they exert pervasive impacts on various antagonistic and mutualistic interactions among species. In this review, we synthesize data from 688 published studies to show that these drivers often alter competitive interactions among plants and animals, exert multitrophic effects on the decomposer food web, increase intensity of pathogen infection, weaken mutualisms involving plants, and enhance herbivory while having variable effects on predation. A recurrent finding is that there is substantial variability among studies in both the magnitude and direction of effects of any given GEC driver on any given type of biotic interaction. Further, we show that higher order effects among multiple drivers acting simultaneously create challenges in predicting future responses to global environmental change, and that extrapolating these complex impacts across entire networks of species interactions yields unanticipated effects on ecosystems. Finally, we conclude that in order to reliably predict the effects of GEC on community and ecosystem processes, the greatest single challenge will be to determine how biotic and abiotic context alters the direction and magnitude of GEC effects on biotic interactions.}, author = {Tylianakis, Jason M. and Didham, Raphael K. and Bascompte, Jordi and Wardle, David A.}, doi = {10.1111/j.1461-0248.2008.01250.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Tylianakis et al. - 2008 - Global change and species interactions in terrestrial ecosystems.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {CO2,Climate change,Competition,Disease,Food web,Global warming,Interaction effect,Land-use change,Mycorrhiza,Nitrogen deposition,Parasite,Pollination,Seed dispersal}, number = {12}, pages = {1351--1363}, pmid = {19062363}, title = {{Global change and species interactions in terrestrial ecosystems}}, volume = {11}, year = {2008} } @article{Tonkin2017, abstract = {Introduction: D-dimer assay, generally evaluated according to cutoff points calibrated for VTE exclusion, is used to estimate the individual risk of recurrence after a first idiopathic event of venous thromboembolism (VTE). Methods: Commercial D-dimer assays, evaluated according to predetermined cutoff levels for each assay, specific for age (lower in subjects {\textless}70 years) and gender (lower in males), were used in the recent DULCIS study. The present analysis compared the results obtained in the DULCIS with those that might have been had using the following different cutoff criteria: traditional cutoff for VTE exclusion, higher levels in subjects aged ≥60 years, or age multiplied by 10. Results: In young subjects, the DULCIS low cutoff levels resulted in half the recurrent events that would have occurred using the other criteria. In elderly patients, the DULCIS results were similar to those calculated for the two age-adjusted criteria. The adoption of traditional VTE exclusion criteria would have led to positive results in the large majority of elderly subjects, without a significant reduction in the rate of recurrent event. Conclusion: The results confirm the usefulness of the cutoff levels used in DULCIS.}, author = {Tonkin, Jonathan D. and Bogan, Michael T. and Bonada, N{\'{u}}ria and Rios-Touma, Blanca and Lytle, David A.}, doi = {10.1002/ecy.1761}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Tonkin et al. - 2017 - Seasonality and predictability shape temporal species diversity.pdf:pdf}, isbn = {4955139574}, issn = {00129658}, journal = {Ecology}, keywords = {climate,communities,desert annuals,migratory waterfowl,periodicity,seasons,stream invertebrates,temporal beta diversity,turnover,wavelets}, number = {5}, pages = {1201--1216}, title = {{Seasonality and predictability shape temporal species diversity}}, volume = {98}, year = {2017} } @article{Pellet2007, abstract = {Much of metapopulation theory assumes that the persistence of individual populations in a metapopulation, and persistence of the metapopulation as a whole, is best modeled by the area of habitat patches and their isolation. Estimates of isolation typically include a measure of geographic distance and a measure of either population size or patch area. This "area and isolation paradigm" assumes a functional relationship between the area of a patch and its extinction probability, and between isolation of a patch and its colonization probability. Although these assumptions are fundamental to use of incidence function models of metapopulation dynamics, the assumptions have been validated in only a small number of studies. We tested the ability of area and isolation to predict extinction and colonization patterns using multiple-year occupancy data for 10 species from three taxonomic groups (butterflies, amphibians, and birds). We examined 13 potential models of metapopulation dynamics. All models included four basic parameters: occupancy during the first year of the survey, probability of extinction, probability of colonization, and single-visit detection probability. In eight models, each parameter was either constant or time-dependent. Five models included a patch-level covariate of extinction probability (patch area or population size), colonization probability (connectivity, the inverse of isolation), or both. Extinction patterns generally were predicted more effectively as a function of local population size than as a function of patch area, a constant probability of extinction, or a time-dependent probability of extinction. In most cases, inclusion of connectivity as a patch-level covariate did not improve predictions of colonization patterns. We estimated single-visit detection probabilities for all species in our analyses, thus providing evidence-based guidelines for the refinement of future monitoring protocols. ?? 2007 Elsevier Ltd. All rights reserved.}, annote = {- we d}, author = {Pellet, J{\'{e}}r{\^{o}}me and Fleishman, Erica and Dobkin, David S. and Gander, Antoine and Murphy, Dennis D.}, doi = {10.1016/j.biocon.2006.12.020}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pellet et al. - 2007 - An empirical evaluation of the area and isolation paradigm of metapopulation dynamics.pdf:pdf}, isbn = {0006-3207}, issn = {00063207}, journal = {Biological Conservation}, keywords = {Amphibians,Birds,Bufo calamita,Butterflies,Colonization,Connectivity,Dendroica petechia,Extinction,Great Basin,Hyla arborea,Maculinea nausithous,Melospiza melodia,Passerina amoena,Patch area,Picoides villosus,Selasphorus platycercus,Speyeria nokomis,Switzerland,Troglodytes aedon}, number = {3}, pages = {483--495}, pmid = {2044}, title = {{An empirical evaluation of the area and isolation paradigm of metapopulation dynamics}}, volume = {136}, year = {2007} } @article{Castillo2016, abstract = {Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed. We used a landscape genetics approach to evaluate resistance to gene flow and, thus, to determine how landscape and climate-related variables influence gene flow for American pikas (Ochotona princeps) in eight federally managed sites in the western United States. We used empirically derived, individual-based landscape resistance models in conjunction with predictive occupancy models to generate patch-based network models describing functional landscape connectivity. Metareplication across landscapes enabled identification of limiting factors for dispersal that would not otherwise have been apparent. Despite the cool microclimates characteristic of pika habitat, south-facing aspects consistently represented higher resistance to movement, supporting the previous hypothesis that exposure to relatively high temperatures may limit dispersal in American pikas. We found that other barriers to dispersal included areas with a high degree of topographic relief, such as cliffs and ravines, as well as streams and distances greater than 1-4 km depending on the site. Using the empirically derived network models of habitat patch connectivity, we identified habitat patches that were likely disproportionately important for maintaining functional connectivity, areas in which habitat appeared fragmented, and locations that could be targeted for management actions to improve functional connectivity. We concluded that climate change, besides influencing patch occupancy as predicted by other studies, may alter landscape resistance for pikas, thereby influencing functional connectivity through multiple pathways simultaneously. Spatial autocorrelation among genotypes varied across study sites and was largest where habitat was most dispersed, suggesting that dispersal distances increased with habitat fragmentation, up to a point. This study demonstrates how landscape features linked to climate can affect functional connectivity for species with naturally fragmented distributions, and reinforces the importance of replicating studies across landscapes.}, author = {Castillo, Jessica A. and Epps, Clinton W. and Jeffress, Mackenzie R. and Ray, Chris and Rodhouse, Thomas J. and Schwalm, Donelle}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Castillo et al. - 2016 - Replicated Landscape genetic and network analyses reveal wide variation in functional connectivity for American.pdf:pdf}, isbn = {1939-5582}, issn = {19395582}, journal = {Ecological Applications}, keywords = {American pika (ochotona princeps),Climate change,Dispersal,Functional connectivity,Graph theory,Landscape genetics,Metareplication}, number = {6}, pages = {1660--1676}, pmid = {27755691}, title = {{Replicated Landscape genetic and network analyses reveal wide variation in functional connectivity for American pikas}}, volume = {26}, year = {2016} } @article{Millar2018, author = {Millar, Constance I and Delany, Diane L and Hersey, Kimberly A and Jeffress, Mackenzie R and Smith, Andrew T and VanGunst, Jane and Westfall, Robert D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Millar et al. - Unknown - Distribution, climatic relationships, and status of American pikas (emph{\{}Ochotona princeps{\}}) in the Great Basi.pdf:pdf}, journal = {Western North American Naturalist}, title = {{Distribution, climatic relationships, and status of American pikas ($\backslash$emph{\{}Ochotona princeps{\}}) in the Great Basin, USA}} } @article{Swihart2003, author = {Swihart, Robert K and Atwood, Todd C and Goheen, Jacob R and Scheiman, Daniel M and Munroe, Karen E. and Gehring, Thomas M.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Swihart et al. - 2003 - Patch occupancy of North American mammals is patchiness in the eye of the beholder.pdf:pdf}, journal = {Journal of Biogeography}, pages = {1--21}, title = {{Patch occupancy of North American mammals: is patchiness in the eye of the beholder?}}, volume = {30}, year = {2003} } @incollection{Diamond1984, abstract = {Revisao sobre a taxa de extincao de especies (principalmente aves) em ilhas oceanicas e em habitats isolados. Inclui discussao sobre Barro Colorado island, Southern Brazilian Woodlots, Rio Palenque Field Station (Ecuador), Banks Peninsula (New Zealand),and Eastern North American Deciduous Forest}, author = {Diamond, J M}, booktitle = {Extinctions}, isbn = {0-226-58690-1}, keywords = {AUTOECOL HABITAT,BIOGEOGR INSULAR,CONSERV FRAGMENT,DOUT,METAPOPUL}, pages = {191--246}, title = {{Normal extinctions of isolated populations}}, year = {1984} } @article{Nichols2016, abstract = {American pikas (Ochotona princeps) are small alpine lagomorphs and talus obligates with a narrow range of temperature tolerance, along with physiological and ecological characteristics that make them especially vulnerable to local extirpation in the face of climate change. Since their initial colonization of the Great Basin during the Pleistocene geological epoch, the distribution of pikas in this region has become more restricted, with population losses occurring especially in lower-elevation sites characterized by relatively low precipitation and high temperatures. Even where pikas have persisted, many populations are now restricted to higher elevations. We surveyed several sites in the Bodie Hills of eastern California known to have been recently occupied by pikas. Here we report the recent extirpations of 2 of these sites: one small cluster of anthropogenic patches in the historic Masonic Mining District and one natural patch on Masonic Mountain. These extirpations are consistent with those reported in California and across the Great Basin and may indicate the impending loss of pikas from this region due to impacts from global climate change.}, author = {Nichols, Lyle B and Klingler, Kelly B and Peacock, Mary M and Western, Source and American, North}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nichols et al. - 2016 - American pikas (emph{\{}Ochotona princeps{\}}) extirpated from the historic masonic mining district of eastern Califor.pdf:pdf}, isbn = {1527-0904}, issn = {1527-0904}, journal = {Western North American Naturalist}, number = {2}, pages = {163--171}, title = {{American pikas ($\backslash$emph{\{}Ochotona princeps{\}}) extirpated from the historic masonic mining district of eastern California}}, volume = {76}, year = {2016} } @article{Didham2012, abstract = {Th e conceptual foundations of habitat fragmentation research have not kept pace with empirical advances in our under- standing of species responses to landscape change, nor with theoretical advances in the wider disciplines of ecology. Th ere is now real debate whether explicit recognition of ‘ habitat fragmentation ' as an over-arching conceptual domain will stimulate or hinder further progress toward understanding and mitigating the eff ects of landscape change. In this paper, we critically challenge the conceptual foundations of the discipline, and attempt to derive an integrated perspective on the best way to advance mechanistic understanding of fragmentation processes. We depict the inherent assumptions underly- ing the discipline as a ‘ conceptual phase space ' of contrasting false dichotomies in fragmentation ‘ problem space ' . In our opinion, the key determinant of whether ‘ habitat fragmentation ' can remain a cohesive framework lies in the concept of ‘ interdependence ' : 1) interdependence of landscape eff ects on species and 2) interdependence of species responses to landscape change. If there is non-trivial interdependence among the various sub-components of habitat fragmentation, or non-trivial interdependence among species responses to landscape change, then there will be real heuristic value in ‘ habitat fragmentation ' as a single conceptual domain. At present, the current paradigms entrenched in the fragmentation literature are implicitly founded on strict independence of landscape eff ects (e.g. the debate about the independent eff ects of habitat loss versus fragmentation per se) and strict independence of species responses (e.g. the individualistic species response models underpinning landscape continuum models), despite compelling evidence for interdependence in both eff ects and responses to fragmentation. We discuss how strong ‘ interdependence ' of eff ects and responses challenges us to rethink long- held views, and re-cast the conceptual foundations of habitat fragmentation in terms of spatial context-dependence in the eff ects of multiple interacting spatial components of fragmentation, and community context-dependence in the responses of multiple interacting species to landscape change. In}, author = {Didham, Raphael K. and Kapos, Valerie and Ewers, Robert M.}, doi = {10.1111/j.1600-0706.2011.20273.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Didham, Kapos, Ewers - 2012 - Rethinking the conceptual foundations of habitat fragmentation research.pdf:pdf}, isbn = {1600-0706}, issn = {00301299}, journal = {Oikos}, number = {2}, pages = {161--170}, title = {{Rethinking the conceptual foundations of habitat fragmentation research}}, volume = {121}, year = {2012} } @article{Hughes2018, abstract = {Tropical reef systems are transitioning to a new era in which the interval between recurrent bouts of coral bleaching is too short for a full recovery of mature assemblages.We analyzed bleaching records at 100 globally distributed reef locations from 1980 to 2016. The median return time between pairs of severe bleaching events has diminished steadily since 1980 and is now only 6 years. As global warming has progressed, tropical sea surface temperatures are warmer now during current La Ni{\~{n}}a conditions than they were during El Ni{\~{n}}o events three decades ago. Consequently, as we transition to the Anthropocene, coral bleaching is occurring more frequently in all El Ni{\~{n}}o–Southern Oscillation phases, increasing the likelihood of annual bleaching in the coming decades}, annote = {- how frequent is too frequent? - extreme heat, not geneneral warming, is what is important here}, author = {Hughes, Terry P and Anderson, Kristen D and Connolly, Sean R and Heron, Scott F and Kerry, James T and Lough, Janice M and Baird, Andrew H and Baum, Julia K and Berumen, Michael L and Bridge, Tom C and Claar, Danielle C and Eakin, C Mark and Gilmour, James P and Graham, Nicholas A J and Harrison, Hugo and Hobbs, Jean-Paul A and Hoey, Andrew S and Hoogenboom, Mia and Lowe, Ryan J and Mcculloch, Malcolm T and Pandolfi, John M and Pratchett, Morgan and Schoepf, Verena and Torda, Gergely and Wilson, Shaun K}, doi = {10.1126/science.aan8048}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hughes et al. - 2018 - Spatial and temporal patterns of mass bleaching of corals in the Anthropocene.pdf:pdf}, issn = {0036-8075}, journal = {Science}, number = {80}, pages = {80--83}, pmid = {29302011}, title = {{Spatial and temporal patterns of mass bleaching of corals in the Anthropocene}}, url = {www.sciencemag.org/content/359/6371/80/suppl/DC1}, volume = {5}, year = {2018} } @incollection{Jordano2013, annote = {- definitely need to account for phylogenetics - showed that ecological networks are often broad or scale free, interactions are often nested, networks are typpically modular Forbidden links driven by biological constraits (may explain upwards of 75{\%} of nonobaserved insteractions) - temporal uncoupling (match/mismatch hypothesis) - size mismatching (like bird beaks) - could also include habitat selection, foraging constraits, or physiological constraints Species abundance will also structure ecological networks Evolutionary history can affect position of species within network and the interaction strength between different patterns - ecology tied more strongly to evolutionary patterns for animals (probability mobility traits)}, author = {Jordano, Pedro and Networks, Mutualistic and Central, Proquest Ebook}, booktitle = {Mutualistic Networks}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Jordano, Networks, Central - 2013 - Chapter 4 Ecological and evolutionary mechanisms.pdf:pdf}, pages = {12291--12291}, title = {{Chapter 4: Ecological and evolutionary mechanisms}}, year = {2013} } @article{Martin2017, abstract = {With many conservation issues requiring urgent action, determining how much data are needed to inform good decisions is a common problem. We examine this problem in relation to the protection of critical habitat, the habitat required for species' recovery and persistence. The protection of critical habitat is an essential step in the threatened species recovery process. It is also one of the most contentious and protracted decisions faced by environmental agencies. Uncertainty about what constitutes critical habitat, and the challenges of balancing competing societal objectives and of protecting critical habitat once identified are stalling the recovery process. We offer insight into this challenge by investigating how long we can afford to spend identifying critical habitat before opportunities to recover a species are lost. We illustrate our decision model using Canada's threatened northern abalone (Haliotis kamtschatkana). Our method delivers the stopping time at which habitat protection must begin, despite uncertainty, in order to avoid an unacceptable risk of extinction.}, annote = {This paper uses simulations of an abalone population to demonstrate when a choice about habitat protectino needs to be made. The model includes a function for how confident we are about which habitat is critical and the population dynamics of the species involved. The paper points out that it is often neccessary to make a decision about protecting crtiical habitat before all "neccessary" data has been collected. In this case, more data is always better is not actually true. Use Receiver operator curves to make decisions on balance between false positves and false negatives in regards to conservation decisions}, author = {Martin, Tara G. and Camaclang, Abbey E. and Possingham, Hugh P. and Maguire, Lynn A. and Chad{\`{e}}s, Iadine}, doi = {10.1111/conl.12266}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Martin et al. - 2017 - Timing of Protection of Critical Habitat Matters.pdf:pdf}, isbn = {1755263X}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Decision making,Endangered Species Act,Environment Protection and Biodiversity Act,Haliotis kamtschatkana,decision model,extinction risk,habitat protection,learning, northern abalone,species at risk}, number = {3}, pages = {308--316}, title = {{Timing of Protection of Critical Habitat Matters}}, volume = {10}, year = {2017} } @article{Martin2012, abstract = {Failure to act quickly on evidence of rapid population decline has led to the first mammal extinction in Australia in the last 50 years, the Christmas Island Pipistrelle (Pipistrellus murrayi). The fate of another iconic species, the migratory Orange-bellied Parrot (Neophema chrysogaster), monitored intensively for over 20 years, hangs in the balance. To inform future conservation management and decision making, we investigate the decision process that has led to the plight of both species. Our analysis suggests three globally relevant recommendations for minimizing species extinction worldwide: (1) informed, empowered, and responsive governance and leadership is essential; (2) processes that ensure institutional accountability must be in place, and; (3) decisions must be made whilst there is an opportunity to act. The bottom line is that, unless responsive and accountable institutional processes are in place, decisions will be delayed and extinction will occur.}, annote = {This paper documents the conservation and decision makjing processes to several species of conservation concern. They argue that waiting to collect more data can imperil an endagered species Point to three key lessons: 1) organized and efffective leadership is important 2) recovery plans should include specific triggers to indicate when a new policy should be enacted...prevents delay in deciding what to do 3) delaying decisions removes opportunities and choices for species management}, author = {Martin, Tara G. and Nally, Simon and Burbidge, Andrew A. and Arnall, Sophie and Garnett, Stephen T. and Hayward, Matt W. and Lumsden, Linda F. and Menkhorst, Peter and Mcdonald-Madden, Eve and Possingham, Hugh P.}, doi = {10.1111/j.1755-263X.2012.00239.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Martin et al. - 2012 - Acting fast helps avoid extinction.pdf:pdf}, isbn = {1755-263X}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Captive breeding,Christmas Island Pipistrelle,Endangered species,Governance,Leadership,Monitoring,Orange-bellied Parrot}, number = {4}, pages = {274--280}, title = {{Acting fast helps avoid extinction}}, volume = {5}, year = {2012} } @article{Kessel2014a, abstract = {{\textcopyright} Inter-Research 2014. Understanding how and why animals are distributed through time and space has always been a fundamental component of ecology and is an essential prerequisite for effective conservation and/or management. However, for highly mobile K-selected species, behavioural predictability is rarely considered over appropriate scales relative to life history. To address this point, a multidisciplinary approach combining telemetry, external tagging, physical assessment, environmental monitoring and genetic analysis was adopted to determine a spatial framework for the movements of adult lemon sharks Negaprion brevirostris at multiple spatial and temporal scales from 2007 to 2011. Lemon sharks (n = 83) were tracked with passive acoustic telemetry, revealing a winter residency in the southeast Florida region. Detections from individuals recorded within the core winter habitat for {\textgreater} 20 d (n = 56) were incorporated into generalized linear mixedeffects models to investigate the influence of water temperature, photoperiod, moon phase, month and year on presence. The findings of this study suggest a temperature driven 'migrationresidency' model for mature lemon shark distribution across the USA eastern seaboard. Lemon sharks are distributed across a wide geographical area in the summer months and migrate south concentrating off southeast Florida in the winter, with this pattern repeated each year. From comparative genetic analysis and the absence of any evidence of mating behaviour during the winter residency period, mating and parturition most probably occur in May/June between northern Florida and the Carolinas. This study highlights the importance of determining the specific dynamics and proximate causes of animal movement and distribution over appropriate spatial and temporal scales relative to life history.}, author = {Kessel, S.T. and Chapman, D.D. and Franks, B.R. and Gedamke, T. and Gruber, S.H. and Newman, J.M. and White, E.R. and Perkins, R.G.}, doi = {10.3354/meps10966}, issn = {01718630}, journal = {Marine Ecology Progress Series}, keywords = {Acoustic telemetry,GLMM,Lemon shark,Seasonal migration,Seasonal residency,Temperature preference}, title = {{Predictable temperature-regulated residency, movement and migration in a large, highly mobile marine predator (Negaprion brevirostris)}}, volume = {514}, year = {2014} } @article{Robinson2014a, abstract = {Biodiversity hotspots have been used extensively in setting conservation priorities for marine ecosystems. A recent Nature publication claims to have uncovered new latitudinal gradients in the evenness of reef communities and new reef hotspots based on functional diversity. Simulation models show that the purported evenness gradient is a mathematical inevitability of differences in species richness and detectability between vastly different marine ecosystems, namely 'reefs' in tropical, temperate, and polar regions. Constraints on evenness, along with disparity amongst communities in possible functional traits, cast doubt on the utility of global functional diversity comparisons for management of marine systems. {\textcopyright} 2014 Elsevier Ltd.}, author = {Robinson, J.P.W. and White, E.R. and Wiwchar, L.D. and Claar, D.C. and Suraci, J.P. and Baum, J.K.}, doi = {10.1016/j.marpol.2014.03.012}, issn = {0308597X}, journal = {Marine Policy}, keywords = {Evenness,Functional diversity,Macroecology,Marine fish,Reef ecosystems,Underwater visual census}, title = {{The limitations of diversity metrics in directing global marine conservation}}, volume = {48}, year = {2014} } @article{White2015a, abstract = {{\textcopyright} 2015 Society for Conservation Biology. Fishing pressure has increased the extinction risk of many elasmobranch (shark and ray) species. Although many countries have established no-take marine reserves, a paucity of monitoring data means it is still unclear if reserves are effectively protecting these species. We examined data collected by a small group of divers over the past 21 years at one of the world's oldest marine protected areas (MPAs), Cocos Island National Park, Costa Rica. We used mixed effects models to determine trends in relative abundance, or probability of occurrence, of 12 monitored elasmobranch species while accounting for variation among observers and from abiotic factors. Eight of 12 species declined significantly over the past 2 decades. We documented decreases in relative abundance for 6 species, including the iconic scalloped hammerhead shark (Sphyrna lewini) (-45{\%}), whitetip reef shark (Triaenodon obesus) (-77{\%}), mobula ray (Mobula spp.) (-78{\%}), and manta ray (Manta birostris) (-89{\%}), and decreases in the probability of occurrence for 2 other species. Several of these species have small home ranges and should be better protected by an MPA, which underscores the notion that declines of marine megafauna will continue unabated in MPAs unless there is adequate enforcement effort to control fishing. In addition, probability of occurrence at Cocos Island of tiger (Galeocerdo cuvier), Galapagos (Carcharhinus galapagensis), blacktip (Carcharhinus limbatus), and whale (Rhincodon typus) sharks increased significantly. The effectiveness of MPAs cannot be evaluated by examining single species because population responses can vary depending on life history traits and vulnerability to fishing pressure.}, author = {White, E.R. and Myers, M.C. and Flemming, J.M. and Baum, J.K.}, doi = {10.1111/cobi.12478}, issn = {15231739}, journal = {Conservation Biology}, keywords = {Citizen science,Eastern tropical Pacific,Fisheries,Generalized linear mixed models,MPA,Marine reserve,Sharks,Zero-inflated}, number = {4}, title = {{Shifting elasmobranch community assemblage at Cocos Island-an isolated marine protected area}}, volume = {29}, year = {2015} } @article{Senko2014, abstract = {Marine megafauna such as seabirds, marine mammals and sea turtles are subject to high mortality from incidental capture or bycatch in fisheries. Recent research suggests that fishing effort is increasing worldwide, highlighting the need to evaluate strategies intended to reduce marine megafauna bycatch. Here, we use three focal species (i.e. leatherback turtle Dermochelys coriacea, black-footed albatross Phoebastria nigripes and vaquita porpoise Phocoena sinus) as case studies to compare management outcomes of four bycatch mitigation measures: time-area closures, individual bycatch limits, gear modifications and buy-outs. Time-area closures were used for leatherbacks and vaquitas with limited effectiveness, although timing, size and enforcement influenced their efficacy. Individual bycatch limits were employed for leatherbacks in one fishery, sometimes simultaneously with gear modifications and closures. Gear modificati ons consistently reduced bycatch of leatherbacks and black-footed albatross and showed strong promise for vaquitas. True buy-outs were only used for vaquitas and were costly, most fishers were unwilling to be bought out, and it is unclear if they reduced bycatch. Our review suggests that gear modifications were the most widely used and generally most promising technique for these species, although management outcomes of each strategy depended largely on the species-fishery interaction, fishery characteristics and socioeconomic context. Based on lessons learned from our case studies, we outline when and where a particular approach may be most effective, provide recommendations for improving each strategy and highlight priorities for future research. {\textcopyright} 2013 The Zoological Society of London.}, author = {Senko, J. and White, E.R. and Heppell, S.S. and Gerber, L.R.}, doi = {10.1111/acv.12051}, issn = {13679430}, journal = {Animal Conservation}, keywords = {Buy-outs,Bycatch limits,Bycatch mitigation,Gear modifications,Marine megafauna,Time-area closures}, number = {1}, title = {{Comparing bycatch mitigation strategies for vulnerable marine megafauna}}, volume = {17}, year = {2014} } @article{Gerber2014b, abstract = {While most demographic population models used in conservation rely on female vital rates, recent empirical evidence suggests that male dynamics should be included in population models used for assessing extinction risk. Using California sea lions Zalophus californianus as an applied example, we demonstrate that there are situations in which two-sex models are more appropriate than the commonly used female-based model. Two-sex models are relevant in cases where vital rates for sexes differ and for polygamous species such as sea lions. Vital rates targeted for management may therefore respond differently for males and females and for different assumptions about sex ratio. Synthesis and applications. Conservation biologists should carefully consider the social structure and sex ratio of focal species in order to determine whether a two-sex matrix model will yield more accurate estimates of extinction risk than standard one-sex models. {\textcopyright} 2013 The Authors. Journal of Applied Ecology {\textcopyright} 2013 British Ecological Society.}, author = {Gerber, L.R. and White, E.R.}, doi = {10.1111/1365-2664.12177}, issn = {00218901}, journal = {Journal of Applied Ecology}, keywords = {Extinction risk,Sex ratio,Two-sex models,Zalophus californianus}, number = {1}, title = {{Two-sex matrix models in assessing population viability: When do male dynamics matter?}}, volume = {51}, year = {2014} } @article{Rassweiler2012, abstract = {There is a growing focus around the world on marine spatial planning, including spatial fisheries management. Some spatial management approaches are quite blunt, as when marine protected areas (MPAs) are established to restrict fishing in specific locations. Other management tools, such as zoning or spatial user rights, will affect the distribution of fishing effort in a more nuanced manner. Considerable research has focused on the ability of MPAs to increase fishery returns, but the potential for the broader class of spatial management approaches to outperform MPAs has received far less attention. We use bioeconomic models of seven nearshore fisheries in Southern California to explore the value of optimized spatial management in which the distribution of fishing is chosen to maximize profits. We show that fully optimized spatial management can substantially increase fishery profits relative to optimal nonspatial management but that the magnitude of this increase depends on characteristics of the fishing fleet and target species. Strategically placed MPAs can also increase profits substantially compared with nonspatial management, particularly if fishing costs are low, although profit increases available through optimal MPA-based management are roughly half those from fully optimized spatial management. However, if the same total area is protected by randomly placing MPAs, starkly contrasting results emerge: most random MPA designs reduce expected profits. The high value of spatial management estimated here supports continued interest in spatially explicit fisheries regulations but emphasizes that predicted increases in profits can only be achieved if the fishery is well understood and the regulations are strategically designed.}, author = {Rassweiler, A. and Costello, C. and Siegel, D. A.}, doi = {10.1073/pnas.1116193109}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rassweiler, Costello, Siegel - 2012 - Marine protected areas and the value of spatially optimized fishery management.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rassweiler, Costello, Siegel - 2012 - Marine protected areas and the value of spatially optimized fishery management(2).pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {29}, pages = {11884--11889}, pmid = {22753469}, title = {{Marine protected areas and the value of spatially optimized fishery management}}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1116193109}, volume = {109}, year = {2012} } @book{Billeb1986, author = {Billeb, Emil W.}, publisher = {Gem Guides Book Company}, title = {{Mining Camp Days}}, year = {1986} } @book{Wedertz1969, address = {Bishop, California}, author = {Wedertz, Frank S.}, publisher = {Community Printing and Publishing}, title = {{Bodie, 1859-1900}}, year = {1969} } @article{Smith1980, abstract = {Temporal change in size of populations of a small alpine mammal, the pika (O. princeps), at Bodie, California, USA, was analyzed by comparing a 1972 census of the observed spacing of pikas on discrete islands of habitat to a similar 1977 census. The islands of habitat varied in size and distance from one another. Overall results from each census were strikingly similar. Not all of the islands were occupied and most seemed to contain fewer individuals than they could hold. The populations apparently represent dynamic equilibria between extinction (which was inversely related to island size), and recolonization (which was inversely related to inter-island distance). In spite of these similarities, the population size of individual islands changed dramatically. Eight previously unocuppied islands were colonized and 11 island populations became extinct. Of 77 islands compared, 53{\%} changed their degree of saturation within the 5 yr period. Changes in percent saturation of available habitat on islands varied among island sizes and degrees of isolations. All cases of turnover (extinction or recolonization) occurred on small or medium-size islands. Within these island size categories, turnover increased with isolation. Extinction of populations on islands close to a source of potential colonists are apparently minimized by recurrent colonization, a verification of the rescue effect.}, author = {Smith, Andrew T}, doi = {10.2307/1937147}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {1,1980,61,8-13,andrew t,author,ecological society of america,ecology,feb,no,ochotona princeps,populations of the pika,poral changes in insular,pp,published by,s,smith,source,vol}, number = {1}, pages = {8--13}, title = {{Temporal changes in insular populations of the pika ($\backslash$emph{\{}Ochotona princeps{\}})}}, volume = {61}, year = {1980} } @article{Stefan2015, abstract = {The past decade has seen a rapid increase in the ability of biologists to collect large amounts of data. It is therefore vital that research biologists acquire the necessary skills during their training to visualize, analyze, and interpret such data. To begin to meet this need, we have developed a "boot camp" in quantitative methods for biology graduate students at Harvard Medical School. The goal of this short, intensive course is to enable students to use computational tools to visualize and analyze data, to strengthen their computational thinking skills, and to simulate and thus extend their intuition about the behavior of complex biological systems. The boot camp teaches basic programming using biological examples from statistics, image processing, and data analysis. This integrative approach to teaching programming and quantitative reasoning motivates students' engagement by demonstrating the relevance of these skills to their work in life science laboratories. Students also have the opportunity to analyze their own data or explore a topic of interest in more detail. The class is taught with a mixture of short lectures, Socratic discussion, and in-class exercises. Students spend approximately 40{\%} of their class time working through both short and long problems. A high instructor-to-student ratio allows students to get assistance or additional challenges when needed, thus enhancing the experience for students at all levels of mastery. Data collected from end-of-course surveys from the last five offerings of the course (between 2012 and 2014) show that students report high learning gains and feel that the course prepares them for solving quantitative and computational problems they will encounter in their research. We outline our course here which, together with the course materials freely available online under a Creative Commons License, should help to facilitate similar efforts by others.}, author = {Stefan, Melanie I. and Gutlerner, Johanna L. and Born, Richard T. and Springer, Michael}, doi = {10.1371/journal.pcbi.1004208}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stefan et al. - 2015 - The Quantitative Methods Boot Camp Teaching Quantitative Thinking and Computing Skills to Graduate Students in th.pdf:pdf}, isbn = {1553-734x}, issn = {15537358}, journal = {PLoS Computational Biology}, number = {4}, pmid = {25880064}, title = {{The Quantitative Methods Boot Camp: Teaching Quantitative Thinking and Computing Skills to Graduate Students in the Life Sciences}}, url = {http://dx.doi.org/10.1371/journal.pcbi.1004208}, volume = {11}, year = {2015} } @article{Feldon2017, abstract = {Many PhD programs incorporate boot camps and summer bridge programs to accelerate the development of doctoral students' research skills and acculturation into their respective disciplines. These brief, high-intensity experiences span no more than several weeks and are typically designed to expose graduate students to data analysis techniques, to develop scientific writing skills, and to better embed incoming students into the scholarly community. However, there is no previous study that directly measures the outcomes of PhD students who participate in such programs and compares them to the outcomes of students who did not participate. Likewise, no previous study has used a longitudinal design to assess these outcomes over time. Here we show that participation in such programs is not associated with detectable benefits related to skill development, socialization into the academic community, or scholarly productivity for students in our sample. Analyzing data from 294 PhD students in the life sciences from 53 US institutions, we found no statistically significant differences in outcomes between participants and nonparticipants across 115 variables. These results stand in contrast to prior studies presenting boot camps as effective interventions based on participant satisfaction and perceived value. Many universities and government agencies (e.g., National Institutes of Health and National Science Foundation) invest substantial resources in boot camp and summer bridge activities in the hopes of better supporting scientific workforce development. Our findings do not reveal any measurable benefits to students, indicating that an allocation of limited resources to alternative strategies with stronger empirical foundations warrants consideration.}, author = {Feldon, David F. and Jeong, Soojeong and Peugh, James and Roksa, Josipa and Maahs-Fladung, Cathy and Shenoy, Alok and Oliva, Michael}, doi = {10.1073/pnas.1705783114}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Feldon et al. - 2017 - Null effects of boot camps and short-format training for PhD students in life sciences.pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {37}, pages = {201705783}, pmid = {28847929}, title = {{Null effects of boot camps and short-format training for PhD students in life sciences}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1705783114}, volume = {114}, year = {2017} } @article{Ferriere2004, abstract = {As human threats to the Earth's biota span unprecedented temporal and spatial scales, it has become urgent to integrate currently disparate areas of conservation biology into a unified framework. Combining conservation genetics, demography, and ecology, this book presents an integrative approach to managing species as well as ecological and evolutionary processes. The contributions are intended for students, professionals, and researchers in conservation biology, ecology, genetics, and evolution.}, annote = {Chapter 11: Adaptive dynamics and evolving biodviersity -}, author = {Ferri{\`{e}}re, R and Dieckmann, U and Couvet, D}, doi = {10.1017/CBO9780511542022}, isbn = {9780511542022}, journal = {Evolutionary Ecology}, number = {3}, pages = {428}, title = {{Evolutionary Conservation Biology}}, url = {http://ebooks.cambridge.org/ref/id/CBO9780511542022}, volume = {55}, year = {2004} } @article{Freeman2014, abstract = {To test the hypothesis that lecturing maximizes learning and course performance, we metaanalyzed 225 studies that reported data on examination scores or failure rates when comparing student performance in undergraduate science, technology, engineering, and mathematics (STEM) courses under traditional lecturing versus active learning. The effect sizes indicate that on average, student performance on examinations and concept inventories increased by 0.47 SDs under active learning (n = 158 studies), and that the odds ratio for failing was 1.95 under traditional lecturing (n = 67 studies). These results indicate that average examination scores improved by about 6{\%} in active learning sections, and that students in classes with traditional lecturing were 1.5 times more likely to fail than were students in classes with active learning. Heterogeneity analyses indicated that both results hold across the STEM disciplines, that active learning increases scores on concept inventories more than on course examinations, and that active learning appears effective across all class sizes--although the greatest effects are in small (n [{\&}le;] 50) classes. Trim and fill analyses and fail-safe n calculations suggest that the results are not due to publication bias. The results also appear robust to variation in the methodological rigor of the included studies, based on the quality of controls over student quality and instructor identity. This is the largest and most comprehensive metaanalysis of undergraduate STEM education published to date. The results raise questions about the continued use of traditional lecturing as a control in research studies, and support active learning as the preferred, empirically validated teaching practice in regular classrooms.}, archivePrefix = {arXiv}, arxivId = {arXiv:1408.1149}, author = {Freeman, S. and Eddy, S. L. and McDonough, M. and Smith, M. K. and Okoroafor, N. and Jordt, H. and Wenderoth, M. P.}, doi = {10.1073/pnas.1319030111}, eprint = {arXiv:1408.1149}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Freeman et al. - 2014 - Active learning increases student performance in science, engineering, and mathematics.pdf:pdf}, isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {23}, pages = {8410--8415}, pmid = {24821756}, title = {{Active learning increases student performance in science, engineering, and mathematics}}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.1319030111}, volume = {111}, year = {2014} } @article{Larsen2001, abstract = {We describe a framework for evaluating the effects of spatial and temporal variation on the sensitivity of alternative ecological survey designs to detect regional temportal trends}, annote = {need to cite this an another paper within this article}, author = {Larsen, David P. and Kincaid, Thomas M. and Jacobs, Steven E. and Urquhart, N. Scott}, doi = {10.1641/0006-3568(2001)051[1069:DFELAR]2.0.CO;2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Larsen et al. - 2001 - Designs for Evaluating Local and Regional Scale Trends.pdf:pdf}, isbn = {0006-3568}, issn = {0006-3568}, journal = {BioScience}, number = {12}, pages = {1069}, title = {{Designs for Evaluating Local and Regional Scale Trends}}, volume = {51}, year = {2001} } @article{Regan2017, abstract = {Population viability analysis (PVA) is a reliable tool for ranking management options for a range of species despite parameter uncertainty. No one has yet investigated whether this holds true for model uncertainty for species with complex life histories and for responses to multiple threats. We tested whether a range of model structures yielded similar rankings of management and threat scenarios for 2 plant species with complex postfire responses. We examined 2 contrasting species from different plant functional types: an obligate seeding shrub and a facultative resprouting shrub. We exposed each to altered fire regimes and an additional, species-specific threat. Long-term demographic data sets were used to construct an individual-based model (IBM), a complex stage-based model, and a simple matrix model that subsumes all life stages into 2 or 3 stages. Agreement across models was good under some scenarios and poor under others. Results from the simple and complex matrix models were more similar to each other than to the IBM. Results were robust across models when dominant threats are considered but were less so for smaller effects. Robustness also broke down as the scenarios deviated from baseline conditions, likely the result of a number of factors related to the complexity of the species' life history and how it was represented in a model. Although PVA can be an invaluable tool for integrating data and understanding species' responses to threats and management strategies, this is best achieved in the context of decision support for adaptive management alongside multiple lines of evidence and expert critique of model construction and output.}, author = {Regan, Helen M. and Boh{\'{o}}rquez, Clara I. and Keith, David A. and Regan, Tracey J. and Anderson, Kurt E.}, doi = {10.1111/cobi.12831}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Regan et al. - 2017 - Implications of different population model structures for management of threatened plants.pdf:pdf}, issn = {15231739}, journal = {Conservation Biology}, keywords = {Grevillea caleyi,Xanthorrhoea resinosa,an{\'{a}}lisis de viabilidad poblacional,conservation management,incertidumbre de modelo,individual-based model,manejo de la conservaci{\'{o}}n,matrix model,model uncertainty,modelo basado en el individuo,modelo matricial,population viability analysis}, number = {2}, pages = {459--468}, title = {{Implications of different population model structures for management of threatened plants}}, volume = {31}, year = {2017} } @article{Fahrig2013, abstract = {I challenge (1) the assumption that habitat patches are natural units of measurement for species richness, and (2) the assumption of distinct effects of habitat patch size and isolation on species richness. I propose a simpler view of the relationship between habitat distribution and species richness, the ‘habitat amount hypothesis', and I suggest ways of testing it. The habitat amount hypothesis posits that, for habitat patches in a matrix of non-habitat, the patch size effect and the patch isolation effect are driven mainly by a single underlying process, the sample area effect. The hypothesis predicts that species richness in equal-sized sample sites should increase with the total amount of habitat in the ‘local landscape' of the sample site, where the local landscape is the area within an appropriate distance of the sample site. It also predicts that species richness in a sample site is independent of the area of the particular patch in which the sample site is located (its ‘local patch'), except insofar as the area of that patch contributes to the amount of habitat in the local landscape of the sample site. The habitat amount hypothesis replaces two predictor variables, patch size and isolation, with a single predictor variable, habitat amount, when species richness is analysed for equal-sized sample sites rather than for unequal-sized habitat patches. Studies to test the hypothesis should ensure that ‘habitat' is correctly defined, and the spatial extent of the local landscape is appropriate, for the species group under consideration. If supported, the habitat amount hypothesis would mean that to predict the relationship between habitat distribution and species richness: (1) distinguishing between patch-scale and landscape-scale habitat effects is unnecessary; (2) distinguishing between patch size effects and patch isolation effects is unnecessary; (3) considering habitat configuration independent of habitat amount is unnecessary; and (4) delineating discrete habitat patches is unnecessary.}, author = {Fahrig, Lenore}, doi = {10.1111/jbi.12130}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fahrig - 2013 - Rethinking patch size and isolation effects The habitat amount hypothesis.pdf:pdf}, isbn = {1365-2699}, issn = {03050270}, journal = {Journal of Biogeography}, keywords = {Edge effect,Habitat fragmentation,Habitat loss,Local landscape,Local patch,Matrix quality,Nested subsets,SLOSS,Species accumulation curve,Species-area relationship}, number = {9}, pages = {1649--1663}, title = {{Rethinking patch size and isolation effects: The habitat amount hypothesis}}, volume = {40}, year = {2013} } @article{Pechmann1991, author = {Pechmann, Joseph H K and Scott, David E and Semlitsch, Raymond D and Janalee, P and Vitt, Laurie J and Gibbons, J Whitfield}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pechmann et al. - 1991 - Declining amphibian populations the problem of separating human impacts from natural fluctuations.pdf:pdf}, journal = {Science}, number = {4}, pages = {1--5}, title = {{Declining amphibian populations : the problem of separating human impacts from natural fluctuations}}, volume = {892}, year = {1991} } @article{Inchausti2001, author = {Inchausti, P and Halley, J}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Inchausti, Halley - 2001 - Investigating long-term ecological variability using the global population dynamics database.pdf:pdf}, journal = {Science}, number = {5530}, pages = {1999--2002}, title = {{Investigating long-term ecological variability using the global population dynamics database}}, volume = {293}, year = {2001} } @article{Chickering1987, author = {Chickering, Arthur W. and Gamson, Zelda F.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chickering, Gamson - 1987 - Seven principles for good practice in undergraduate education.pdf:pdf}, isbn = {0876522347}, journal = {AAHE Bulletin}, pages = {6}, title = {{Seven principles for good practice in undergraduate education}}, volume = {Mar}, year = {1987} } @article{Beever2011, abstract = {Contemporary climate change is expected to affect the distributions of most species, but the nature, tempo, and mechanics of contemporary range shifts are still largely speculative. Here, we use fine-scale distributional records developed over the past Century, combined with spatially comprehensive microclimatic data, to demonstrate a dramatic shift in the range of a climate-sensitive mammal and to infer the increasingly important role of climate in local extinctions of this species across a 38.2 million-ha area. Changes in the distribution of the American pika (Ochotona princeps) throughout the Great Basin ecoregion were characterized using records from 1898-2008, revealing a nearly five-fold increase in the rate of local extinction and an 11-fold increase in the rate of upslope range retraction during the last ten years, compared with during the 20th Century. Four of ten local pika extinctions have occurred since 1999, and across this ecoregion the low-elevation range boundary for this species is now moving upslope at an average rate of about 145 m per decade. The rapid, ecoregional range shift of this small, talus-dwelling species stands in remarkable contrast with the dynamics and determinants of endangerment previously observed for most terrestrial species, and to earlier extinction determinants for O. princeps in this region. Further investigation of widely distributed species will clarify rates at which biotic response to environmental change is occurring, and how factors driving that change are evolving in different portions of the earth.}, annote = {This paper resurveyed old sights to look for pika extirpations. They then used statistical models to determine potential correlations between predicted and actual extirpated sights. They found that elevational distributions of pikas shifted upwards..}, author = {Beever, Erik A. and Ray, Chris and Wilkening, Jenifer L. and Brussard, Peter F. and Mote, Philip W.}, doi = {10.1111/j.1365-2486.2010.02389.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Beever et al. - 2011 - Contemporary climate change alters the pace and drivers of extinction.pdf:pdf}, isbn = {1354-1013}, issn = {13541013}, journal = {Global Change Biology}, keywords = {American pika,Environmental change,Great Basin ecoregion,Information-theoretic analysis,Local-extinction determinants,Model updating,Montane biotas,Ochotona princeps,Upslope range retraction}, number = {6}, pages = {2054--2070}, title = {{Contemporary climate change alters the pace and drivers of extinction}}, volume = {17}, year = {2011} } @article{Tanner2009, abstract = {Pedagogical strategies have been experimentally applied in large-enrollment biology courses in an attempt to amplify what teachers do best in effecting deep learning, thus more closely approximating a one-on-one interaction with students. Carefully orchestrated in-class formative assessments were conducted to provide frequent, high-quality feedback that allows students to accurately diagnose the current state of their understanding of fundamental biological concepts and make specific plans to remedy any deficiencies. Teachers can also assume responsibility to guide out-of-class study among classmates by promoting Elaborative Questioning, an inquiry exchange that permits misconceptions to be identified and corrected and that promotes long- lasting metacognitive and analytical thinking skills. Data are presented that demonstrate the positive impact of these innovations on student performance and affect.}, author = {Tanner, Kimberly D.}, doi = {10.1187/cbe.09}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Tanner - 2009 - Active Learning and Student-centered Pedagogy Improve Student Attitdues and Performance in Introductory Biology.pdf:pdf}, isbn = {1931-7913}, issn = {1931-7913}, journal = {CBE-Life Science Education}, pages = {203--213}, pmid = {19723819}, title = {{Active Learning and Student-centered Pedagogy Improve Student Attitdues and Performance in Introductory Biology}}, volume = {8}, year = {2009} } @article{Brashares2005, annote = {This is an interesting paper that used sub-sampling techniques to estimate how many surveys should be conducted each year to ensure a high enough statistical power. They use reserve data on four species to estimate how frequently and how spatially sampling should be done}, author = {Brashares, Justin S and Sam, Moses K}, doi = {10.1007/s10531-005-8404-z}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brashares, Sam - 2005 - How much is enough Estimating the minimum sampling required for effective monitoring of African reserves.pdf:pdf}, journal = {Biodiversity and Conservation}, keywords = {abstract,balance of rigour and,design moni-,developing countries,developing countries requires a,effective biological monitoring in,guidelines to help practitioners,locally-based monitoring,population trends,power analysis,practicality,ranger-based monitoring,sampling effort,sustainability,there exist few general,unfortunately,wildlife monitoring}, pages = {2709--2722}, title = {{How much is enough? Estimating the minimum sampling required for effective monitoring of African reserves}}, volume = {14}, year = {2005} } @article{Blanchard2007, annote = {This paper using detailed simiulations to determine which mointoring schemes (random, fixed stratified, etc) to determine the best approach to monitoring. They also include things like temperature preferences and local patiness to see how this type of biological information may affect sampling. They find that 15 or more years is usually neccessary to detect trends, but this of course depends on sampling design, type I and II error rates, temperature, and patchiness}, author = {Blanchard, Julia L and Maxwell, David L and Jennings, Simon}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Blanchard, Maxwell, Jennings - 2007 - Power of monitoring surveys to detect abundance trends in depleted populations the effects of dens.pdf:pdf}, journal = {ICES Journal of Marine Science}, keywords = {climate change,density-dependent habitat use,ecosystem approach to fisheries,fish population,monitoring,survey design,trawl}, number = {1}, pages = {111--120}, title = {{Power of monitoring surveys to detect abundance trends in depleted populations: the effects of density-dependent habitat use, patchiness, and climate change}}, volume = {65}, year = {2007} } @article{Thompson2000, annote = {This paper uses a PVA approach to assess the risks of waiting to long to enact conservation or management practices. It may take a number of years to detect a trend, and it may be too late by the time the trend is actually detected. Argues for the precautionary approach based on these results.}, author = {Thompson, Paul M and Wilson, Ben and Grellier, Kate and Hammond, Philip S}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thompson et al. - 2000 - Combining power analysis and population viability analysis to compare traditional and precautionary approaches.pdf:pdf}, journal = {Conservation Biology}, number = {5}, pages = {1253--1263}, title = {{Combining power analysis and population viability analysis to compare traditional and precautionary approaches to conservation of coastal cetaceans}}, volume = {14}, year = {2000} } @article{Hughes2007, author = {Hughes, A. Randall and Byrnes, Jarrett E and Kimbro, David L. and Stachowicz, John J.}, doi = {10.1111/j.1461-0248.2007.01075.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hughes et al. - 2007 - Reciprocal relationships and potential feedbacks between biodiversity and disturbance.pdf:pdf}, journal = {Ecology Letters}, keywords = {10,2007,849,864,biodiversity,disturbance,ecology letters,ecosystem function,feedback,hypothesis,intermediate disturbance,stability}, pages = {849--864}, title = {{Reciprocal relationships and potential feedbacks between biodiversity and disturbance}}, volume = {10}, year = {2007} } @article{Hastings2014a, author = {Hastings, Alan}, doi = {10.1007/s10144-013-0416-z}, journal = {Pop}, keywords = {connectivity {\'{a}} dispersal {\'{a}},extinction {\'{a}}}, pages = {21--26}, title = {{Persistence and management of spatially distributed populations}}, volume = {56}, year = {2014} } @article{Ward-paige2010, author = {Ward-paige, Christine A and Pattengill-Semmens, Christy and Myers, Ransom A and Lotze, Heike K.}, doi = {10.1007/s10641-010-9739-1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ward-paige et al. - 2010 - Spatial and temporal trends in yellow stingray abundance evidence from diver surveys.pdf:pdf}, isbn = {1064101097}, journal = {Environ Biol Fish}, keywords = {citizen science,diver survey,elasmobranch,monitoring,population,trend,trophic interactions,yellow stingray}, title = {{Spatial and temporal trends in yellow stingray abundance : evidence from diver surveys}}, year = {2010} } @article{McCain2016, annote = {This study used simulations to see estimate the probability of detecting the ffects of climate change. They show that for species with high levels of population variability, it is very diffuclt to detect changes in abundance or range shifts over time. They argue that more sampling has to be done for species iwht large variability There work shows that for species like pikas, a one-year resampling of historical sites is probably inappropriate. You would likely detect a high number of extirpations}, author = {McCain, Christy Marie and Szewczyk, Tim and Knight, Kevin Bracy}, doi = {10.1111/gcb.13211}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McCain, Szewczyk, Knight - 2016 - Population variability complicates the accurate detection of climate change responses.pdf:pdf}, journal = {Global Change Biology}, keywords = {abundance change,demography,extinction risk,local extirpation,population monitoring,range,range contractions}, number = {6}, pages = {2081--2093}, title = {{Population variability complicates the accurate detection of climate change responses}}, volume = {22}, year = {2016} } @article{EditorialStaff2017, annote = {This short editorial just argues that long term data is important. They point out thtat long term data is difficult to come by because of funding cycles}, author = {{Editorial Staff}}, doi = {10.1038/s41559-017-0306-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Editorial Staff - 2017 - Long-term relationships.pdf:pdf}, journal = {Nature Ecology and Evolution}, pages = {1209--1210}, title = {{Long-term relationships}}, volume = {1}, year = {2017} } @article{Taylor2004, author = {Taylor, C A Z M and Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Taylor, Hastings - 2004 - Finding optimal control strategies for invasive species a density-structured model for Spartina alterniflora.pdf:pdf}, pages = {1049--1057}, title = {{Finding optimal control strategies for invasive species : a density-structured model for Spartina alterniflora}}, year = {2004} } @article{Allendorf2003, author = {Allendorf, Fred W and Lundquist, Laura L}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Allendorf, Lundquist - 2003 - Introduction Population Biology, Evolution, and Control of Invasive Species.pdf:pdf}, journal = {Conservation Biology}, number = {1}, pages = {24--30}, title = {{Introduction: Population Biology, Evolution, and Control of Invasive Species}}, volume = {17}, year = {2003} } @article{Simpfendorfer2011, author = {Simpfendorfer, Colin A and Heupel, M.R. and White, W.T. and Dulvy, N.K.}, doi = {10.1071/MF11086}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Simpfendorfer et al. - 2011 - The importance of research and public opinion to conservation management of sharks and rays A synthesis.pdf:pdf}, journal = {Marine and Freshwater Research}, pages = {518--527}, title = {{The importance of research and public opinion to conservation management of sharks and rays: A synthesis}}, volume = {62}, year = {2011} } @article{Wischusen2007, author = {Wischusen, Sheri Maples and Wischusen, E William}, doi = {10.1187/cbe.06}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wischusen, Wischusen - 2007 - Biology Intensive Orientation for Students (BIOS) A Biology “Boot Camp”.pdf:pdf}, journal = {CBE-Life Science Education}, pages = {172--178}, title = {{Biology Intensive Orientation for Students (BIOS): A Biology “Boot Camp”}}, volume = {6}, year = {2007} } @article{Topelko2005, author = {Topelko, Karen N and Dearden, Philip}, doi = {10.1080/14724040409480343}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Topelko, Dearden - 2005 - The shark watching industry and its potential contribution to shark conservation.pdf:pdf}, journal = {Journal of Ecotourism}, number = {2}, pages = {108--128}, title = {{The shark watching industry and its potential contribution to shark conservation}}, volume = {4}, year = {2005} } @article{White2019, author = {White, Easton R.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White - 2019 - Minimum time required to detect population trends the need for long-term monitoring programs.pdf:pdf}, journal = {BioScience}, number = {1}, pages = {40--46}, title = {{Minimum time required to detect population trends: the need for long-term monitoring programs}}, volume = {69}, year = {2019} } @article{Hastings2017, author = {Hastings, Alan and Gaines, Steven D and Costello, Christopher}, doi = {10.1073/pnas.1705169114}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Gaines, Costello - 2017 - Marine reserves solve an important bycatch problem in fisheries.pdf:pdf}, journal = {Proceedings of the National Academy of Sciences}, pages = {1--8}, title = {{Marine reserves solve an important bycatch problem in fisheries}}, year = {2017} } @book{Wood2006, author = {Wood, S.N.}, publisher = {Chapman Hall/CRC}, title = {{Generalized Additive Models: An Introduction with R}}, year = {2006} } @article{Wickham2011, author = {Wickham, H.}, journal = {Journal of Statistical Software}, number = {1}, pages = {1--29}, title = {{The split-apply-combine strategy for data analysis}}, volume = {40}, year = {2011} } @article{Flanagan2017, annote = {Could I have all BIS2B students do similar set of assessment?}, author = {Flanagan, K M and Einarson, J}, doi = {10.1187/cbe.16-08-0253}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Flanagan, Einarson - 2017 - Gender, math confidence , and grit Relationships with quantitative skills and performance in an undergraduat.pdf:pdf}, journal = {CBE-Life Science Education}, number = {ar47}, pages = {1--11}, title = {{Gender, math confidence , and grit: Relationships with quantitative skills and performance in an undergraduate biology coursae}}, volume = {16}, year = {2017} } @article{Blackwood2010, author = {Blackwood, Julie and Hastings, Alan and Costello, Christopher}, doi = {10.1016/j.ecolecon.2009.08.029}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Blackwood, Hastings, Costello - 2010 - Cost-effective management of invasive species using linear-quadratic control.pdf:pdf}, issn = {0921-8009}, journal = {Ecological Economics}, keywords = {linear-quadratic control}, number = {3}, pages = {519--527}, title = {{Cost-effective management of invasive species using linear-quadratic control}}, url = {http://dx.doi.org/10.1016/j.ecolecon.2009.08.029}, volume = {69}, year = {2010} } @article{Vann-sander2016, author = {Vann-sander, Sarah and Clifton, Julian and Harvey, Euan}, doi = {10.1016/j.marpol.2016.06.026}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vann-sander, Clifton, Harvey - 2016 - Can citizen science work Perceptions of the role and utility of citizen science in a marine policy.pdf:pdf}, issn = {0308-597X}, journal = {Marine Policy}, keywords = {Citizen science,Marine resource management,Stakeholder attitudes,Systems thinking}, pages = {82--93}, publisher = {Elsevier}, title = {{Can citizen science work? Perceptions of the role and utility of citizen science in a marine policy and management context}}, url = {http://dx.doi.org/10.1016/j.marpol.2016.06.026}, volume = {72}, year = {2016} } @article{Kosmala2016, author = {Kosmala, Margaret and Wiggins, Andrea and Swanson, Alexandra and Simmons, Brooke}, doi = {10.1002/fee.1436}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kosmala et al. - 2016 - Assessing data quality in citizen science.pdf:pdf}, journal = {Frontiers in Ecology and the Environment}, number = {Show 2015}, title = {{Assessing data quality in citizen science}}, year = {2016} } @article{Cisneros-Montemayor2013, author = {Cisneros-Montemayor, Andr{\'{e}}s M. and Barnes-Mauthe, Michele and Al-Abdulrazzak, Dalal and Navarro-Holm, Estrella and Sumaila, U. Rashid}, doi = {10.1017/S0030605312001718}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cisneros-Montemayor et al. - 2013 - Global economic value of shark ecotourism implications for conservation.pdf:pdf}, journal = {Oryx}, keywords = {economic value,fi sheries,marine ecotourism}, pages = {1--8}, title = {{Global economic value of shark ecotourism: implications for conservation}}, year = {2013} } @article{Mota2014, author = {Mota, Luis and Mota, L and Frausto, O}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mota, Mota, Frausto - 2014 - Protected Area Management The Use of Scuba Diving Tourism for Marine Protected Area Management.pdf:pdf}, journal = {International Journal of Social, Management, Economics and Business Engineering}, number = {10}, pages = {3159--3164}, title = {{Protected Area Management The Use of Scuba Diving Tourism for Marine Protected Area Management}}, volume = {8}, year = {2014} } @article{Dickinson2012, author = {Dickinson, Janis L and Shirk, Jennifer and Bonter, David and Bonney, Rick and Crain, Rhiannon L and Martin, Jason and Phillips, Tina and Purcell, Karen}, doi = {10.1890/110236}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dickinson et al. - 2012 - The current state of citizen science as a tool for ecological research and public engagement.pdf:pdf}, journal = {Frontiers in Ecology and the Environment}, number = {6}, pages = {291--297}, title = {{The current state of citizen science as a tool for ecological research and public engagement}}, volume = {10}, year = {2012} } @article{Vianna2012, author = {Vianna, G M S and Meekan, M G and Pannell, D J and Marsh, S P and Meeuwig, J J}, doi = {10.1016/j.biocon.2011.11.022}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vianna et al. - 2012 - Socio-economic value and community benefits from shark-diving tourism in Palau A sustainable use of reef shark po.pdf:pdf}, journal = {Biological Conservation}, keywords = {conservation incentives}, pages = {267--277}, title = {{Socio-economic value and community benefits from shark-diving tourism in Palau: A sustainable use of reef shark populations}}, volume = {145}, year = {2012} } @book{Wood2017, address = {Boca Raton, FL}, author = {Wood, Simon N.}, pages = {496}, publisher = {CRC Press - Taylor and Francis Group}, title = {{Generalized additive models: an introduction with R}}, year = {2017} } @article{Bart2004, author = {Bart, Jonathon and Burnham, Kenneth P. and Dunn, Erica H. and Francis, Charles M. and Ralph, C. John}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bart et al. - 2004 - Goals and strategies for estimating trends in landbird abundance.pdf:pdf}, journal = {Journal of Wildlife Management}, keywords = {all major,and thou-,birds,cal information for nearly,monitoring,north american breeding bird,past,population size monitoring has,population trends,provided criti-,sands of minor,survey,surveys,trend estimation,wildlife issues during the}, number = {3}, pages = {611--626}, title = {{Goals and strategies for estimating trends in landbird abundance}}, volume = {68}, year = {2004} } @article{Myhrvold2015, author = {Myhrvold, Nathan P. and Baldridge, Elita and Chan, Benjamin and Sivam, Dhileep and Freeman, Daniel L. and Ernest, S.K. Morgan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Myhrvold et al. - 2015 - An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles.pdf:pdf}, journal = {Ecology}, number = {11}, pages = {3109}, title = {{An amniote life-history database to perform comparative analyses with birds, mammals, and reptiles}}, volume = {96}, year = {2015} } @article{Bartsch2017, abstract = {Background Mathematical models can help aid public health responses to Chagas disease. Models are typically developed to fulfill a particular need, and comparing outputs from different models addressing the same question can help identify the strengths and weaknesses of the models in answering particular questions, such as those for achieving the 2020 goals for Chagas disease. Methods Using two separately developed models (PHICOR/CIDMA model and Princeton model), we simulated dynamics for domestic transmission of Trypanosoma cruzi (T. cruzi). We compared how well the models targeted the last 9 years and last 19 years of the 1968–1998 historical seroprevalence data from Venezuela. Results Both models were able to generate the T. cruzi seroprevalence for the next time period within reason to the historical data. The PHICOR/CIDMA model estimates of the total population seroprevalence more closely followed the trends seen in the historic data, while the Princeton model estimates of the age-specific seroprevalence more closely followed historic trends when simulating over 9 years. Additionally, results from both models overestimated T. cruzi seroprevalence among younger age groups, while underestimating the seroprevalence of T. cruzi in older age groups. Conclusion The PHICOR/CIDMA and Princeton models differ in level of detail and included features, yet both were able to generate the historical changes in T. cruzi seroprevalence in Venezuela over 9 and 19-year time periods. Our model comparison has demonstrated that different model structures can be useful in evaluating disease transmission dynamics and intervention strategies.}, author = {Bartsch, Sarah M. and Peterson, Jennifer K. and Hertenstein, Daniel L. and Skrip, Laura and Ndeffo-Mbah, Martial and Galvani, Alison P. and Dobson, Andrew P. and Lee, Bruce Y.}, doi = {10.1016/j.epidem.2017.02.004}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bartsch et al. - 2017 - Comparison and validation of two computational models of Chagas disease A thirty year perspective from Venezuela.pdf:pdf}, issn = {18780067}, journal = {Epidemics}, keywords = {Chagas disease,Model,Model comparison,Simulation,Trypanosoma cruzi}, pages = {81--91}, publisher = {Elsevier B.V.}, title = {{Comparison and validation of two computational models of Chagas disease: A thirty year perspective from Venezuela}}, url = {http://dx.doi.org/10.1016/j.epidem.2017.02.004}, volume = {18}, year = {2017} } @article{Smith2016, author = {Smith, Andrew T and Nagy, John D and Millar, Constance I}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Nagy, Millar - 2016 - Behavioral ecology of American pikas (emph{\{}Ochotona princeps{\}}) at Mono Craters, California Living on the ed.pdf:pdf}, journal = {Western North American Naturalist}, number = {4}, pages = {459--484}, title = {{Behavioral ecology of American pikas ($\backslash$emph{\{}Ochotona princeps{\}}) at Mono Craters, California: Living on the edge}}, volume = {76}, year = {2016} } @article{Pizarro-Novoa1998, author = {Pizarro-Novoa, Juan and Roma{\~{n}}a, Cristina}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pizarro-Novoa, Roma{\~{n}}a - 1998 - Variaci{\'{o}}n estacional de una poblaci{\'{o}}n silvestre de Rhodnius pallences Barber 1932 (Heteroptera Triatom.pdf:pdf}, issn = {0303-7495}, journal = {Bulletin de l'Institut Fran{\c{c}}ais d'Etudes Andines}, keywords = {Rhodnius pallescens,Triatominae,ecolog{\'{i}}a,enfermedad de Chagas,palmeras}, number = {2}, pages = {309--325}, title = {{Variaci{\'{o}}n estacional de una poblaci{\'{o}}n silvestre de Rhodnius pallences Barber 1932 (Heteroptera: Triatominae) en la costa Caribe Colombiana.}}, url = {http://www.redalyc.org/pdf/126/12627206.pdf}, volume = {27}, year = {1998} } @book{Bolker2008, address = {Princeton, New Jersey}, author = {Bolker, Benjamin M.}, edition = {1}, pages = {395}, publisher = {Princeton University Press}, title = {{Ecological Models and Data in R}}, year = {2008} } @misc{RCoreTeam2017, address = {Vienna, Austria}, author = {{R Core Team}}, publisher = {R Foundation for Statistical Computing}, title = {{R: A language and environment for statistical computing}}, url = {https://www.r-project.org/}, year = {2017} } @article{Castanera2003, abstract = {We present a stage-structured mathematical model of the population dynamics of Triatoma infestans in a single house, as part of a more complex model incorporating domestic Trypanosoma cruzi transmission. Novel features of this model are a formulation in continuous time accounting for demographic stochasticity, temperature-dependent female fecundity and developmental times, and insect stage-dependent host irritability. The model assumes a closed domestic insect population regulated by insect density and stage-dependent host irritability depressing the insects' feeding success and female fecundity. The model describes that the abundance of T. infestans insects fluctuates seasonally with only one peak in summer, whereas eggs show one peak in spring and another in the fall as a result of two peaks in female fecundity. The proportion of recently fed adult insects peaks in summer and falls close to zero in winter only when the intensity of host irritability differs markedly between small and large insect stages. In our model, the insect carrying capacity is the joint result of density-dependent access to hosts and density-independent mortality rates. Our hypothesis is that refuge quality in the house, not the absolute number of refuges, determined by construction features would translate into differential insect stage mortalities. The presence of only one hen brooding indoors during spring and summer increases insect numbers in a clearly detectable way. Sensitivity analysis showed strong effects on timed-averaged insect abundance of prolonged developmental time induced by low temperatures, the threshold insect density for host irritability, and mean female fecundity. {\textcopyright} 2002 Elsevier Science B.V. All rights reserved.}, author = {Casta{\~{n}}era, M{\'{o}}nica B. and Aparicio, Juan P. and G{\"{u}}rtler, Ricardo E.}, doi = {10.1016/S0304-3800(02)00388-5}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Casta{\~{n}}era, Aparicio, G{\"{u}}rtler - 2003 - A stage-structured stochastic model of the population dynamics of Triatoma infestans, the main v.pdf:pdf}, isbn = {0304-3800}, issn = {03043800}, journal = {Ecological Modelling}, keywords = {Chagas disease,Population dynamics,Stochastic model,Triatoma infestans,Trypanosoma cruzi,Vector}, number = {1-2}, pages = {33--53}, title = {{A stage-structured stochastic model of the population dynamics of Triatoma infestans, the main vector of Chagas disease}}, volume = {162}, year = {2003} } @article{Barbu2009, abstract = {{\{}BACKGROUND{\}}: Chagas disease is the most important vector-borne disease in Latin America. Regional initiatives based on residual insecticide spraying have successfully controlled domiciliated vectors in many regions. Non-domiciliated vectors remain responsible for a significant transmission risk, and their control is now a key challenge for disease control.$\backslash$n{\{}METHODOLOGY{\}}/{\{}PRINCIPAL{\}} {\{}FINDINGS{\}}: A mathematical model was developed to predict the temporal variations in abundance of non-domiciliated vectors inside houses. Demographic parameters were estimated by fitting the model to two years of field data from the Yucatan peninsula, Mexico. The predictive value of the model was tested on an independent data set before simulations examined the efficacy of control strategies based on residual insecticide spraying, insect screens, and bednets. The model accurately fitted and predicted field data in the absence and presence of insecticide spraying. Pyrethroid spraying was found effective when 50 mg/m(2) were applied yearly within a two-month period matching the immigration season. The {\{}$\backslash$textgreater{\}}80{\%} reduction in bug abundance was not improved by larger doses or more frequent interventions, and it decreased drastically for different timing and lower frequencies of intervention. Alternatively, the use of insect screens consistently reduced bug abundance proportionally to the reduction of the vector immigration rate.$\backslash$n{\{}CONCLUSION{\}}/{\{}SIGNIFICANCE{\}}: Control of non-domiciliated vectors can hardly be achieved by insecticide spraying, because it would require yearly application and an accurate understanding of the temporal pattern of immigration. Insect screens appear to offer an effective and sustainable alternative, which may be part of multi-disease interventions for the integrated control of neglected vector-borne diseases.}, annote = {Barbu et al (2009) use simple matrix models combined with field data to examine different control strategies of non-domicilied triatomine bugs. Their field site was in a remote village in the Yucatan. They found that the spray timing and half life of the pesticide was really important. Furthermore, they found that spraying was more costly than simply using window screens. The addition of bednets had little effect b/c the low amount of reporudciton within houses. They argue insect screens are the most cost effective, and they would be useful in combatting other vector-bourne diseases. Barbu et al (2009) also noted the importance of seasonal movement of bugs into houses. What drives this seasonal movement period? Is it their prey resource or environmental conditions? The number of dispersers could then be affected by stochastic variables.}, author = {Barbu, Corentin and Dumonteil, Eric and Gourbi{\`{e}}re, S{\'{e}}bastien}, doi = {10.1371/journal.pntd.0000416}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barbu, Dumonteil, Gourbi{\`{e}}re - 2009 - Optimization of control strategies for non-domiciliated Triatoma dimidiata, Chagas disease vector.pdf:pdf}, isbn = {1935-2735}, issn = {1935-2735}, journal = {PLoS Neglected Tropical Diseases}, number = {4}, pmid = {19365542}, title = {{Optimization of control strategies for non-domiciliated Triatoma dimidiata, Chagas disease vector in the Yucat{\'{a}}n Peninsula, Mexico}}, volume = {3}, year = {2009} } @article{Field2007, author = {Field, Scott A and Connor, Patrick J O and Tyre, Andrew J and Possingham, Hugh P}, doi = {10.1111/j.1442-9993.2007.01715.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Field et al. - 2007 - Making monitoring meaningful.pdf:pdf}, journal = {Austral Ecology}, keywords = {conservation,management,sampling design,statistical analysis,statistical power}, pages = {485--491}, title = {{Making monitoring meaningful}}, volume = {32}, year = {2007} } @article{Wagner2009, author = {Wagner, Tyler and Vandergoot, Christopher S. and Tyson, Jeff}, doi = {10.1577/M08-197.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wagner, Vandergoot, Tyson - 2009 - Evaluating the power to detect temporal trends in fishery-independent surveys - A case study based on.pdf:pdf}, journal = {North American Journal of Fisheries Management}, pages = {805--816}, title = {{Evaluating the power to detect temporal trends in fishery-independent surveys - A case study based on gill nets set in the Ohio waters of Lake Erie for walleyes}}, volume = {29}, year = {2009} } @article{Hauser2006, author = {Hauser, Cindy E. and Pople, Anthony R. and Possingham, Hugh P.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hauser, Pople, Possingham - 2006 - Should managed populations be monitored every year.pdf:pdf}, journal = {Ecological Applications}, keywords = {decision theory,harvest,macropus rufus,managed populations,monitoring regime,optimization,population model,red kangaroo,south australia}, number = {2}, pages = {807--819}, title = {{Should managed populations be monitored every year?}}, volume = {16}, year = {2006} } @article{Marsh2008, author = {Marsh, David M and Trenham, Peter C}, doi = {10.1111/j.1523-1739.2008.00927.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Marsh, Trenham - 2008 - Current trends in plant and animal population monitoring.pdf:pdf}, journal = {Conservation Biology}, keywords = {biodiversity,de poblaciones de animales,government agencies,los programas de monitoreo,monitoreo de poblaciones de,monitoring programs,nongovernmental organizations,plantas y animales,popula-,population monitoring,resumen,sampling designs,tendencias actuales en el,tion decline,y plantas son cr}, number = {3}, pages = {647--655}, title = {{Current trends in plant and animal population monitoring}}, volume = {22}, year = {2008} } @article{Nichols2006, author = {Nichols, James D. and Williams, Bryon K.}, doi = {10.1016/j.tree.2006.08.007}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nichols, Williams - 2006 - Monitoring for conservation.pdf:pdf}, journal = {Trends in Ecology and Evolution}, number = {12}, pages = {668--673}, title = {{Monitoring for conservation}}, volume = {21}, year = {2006} } @article{Hughes2017, author = {Hughes, Brent B and Beas-luna, Rodrigo and Barner, Allison K and Brewitt, Kimberly and Brumbaugh, Daniel R and Cerny-Chipman, Elizabeth B. and Close, Sarah L. and Coblentz, Kyle E. and Nesnera, Kristin L. De and Drobnitch, Sarah T. and Figurski, Jared D. and Focht, Becky and Friedman, Maya and Freiwald, Jan and Heady, Kristen K. and Heady, Walter N. and Hettinger, Annaliese and Johnson, Angela and Karr, Kendra A. and Mahoney, Brenna and Moritsch, Monica M. and Osterback, Ann-Marie K. and Reimer, Jessica and Robinson, Jonathan and Rohrer, Tully and Rose, Jeremy M. and Sabal, Megan and Segui, Leah M. and Shen, Chenchen and Sullivan, Jenna and Zuercher, Rachel and Raimondi, Peter T. and Menge, Bruce A. and Grorud-Colvert, Kirsten and Novak, Mark and Carr, Mark H.}, doi = {10.1093/biosci/biw185}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hughes et al. - 2017 - Long-term studies contribute disproportionately to ecology and policy.pdf:pdf}, journal = {BioScience}, keywords = {citation rate,climate change,impact factor,national research council,study duration}, number = {3}, pages = {271--281}, title = {{Long-term studies contribute disproportionately to ecology and policy}}, volume = {67}, year = {2017} } @article{White2014b, abstract = {BACKGROUND: Long-lived marine megavertebrates (e.g. sharks, turtles, mammals, and seabirds) are inherently vulnerable to anthropogenic mortality. Although some mathematical models have been applied successfully to manage these animals, more detailed treatments are often needed to assess potential drivers of population dynamics. In particular, factors such as age-structure, density-dependent feedbacks on reproduction, and demographic stochasticity are important for understanding population trends, but are often difficult to assess. Lemon sharks (Negaprion brevirostris) have a pelagic adult phase that makes them logistically difficult to study. However, juveniles use coastal nursery areas where their densities can be high. RESULTS: We use a stage-structured, Markov-chain stochastic model to describe lemon shark population dynamics from a 17-year longitudinal dataset at a coastal nursery area at Bimini, Bahamas. We found that the interaction between delayed breeding, density-dependence, and demographic stochasticity accounts for 33 to 49{\%} of the variance in population size. CONCLUSIONS: Demographic stochasticity contributed all random effects in this model, suggesting that the existence of unmodeled environmental factors may be driving the majority of interannual population fluctuations. In addition, we are able to use our model to estimate the natural mortality rate of older age classes of lemon sharks that are difficult to study. Further, we use our model to examine what effect the length of a time series plays on deciphering ecological patterns. We find that-even with a relatively long time series-our sampling still misses important rare events. Our approach can be used more broadly to infer population dynamics of other large vertebrates in which age structure and demographic stochasticity are important. REVIEWERS: This article was reviewed by Yang Kuang, Christine Jacob, and Ollivier Hyrien.}, author = {White, E.R. and Nagy, J.D. and Gruber, S.H.}, doi = {10.1186/1745-6150-9-23}, issn = {17456150}, journal = {Biology direct}, number = {1}, title = {{Modeling the population dynamics of lemon sharks}}, volume = {9}, year = {2014} } @article{Barbu2011, abstract = {BACKGROUND: Chagas disease is a major neglected tropical disease with deep socio-economical effects throughout Central and South America. Vector control programs have consistently reduced domestic populations of triatomine vectors, but non-domiciliated vectors still have to be controlled efficiently. Designing control strategies targeting these vectors is challenging, as it requires a quantitative description of the spatio-temporal dynamics of village infestation, which can only be gained from combinations of extensive field studies and spatial population dynamic modelling.$\backslash$n$\backslash$nMETHODOLOGY/PRINCIPAL FINDINGS: A spatially explicit population dynamic model was combined with a two-year field study of T. dimidiata infestation dynamics in the village of Teya, Mexico. The parameterized model fitted and predicted accurately both intra-annual variation and the spatial gradient in vector abundance. Five different control strategies were then applied in concentric rings to mimic spatial design targeting the periphery of the village, where vectors were most abundant. Indoor insecticide spraying and insect screens reduced vector abundance by up to 80{\%} (when applied to the whole village), and half of this effect was obtained when control was applied only to the 33{\%} of households closest to the village periphery. Peri-domicile cleaning was able to eliminate up to 60{\%} of the vectors, but at the periphery of the village it has a low effect, as it is ineffective against sylvatic insects. The use of lethal traps and the management of house attractiveness provided similar levels of control. However this required either house attractiveness to be null, or ≥ 5 lethal traps, at least as attractive as houses, to be installed in each household.$\backslash$n$\backslash$nCONCLUSION/SIGNIFICANCE: Insecticide and insect screens used in houses at the periphery of the village can contribute to reduce house infestation in more central untreated zones. However, this beneficial effect remains insufficient to allow for a unique spatially targeted strategy to offer protection to all households. Most efficiently, control should combine the use of insect screens in outer zones to reduce infestation by both sylvatic and peri-domiciliated vectors, and cleaning of peri-domicile in the centre of the village where sylvatic vectors are absent. The design of such spatially mixed strategies of control offers a promising avenue to reduce the economic cost associated with the control of non-domiciliated vectors.}, annote = {Barbu et al 2011 build on their 2009 by exploring how different management strategies can be used in a spatially explicent framework to combat Chagas disease. Again, they focus on non-domicialed Triatomine bugs. Using a spatially explicent model, they examine insect sprayinh, insect screens, peri-domicile cleaning, manipulation of houses' attractiveness, and Triatomine lethal traps. They applied these strategies in rings around the city center. They found that a combination of strategies is best. Specifically, they found that spraying or screens on the outer edge of town and peri-domicile cleaning in the center provided the optimal vector control. They do not explicently look at the cost of the strategies, nor do they examine palms specifically. - point out importance of non-domiciliated triatomines in sustaining Chagas -{\textgreater} makes it hard to do control measures at houses then - can insects visit multiple houses in a night? Or will they die after first failed attempt - tested different control strategies on different zones (rings) around the core of the village. Found that spraying or insect screens in outer zones combined with peri-domicile cleaning in center provided optimumm vector control at the lowest cost}, author = {Barbu, Corentin and Dumonteil, Eric and Gourbi{\`{e}}re, S{\'{e}}bastien}, doi = {10.1371/journal.pntd.0001045}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barbu, Dumonteil, Gourbi{\`{e}}re - 2011 - Evaluation of spatially targeted strategies to control non-domiciliated Triatoma dimidiata vector.pdf:pdf}, isbn = {1935-2735 (Electronic)$\backslash$r1935-2727 (Linking)}, issn = {19352727}, journal = {PLoS Neglected Tropical Diseases}, number = {5}, pmid = {21610862}, title = {{Evaluation of spatially targeted strategies to control non-domiciliated Triatoma dimidiata vector of chagas disease}}, volume = {5}, year = {2011} } @article{Nouvellet2015, abstract = {More than 100years after its formal description, Chagas disease remains a major public health concern in Latin America with a yearly burden of 430,000 Disability-Adjusted Life Years (DALYs). The aetiological agent, a protozoan named Trypanosoma cruzi, is mainly transmitted to mammalian hosts by triatomine vectors. Multiple species of mammals and triatomines can harbour and transmit the parasite, and the feeding range of triatomine species typically includes many noncompetent hosts. Furthermore, the transmission of the pathogen can occur via several routes including the typical vector's faeces, but also oral, congenital and blood transfusion routes. These ecological and epidemiological complexities of the disease have hindered many control initiatives. In such a context, mathematical models provide invaluable tools to explore and understand the dynamics of T. cruzi transmission, and to design, optimize and monitor the efficacy of control interventions. We intend here to provide the first review of the mathematical models of Chagas disease, focussing on how they have contributed to our understanding of (1) the population dynamics and control of triatomine vectors, and (2) the epidemiology of T. cruzi infections. We also aim at suggesting promising lines of modelling that could further improve our understanding of the ecology, evolution, and control of the disease.}, annote = {- 40 different species of triatomines can transmit T. cruzi - review modeling work but do not look at ecological niche models or overly abstract math papers - argue no one has used stage structured models to look at Chagas... -argue there are few studies looking at dispersal kernel explicently - models do incorporate population regulation including intraspecifc interference on blood feeding hosts and competition for refuges within houses - models have evaluated ideal times of insectidce applicaiton - also discuss epidemiological models: force of infection approach and compartmental models - some models look at dogs, chickens, and other animals too - should probably have many host types (like Susceptbe, acute, and chronic infections) - explore cost benefit and cost effectiveness analyses - argue there is a lack of combining dynamical models with economic evaluations}, author = {Nouvellet, Pierre and Cucunub{\'{a}}, Zulma M. and Gourbi{\`{e}}re, S{\'{e}}bastien}, doi = {10.1016/bs.apar.2014.12.004}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nouvellet, Cucunub{\'{a}}, Gourbi{\`{e}}re - 2015 - Ecology, Evolution and Control of Chagas Disease A Century of Neglected Modelling and a Promis.pdf:pdf}, isbn = {9780128032565}, issn = {0065308X}, journal = {Advances in Parasitology}, keywords = {Control,Dynamical model,Latin America,Mathematics,Neglected tropical disease,Public health,Statistics,Triatomine,Trypanosoma cruzi,Vector-borne}, pages = {135--191}, pmid = {25765195}, title = {{Ecology, Evolution and Control of Chagas Disease: A Century of Neglected Modelling and a Promising Future}}, volume = {87}, year = {2015} } @article{Erazo2016a, abstract = {BACKGROUND: Chagas disease is the most important vector-borne disease in Latin America and Rhodnius prolixus is the main vector in Colombia. Control strategies in this region have shown poor outcomes due to the insect's ability to disperse between the sylvatic and the domestic habitat. Because insect migration to houses is responsible to sustain contact rates between vectors and humans, understanding the risk factors that promote migration could be important in designing control strategies. In this respect, it has been reported that adult triatomines have the ability to move over long ranges at night attracted by artificial light. Thus, light bulbs could be playing a critical role in house invasion. The main objective of this study is to understand the role of artificial light, or simply light, in house infestation by R. prolixus.$\backslash$n$\backslash$nMETHODS: To investigate the role of light, we combined fieldwork in the village of Chavinave, Casanare, Colombia and a mathematical model of Rhodnius prolixus dynamics. The model allowed us to simulate insect mobility and distribution in the village based on field results. We created 11 scenarios representing different amounts of light in the village (from 0 to 100 {\%}, with increments of 10 {\%}) with 100 simulations each for a time of 1000 days (2.7 years) and compare the results between the scenarios.$\backslash$n$\backslash$nRESULTS: None of the Gomez-Nu{\~{n}}ez traps were positive at any stage of the study, suggesting that insects do not colonize houses. The model predicts that with current village connections the proportion of houses that have visiting insects should be around 98 {\%}. Additionally we showed that an increase in light allows for insect spreading and migration to previously un-infested areas.$\backslash$n$\backslash$nCONCLUSIONS: Increments in light could increase the contact rates between vectors and humans; a two-fold increase in human cases for a 30 {\%} increase in the use and visibility of light on this particular village was estimated with the model.}, author = {Erazo, Diana and Cordovez, Juan}, doi = {10.1186/s13071-015-1240-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Erazo, Cordovez - 2016 - The role of light in Chagas disease infection risk in Colombia.pdf:pdf}, issn = {1756-3305}, journal = {Parasites {\&} Vectors}, keywords = {chagas disease,domestic lights,house infestation,mathematical modeling,rhodnius prolixus,risk factors}, number = {1}, pages = {9}, pmid = {26732186}, title = {{The role of light in Chagas disease infection risk in Colombia}}, url = {http://www.parasitesandvectors.com/content/9/1/9}, volume = {9}, year = {2016} } @article{Erazo2016, abstract = {BACKGROUND Chagas disease is a major public health concern in Latin America and it is transmitted by insects of the subfamily Triatominae, including Rhodnius spp. Since palm trees are ubiquitous in Colombia and a habitat for Rhodnius spp., the presence of palms near villages could increase contact rates between vectors and humans. Therefore, knowing whether a relationship exists between the proximity of palms to villages and the abundance and distribution of vectors therein, may be critical for Chagas disease prevention programs. Adapting a mathematical model for R. prolixus population dynamics in a small village, we model the implications of changing distances between palms and dwellings, to the risk of Chagas disease infection. METHODS We implemented a mathematical model that reflects R. prolixus population dynamics in a small village located in the department of Casanare (Colombia) to study the role of palm-house proximity. We varied the distance between palms and houses by monitoring the network global efficiency metric. We constructed 1,000 hypothetical villages varying distances and each one was run 100 times. RESULTS According to the model, as palm-house proximity increases, houses were more likely to be visited by triatomine bugs. The number of bugs per unit time increased progressively in a non-linear fashion with high variability. We stress the importance of village configuration on the model output. CONCLUSIONS From a theoretical perspective, palm-house proximity may have a positive effect on the incidence of Chagas disease. The model predicts a 1{\%} increase in new human cases per year when houses and palms are brought closer by 75{\%}.}, annote = {- as you decrease palm-house distances, increased disease risk}, author = {Erazo, Diana and Cordovez, Juan}, doi = {10.1186/s13071-016-1884-8}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Erazo, Cordovez - 2016 - Modeling the effects of palm-house proximity on the theoretical risk of Chagas disease transmission in a rural.pdf:pdf}, issn = {1756-3305}, journal = {Parasites {\&} Vectors}, keywords = {Mathematical modeling,Chagas disease,Rhodnius prol,chagas disease,house infestation,mathematical modeling,palm,rhodnius prolixus,risk factors}, number = {1}, pages = {592}, pmid = {27863520}, publisher = {Parasites {\&} Vectors}, title = {{Modeling the effects of palm-house proximity on the theoretical risk of Chagas disease transmission in a rural locality of the Orinoco basin, Colombia}}, url = {http://parasitesandvectors.biomedcentral.com/articles/10.1186/s13071-016-1884-8}, volume = {9}, year = {2016} } @article{Rendon2015, abstract = {Rhodnius prolixus, a blood-sucking triatomine with domiciliary anthropophilic habits, is the main vector of Chagas disease. The current paradigm of Trypanosoma cruzi transmission in Columbia includes a sylvatic and domiciliary cycle co-existing with domestic and sylvatic populations of reservoirs. The aim of this study is to evaluate the population densities and relative abundance of triatomines and mammals that may be involved in the sylvatic cycle of Chagas disease to clarify the epidemiological scenario in an endemic area in the province of Casanare. Insect vectors on Attalea butyracea palms were captured using both manual searches and bait traps. The capture of mammals was performed using Sherman and Tomahawk traps. We report an infestation index of 88.5{\%} in 148 palms and an index of T. cruzi natural infection of 60.2{\%} in 269 dissected insects and 11.9{\%} in 160 captured mammals. High population densities of triatomines were observed in the sylvatic environment and there was a high relative abundance of reservoirs in the area, suggesting a stable enzootic cycle. We found no evidence of insect domiciliation. Taken together, these observations suggest that eco-epidemiological factors shape the transmission dynamics of T. cruzi, creating diverse scenarios of disease transmission.}, annote = {- point out thatt different species of triatomine insect can have different behavior - point out that there are seasonal differences in abundance because of rain}, author = {Rend{\'{o}}n, Lina Mar{\'{i}}a and Guhl, Felipe and Cordovez, Juan Manuel and Erazo, Diana}, doi = {10.1590/0074-02760140403}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rend{\'{o}}n et al. - 2015 - New scenarios of Trypanosoma cruzi transmission in the Orinoco region of Colombia.pdf:pdf}, issn = {16788060}, journal = {Memorias do Instituto Oswaldo Cruz}, keywords = {Attalea butyracea,Chagas disease,Infection index,Infestation index,Insect domiciliation,Rhodnius prolixus}, number = {3}, pages = {283--288}, pmid = {25830543}, title = {{New scenarios of Trypanosoma cruzi transmission in the Orinoco region of Colombia}}, volume = {110}, year = {2015} } @article{Giron-Nava2017, author = {Giron-Nava, Alfredo and James, Chase C and Johnson, Andrew F and Dannecker, David and Kolody, Bethany and Lee, Adrienne and Nagarkar, Maitreyi and Pao, Gerald M and Ye, Hao and Johns, David G and Sugihara, George}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Giron-Nava et al. - 2017 - Quantitative argument for long-term ecological monitoring.pdf:pdf}, journal = {Marine Ecology Progress Series}, keywords = {dynamics,ecological data,long-term monitoring,nonlinearity,population,predictability,time series}, pages = {269--274}, title = {{Quantitative argument for long-term ecological monitoring}}, volume = {572}, year = {2017} } @incollection{Thomson2014, abstract = {Global Environmental Change is a peer-reviewed international journal publishing high quality, theoretically and empirically rigorous articles, which...}, author = {Thomson, Madeleine C}, booktitle = {Global Environmental Change}, doi = {10.1007/978-94-007-5784-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thomson - 2014 - Emerging infectious diseases, vector-borne diseases, and climate change.pdf:pdf}, isbn = {978-94-007-5783-7}, keywords = {adaptation,climate change,climate variability,emerging infectious disease,vector-borne disease}, pages = {623--628}, publisher = {Springer Netherlands}, title = {{Emerging infectious diseases, vector-borne diseases, and climate change}}, url = {http://link.springer.com/10.1007/978-94-007-5784-4}, year = {2014} } @article{Gage2008, abstract = {Abstract: Climate change could significantly affect vectorborne disease in humans. Temperature, precipitation, humidity, and other climatic factors are known to affect the reproduction, development, behavior, and population dynamics of the arthropod vectors of these diseases. Climate also can affect the development of pathogens in vectors, as well as the population dynamics and ranges of the nonhuman vertebrate reservoirs of many vectorborne diseases. Whether climate changes increase or decrease the incidence of vectorborne diseases in humans will depend not only on the actual climatic conditions but also on local nonclimatic epidemiologic and ecologic factors. Predicting the relative impact of sustained climate change on vectorborne diseases is difficult and will require long-term studies that look not only at the effects of climate change but also at the contributions of other agents of global change such as increased trade and travel, demographic shifts, civil unrest, changes in land use, water availability, and other issues. Adapting to the effects of climate change will require the development of adequate response plans, enhancement of surveillance systems, and development of effective and locally appropriate strategies to control and prevent vectorborne diseases. {\textcopyright} 2008.}, author = {Gage, Kenneth L. and Burkot, Thomas R. and Eisen, Rebecca J. and Hayes, Edward B.}, doi = {10.1016/j.amepre.2008.08.030}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gage et al. - 2008 - Climate and Vectorborne Diseases.pdf:pdf}, isbn = {0749-3797}, issn = {07493797}, journal = {American Journal of Preventive Medicine}, number = {5}, pages = {436--450}, pmid = {18929970}, title = {{Climate and Vectorborne Diseases}}, volume = {35}, year = {2008} } @misc{Ruel1999, abstract = {Many biologists now recognize that environmental variance can exert important effects on patterns and processes in nature that are independent of average conditions. Jensen's inequality is a mathematical proof that is seldom mentioned in the ecological literature but which provides a powerful tool for predicting some direct effects of environmental variance in biological systems. Qualitative predictions can be derived from the form of the relevant response functions (accelerating versus decelerating). Knowledge of the frequency distribution (especially the variance) of the driving variables allows quantitative estimates of the effects. Jensen's inequality has relevance in every field of biology that includes nonlinear processes.}, author = {Ruel, Jonathan J. and Ayres, Matthew P.}, booktitle = {Trends in Ecology and Evolution}, doi = {10.1016/S0169-5347(99)01664-X}, isbn = {0169-5347}, issn = {01695347}, number = {9}, pages = {361--366}, pmid = {10441312}, title = {{Jensen's inequality predicts effects of environmental variation}}, volume = {14}, year = {1999} } @inproceedings{Zhu2008, abstract = {This paper studies the problem of stability anal- ysis for discrete-time delay systems. By using new Lyapunov functional and the discrete Jensen inequality, new stability criteria are presented in terms of linear matrix inequalities (LMIs) and proved to be less conservative than the existing ones. Compared with the existing results, the computational complexity of the obtained stability criteria is reduced greatly since less decision variables are involved. Numerical examples are given to illustrate the effectiveness and advantages of the proposed method. I.}, author = {Zhu, Xun-lin and Yang, Guang-hong}, booktitle = {2008 American Control Conference}, doi = {10.1109/ACC.2008.4586727}, isbn = {978-1-4244-2078-0}, keywords = {Delay systems,LMIs,Stability of linear systems}, number = {1}, pages = {1644--1649}, title = {{Jensen inequality approach to stability analysis of discrete-time systems with time-varying delay}}, url = {http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=4586727}, year = {2008} } @misc{IUCN2012, abstract = {The new Canid Action Plan synthesises the current knowledge on the biology, ecology and status of all wild canid species, and outlines the conservation actions and projects needed to secure their long-term survival. Aiming at conservation biologists, ecologists, local conservation officials, administrators, educators, and all others dealing with canids in their jobs, the authors aspire to stimulate the conservation of all canids by highlighting problems, debating priorities and suggesting action. The 36 taxa of wild canids that comprise the family Canidae, ranging in size from the tiny fennec fox to the mighty grey wolf, and found in every continent except Antarctica, are special. They are special because they have, as perceived friend or foe, preoccupied the imaginations of mankind for millennia; because the breadth of their adaptations makes them enthralling to science; and because the contradictory facets of their relations with people perplex the conservationist. The increase in numbers of people, the spread of settlement, and the exploitation of natural resources of previously little-disturbed wild lands, together with persecution, are threatening some of these canids with extinction. The possibility that we are heedlessly, perhaps needlessly, mismanaging many of them is saddening; the probability that our negligence will force several more to extinction should fill us with bottomless dismay. It demands action, and that is why we have compiled this new Canid Action Plan. Following a short introduction and a chapter on phylogeny, classification, and evolutionary ecology of the Canidae (Part 1), Part 2 provides the latest information on the distribution, biology and conservation status of each species, organised by geographical region. The accounts also list current field projects, and their contact details are provided in an appendix. The Canid Specialist Groups members are active worldwide. Nine of the 36 taxa covered are threatened (3 Critically Endangered, 3 Endangered and 3 Vulnerable), and one is considered Near Threatened. Six species (7{\%}) were listed as Data Deficient, and 20 (56{\%}) species as Least Concern (Appendix 1). The threatened canids are: Darwins fox (CR). Until recently, known only from the Island of Chilo (Chile) until rediscovered 600km away in the coastal mountains, where domestic dogs threaten them with disease or direct attack. Red wolf (CR). Currently the subject of taxonomic debate, red wolves were declared Extinct in the Wild by 1980, but have been reintroduced into eastern North Carolina, where they are now locally common. Hybridisation with coyotes is the primary threat. Island fox (CR). Restricted to the six largest of the eight California Channel Islands, each island population is considered a separate subspecies, and four have declined precipitously. Threats include hyperpredation by golden eagles and the introduction of canine diseases. Ethiopian wolf (EN). Less than 500 individuals remain, confined to eight locations in the Ethiopian Highlands. Previously listed as Critically Endangered, continuous loss of habitat due to high-altitude subsistence agriculture remains the major threat, along with disease (particularly rabies). African wild dog (EN). Formerly distributed throughout sub-Saharan Africa, excluding rainforests, wild dogs have disappeared from 25 of the former 39 range states. More than half of the mortality recorded among adults is caused directly by human activity. Dhole (EN). Formerly distributed across Asia, dholes have undergone widespread decline and are threatened by depletion of their prey base, habitat loss, persecution, competition and disease. Dingo (VU). Austronesian people transported the dingo from Asia to Australia and other islands in between 1,000 and 5,000 years ago. Pure dingoes occur only as remnant populations in central and northern Australia and in Thailand, and they are threatened by cross-breeding with domestic dogs. Bush dog (VU). Despite a supposedly widespread distribution in South American forests, this species is perceived as rare, and threatened by habitat conversion and human encroachment. Blanfords fox (VU). Present in arid mountainous regions of the Middle East and north-eastern Egypt eastwards to Afghanistan, where human development could pose a threat. In contrast to the threats faced by threatened canids, several species are thriving in human-dominated landscapes and incur the loathing of farmers and hunters alike. Red foxes are notoriously successful in urban settings, and coyotes, golden jackals, crab-eating and kit foxes seem able to thrive amidst human settlements. Management prompted by rabies control, fur harvest, and livestock predation leads to the slaughter of hundreds of thousands of canids annually. Part 3 of the Plan considers nine major issues in canid conservation, namely canid society, conservation genetics, assessing and managing diseases, management of canids near people, impact of exploitation and trade, survey and census techniques, captive conservation, reintroduction and metapopulation management, and conservation education. Part 4 is arguably the most important section. It includes a chapter on the need for setting priorities and measuring success in canid conservation, and the detailed Action Plan for canid conservation into the 21st century. Although we have sought to refine and consolidate these entries, they represent the views of the many experts around the world who suggested them, who debated them in our workshops and in the forum of our international congress, hosted by the WildCRU in Oxford in September 2001. The list of proposed projects makes no claim to be comprehensive, but it is the result of extremely wide consultation. The plan itself, together with the databases concerning existing members and research projects, are all available on the web at http://www.canids.org. The Action Plan was prepared in parallel with our edited monograph entitled The Biology and Conservation of Wild Canids (Oxford University Press, 2004) which contains comprehensive reviews of the science underpinning this Action Plan, together with 14 case studies of wild canid biology. David W. Macdonald, Chairman IUCN/S SC Canid Specialist Group Claudio Sillero-Zubiri, Deputy Chair IUCN/S SC Canid Specialist Group}, author = {IUCN}, doi = {10.9782-8317-0633-5}, isbn = {2831707862}, issn = {28317078}, keywords = {and,n red list categories}, number = {version 13}, pages = {38}, pmid = {2734}, title = {{IUCN Red List Categories and Criteria: Version 3.1}}, urldate = {2017-06-02}, year = {2012} } @article{Regan2002, author = {Regan, Helen M. and Colyvan, Mark and Burgman, Mark A. and Applications, Ecological and Apr, No}, doi = {10.2307/3060967}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Regan et al. - 2002 - A taxonomy and treatment of uncertainty for ecology and conservation biology.pdf:pdf}, isbn = {10510761}, issn = {10510761}, journal = {Ecological applications}, keywords = {episremic uncertainty,linguistic uncertaint,uncertainty,vagueness}, number = {2}, pages = {618--628}, title = {{A taxonomy and treatment of uncertainty for ecology and conservation biology}}, url = {http://www.esajournals.org/doi/abs/10.1890/1051-0761(2002)012[0618:ATATOU]2.0.CO;2{\%}5Cnhttp://www.esajournals.org/action/cookieAbsent}, volume = {12}, year = {2002} } @article{Hilborn1987, abstract = {An analysis of the types of uncertainties faced by resource managers is presented. Uncertainties are classified by the frequency of occurrence. Managers develop ways for dealing with frequently occurring uncertainties that do not commonly present extraordinary problems. Uncertainties that occur infrequently require an adaptive learning approach to management where we must learn about the true states of nature by careful monitoring, evaluation, and experimentation. In an undesirable situation, the ability to respond rapidly is most important. Uncertainties that occur rarely, called surprise, are very difficult to deal with. Suggested responses include holding some resources in reserve to cope with the unexpected and developing broadly based monitoring systems to detect surprises as early as possible.}, author = {Hilborn, Ray}, doi = {10.1577/1548-8659(1987)7<1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hilborn - 1987 - Living with uncertainty in resource management.pdf:pdf}, isbn = {0275-5947}, issn = {0275-5947}, journal = {North American Journal of Fisheries Management}, number = {January 2014}, pages = {37--41}, title = {{Living with uncertainty in resource management}}, volume = {5947}, year = {1987} } @article{Costantino1997, abstract = {A nonlinear demographic model was used to predict the population dynamics of the flour beetle Tribolium under laboratory conditions and to establish the experimental protocol that would reveal chaotic behavior. With the adult mortality rate experimentally set high, the dynamics of animal abundance changed from equilibrium to quasiperiodic cycles to chaos as adult-stage recruitment rates were experimentally manipulated. These transitions in dynamics corresponded to those predicted by the mathematical model. Phase-space graphs of the data together with the deterministic model attractors provide convincing evidence of transitions to chaos.}, author = {Costantino, R. F. and Desharnais, R A and Cushing, J M and Dennis, Brian}, doi = {10.1126/science.275.5298.389}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Costantino et al. - 1997 - Chaotic dynamics in an insect population.pdf:pdf}, isbn = {9783642220234}, issn = {00368075}, journal = {Science}, number = {5298}, pages = {389--391}, pmid = {8994036}, title = {{Chaotic dynamics in an insect population}}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.275.5298.389}, volume = {275}, year = {1997} } @article{Strevens2011, abstract = {P{\textgreater}1. The majority of our knowledge of harvested populations has been$\backslash$ndrawn from studies on single-species occupying continuous landscapes.$\backslash$nPopulation dynamics in spatially structured landscapes are markedly$\backslash$ndifferent from those in continuous habitats. We investigate the effects$\backslash$nof several harvesting strategies on the metapopulation dynamics of the$\backslash$nbruchid beetle Callosobruchus maculatus and its parasitoid$\backslash$nAnisopteromalus calandrae, when locally extinction prone populations of$\backslash$nbruchids were harvested. By harvesting the resource in this closed$\backslash$nresource-consumer interaction, we could examine the scenario where$\backslash$nhumans and natural predators share a common resource.$\backslash$n2. Using population-level models in single and coupled-patch systems,$\backslash$nsimulations were run to estimate sustainable harvesting levels for each$\backslash$nharvesting strategy. These harvesting levels were then implemented in$\backslash$nexperimental metapopulation microcosms. Experiments were run for$\backslash$nmultiple generations and long-term time series of population size and$\backslash$nharvest yield were collected.$\backslash$n3. Controversially, harvesting resulted in larger regional population$\backslash$nsizes in harvested metapopulations than in unharvested metapopulations.$\backslash$nSimilarly, conservative harvesting strategies such as fixed escapement$\backslash$nharvesting and harvesting with refuges resulted in smaller population$\backslash$nsizes than fixed quota or fixed proportion harvesting strategies. Fixed$\backslash$nproportion harvesting gave rise to the largest population sizes, fewest$\backslash$nlocal extinctions and largest yields. Assuming both species are of$\backslash$necological importance, fixed proportion is therefore the optimal$\backslash$nharvesting strategy for this model system.$\backslash$n4. Synthesis and applications. We demonstrate that, under certain$\backslash$nconditions, increasing local mortality can increase population sizes.$\backslash$nThis `hydra effect' may be caused by the advantage of higher rates of$\backslash$nlocal population turnover for dispersive species in patchy landscapes,$\backslash$nor due to the interruption of overcompensatory density-dependence in the$\backslash$nhost populations. These results are of particular relevance both in the$\backslash$ndevelopment of sustainable harvesting policies in multi-species$\backslash$ncommunities or, conversely, the control of pest species inhabiting$\backslash$nspatially structured landscapes. We have shown that predictive models$\backslash$ncan be a useful tool in the estimation of sustainable harvesting limits$\backslash$nwhere no a priori knowledge of the system exists. We also demonstrate$\backslash$nthat spatial structure, the effects of interspecific interactions and$\backslash$nknowledge of density-dependent population dynamics must be included in$\backslash$nthe generation of sustainable harvesting theory.}, annote = {- found fixed proportion harvesting maximized both species Classsic harvesting strategies: MSY, fixed quota, fixed proportion, fixed escapement, harvesting refuges}, author = {Strevens, Chlo{\"{e}} M J and Bonsall, Michael B.}, doi = {10.1111/j.1365-2664.2010.01907.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Strevens, Bonsall - 2011 - The impact of alternative harvesting strategies in a resource-consumer metapopulation.pdf:pdf}, isbn = {0021-8901}, issn = {00218901}, journal = {Journal of Applied Ecology}, keywords = {Anisopteromalus calandrae,Callosobruchus maculatus,Escapement,Host-parasitoid,Proportion,Quota,Refuges}, number = {1}, pages = {102--111}, title = {{The impact of alternative harvesting strategies in a resource-consumer metapopulation}}, volume = {48}, year = {2011} } @article{Hatch2003, author = {Hatch, S A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hatch - 2003 - Statistical power for detecting trends with applications to seabirds monitoring.pdf:pdf}, journal = {Biological Conservation}, keywords = {Alaska,Biological significance,Components of variance,Computer software,Exponential models,Linear regression,Pseudoreplication,Seabird monitoring,Statistical power,Study design,Time series,Trend analysis}, pages = {317--329}, title = {{Statistical power for detecting trends with applications to seabirds monitoring.}}, volume = {111}, year = {2003} } @article{Johnstone2010, abstract = {Biogeographical, physiological, and paleoecological evidence suggests that the coast redwood [Sequoia sempervirens (D. Don) Endl.] is closely associated with the presence of summer marine fog along the Pacific coast of California. Here we present a novel record of summer fog frequency in the coast redwood region upon the basis of direct hourly measurements of cloud ceiling heights from 1951 to 2008. Our analysis shows that coastal summer fog frequency is a remarkably integrative measure of United States Pacific coastal climate, with strong statistical connections to the wind-driven upwelling system of the California Current and the broad ocean temperature pattern known as the Pacific Decadal Oscillation. By using a long-term index of daily maximum land temperatures, we infer a 33{\%} reduction in fog frequency since the early 20th century. We present tree physiological data suggesting that coast redwood and other ecosystems along the United States west coast may be increasingly drought stressed under a summer climate of reduced fog frequency and greater evaporative demand.}, author = {Johnstone, J. A. and Dawson, T. E.}, doi = {10.1073/pnas.0915062107}, isbn = {1091-6490 (Electronic)$\backslash$n0027-8424 (Linking)}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {10}, pages = {4533--4538}, pmid = {20160112}, title = {{Climatic context and ecological implications of summer fog decline in the coast redwood region}}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.0915062107}, volume = {107}, year = {2010} } @article{Metcalf2009, abstract = {Seasonal variation in infection transmission is a key determinant of epidemic dynamics of acute infections. For measles, the best-understood strongly immunizing directly transmitted childhood infection, the perception is that term-time forcing is the main driver of seasonality in developed countries. The degree to which this holds true across other acute immunizing childhood infections is not clear. Here, we identify seasonal transmission patterns using a unique long-term dataset with weekly incidence of six infections including measles. Data on age{\{}$\backslash$textendash{\}}incidence allow us to quantify the mean age of infection. Results indicate correspondence between dips in transmission and school holidays for some infections, but there are puzzling discrepancies, despite close correspondence between average age of infection and age of schooling. Theoretical predictions of the relationship between amplitude of seasonality and basic reproductive rate of infections that should result from term-time forcing are also not upheld. We conclude that where yearly trajectories of susceptible numbers are perturbed, e.g. via waning of immunity, seasonality is unlikely to be entirely driven by term-time forcing. For the three bacterial infections, pertussis, scarlet fever and diphtheria, there is additionally a strong increase in transmission during the late summer before the end of school vacations. {\{}{\textcopyright}{\}} 2009 The Royal Society}, author = {Metcalf, C. J. E. and Bjornstad, O. N. and Grenfell, B. T. and Andreasen, V.}, doi = {10.1098/rspb.2009.1058}, isbn = {0962-8452}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, number = {1676}, pages = {4111--4118}, pmid = {19740885}, title = {{Seasonality and comparative dynamics of six childhood infections in pre-vaccination Copenhagen}}, url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2009.1058}, volume = {276}, year = {2009} } @article{Shaman2010, abstract = {Much of the observed wintertime increase of mortality in temperate regions is attributed to seasonal influenza. A recent reanalysis of laboratory experiments indicates that absolute humidity strongly modulates the airborne survival and transmission of the influenza virus. Here, we extend these findings to the human population level, showing that the onset of increased wintertime influenza-related mortality in the United States is associated with anomalously low absolute humidity levels during the prior weeks. We then use an epidemiological model, in which observed absolute humidity conditions temper influenza transmission rates, to successfully simulate the seasonal cycle of observed influenza-related mortality. The model results indicate that direct modulation of influenza transmissibility by absolute humidity alone is sufficient to produce this observed seasonality. These findings provide epidemiological support for the hypothesis that absolute humidity drives seasonal variations of influenza transmission in temperate regions.}, author = {Shaman, Jeffrey and Pitzer, Virginia E. and Viboud, C{\'{e}}cile and Grenfell, Bryan T. and Lipsitch, Marc}, doi = {10.1371/journal.pbio.1000316}, isbn = {2157-3999 (Electronic)}, issn = {15449173}, journal = {PLoS Biology}, number = {2}, pmid = {20186267}, title = {{Absolute humidity and the seasonal onset of influenza in the continental United States}}, volume = {8}, year = {2010} } @article{Wesolowski2015, abstract = {Changing patterns of human aggregation are thought to drive annual and multiannual outbreaks of infectious diseases, but the paucity of data about travel behavior and population flux over time has made this idea difficult to test quantitatively. Current measures of human mobility, especially in low-income settings, are often static, relying on approximate travel times, road networks, or cross-sectional surveys. Mobile phone data provide a unique source of information about human travel, but the power of these data to describe epidemiologically relevant changes in population density remains unclear. Here we quantify seasonal travel patterns using mobile phone data from nearly 15 million anonymous subscribers in Kenya. Using a rich data source of rubella incidence, we show that patterns of population travel (fluxes) inferred from mobile phone data are predictive of disease transmission and improve significantly on standard school term time and weather covariates. Further, combining seasonal and spatial data on travel from mobile phone data allows us to characterize seasonal fluctuations in risk across Kenya and produce dynamic importation risk maps for rubella. Mobile phone data therefore offer a valuable previously unidentified source of data for measuring key drivers of seasonal epidemics.}, archivePrefix = {arXiv}, arxivId = {0706.1062v1}, author = {Wesolowski, Amy and Metcalf, C. J. E. and Eagle, Nathan and Kombich, Janeth and Grenfell, Bryan T. and Bj{\o}rnstad, Ottar N. and Lessler, Justin and Tatem, Andrew J. and Buckee, Caroline O.}, doi = {10.1073/pnas.1423542112}, eprint = {0706.1062v1}, isbn = {0902262106}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {35}, pages = {11114--11119}, pmid = {26283349}, title = {{Quantifying seasonal population fluxes driving rubella transmission dynamics using mobile phone data}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1423542112}, volume = {112}, year = {2015} } @article{Altizer2013, abstract = {Scientists have long predicted large-scale responses of infectious diseases to climate change, giving rise to a polarizing debate, especially concerning human pathogens for which socioeconomic drivers and control measures can limit the detection of climate-mediated changes. Climate change has already increased the occurrence of diseases in some natural and agricultural systems, but in many cases, outcomes depend on the form of climate change and details of the host-pathogen system. In this review, we highlight research progress and gaps that have emerged during the past decade and develop a predictive framework that integrates knowledge from ecophysiology and community ecology with modeling approaches. Future work must continue to anticipate and monitor pathogen biodiversity and disease trends in natural ecosystems and identify opportunities to mitigate the impacts of climate-driven disease emergence.}, author = {Altizer, S. and Ostfeld, R. S. and Johnson, P. T. J. and Kutz, S. and Harvell, C. D.}, doi = {10.1126/science.1239401}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Altizer et al. - 2013 - Climate Change and Infectious Diseases From Evidence to a Predictive Framework.pdf:pdf}, isbn = {0036-8075}, issn = {0036-8075}, journal = {Science}, number = {6145}, pages = {514--519}, pmid = {23908230}, title = {{Climate Change and Infectious Diseases: From Evidence to a Predictive Framework}}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1239401}, volume = {341}, year = {2013} } @article{Bjørnstad2002, abstract = {Before the development of mass-vaccination campaigns, measles exhibited persistent fluctuations (endemic dynamics) in large British cities, and recurrent outbreaks (episodic dynamics) in smaller communities. The critical community size separating the two regimes was {\~{}}300 000-500 000. We develop a model, the TSIR (Time-series Susceptible-Infected-Recovered) model, that can capture both endemic cycles and episodic outbreaks in measles. The model includes the stochasticity inherent in the disease transmission (giving rise to a negative binomial conditional distribution) and random immigration. It is thus a doubly stochastic model for disease dynamics. It further includes seasonality in the transmission rates. All parameters of the model are estimated on the basis of time series data on reported cases and reconstructed susceptible numbers from a set of cities in England and Wales in the prevaccination era (1944-1966). The 60 cities analyzed span a size range from London (3.3× 106 inhabitants) to Teignmouth (10 500 inhabitants). The dynamics of all cities fit the model well. Transmission rates scale with community size, as expected from dynamics adhering closely to frequency dependent transmission ("true mass action"). These rates are further found to reveal strong seasonal variation, corresponding to high transmission during school terms and lower transmission during the school holidays. The basic reproductive ratio, R0, is found to be invariant across the observed range of host community size, and the mean proportion of susceptible individuals also appears to be constant. Through the epidemic cycle, the susceptible population is kept within a 3{\%} interval. The disease is, thus, efficient in "regulating" the susceptible population-even in small cities that undergo recurrent epidemics with frequent extinction of the disease agent. Recolonization is highly sensitive to the random immigration process. The initial phase of the epidemic is also stochastic (due to demographic stochasticity and random immigration). However, the epidemic is nearly "deterministic" through most of the growth and decline phase.}, author = {Bj{\o}rnstad, Ottar N. and Finkenst{\"{a}}dt, B{\"{a}}rbel F. and Grenfell, Bryan T.}, doi = {10.1890/0012-9615(2002)072[0169:DOMEES]2.0.CO;2}, isbn = {0012-9615}, issn = {00129615}, journal = {Ecological Monographs}, keywords = {Epidemic birth-death process,Extinction-recolonization,Noise and determinism,Nonlinear stochastic dynamics,Persistence thresholds,Population cycles,R0,Spatial coupling,TSIR model,Time series analysis}, number = {2}, pages = {169--184}, title = {{Dynamics of measles epidemics: Estimating scaling of transmission rates using a Time series SIR model}}, volume = {72}, year = {2002} } @article{Grenfell2002, abstract = {Two key linked questions in population dynamics are the relative importance of noise vs. density-dependent nonlinearities and the limits on temporal predictability of population abundance. We propose that childhood microparasitic infections, notably mea-sles, provide an unusually suitable empirical and theoretical test bed for addressing these issues. We base our analysis on a new mechanistic time series model for measles, the TSIR model, which captures the mechanistic essence of epidemic dynamics. The model, and parameter estimates based on short-term fits to prevaccination measles time series for 60 towns and cities in England and Wales, is introduced in a companion paper. Here, we explore how well the model predicts the long-term dynamics of measles and the balance between noise and determinism, as a function of population size. The TSIR model captures the basic dynamical features of the long-term pattern of measles epidemics in large cities remarkably well (based on time and frequency domain analyses). In particular, the model illustrates the impact of secular increases in birth rates, which cause a transition from biennial to annual dynamics. The model also captures the observed increase in epidemic irregularity with decreasing population size and the onset of local extinction below a critical community size. Decreased host population size is shown to be associated with an increased impact of demographic stochasticity. The interaction between nonlinearity and noise is explored using local Lyapunov exponents (LLE). These testify to the high level of stability of the biennial attractor in large cities. Irregularities are due to the limit cycle evolving with changing human birth rates and not due to complex dynamics. The geometry of the dynamics (sign and magnitude of the LLEs across phase space) is similar in the cities and the smaller urban areas. The qualitative difference in dynamics between small and large host communities is that demographic and extinction–recolonization stochasticities are much more influential in the former. The regional dynamics can therefore only be understood in terms of a core–satellite metapopulation structure for this host–enemy system. We also make a preliminary exploration of the model's ability to predict the dynamic consequences of measles vaccination.}, author = {Grenfell, Bryan T. and Bj{\o}rnstad, Ottar N. and Finkenst{\"{a}}dt, B{\"{a}}rbel F.}, doi = {10.1890/0012-9615(2002)072[0185:DOMESN]2.0.CO;2}, isbn = {0012-9615}, issn = {00129615}, journal = {Ecological Monographs}, keywords = {Attractor evolution,Core-satellite metapopulation,Epidemic birth-death process,Extinction-recolonization,Nonlinear stochastic dynamics,Persistence thresholds,Population cycles,TSIR model,Time series analysis,Transience,Vaccination}, number = {2}, pages = {185--202}, title = {{Dynamics of measles epidemics: Scaling noise, determinism, and predictability with the TSIR model}}, volume = {72}, year = {2002} } @misc{GPDD2010, abstract = {"NERC Centre for Population Biology, Imperial College (2010) The Global Population Dynamics Database. http://www.sw.ic.ac.uk/cpb/cpb/gpdd.html".}, author = {{NERC Centre for Population Biology Imperial College}}, booktitle = {NERC Centre for Population Biology, Imperial College}, keywords = {biology,dynamics,population,population biology,population dynamics,population-dynamics}, title = {{The Global Population Dynamics Database Version 2. http://www3.imperial.ac.uk/cpb/databases/gpdd}}, url = {http://www3.imperial.ac.uk/cpb/databases/gpdd}, year = {2010} } @incollection{Schmit2011, author = {Schmit, Lara M. and Schmidt, John C.}, booktitle = {Effects of Three High-Flow Experiments on the Colorado River Ecosystem Downstream from Glen Canyon Dam, Arizona}, chapter = {1}, editor = {Melis, T.S.}, publisher = {U.S. Geological Survey Circular}, title = {{Introduction and Overview}}, year = {2011} } @incollection{Kennedy2011, author = {Kennedy, Theodore A and Ralston, Barbara E.}, booktitle = {Effects of Three High-Flow Experiments on the Colorado River Ecosystem Downstream from Glen Canyon Dam, Arizona}, chapter = {5}, editor = {Melis, T.S.}, publisher = {U.S. Geological Survey Circular}, title = {{Biological Responses to High-Flow Experiments at Glen Canyon Dam}}, year = {2011} } @incollection{Schmidt2011, author = {Schmidt, John C. and Grams, Paul E.}, booktitle = {Effects of Three High-Flow Experiments on the Colorado River Ecosystem Downstream from Glen Canyon Dam, Arizona}, chapter = {2}, editor = {Melis, T.S.}, publisher = {U.S. Geological Survey Circular}, title = {{Understanding Physical Processes of the Colorado River}}, year = {2011} } @article{Korman2011, abstract = {Hourly fluctuations in flow from Glen Canyon Dam were increased in an attempt to limit the population of nonnative rainbow trout Oncorhynchus mykiss in the Colorado River, Arizona, due to concerns about negative effects of nonnative trout on endangered native fishes. Controlled floods have also been conducted to enhance native fish habitat. We estimated that rainbow trout incubation mortality rates resulting from greater fluctuations in flow were 23-49{\%} (2003 and 2004) compared with 5-11{\%} under normal flow fluctuations (2006-2010). Effects of this mortality were apparent in redd excavations but were not seen in hatch date distributions or in the abundance of the age-0 population. Multiple lines of evidence indicated that a controlled flood in March 2008, which was intended to enhance native fish habitat, resulted in a large increase in early survival rates of age-0 rainbow trout. Age-0 abundance in July 2008 was over fourfold higher than expected given the number of viable eggs that produced these fish. A hatch date analysis indicated that early survival rates were much higher for cohorts that hatched about 1 month after the controlled flood (approx. April 15) relative to those that hatched before this date. The cohorts that were fertilized after the flood were not exposed to high flows and emerged into better-quality habitat with elevated food availability. Interannual differences in age-0 rainbow trout growth based on otolith microstructure supported this hypothesis. It is likely that strong compensation in survival rates shortly after emergence mitigated the impact of incubation losses caused by increases in flow fluctuations. Control of nonnative fish populations will be most effective when additional mortality is applied to older life stages after the majority of density-dependent mortality has occurred. Our study highlights the need to rigorously assess instream flow decisions through the evaluation of population-level responses.}, author = {Korman, Josh and Kaplinski, Matthew and Melis, Theodore S. TS}, doi = {10.1080/00028487.2011.572015}, isbn = {0002-8487}, issn = {0002-8487}, journal = {Transactions of the American Fisheries Society}, number = {2}, pages = {487--505}, title = {{Effects of fluctuating flows and a controlled flood on incubation success and early survival rates and growth of age-0 rainbow trout in a large regulated river}}, url = {http://www.tandfonline.com/doi/abs/10.1080/00028487.2011.572015}, volume = {140}, year = {2011} } @article{Donohue2005, abstract = {Because seed dispersal influences the environment experienced by seeds, that environment can change as dispersal evolves. The evolutionary potential of dispersal can in turn change as dispersal evolves, if its expression of genetic variation depends on the postdispersal environment. We examined whether seed dispersion patterns have a detectable genetic basis (and therefore evolutionary potential) and determined whether that genetic basis changed depending on one postdispersal environmental factor: conspecific density. We grew replicates of 12 ecotypes of Arabidopsis thaliana at high and low density and measured seed dispersion patterns and maternal traits associated with dispersal under controlled conditions. We found density-dependent ecotypic variation for maternal traits that influence dispersal. Significant genetic variation for postdispersal sibling density was detected only when plants were grown at high density, suggesting that if dispersal evolves to result in lower postdispersal densities, the expression of genetic variation for dispersal would be reduced. This dynamic could lead to a plasticity-induced constraint on the evolution of dispersal. The ability of organisms to alter the environment they experience and the ability of that environment to evolve can alter evolutionary dynamics by augmenting or reducing evolutionary potential and thereby facilitating or constraining evolutionary responses to selection.}, annote = {Discussion in class: - outcomes vs traits - niche constructino can also be more subtle (like locaiton choice) as opposed to actual habitat modification - seasonal phenology is form of temporal niche construction - niche construction and evolution - increases SD of dispersal distance when you are at high density - higher variance of traits between ecotypes at low popualtion size (could then drive evolution) - H2 and broad vs narrow sense heritability Table 3: g matrices are not symmetrical -}, author = {Donohue, Kathleen and Polisetty, Chandra R and Wender, Naomi J}, doi = {10.1086/429162}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Donohue, Polisetty, Wender - 2005 - Genetic basis and consequences of niche construction plasticity-induced genetic constraints on the e.pdf:pdf}, isbn = {0003-0147}, issn = {1537-5323}, journal = {The American Naturalist}, keywords = {corresponding author,e-mail kdonohue,edu,evolutionary constraints,habitat choice,habitat selection,harvard,maternal effects,oeb,phenotypic plasticity}, number = {5}, pages = {537--550}, pmid = {15795851}, title = {{Genetic basis and consequences of niche construction: plasticity-induced genetic constraints on the evolution of seed dispersal in Arabidopsis thaliana.}}, volume = {165}, year = {2005} } @article{Dodrill2016, author = {Dodrill, Michael J and Yard, Michael D and III, WIlliam E. Pine}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dodrill, Yard, III - 2016 - Assessing Predation Risks for Small Fish in a Large River Ecosystem between Contrasting Habitats and Turbidi.pdf:pdf}, journal = {The American Midland Naturalist Journal}, number = {2}, pages = {206--221}, title = {{Assessing Predation Risks for Small Fish in a Large River Ecosystem between Contrasting Habitats and Turbidity Conditions}}, url = {http://web.a.ebscohost.com/ehost/pdfviewer/pdfviewer?vid=1{\&}sid=823f14b4-e0bf-4194-bb45-5ad9d6fd7935{\%}40sessionmgr4010{\&}hid=4209}, volume = {175}, year = {2016} } @article{Yao2017, author = {Yao, Weiwei and Liu, Huaxian and Chen, Yuansheng and Zhang, Wenyi and Zhong, Yu and Fan, Haiyan and Li, Linkai and Bamal, Sudeep}, doi = {10.3390/w9020150}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yao et al. - 2017 - Simulating Spawning and Juvenile Rainbow Trout (Oncorhynchus mykiss) Habitat in Colorado River Based on High-Flow Ef.pdf:pdf}, issn = {2073-4441}, journal = {Water}, keywords = {and juvenile rainbow trout,cfd model,fish habitat model,high flow effects,spawning,temperature distribution}, number = {3}, pages = {150}, title = {{Simulating Spawning and Juvenile Rainbow Trout (Oncorhynchus mykiss) Habitat in Colorado River Based on High-Flow Effects}}, url = {http://www.mdpi.com/2073-4441/9/2/150}, volume = {9}, year = {2017} } @article{Yard2011, abstract = {Introductions of nonnative salmonids, such as rainbow trout Oncorhynchus mykiss and brown trout Salmo trutta, have affected native fishes worldwide in unforeseen and undesirable ways. Predation and other interactions with nonnative rainbow trout and brown trout have been hypothesized as contributing to the decline of native fishes (including the endangered humpback chub Gila cypha) in the Colorado River, Grand Canyon. A multiyear study was conducted to remove nonnative fish from a 15-km segment of the Colorado River near the Little Colorado River confluence. We evaluated how sediment, temperature, fish prey availability, and predator abundance influenced the incidence of piscivory (IP) by nonnative salmonids. Study objectives were addressed through spatial (upstream and downstream of the Little Colorado River confluence) and temporal (seasonal and annual) comparisons of prey availability and predator abundance. Data were then evaluated by modeling the quantity of fish prey ingested by trout during the first 2 years (2003–2004) of the mechanical removal period. Field effort resulted in the capture of 20,000 nonnative fish, of which 90{\%} were salmonids. Results indicated that the brown trout IP was higher (8–70{\%}) than the rainbow trout IP (0.5–3.3{\%}); however, rainbow trout were 50 times more abundant than brown trout in the study area. We estimated that during the study period, over 30,000 fish (native and nonnative species combined) were consumed by rainbow trout (21,641 fish) and brown trout (11,797 fish). On average, rainbow trout and brown trout ingested 85{\%} more native fish than nonnative fish in spite of the fact that native fish constituted less than 30{\%} of the small fish available in the study area. Turbidity may mediate piscivory directly by reducing prey detection, but this effect was not apparent in our data, as rainbow trout IP was greater when suspended sediment levels (range = 5.9–20,000 mg/L) were higher.}, author = {Yard, Michael D. and Coggins, Lewis G. and Baxter, Colden V. and Bennett, Glenn E. and Korman, Josh}, doi = {10.1080/00028487.2011.572011}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yard et al. - 2011 - Trout Piscivory in the Colorado River, Grand Canyon Effects of Turbidity, Temperature, and Fish Prey Availability.pdf:pdf}, issn = {0002-8487}, journal = {Transactions of the American Fisheries Society}, number = {2}, pages = {471--486}, title = {{Trout Piscivory in the Colorado River, Grand Canyon: Effects of Turbidity, Temperature, and Fish Prey Availability}}, volume = {140}, year = {2011} } @incollection{Melis2016, author = {Melis, Theodore S and Pine, William E and Korman, Josh and Yard, Michael D and Jain, Shaleen and Pulwarty, Roger S}, booktitle = {Water policy and planning in a variable and changing climate}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Melis et al. - 2016 - Using Large-Scale Flow Experiments to Rehabilitate Colorado River Ecosystem Function in Grand Canyon Basis for an.pdf:pdf}, pages = {315--345}, publisher = {CRC Press - Taylor and Francis Group}, title = {{Using Large-Scale Flow Experiments to Rehabilitate Colorado River Ecosystem Function in Grand Canyon: Basis for an Adaptive Climate-Resilient Strategy}}, year = {2016} } @article{Yao2015, abstract = {In recent years, dam management guidelines need to estimate the effects of downstream flow on environment. However, high-flow alters physical conditions such as water depth, flow velocity and water temperature in the downstream side of the river. These changes will lead to alteration in fish habitat of the river. In this paper, an eco-hydraulic model was used to determine the levels of fish habitat in the Colorado River downstream from the Glen Canyon Dam. This model has been proposed by combining hydrodynamic and heat transfer model with a habitat suitability index model based on fish preference curves. Rainbow trout (Oncorhynchus mykiss) and flannelmouth sucker (Catostomus latipinnis) were chosen as target species because they represent both native and non-native fish in the study area. Flow velocity, water depth and water temperature were selected as the suitability indicators. The hydrological data from three high-flow experiments were analyzed to determine the effects of high-flow on the Colorado River ecosystem. Numerical model simulations were undertaken as follows: firstly, based on the hydrodynamic and heat transfer equation, three hydraulic factors including water depth, velocity and temperature distribution were simulated and the associated suitability for each was obtained based on the fish preference curves. Later, the habitat suitability equation was developed to simulate the target species' habitat situation in high flow effects. Finally, the WUA (weighted usable area) and OSI (overall suitability index) of the spawning fish species were quantitatively calculated to evaluate the sensitivity of the high flow. The results show that the effects of three HFE are more severe in spawning flannelmouth sucker than in spawning rainbow trout. It is worth noting that the one day HFE was beneficial to spawning rainbow trout and harmful to spawning flannelmouth sucker but in the HFE of more than 8 days, both the spawning habitats were completely destroyed.}, author = {Yao, Weiwei and Rutschmann, Peter and Sudeep}, doi = {10.1016/j.ecoleng.2014.11.024}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yao, Rutschmann, Sudeep - 2015 - Three high flow experiment releases from Glen Canyon Dam on rainbow trout and flannelmouth sucker habit.pdf:pdf}, issn = {09258574}, journal = {Ecological Engineering}, keywords = {CFD model,Fish habitat model,High-flow experiment,Spawning flannelmouth sucker,Spawning rainbow trout,Temperature distribution}, pages = {278--290}, publisher = {Elsevier B.V.}, title = {{Three high flow experiment releases from Glen Canyon Dam on rainbow trout and flannelmouth sucker habitat in Colorado River}}, url = {http://dx.doi.org/10.1016/j.ecoleng.2014.11.024}, volume = {75}, year = {2015} } @article{Finch2015, abstract = {The upstream migration of adult anadromous salmonids in the Columbia River Basin (CRB) has been dramatically altered and fish may be experiencing energetically costly delays at dams. To explore this notion, we estimated the energetic costs of migration and reproduction of Yakima River-bound spring Chinook salmon Oncorhynchus tshawytscha using a sequential analysis of their proximate composition (i.e., percent water, fat, protein, and ash). Tissues (muscle, viscera, and gonad) were sampled from fish near the start of their migration (Bonneville Dam), at a mid point (Roza Dam, 510km upstream from Bonneville Dam) and from fresh carcasses on the spawning grounds (about 100km above Roza Dam). At Bonneville Dam, the energy reserves of these fish were remarkably high, primarily due to the high percentage of fat in the muscle (18–20{\%}; energy content over 11 kJ g?1). The median travel time for fish from Bonneville to Roza Dam was 27 d and ranged from 18 to 42 d. Fish lost from 6 to 17{\%} of their energy density in muscle, depending on travel time. On average, fish taking a relatively long time for migration between dams used from 5 to 8{\%}more energy from the muscle than faster fish. From the time they passed Bonneville Damto death, these fish, depending on gender, used 95–99{\%} of their muscle and 73–86{\%} of their visceral lipid stores. Also, both sexes used about 32{\%} of their muscular and very little of their visceral protein stores. However, we were unable to relate energy use and reproductive success to migration history. Our results suggest a possible influence of the CRB hydroelectric system on adult salmonid energetics}, author = {Finch, C. and III, W.E. Pine and Yackulic, C.B. and Dodrill, M.J. and Yard, M. and Gerig, B.S. and JR., L.G. Coggins and Korman, J.}, doi = {10.1002/rra}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Finch et al. - 2015 - Hydrogeomorphology- Ecology Interactions in River Systems.pdf:pdf}, isbn = {1535-1459}, issn = {{\textless}null{\textgreater}}, journal = {River Research and Applications}, keywords = {chinook salmon,columbia river,energetics,hydroelectric dams,lipid,passive integrated,protein,proximate analysis}, pages = {1085--1095}, pmid = {2717}, title = {{Hydrogeomorphology- Ecology Interactions in River Systems}}, url = {http://doi.wiley.com/10.1002/rra.1112{\%}5Cnpapers2://publication/doi/10.1002/rra.1112}, volume = {22}, year = {2015} } @article{Haak2011, annote = {- EOP specific programs to close achievement gaps are often costly - they share that a highly structured active learning course can be just as effective as more expensive programs - they looked at different quaters of student success while taking into acount differences between quarters - found that everyone did better in new classroom envionment, and EOP students did particuraly better - also ranked questions according to Blooms taxonmoy and found the new format also helped student achieve higher levels on that pyramid - what was difference between low, mid, and high - can we get BIS2b data? can we have list of students in EOP program or the BUSP program? - math exercises?}, author = {Haak, David C. and HilleRisLambers, Janneke and Pitre, Emile and Freeman, Scott}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Haak et al. - 2011 - Increased structure and active learning reduce the achievement gap in introductory biology.pdf:pdf}, number = {June}, title = {{Increased structure and active learning reduce the achievement gap in introductory biology}}, year = {2011} } @book{Brewer2011, abstract = {A SUMMARY OF RECOMMENDATIONS MADE AT A NATIONAL CONFERENCE ORGANIZED BY THE AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE}, annote = {recommendations: - integrate core concepts across curriculum - focus on a student-centured approach - promote campuswide commitment to change - engage biology community in implementing change - Need better metrics to track change - Updated 2015 report as well Core concepts for Biological literacy: - evolution, structure and function, information flow, transformation of energy and matter, systems thinking Core conpetencies: 1. apply process of science, 2. ability to use quantitatve reasoning,3. ability to use modeling and simulation, 4. interdisiplinary nature of science, 5. communicatign beyond disiplie and 6 relationship between science and scoeity}, author = {Brewer, Carol and Smith, Diane}, booktitle = {American Association for the Advancement of Science}, doi = {10.1002/(SICI)1098-2736(200004)37:4<295::AID-TEA2>3.0.CO;2-2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brewer, Smith - 2011 - Vision and change in undergraduate biology education a call to action.pdf:pdf}, isbn = {9780871687418}, issn = {0022-4308}, pages = {1--100}, pmid = {8655374}, title = {{Vision and change in undergraduate biology education: a call to action}}, url = {http://oreos.dbs.umt.edu/workshop/sharedfiles/Final{\_}VandC{\_}Draft{\_}Dec1.pdf}, year = {2011} } @article{Saino2017, annote = {DIscussion amongst group: -references VIsser et al 2010 paper that tries to bring together different fields in phenology research -clock gene controls set of genes that control circadium -most birds at study site had same genotype but there was high variation in migraiton -{\textgreater} could it be methylation instead? -1-7 eggs per clutch, up to 3 clutches per year - Why differences betweeen males and females?}, author = {Saino, Nicola and Ambrosini, Roberto and Albetti, Benedetta and Caprioli, Manuela and {De Giorgio}, Barbara and Gatti, Emanuele and Liechti, Felix and Parolini, Marco and Romano, Andrea and Romano, Maria and Scandolara, Chiara and Gianfranceschi, Luca and Bollati, Valentina and Rubolini, Diego}, doi = {10.1038/srep45412}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Saino et al. - 2017 - Migration phenology and breeding success are predicted by methylation of a photoperiodic gene in the barn swallow.pdf:pdf}, issn = {2045-2322}, journal = {Scientific Reports}, number = {February}, pages = {45412}, publisher = {Nature Publishing Group}, title = {{Migration phenology and breeding success are predicted by methylation of a photoperiodic gene in the barn swallow}}, url = {http://www.nature.com/articles/srep45412}, volume = {7}, year = {2017} } @article{Fryxell2006, abstract = {Overharvesting by humans threatens a substantial fraction of endangered species. Reserves have recently received enormous attention as a means of better conserving harvested resources, despite limited empirical evidence of their efficacy. We used manipulated microcosms to test whether reserves reduce extinction risk in mobile populations of harvested Tetrahymena thermophila, a ciliate. Here we show that patterns of population distribution inside and outside reserves can be accurately predicted on the basis of simple models of diffusion coupled with logistic controls on local population growth. No extinctions occurred in eight experimental trials with reserves, whereas extinction occurred in seven of eight trials without reserves, as predicted by population viability models based on stochastic population processes. These results suggest that marine reserves may be an effective means of improving long-term viability in heavily harvested fish species.}, author = {Fryxell, John M. and Lynn, Denis H. and Chris, Philip J.}, doi = {10.1111/j.1461-0248.2006.00960.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fryxell, Lynn, Chris - 2006 - Harvest reserves reduce extinction risk in an experimental microcosm.pdf:pdf}, isbn = {1461-023X}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Ciliate,Extinction,Fisheries,Harvest,Logistic,Model,Population viability,Reserve,Tetrahymena}, number = {9}, pages = {1025--1031}, pmid = {16925651}, title = {{Harvest reserves reduce extinction risk in an experimental microcosm}}, volume = {9}, year = {2006} } @article{Snyder2014a, abstract = {Harvesting for food or sport is often non-random with respect to demographic state, such as size or life stage. The population-level consequences of such selective harvesting depend upon which states are harvested and how those states contribute to population dynamics. We focused on a form of selective harvesting that has not previously been investigated in an experimental context: sex-selective harvesting, a common feature of exploited, dioecious populations. Using simple metapopulations (two patches connect by dispersal) of sexually dimorphic Bruchid beetles in the laboratory, we contrasted the effects of female-selective, male-selective, and non-selective harvesting over six generation of population dynamics. We also tested the ability of a harvest refuge (one patch of the metapopulation free from harvesting) to mitigate the effects of harvesting, and whether refuge effects interacted with sex selectivity. Sex-selective harvesting significantly perturbed operational sex ratios and harvest refuges dampened these perturbations. Metapopulations assigned to male-selective and non-selective treatments were able to fully compensate for harvesting, such that their dynamics did not differ from non-harvested controls. Only female-selective harvesting led to significant reductions in population size and this effect was completely offset by dispersal from a harvest refuge. A two-sex model confirmed that population dynamics are more sensitive to female vs. male harvesting, but suggested that higher levels of male harvest than included in our experiment would cause population decline. We discuss the roles of density-dependent competition and frequency-dependent sexual processes in the population response to sex-selective harvesting.}, annote = {- removed fixed fraction of adults each generation}, author = {Snyder, Kate T. and Freidenfelds, Nicole A. and Miller, Tom E X}, doi = {10.1111/j.1600-0706.2013.00662.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Snyder, Freidenfelds, Miller - 2014 - Consequences of sex-selective harvesting and harvest refuges in experimental meta-populations.pdf:pdf}, isbn = {1600-0706}, issn = {00301299}, journal = {Oikos}, number = {3}, pages = {309--314}, title = {{Consequences of sex-selective harvesting and harvest refuges in experimental meta-populations}}, volume = {123}, year = {2014} } @article{Lindh2016, abstract = {Phenological changes among plants due to climate change are well documented, but often hard to interpret. In order to assess the adaptive value of observed changes, we study how annual plants with and without growth constraints should optimize their flowering time when productivity and season length changes. We consider growth constraints that depend on the plant's vegetative mass: self-shading, costs for nonphotosynthetic structural tissue and sibling competition. We derive the optimal flowering time from a dynamic energy allocation model using optimal control theory. We prove that an immediate switch (bang-bang control) from vegetative to reproductive growth is optimal with constrained growth and constant mortality. Increasing mean productivity, while keeping season length constant and growth unconstrained, delayed the optimal flowering time. When growth was constrained and productivity was relatively high, the optimal flowering time advanced instead. When the growth season was extended equally at both ends, the optimal flowering time was advanced under constrained growth and delayed under unconstrained growth. Our results suggests that growth constraints are key factors to consider when interpreting phenological flowering responses. It can help to explain phenological patterns along productivity gradients, and links empirical observations made on calendar scales with life-history theory.}, annote = {- they find that with global warming, optimal flowering is delayed for plants with unconstrained growth - as season length gets longer, optimal flowering for plants is delayed if they have constrained growth - Pikas would have constrained growth -find that increased productivity should delay flowering tie}, author = {Lindh, Magnus and Johansson, Jacob and Bolmgren, Kjell and Lundstr??m, Niklas L P and Br??nnstr??m, ??ke and Jonz??n, Niclas}, doi = {10.1111/nph.13706}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lindh et al. - 2016 - Constrained growth flips the direction of optimal phenological responses among annual plants.pdf:pdf}, issn = {14698137}, journal = {New Phytologist}, keywords = {Climate change,Constrained growth,Flowering,Life history,Optimal control theory,Phenology,Productivity,Season}, number = {4}, pages = {1591--1599}, pmid = {26548947}, title = {{Constrained growth flips the direction of optimal phenological responses among annual plants}}, volume = {209}, year = {2016} } @article{Anderson2012, abstract = {Anthropogenic climate change has already altered the timing of major life-history transitions, such as the initiation of reproduction. Both phenotypic plasticity and adaptive evolution can underlie rapid phenological shifts in response to climate change, but their relative contributions are poorly understood. Here, we combine a continuous 38 year field survey with quantitative genetic field experiments to assess adaptation in the context of climate change. We focused on Boechera stricta (Brassicaeae), a mustard native to the US Rocky Mountains. Flowering phenology advanced significantly from 1973 to 2011, and was strongly associated with warmer temperatures and earlier snowmelt dates. Strong directional selection favoured earlier flowering in contemporary environments (2010-2011). Climate change could drive this directional selection, and promote even earlier flowering as temperatures continue to increase. Our quantitative genetic analyses predict a response to selection of 0.2 to 0.5 days acceleration in flowering per generation, which could account for more than 20 per cent of the phenological change observed in the long-term dataset. However, the strength of directional selection and the predicted evolutionary response are likely much greater now than even 30 years ago because of rapidly changing climatic conditions. We predict that adaptation will likely be necessary for long-term in situ persistence in the context of climate change.}, annote = {Notes from discussion: -early may be better most years but the rare year is bad - this system doesn't deal with pollinators which is nice - look at fitness shape vs trait of interest - RILs were b/w Colorado and Montana to express more variance -detrending helps you identify plasticity -what other variables matter? freezing rains -could track individuals and look at plasticity in breeding time. Could we do this in lemon sharks?}, author = {Anderson, J. T. and Inouye, D. W. and McKinney, a. M. and Colautti, R. I. and Mitchell-Olds, T.}, doi = {10.1098/rspb.2012.1051}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Anderson et al. - 2012 - Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate.pdf:pdf}, isbn = {1471-2954 (Electronic)$\backslash$r0962-8452 (Linking)}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {adaptive evolution,boechera stricta,flowering phenology,natural selection,response to selection,rocky mountain biological laboratory}, number = {1743}, pages = {3843--3852}, pmid = {22787021}, title = {{Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change}}, volume = {279}, year = {2012} } @article{Lof2012, abstract = {Adaptation in dynamic environments depends on the grain, magnitude and predictability of ecological fluctuations experienced within and across generations. Phenotypic plasticity is a well-studied mechanism in this regard, yet the potentially complex effects of stochastic environmental variation on optimal mean trait values are often overlooked. Using an optimality model inspired by timing of reproduction in great tits, we show that temporal variation affects not only optimal reaction norm slope, but also elevation. With increased environmental variation and an asymmetric relationship between fitness and breeding date, optimal timing shifts away from the side of the fitness curve with the steepest decline. In a relatively constant environment, the timing of the birds is matched with the seasonal food peak, but they become adaptively mismatched in environments with temporal variation in temperature whenever the fitness curve is asymmetric. Various processes affecting the survival of offspring and parents influence this asymmetry, which collectively determine the 'safest' strategy, i.e. whether females should breed before, on, or after the food peak in a variable environment. As climate change might affect the (co)variance of environmental variables as well as their averages, risk aversion may influence how species should shift their seasonal timing in a warming world.}, annote = {- arre there examples in nature of cues becoming less reliable? - with temporal variation, optimal timing shifts away from peak of fitness curve to less steap side Important paper to cite in my work. They examine similar questions to my IIASA work, but they use a much different approach and framework based on pure optimality...I should dig into their methods and results more How can I calculate a fitness curve for different reproductive dates in my model?}, author = {Lof, M. E. and Reed, T. E. and McNamara, J. M. and Visser, M. E.}, doi = {10.1098/rspb.2012.0431}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lof et al. - 2012 - Timing in a fluctuating environment environmental variability and asymmetric fitness curves can lead to adaptively m.pdf:pdf}, isbn = {1471-2954 (Electronic)$\backslash$r0962-8452 (Linking)}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B}, keywords = {bet-hedging,climate,dynamic optimization,fitness curve,plasticity,stochasticity}, number = {1741}, pages = {3161--3169}, pmid = {22628472}, title = {{Timing in a fluctuating environment: environmental variability and asymmetric fitness curves can lead to adaptively mismatched avian reproduction}}, volume = {279}, year = {2012} } @article{Wilkening2016, abstract = {See, stats, and : https : / / www . researchgate . net / publication / 304070850 Characterizing American (Ochotona) Article Impact : 1 . 84 : 10 . 1093 / jmammal / gyw097 READS 25 2 : Jennifer U . S . Fish 20 SEE Chris Institute 70 , 491 SEE All - text, letting . Available : Jennifer Retrieved : 27 1 The measurement of stress hormone (glucocorticoid [ GC ]) concentration is increasingly used to assess the health of wildlife populations . However , for many species , we do not have a good understanding of the range of GC concentrations that might indicate a compromised individual . A temporary increase in GC concentration can prompt the adoption of behavior or activities to promote individual survival . However , chronic GC elevation results in deleterious effects on health that can reduce survival . In order to use GC concentration as a metric of individual fitness for a given species , it will be necessary to relate individual demographic rates to GC concentration . We related survival in American pikas (Ochotona princeps) to 2 different stress metrics , glucocorticoid metabolite (GCM) concentration in fecal samples and GC concentration in plasma samples . Annual survival was analyzed in relation to each of these stress metrics as well as other physiological metrics and habitat characteristics at several sites in the Rocky Mountains . Among the predictors considered , GCM concentration was by far the strongest predictor of annual survival in pikas , and individuals with higher baseline GCM were less likely to survive . Our metric of flea load was also negatively related to annual survival . Given the limited time and resources that characterize many wildlife conservation projects , it is important to establish which endocrine metrics are the most informative for a species . American pikas have been identified as a sentinel species for detecting effects of climate change , and several correlational studies have projected range contraction for the species . Our results suggest that more mechanistic projections might be possible given further study of the relationship between GCM and climate . Our approach contributes to a better understanding of factors affecting survival in this species and provides a basis for further research relating individual stress response andsurvivaltoenvironmentalchange.}, author = {Wilkening, Jennifer L. and Ray, Chris}, doi = {10.1093/jmammal/gyw097}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wilkening, Ray - 2016 - Characterizing predictors of survival in the American pika (emph{\{}Ochotona princeps{\}}).pdf:pdf}, issn = {15451542}, journal = {Journal of Mammalogy}, keywords = {Rocky Mountains,climate change,ecophysiology,glucocorticoids,mark-resight,sentinel species,stress response}, number = {5}, pages = {1366--1375}, title = {{Characterizing predictors of survival in the American pika ($\backslash$emph{\{}Ochotona princeps{\}})}}, volume = {97}, year = {2016} } @article{Patten2015, abstract = {Aspects of ecology-based environmentalism may run counter to how nature works; it is important to get the science right. The Janus Enigma Hypothesis is formulated as a flow???storage network approach to holistic ecological understanding. It proceeds from primary energy???matter consumption toward maximization of throughflow. When transferred material is energy, the goal function is maximum power (energy flow). The Janus Hypothesis has the following line of development: 1. The 2nd Law of Thermodynamics requires that the environments of aggrading (anti-entropic) processes become themselves degraded. To restrict such degradation is to limit life's processes.2. A maximum power conjecture holds that aggrading systems self-organize to maximize power generating work. Maximal resource use, work production, and environmental degradation necessarily follow. This applies also to material flow in generalized energy???matter (throughflow) processing.3. In maximizing power (throughflow), biota perform work to maximize their fitness (Type I, biological), but at the expense of degraded environments. Zero-sumness of conservative, consumptive transfers produces a proximate life???environment relationship that is win???lose.4. But covert mechanisms also operate such that maximizing throughflow also maximizes a system-wide, nonzero-sum, network property???dominant indirect effects.5. These maximize another property of network organization, network synergism. This transforms proximate, tangible, zero-sum, agonistic, (+, ???) transactions into ultimate, intangible, nonzero-sum, mainly positive (+, +) and synergistic relations. The proximate transactions lead by network processes to ultimate nonzero-sum benefits??{\textgreater}??costs, which is network synergism.6. By the indirect line from maximum power (throughflow) to network synergism, biotic work maximizes both biological and ecological fitness (Type II), and the life???environment relationship becomes win???win. This cannot be seen from pure empiricism because it plays out diffusely as limit processes in networks that are virtual.Three lines of evidence are presented in support of the Janus Hypothesis: (1) ???Building a biosphere??? by progressively adding nodes and links in simple compartment models shows throughflow and network synergism to be positively correlated. (2) Decomposing the utility measure of network synergism in these models into its constituents shows them to be largely made up of throughflows; maximum network synergism likely follows from the maximization of throughflow. (3) Comparing total system throughflow with network synergism in 31 food webs described for Ukrainian pasturelands shows the two measures to be positively correlated in this large empirical database. The Janus Hypothesis has a built-in paradox. Because the positive benefits derived from the nonzero-sum maximum throughflow???????network synergism???????Fitness-II line exceed the negative costs generated by the zero-sum maximum throughflow???????Fitness-I line, applied programs designed to reduce environmental degradation will reduce not only Fitness-I, but also Fitness-II by foregoing the implicit benefits of network synergism that inherently exceed the explicit costs of maximizing throughflow. This is the Janus Enigma. It means that well-meaning but misguided environmental programs may actually, in fact must, induce a lose???lose relationship between life and environment. If the Janus Hypothesis proves scientifically valid, environmentalism must resolve and manage the apparent conflict, and ecology as its parent science must expand its dimensions and become a complex systems science competent in understanding and methodology to meet the challenges of complex, intractable, non-obvious holism in nature's living networks.}, author = {Patten, Bernard C.}, doi = {10.1016/j.ecolmodel.2015.10.020}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Patten - 2015 - Systems ecology and environmentalism Getting the science right. Part II The Janus Enigma Hypothesis.pdf:pdf}, isbn = {0925-8574}, issn = {03043800}, journal = {Ecological Modelling}, keywords = {AWFUL theorem,Environs,Food webs,Janus-1 hypothesis,Maximum power,Networks}, pages = {101--138}, publisher = {Elsevier B.V.}, title = {{Systems ecology and environmentalism: Getting the science right. Part II: The Janus Enigma Hypothesis}}, url = {http://dx.doi.org/10.1016/j.ecolmodel.2014.04.010}, volume = {335}, year = {2015} } @article{DiMarco2017, annote = {NULL}, author = {{Di Marco}, Moreno and Chapman, Sarah and Althor, Glenn and Kearney, Stephen and Besancon, Charles and Butt, Nathalie and Maina, Joseph M. and Possingham, Hugh P. and {Rogalla von Bieberstein}, Katharina and Venter, Oscar and Watson, James E.M.}, doi = {10.1016/j.gecco.2017.01.008}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Di Marco et al. - 2017 - Changing trends and persisting biases in three decades of conservation science.pdf:pdf}, issn = {23519894}, journal = {Global Ecology and Conservation}, pages = {32--42}, publisher = {Elsevier B. V.}, title = {{Changing trends and persisting biases in three decades of conservation science}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S2351989417300148}, volume = {10}, year = {2017} } @article{Maguran2010, abstract = {The growing need for baseline data against which efforts to reduce the rate of biodiversity loss can be judged highlights the importance of long-term datasets, some of which are as old as ecology itself. We review methods of evaluating change in biodiversity at the community level using these datasets, and contrast whole-community approaches with those that combine information from different species and habitats. As all communities experience temporal turnover, one of the biggest challenges is distinguishing change that can be attributed to external factors, such as anthropogenic activities, from underlying natural change.Wealso discussmethodological issues, such as false alerts andmodifications indesign, of which users of these data sets need to be aware.}, annote = {NULL}, author = {Maguran, A E and Baillie, S R and Buckland, S T and Dick, J McP and Elston, D A and Scott, E M and Smith, R I and Somerfield, P and Watt, A D}, doi = {10.1016/j.tree.2010.06.016}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Maguran et al. - 2010 - Long-term datasets in biodiversity research and monitoring assessing change in ecological communities through ti.pdf:pdf}, isbn = {0169-5347}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {10}, pages = {574--582}, pmid = {20656371}, publisher = {Elsevier Ltd}, title = {{Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time}}, url = {http://dx.doi.org/10.1016/j.tree.2010.06.016}, volume = {25}, year = {2010} } @article{Mapstone1995, annote = {- good paper to cite as it discusses how type II erros may be more important than type I in conservation biology/ecology -argues that levels of alpha and beta should be set based on the relative consequences of type I and type II errors}, author = {Mapstone, Bruce D.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mapstone - 1995 - Scalable decision rules for environmental impact studies effect Size , type I , and type II errors.pdf:pdf}, journal = {Ecological Applications}, keywords = {effect size,environ-,environmental impact assessment,environmental management,mental monitoring,statistical decisions,statistical power,type 11 error,type i error}, number = {2}, pages = {401--410}, title = {{Scalable decision rules for environmental impact studies : effect Size , type I , and type II errors}}, volume = {5}, year = {1995} } @article{Gerber2016, abstract = {Listing endangered and threatened species under the US Endangered Species Act is presumed to offer a defense against extinction and a solution to achieve recovery of imperiled populations, but only if effective conservation action ensues after listing occurs. The amount of government funding available for species protection and recovery is one of the best predictors of successful recovery; however, government spending is both insufficient and highly disproportionate among groups of species, and there is significant discrepancy between proposed and actualized budgets across species. In light of an increasing list of imperiled species requiring evaluation and protection, an explicit approach to allocating recovery funds is urgently needed. Here I provide a formal decision-theoretic approach focusing on return on investment as an objective and a transparent mechanism to achieve the desired recovery goals. I found that less than 25{\%} of the {\$}1.21 billion/year needed for implementing recovery plans for 1,125 species is actually allocated to recovery. Spending in excess of the recommended recovery budget does not necessarily translate into better conservation outcomes. Rather, elimination of only the budget surplus for “costly yet futile” recovery plans can provide sufficient funding to erase funding deficits for more than 180 species. Triage by budget compression provides better funding for a larger sample of species, and a larger sample of adequately funded recovery plans should produce better outcomes even if by chance. Sharpening our focus on deliberate decision making offers the potential to achieve desired outcomes in avoiding extinction for Endangered Species Act-listed species. }, annote = {NULL}, author = {Gerber, Leah R.}, doi = {10.1073/pnas.1525085113}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gerber - 2016 - Conservation triage or injurious neglect in endangered species recovery.pdf:pdf}, issn = {0027-8424}, journal = {Pnas}, number = {13}, pages = {201525085}, pmid = {26976572}, title = {{Conservation triage or injurious neglect in endangered species recovery}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1525085113}, volume = {113}, year = {2016} } @incollection{Possingham2001, annote = {- 7 step framework does not have recourse built in (however maybe this is just adaptive management)}, author = {Possingham, H.P. and Andelman, S.J. and Noon, B.R. and Trombulak, S. and Pulliam, H.R.}, booktitle = {Research Priorities for Nature Conservation}, editor = {Soule, Orians and Kohm}, pages = {1--18}, publisher = {Society for Conservation Biology}, title = {{Making Smart Conservation Decisions}}, year = {2001} } @article{Parsons2016, annote = {NULL}, author = {Parsons, E C M}, doi = {10.3389/fmars.2016.00229}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Parsons - 2016 - “Advocacy” and “Activism” Are Not Dirty Words–How Activists Can Better Help Conservation Scientists.pdf:pdf}, isbn = {2296-7745}, issn = {2296-7745}, journal = {Frontiers in Marine Science }, keywords = {activism,advocay,advocay, activism, conservation, slacktivism, whac,conservation,ngos,slacktivism,whacktivism}, number = {November}, pages = {229}, title = {{“Advocacy” and “Activism” Are Not Dirty Words–How Activists Can Better Help Conservation Scientists }}, url = {http://journal.frontiersin.org/article/10.3389/fmars.2016.00229}, volume = {3 }, year = {2016} } @article{Nosek, annote = {NULL}, author = {Nosek, Brian}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nosek - Unknown - Nuzzo and Editorial (2014) - Statistical errors (pvalues).pdf:pdf}, title = {{Nuzzo and Editorial (2014) - Statistical errors (pvalues)}} } @article{Drake2012, abstract = {Microcosm studies of ecological processes have been criticized for being unrealistic. However, since lack of realism is inherent to all experimental science, if lack of realism invalidates microcosm models of ecological processes, then such lack of realism must either also invalidate much of the rest of experimental ecology or its force with respect to microcosm studies must derive from some other limitation of microcosm apparatus. We believe that the logic of the microcosm program for ecological research has been misunderstood. Here, we respond to the criticism that microcosm studies play at most a heuristic role in ecology with a new account of scientific experimentation developed specifically with ecology and other environmental sciences in mind. Central to our account are the concepts of model-based reasoning and analogical inference. We find that microcosm studies are sound when they serve as models for nature and when certain properties, referred to as the essential properties, are in positive analogy. By extension, our account also justifies numerous other kinds of ecological experimentation. These results are important because reliable causal accounts of ecological processes are necessary for sound application of ecological theory to conservation and environmental science. A severe sensitivity to reliable representation of causes is the chief virtue of the microcosm approach.}, annote = {NULL}, author = {Drake, John M. and Kramer, Andrew M.}, doi = {10.1007/s12080-011-0134-0}, isbn = {1874-1738}, issn = {18741738}, journal = {Theoretical Ecology}, keywords = {Analogy,Daphnia,Inference,Mechanism,Microcosm}, number = {3}, pages = {433--444}, title = {{Mechanistic analogy: How microcosms explain nature}}, volume = {5}, year = {2012} } @article{Gates1989, annote = {NULL}, author = {Gates, Timothy K and Member, Associate and Wets, Roger J-b and Grismer, Mark E}, number = {3}, pages = {488--502}, title = {{Stochastic approximation applied to optimal irrigation and drainage planning}}, volume = {115}, year = {1989} } @article{Srivastava2004a, abstract = {Several recent, high-impact ecological studies feature natural microcosms as tools for testing effects of fragmentation, metacommunity theory or links between biodiversity and ecosystem processes. These studies combine the microcosm advantages of small size, short generation times, contained structure and hierarchical spatial arrangement with advantages of field studies: natural environmental variance, 'openness' and realistic species combinations with shared evolutionary histories. This enables tests of theory pertaining to spatial and temporal dynamics, for example, the effects of neighboring communities on local diversity, or the effects of biodiversity on ecosystem function. Using examples, we comment on the position of natural microcosms in the roster of ecological research strategies and tools. We conclude that natural microcosms are as versatile as artificial microcosms, but as complex and biologically realistic as other natural systems. Research to date combined with inherent attributes of natural microcosms make them strong candidate model systems for ecology.}, annote = {NULL}, author = {Srivastava, Diane S. and Kolasa, Jurek and Bengtsson, Jan and Gonzalez, Andrew and Lawler, Sharon P. and Miller, Thomas E. and Munguia, Pablo and Romanuk, Tamara and Schneider, David C. and Trzcinski, M. Kurtis}, doi = {10.1016/j.tree.2004.04.010}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Srivastava et al. - 2004 - Are natural microcosms useful model systems for ecology(2).pdf:pdf}, isbn = {0169-5347}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {7}, pages = {379--384}, pmid = {16701289}, title = {{Are natural microcosms useful model systems for ecology?}}, volume = {19}, year = {2004} } @article{Olden2014, abstract = {Greater scientific knowledge, changing societal values, and legislative mandates have emphasized the importance of implementing large-scale flow experiments (FEs) downstream of dams. We provide the first global assessment of FEs to evaluate their success in advancing science and informing management decisions. Systematic review of 113 FEs across 20 countries revealed that clear articulation of experimental objectives, while not universally practiced, was crucial for achieving management outcomes and changing dam-operating policies. Furthermore, changes to dam operations were three times less likely when FEs were conducted primarily for scientific purposes. Despite the recognized importance of riverine flow regimes, four-fifths of FEs involved only discrete flow events. Over three-quarters of FEs documented both abiotic and biotic outcomes, but only one-third examined multiple taxonomic responses, thus limiting how FE results can inform holistic dam management. Future FEs will present new opportunities to ...}, annote = {NULL}, author = {Olden, Julian D. and Konrad, Christopher P. and Melis, Theodore S. and Kennard, Mark J. and Freeman, Mary C. and Mims, Meryl C. and Bray, Erin N. and Gido, Keith B. and Hemphill, Nina P. and Lytle, David A. and McMullen, Laura E. and Pyron, Mark and Robinson, Christopher T. and Schmidt, John C. and Williams, John G.}, doi = {10.1890/130076}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Olden et al. - 2014 - Are large-scale flow experiments informing the science and management of freshwater ecosystems.pdf:pdf}, isbn = {1540-9295}, issn = {15409309}, journal = {Frontiers in Ecology and the Environment}, number = {3}, pages = {176--185}, title = {{Are large-scale flow experiments informing the science and management of freshwater ecosystems?}}, volume = {12}, year = {2014} } @article{White2017b, annote = {NULL}, author = {White, J. Wilson and Nickols, Kerry J. and Botsford, Louis W.}, doi = {10.1111/conl.12344}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White, Nickols, Botsford - 2017 - Response to O'Leary et al. Misuse of Models Leads to Misguided Conservation Recommendations.pdf:pdf}, isbn = {9109624066}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Global conservation targets,Marine protected areas,Meta‐analysis,Model parameterization,Models}, title = {{Response to O'Leary et al.: Misuse of Models Leads to Misguided Conservation Recommendations}}, url = {http://doi.wiley.com/10.1111/conl.12344}, year = {2017} } @techreport{HFE_Plan_2011, abstract = {The Department of the Interior, acting through the Bureau of Reclamation, is proposing to develop and implement a protocol for high-flow experimental releases from Glen Canyon Dam to better determine whether and how sand conservation can be improved in the Colorado River corridor downstream of Glen Canyon Dam including areas within Grand Canyon National Park. Under the concept of high-flow experimental releases, sand stored in the river channel is suspended by high-volume dam releases and a portion of the sand is redeposited in downstream reaches as sandbars and beaches, while another portion is transported downstream by river flows. These sand features and associated backwater habitats provide key wildlife habitat, protect archaeological sites, enhance riparian vegetation, and provide camping opportunities along the Colorado River in Grand Canyon National Park. This protocol for high-flow experimental releases from Glen Canyon Dam is part of the ongoing implementation of the Glen Canyon Dam Adaptive Management Program. As part of the GCDAMP, the protocol is a component of Interior's compliance with the Grand Canyon Protection Act of 1992 (Public Law 102-575)}, annote = {NULL}, author = {{U.S. Bureau of Reclamation}}, pages = {546}, title = {{Environmental Assessment Development and Implementation of a Protocol for High-flow Experimental Releases from Glen Canyon Dam, Arizona, 2011 - 2020}}, year = {2011} } @article{Melis2015, annote = {NULL}, author = {Melis, Theodore S and Walters, Carl J and Korman, Josh}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Melis, Walters, Korman - 2015 - Surprise and Opportunity for Learning in Grand Canyon the Glen Canyon Dam Adaptive Management Program.pdf:pdf}, journal = {Ecology and Society}, keywords = {adaptive management,colorado river,ecosystem modeling,glen canyon dam,grand canyon,high-flow experiments,humpback chub,rainbow trout,surprise learning}, number = {3}, title = {{Surprise and Opportunity for Learning in Grand Canyon: the Glen Canyon Dam Adaptive Management Program}}, volume = {20}, year = {2015} } @article{Eddy2013, annote = {integrated model of economic choice and fisheries Loo on states once again...... How to you couple models when one more is much more detailed or predictive than the other? e.g. coupled hydrology model and salmon modeling read paper more in depth -{\textgreater} what would you do next? -could make model actually dynamic}, author = {Eddy, S Heila M W R and Entz, A Llison W and Ropeza, O Ctavio A Burto and Axey, M Artin M and Agavarapu, S Riniketh N and Eslie, H Eather M L}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eddy et al. - 2013 - Evidence of market-driven size-selective fishing and the mediating effects of biological and institutional factors.pdf:pdf}, keywords = {coupled natural and human,coupled social-ecological systems,ecosystem,fishing,human behavior,life history traits,population modeling,selective harvest,services,size selection,systems model}, number = {4}, pages = {726--741}, title = {{Evidence of market-driven size-selective fishing and the mediating effects of biological and institutional factors}}, volume = {23}, year = {2013} } @article{Fackler2013, annote = {NULL}, author = {Fackler, Paul L and Marescot, Lucile and Chapron, Guillaume and Chad, Iadine and Duchamp, Christophe and Marboutin, Eric and Gimenez, Olivier}, doi = {10.1111/2041-210X.12082}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fackler et al. - 2013 - Complex decisions made simple a primer on stochastic dynamic programming.pdf:pdf}, journal = {Methods in Ecology and Evolution}, pages = {872--884}, title = {{Complex decisions made simple : a primer on stochastic dynamic programming}}, volume = {4}, year = {2013} } @article{Lade2013, annote = {Model description: - two harvest strategies: one where harvestors cooperate and one where they defect -- depends on prop of each and relative utilies of being in each group --utilities differ by different harvesting strategies between two groups (F), costs incurred by being a defector or cooperator (W), and social ostracise costs of being defector (w) - time scales are same for both groups Generalized modeling: -make general model and then scale it to be per capita or something -then you see if fold bifurcation is possible given generalized parameters - can make statements like if growth is linear, you have no fold bifurcation, but if sigmodial, then fold bifurcation is possible Questions/points to bring up -what does this mean for more complicated systems? Discussion in lab: -Could coupling systems ever negate the complexity?}, author = {Lade, Steven J and Tavoni, Alessandro and Levin, Simon A and Schl, Maja}, doi = {10.1007/s12080-013-0187-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lade et al. - 2013 - Regime shifts in a social-ecological system.pdf:pdf}, journal = {Theoretical Ecology}, keywords = {bifurcation,early warning,ecological system,generalized modeling,regime shifts,signals,social,tipping points}, pages = {359--372}, title = {{Regime shifts in a social-ecological system}}, volume = {6}, year = {2013} } @misc{U.S.FishandWildlife, annote = {NULL}, author = {{U.S. Fish and Wildlife}}, title = {{Upper Colorado River Endangered Fish Recovery Program}}, url = {http://www.coloradoriverrecovery.org/}, urldate = {2017-02-25}, year = {2017} } @article{Ricker1954, annote = {NULL}, author = {Ricker, William}, journal = {Journal of the Fisheries Research Board of Canada}, number = {5}, pages = {559--623}, title = {{Stock and Recuitment}}, volume = {11}, year = {1954} } @article{Munro2015, abstract = {We trace the contributions of Colin Clark from his first book and articles published in the mid-1970s to date and link them to the six papers contained in this Special Issue and the larger fisheries economics literature. We highlight the impacts of Clark's contributions on the theory, empirical, policy and management of fisheries, ranging from particular fisheries applications right through to global studies of the economics of fishing. Our conclusion is that Colin Clark's impact upon fisheries economics has been revolutionary and predict that 100 years from now, his classic contribution, Mathematical Bioeconomics will still be studied with care by economists.}, annote = {NULL}, author = {Munro, Gordon R. and Sumaila, U. Rashid}, doi = {10.1007/s10640-015-9910-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Munro, Sumaila - 2015 - On the Contributions of Colin Clark to Fisheries Economics.pdf:pdf}, isbn = {1064001599}, issn = {15731502}, journal = {Environmental and Resource Economics}, keywords = {Bioeconomics,Capital-theoretic model,Dynamic fishery models,Fisheries economics,Optimal resource investment,Renewable resource management}, number = {1}, pages = {1--17}, publisher = {Springer Netherlands}, title = {{On the Contributions of Colin Clark to Fisheries Economics}}, volume = {61}, year = {2015} } @article{Anderson2017, annote = {how many populations would you expect to find black swan events by chance - 86{\%} of events were unexpected declines - if you ignorre rare significant negative events, more likely to underestimate future extinction risk -argue agains references 12 and 123 - use t distributions and freedom parameter to allow for more rare events - references learning from earhquakes and other fields in wildlife}, author = {Anderson, Sean C and Branch, Trevor A and Cooper, Andrew B and Dulvy, Nicholas K}, doi = {10.1073/pnas.1611525114}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Anderson et al. - 2017 - Black-swan events in animal populations.pdf:pdf}, journal = {PNAS}, title = {{Black-swan events in animal populations}}, year = {2017} } @article{Lee2013, annote = {NULL}, author = {Lee, Duncan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lee - 2013 - CARBayes An R Package for Bayesian Spatial.pdf:pdf}, keywords = {bayesian models,carbayes,conditional autoregressive priors,r}, number = {13}, title = {{CARBayes : An R Package for Bayesian Spatial}}, volume = {55}, year = {2013} } @article{Holyoak2005, annote = {NULL}, author = {Holyoak, Marcel and Lawler, Sharon P.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Holyoak, Lawler - 2005 - The contribution of laboratory experiments on protists to understanding population and metapopulation dynamics.pdf:pdf}, journal = {Advances in Ecological Research}, pages = {245--271}, title = {{The contribution of laboratory experiments on protists to understanding population and metapopulation dynamics}}, volume = {37}, year = {2005} } @article{Benton2007, annote = {NULL Argue microcosms have rich history of increasing our understanding of ecology Question: can you reduce risk of collapse while only having minor reduction in MSY Optimal deisgn and location of MPAs in a variable environment - what about rare events?}, author = {Benton, Tim G and Solan, Martin and Travis, Justin M J and Sait, Steven M}, doi = {10.1016/j.tree.2007.08.003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Benton et al. - 2007 - Microcosm experiments can inform global ecological problems.pdf:pdf}, journal = {Trends in Ecology {\&} Evolution}, number = {10}, title = {{Microcosm experiments can inform global ecological problems}}, volume = {22}, year = {2007} } @article{Cross2011, author = {Cross, Wyatt F and Baxter, Colden V and Donner, Kevin C and Rosi-marshall, Emma J and Kennedy, Theodore A and Hall, Robert O and Kelly, Holly A Wellard and Rogers, R Scott and Cross, Wyatt F and Baxter, Colden V and Donner, Kevin C and Rosi-marshall, Emma J and Kennedy, Theodore A and Hall, Robert O and Kelly, Holly A Wellard and Rogers, R Scott}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cross et al. - 2011 - Ecosystem ecology meets adaptive management food web response to a controlled flood on the Colorado River , Glen.pdf:pdf}, journal = {Ecological Applications}, keywords = {dam,high-flow experiment,organic matter flows,regulated river,secondary production,species interactions,trophic basis of production}, number = {6}, pages = {2016--2033}, title = {{Ecosystem ecology meets adaptive management : food web response to a controlled flood on the Colorado River , Glen Canyon}}, volume = {21}, year = {2011} } @article{Mach2017, annote = {NULL}, author = {Mach, Megan E. and Wedding, Lisa M. and Reiter, Sarah M. and Micheli, Fiorenza and Fujita, Rod M. and Martone, Rebecca G.}, doi = {10.1016/j.ocecoaman.2016.11.028}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mach et al. - 2017 - Assessment and management of cumulative impacts in California's network of marine protected areas.pdf:pdf}, issn = {09645691}, journal = {Ocean {\&} Coastal Management}, pages = {1--11}, publisher = {Elsevier Ltd}, title = {{Assessment and management of cumulative impacts in California's network of marine protected areas}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0964569116303647}, volume = {137}, year = {2017} } @article{Simpfendorfer2017, annote = {NULL}, author = {Simpfendorfer, Colin A and Dulvy, Nicholas K}, doi = {10.1016/j.cub.2016.12.017}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Simpfendorfer, Dulvy - 2017 - Bright spots of sustainable shark fishing.pdf:pdf}, issn = {09609822}, journal = {Current Biology}, pages = {2016--2017}, title = {{Bright spots of sustainable shark fishing}}, year = {2017} } @article{Melis2011, abstract = {Three high-flow experiments (HFEs) were conducted by the U.S. Department of the Interior at Glen Canyon Dam, Arizona, in March 1996, November 2004, and March 2008 (figs. 1 and 2). These experiments, also known as artificial or controlled floods, were large-volume, sched­uled releases of water from Glen Canyon Dam that were designed to mimic some aspects of pre-dam Colorado River seasonal flooding. The goal of these experiments was to determine whether high flows could be used to benefit important physical and biological resources in Glen Canyon National Recreation Area and Grand Canyon National Park (fig. 2) that had been affected by the operation of Glen Canyon Dam. Efforts such as HFEs that seek to maintain and restore downstream resources are undertaken by the U.S. Department of the Interior under the auspices of the Grand Canyon Protection Act of 1992 (GCPA; title XVIII, secs. 1801–1809, of Public Law 102-575). Scientists conducted a wide range of monitoring and research activities before, during, and after the experiments. Initially, research efforts focused on whether HFEs could be used to rebuild and maintain Grand Canyon sandbars, which provide camping beaches for hikers and whitewater rafters, create habitats poten­tially used by native fish and other wildlife, and are the source of windborne sand that may help to protect some archaeological resources from weathering and erosion. As scientists gained a better understanding of how HFEs affect the physical environment, research efforts expanded to include additional investigations about the effects of HFEs on biological resources, such as native fishes, nonnative sports fishes, riverside vegetation, and the aquatic food web. The chapters that follow summarize and synthesize for decisionmakers and the public what has been learned about HFEs to provide a framework for implementing similar future experiments. This report is a product of the Glen Canyon Dam Adaptive Management Program (GCDAMP), a Federal initiative authorized to ensure that the primary mandate of the GCPA (GCPA sec. 1802 (a)) is met through advances in information and resource management. The program and its research efforts focus on a study area that encompasses the Colorado River corridor from the forebay of Glen Canyon Dam to the western boundary of Grand Canyon National Park, which is identified as the Colorado River ecosystem elsewhere in this report. The study area includes the approximately 16-mile river corridor between the dam and Lees Ferry within Glen Canyon National Recreation Area and the entire 277-river mile corridor downstream from Lees Ferry and within Grand Canyon National Park (fig. 2). The U.S. Geological Survey's Grand Canyon Monitoring and Research Center (GCMRC) is responsible for the scientific moni­toring and research efforts of the GCDAMP, including the preparation of this report. The GCMRC gratefully acknowledges the contributions of those scientists with Federal and State resource-management agencies, academic institutions, and private consulting firms who undertook much of the research presented in the chapters that follow.}, annote = {Focuses on high flow experiments in 1996, 2004, and 2008 -main purpose seems to be sandbar building - each experiment costs several million in lost power -campsite area increases by upwards of 50{\%} after high flow experiments - erosion happens quickly (within 6 months) Chapter 4: -snail and humpback chub among most important species -rainbow trout and other non natives important for fishing -temperature and water clarity imoprtant for fish -compettion and predation between two fish species -native fish need backgwaters that come about from sandbar building for reproduction -rainbow trout increases a lot after 2008, probably as result of higher invert biomasss and egg survival}, author = {Melis, T.S.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Melis - 2011 - Effects of Three High-Flow Experiments on the Colorado River Ecosystem Downstream from Glen Canyon Dam, Arizona.pdf:pdf}, journal = {U.S. Geological Survey Circular}, number = {February}, pages = {147 p.}, title = {{Effects of Three High-Flow Experiments on the Colorado River Ecosystem Downstream from Glen Canyon Dam, Arizona}}, url = {http://pubs.usgs.gov/circ/1366/}, volume = {1366}, year = {2011} } @article{White2017a, annote = {NULL}, author = {White, Timothy D. and Carlisle, Aaron B. and Kroodsma, David A. and Block, Barbara A. and Casagrandi, Renato and {De Leo}, Giulio A. and Gatto, Marino and Micheli, Fiorenza and McCauley, Douglas J.}, doi = {10.1016/j.biocon.2017.01.009}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2017 - Assessing the effectiveness of a large marine protected area for reef shark conservation.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {Automatic identification system,Carcharhinus amblyrhynchos,Fisheries,Marine protected areas,Satellite telemetry,Vessel tracking,carcharhinus amblyrhynchos}, pages = {64--71}, publisher = {Elsevier Ltd}, title = {{Assessing the effectiveness of a large marine protected area for reef shark conservation}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006320717300678}, volume = {207}, year = {2017} } @article{Davidson2017, annote = {NULL}, author = {Davidson, Lindsay N K and Dulvy, Nicholas K}, doi = {10.1038/s41559-016-0040}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Davidson, Dulvy - 2017 - Global marine protected areas for avoiding extinctions.pdf:pdf}, issn = {2397-334X}, journal = {Nature Ecology and Evolution}, number = {January}, pages = {1--6}, publisher = {Macmillan Publishers Limited, part of Springer Nature.}, title = {{Global marine protected areas for avoiding extinctions}}, url = {http://dx.doi.org/10.1038/s41559-016-0040}, volume = {1}, year = {2017} } @article{Hilborn2016, abstract = {Efforts to understand how to manage aquatic ecosystems often rely on correlations between human actions and impacts in the ecosystem. We are often warned that correlation does not imply causation and that the gold standard for identify- ing cause and effect relationships is manipulative experiments. History shows us that correlations are often not causal and that managers should not design policies based on the assumption of causality. However, in the absence of manipulation, correlative evidence may be all that is available. Correlative evidence is strongest when (1) correlation is high, (2) it is found consistently across multiple situations, (3) there are not competing explanations, and (4) the correlation is consist- ent with mechanistic explanations that can be supported by experimental evidence. Where possible, manipulative experi- ments and formal adaptive management should be employed, but in large-scale aquatic ecosystems these opportunities are limited. More commonly, we should emphasize identifying the range of possible causal mechanisms and identify poli- cies that are robust to the alternative mechanisms.}, author = {Hilborn, Ray}, doi = {10.1080/03632415.2016.1119600}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hilborn - 2016 - Correlation and Causation in Fisheries and Watershed Management.pdf:pdf}, issn = {0363-2415}, journal = {Fisheries}, number = {1}, pages = {18--25}, title = {{Correlation and Causation in Fisheries and Watershed Management}}, url = {http://www.tandfonline.com/doi/full/10.1080/03632415.2016.1119600}, volume = {41}, year = {2016} } @article{Alexander2006, abstract = {High spawning flows from Hugh Keenleyside Dam (HKD) on the Columbia River results in dewatering of eggs in mountain whitefish (Prosopium williamsoni) populations, but the ultimate effect on adult abundance depends on the shape of the egg-to-adult recruitment curve. Our decision analysis assessed the benefits of alternative flow experiments while accounting for uncertainties in this relationship and in flows in the Columbia and Kootenay rivers. The value of experimenting depended on the true recruitment relationship, how we quantified experimental benefits, and experimental design. With current uncertainty, the optimal HKD spawning flow (out of 11 alternative flows) was 1699.2 m3{\textperiodcentered}s–1. Spawning flows below 1699.2 m3{\textperiodcentered}s–1 did not improve egg survival because lower flows rendered high- quality spawning habitat unavailable and increased scour mortality. Two experimental designs, both with higher preci- sion monitoring, had a high probability of detecting the true recruitment curve at reasonable cost. Information from these experiments suggested an optimal spawning flow of 1699.2 m3{\textperiodcentered}s–1 if adult abundance were sensitive to egg mor- tality or 1982.4 m3{\textperiodcentered}s–1 if the population were insensitive.}, author = {Alexander, Clint A D and Peters, Calvin N and Marmorek, David R and Higgins, Paul}, doi = {10.1139/F06-032}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Alexander et al. - 2006 - A decision analysis of flow management experiments for Columbia River mountain whitefish (Prosopium williamson.pdf:pdf}, isbn = {0706-652X}, issn = {0706-652X}, journal = {Can. J. Fish Aquat. Sci.}, pages = {1142--1156}, title = {{A decision analysis of flow management experiments for Columbia River mountain whitefish (Prosopium williamsoni) management}}, volume = {63}, year = {2006} } @incollection{Morrison2008, abstract = {The European rabbit (Oryctolagus cuniculus) is a well-known species all over the world and occurs in both wild and domestic forms. European rabbits are present in most of Europe, North Africa, parts of South America, Australia and New Zealand, as well as in more than 800 islands, where they occupy a huge variety of ecosystems (Thompson and King 1994). Its domestic counterpart exhibits a remarkable variety of breeds showing variation in colour, size and fertility. Domestic breeds are kept and raised globally for meat, wool and fur, and also as increasing popular pets. However, for most of its history, the European rabbit was confined to the Iberian Peninsula where the species is supposed to have emerged in the mid-Pleistocene. We know this from the analysis of the fossil record that in addition, places also in the Iberian Peninsula the emergence of genus Oryctolagus (Lopez-Martinez 2008, this book). The subsequent geographical expansion and successful colonization of multiple territories is as recent as historical times and has been mostly human-mediated. This expansion eventually ended in a domestication process that is unique to Western Europe.}, annote = {NULL}, author = {Morrison, Shawm and Hik, David S.}, booktitle = {Lagomorph Biology}, doi = {10.1007/978-3-540-72446-9}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Morrison, Hik - 2008 - When Where And for how long Census design considerations for an Alpine Lagomorph, the Collared pika.pdf:pdf}, isbn = {978-3-540-72445-2}, pages = {103--113}, publisher = {Springer Berlin Heidelberg}, title = {{When? Where? And for how long? Census design considerations for an Alpine Lagomorph, the Collared pika}}, year = {2008} } @article{Fiorella2015, abstract = {Women's access to natural resources for food and livelihoods is shaped by resource availability, income, and the gender dynamics that mediate access. In fisheries, where men often fish but women comprise 90{\%} of traders, transactional sex is among the strategies women use to access resources. Using the case of Lake Victoria, we employed mixed methods (in-depth interviews, n=30; cross-sectional survey, n=303) to analyze the influence of fish declines on fish-for-sex relationships. We found that fish declines affect relationship duration and women's bargaining power. Our results have broad implications for the dynamics of economies dependent on increasingly scarce resources throughout the world.}, annote = {discussion in lab:}, author = {Fiorella, Kathryn J. and Camlin, Carol S. and Salmen, Charles R. and Omondi, Ruth and Hickey, Matthew D. and Omollo, Dan O. and Milner, Erin M. and Bukusi, Elizabeth A. and Fernald, Lia C.H. and Brashares, Justin S.}, doi = {10.1016/j.worlddev.2015.05.015}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fiorella et al. - 2015 - Transactional Fish-for-Sex Relationships Amid Declining Fish Access in Kenya.pdf:pdf}, issn = {0305750X}, journal = {World Development}, keywords = {food insecurity,gender,global change,hiv,natural resources,public health}, pages = {323--332}, publisher = {Elsevier Ltd}, title = {{Transactional Fish-for-Sex Relationships Amid Declining Fish Access in Kenya}}, url = {http://dx.doi.org/10.1016/j.worlddev.2015.05.015}, volume = {74}, year = {2015} } @article{Barnes2016, abstract = {SignificanceUnderstanding how social dynamics drive outcomes in environmental systems is critical to advancing global sustainability. We link comprehensive data on fishers information-sharing networks and observed fishing behaviors to demonstrate that social networks are tied to actions that can directly impact ecological health. Specifically, we find evidence that the propensity for individuals to share information primarily with others most similar to themselves creates segregated networks that impede the diffusion of sustainable behaviors--behaviors that could have mitigated the incidental catch of over 46,000 sharks in a single commercial fishery between 2008 and 2012. Our results suggest having a better understanding of social structures and bolstering effective communication across segregated networks has the potential to contribute toward more sustainable environmental outcomes. Social networks can profoundly affect human behavior, which is the primary force driving environmental change. However, empirical evidence linking microlevel social interactions to large-scale environmental outcomes has remained scarce. Here, we leverage comprehensive data on information-sharing networks among large-scale commercial tuna fishers to examine how social networks relate to shark bycatch, a global environmental issue. We demonstrate that the tendency for fishers to primarily share information within their ethnic group creates segregated networks that are strongly correlated with shark bycatch. However, some fishers share information across ethnic lines, and examinations of their bycatch rates show that network contacts are more strongly related to fishing behaviors than ethnicity. Our findings indicate that social networks are tied to actions that can directly impact marine ecosystems, and that biases toward within-group ties may impede the diffusion of sustainable behaviors. Importantly, our analysis suggests that enhanced communication channels across segregated fisher groups could have prevented the incidental catch of over 46,000 sharks between 2008 and 2012 in a single commercial fishery.}, annote = {Discussion notes:}, author = {Barnes, Michele L. and Lynham, John and Kalberg, Kolter and Leung, PingSun}, doi = {10.1073/pnas.1523245113}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barnes et al. - 2016 - Social networks and environmental outcomes.pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {23}, pages = {6466--6471}, title = {{Social networks and environmental outcomes}}, volume = {113}, year = {2016} } @article{Haddad2015, abstract = {We conducted an analysis of global forest cover to reveal that 70{\%} of remaining forest is within 1 km of the forest's edge, subject to the degrading effects of fragmentation. A synthesis of fragmentation experiments spanning multiple biomes and scales, five continents, and 35 years demonstrates that habitat fragmentation reduces biodiversity by 13 to 75{\%} and impairs key ecosystem functions by decreasing biomass and altering nutrient cycles. Effects are greatest in the smallest and most isolated fragments, and they magnify with the passage of time. These findings indicate an urgent need for conservation and restoration measures to improve landscape connectivity, which will reduce extinction rates and help maintain ecosystem services.}, annote = {- they found that changes in abundance were not explained well by alterations to habitat area. However, increased isolation did ahve a negative efect on abundance and species persistence. - argue that fragmentation reduces habitat area, increases isolation, and increases edge effects - For pikas, there is no change in the degree of these factors over time --{\textgreater} In my model, I examine the effect of local population size (habitat area?) and isolation...I do not really deal with edge effects}, author = {Haddad, N. M. and Brudvig, L. a. and Clobert, J. and Davies, K. F. and Gonzalez, A. and Holt, R. D. and Lovejoy, T. E. and Sexton, J. O. and Austin, M. P. and Collins, C. D. and Cook, W. M. and Damschen, E. I. and Ewers, R. M. and Foster, B. L. and Jenkins, C. N. and King, a. J. and Laurance, W. F. and Levey, D. J. and Margules, C. R. and Melbourne, B. a. and Nicholls, a. O. and Orrock, J. L. and Song, D.-X. and Townshend, J. R.}, doi = {10.1126/sciadv.1500052}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Haddad et al. - 2015 - Habitat fragmentation and its lasting impact on Earth's ecosystems.pdf:pdf}, isbn = {doi : 10.1126/sciadv.1500052}, issn = {2375-2548}, journal = {Science Advances}, keywords = {earch article}, number = {2}, pages = {1--9}, pmid = {26601154}, title = {{Habitat fragmentation and its lasting impact on Earth's ecosystems}}, url = {http://advances.sciencemag.org/content/1/2/e1500052.abstract}, volume = {1}, year = {2015} } @article{Scott2016, abstract = {Collaborative environmental governance strategies seek to improve management efforts by involving nongovernmental stakeholders and spanning sectoral and geographic boundaries, but it is unclear whether government funding for such efforts efforts pays off in terms of improved environmental outcomes. This paper explores a common case of collaborative governance—collaborative watershed councils (WCs)—and examines whether the actions of collaborative WCs improve water quality. Coupling longitudinal data concerning 1984 grants given to local WCs in the state of Oregon with water quality monitoring data sampled at 161 sites, this analysis tests whether there is a prima facie case that the actions of local collaborative institutions improve environmental outcomes. Along with presenting some of the first evidence about the impacts of collaborative governance that is based on an objective outcome metric, this paper also contrasts different council actions and considers how institutional capacity impacts council efforts. WC actions are shown to be associated with improved water quality, but the magnitude of improvement is dependent on council attributes and the type of project for which funds are allocated. This paper also makes a methodological contribution by demonstrating the use of hierarchical Bayesian modeling to account for spatial and temporal dependencies present in observational data.}, author = {Scott, Tyler A.}, doi = {10.1093/jopart/muw033}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Scott - 2016 - Is Collaboration a Good Investment Modeling the Link between Funds Given to Collaborative Watershed Councils and Water Qu.pdf:pdf}, issn = {14779803}, journal = {Journal of Public Administration Research and Theory}, number = {4}, pages = {769--786}, title = {{Is Collaboration a Good Investment? Modeling the Link between Funds Given to Collaborative Watershed Councils and Water Quality}}, volume = {26}, year = {2016} } @article{McCrea-Strub2011, abstract = {Given the economic and social importance of fisheries in the Gulf of Mexico large marine ecosystem (LME), it is imperative to quantify the potential impacts of the Deepwater Horizon oil spill. To provide a preliminary perspective of the consequences of this disaster, spatial databases of annual reported commercial catch and landed value prior to the spill were investigated relative to the location of the fisheries closures during July 2010. Recent trends illustrated by this study suggest that more than 20{\%} of the average annual U. S. commercial catch in the Gulf has been affected by postspill fisheries closures, indicating a potential minimum loss in annual landed value of US{\$} 247 million. Lucrative shrimp, blue crab, menhaden, and oyster fisheries may be at greatest risk of economic losses. Overall, it is evident that the oil spill has impacted a highly productive area of crucial economic significance within the Gulf of Mexico LME. This study draws attention to the need for ongoing and thorough investigations into the economic impacts of the oil spill on Gulf fisheries.}, annote = {-they looked at the cost of implementing a closure after the oil spill and how much that may have cost using old catch data - 10 days after spill about 24{\%} of US Gulf EEZ was closed to commericial fishing - this closed area represents a min annual of of {\$}247 million}, author = {McCrea-Strub, A. and Kleisner, K. and Sumaila, U. R. and Swartz, W. and Watson, R. and Zeller, Dirk and Pauly, D.}, doi = {10.1080/03632415.2011.589334}, isbn = {0363-2415}, issn = {0363-2415}, journal = {Fisheries}, number = {7}, pages = {332--336}, title = {{Potential impact of the Deepwater Horizon oil spill on commercial fisheries in the Gulf of Mexico}}, url = {http://apps.webofknowledge.com.proxy.lib.sfu.ca/full{\_}record.do?product=WOS{\&}search{\_}mode=GeneralSearch{\&}qid=9{\&}SID=2AmH5oNckGmfMc91AL9{\&}page=1{\&}doc=4}, volume = {36}, year = {2011} } @article{Pennekamp2016, abstract = {The pervasive influence of human induced global environmental change affects biodiversity across the globe, and there is great uncertainty as to how the biosphere will react on short and longer time scales. To adapt to what the future holds and to manage the impacts of global change, scientists need to predict the expected effects with some confidence and communicate these predictions to policy makers. However, recent reviews found that we currently lack a clear understanding of how predictable ecology is, with views seeing it as mostly unpredictable to potentially predictable, at least over short time frames. However, in applied, ecology-related fields predictions are more commonly formulated and reported, as well as evaluated in hindsight, potentially allowing one to define baselines of predictive proficiency in these fields. We searched the literature for representative case studies in these fields and collected information about modeling approaches, target variables of prediction, predictive proficiency achieved, as well as the availability of data to parameterize predictive models. We find that some fields such as epidemiology achieve high predictive proficiency, but even in the more predictive fields proficiency is evaluated in different ways. Both phenomenological and mechanistic approaches are used in most fields, but differences are often small, with no clear superiority of one approach over the other. Data availability is limiting in most fields, with long-term studies being rare and detailed data for parameterizing mechanistic models being in short supply. We suggest that ecologists adopt a more rigorous approach to report and assess predictive proficiency, and embrace the challenges of real world decision making to strengthen the practice of prediction in ecology.}, annote = {NULL}, author = {Pennekamp, Frank and Adamson, Matthew W. and Petchey, Owen L. and Poggiale, Jean-Christophe and Aguiar, Ma{\'{i}}ra and Kooi, Bob W. and Botkin, Daniel B. and DeAngelis, Donald L.}, doi = {10.1016/j.ecocom.2016.12.005}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pennekamp et al. - 2016 - The practice of prediction What can ecologists learn from applied, ecology-related fields.pdf:pdf}, issn = {1476945X}, journal = {Ecological Complexity}, keywords = {predictive pro fi ciency}, publisher = {Elsevier B.V.}, title = {{The practice of prediction: What can ecologists learn from applied, ecology-related fields?}}, url = {http://dx.doi.org/10.1016/j.ecocom.2016.12.005}, year = {2016} } @article{Reed2004, abstract = {Population models incorporating demographic, environmental and genetic stochasticity were created from long-term data on natural populations of 30 species of vertebrates. The probability of extinction for a single population in a continuous habitat was compared to that of multiple isolated, or semi-isolated, populations occupying a fragmented landscape with an equivalent total carrying capacity. Populations occupying a fragmented landscape were modelled for a range of dispersal rates and levels of asynchrony in the effects of environmental disturbances. Dispersal among subpopulations in the fragmented landscape partially alleviates the effect of fragmentation on extinction rates, despite the models explicitly incorporating disease epidemics which spread between subpopulations through dispersal. Even moderate environmental correlations among subpopulations greatly reduces the viability of the metapopulation relative to the case where the populations are totally independent. Whether a population performed better as a single population or as a metapopulation was strongly affected by the carrying capacity assumed, the time frame examined and the initial fitness of the population. A single population always fared better when the total habitat available was capable of supporting ≤1000 adults. Thus, continued habitat fragmentation can be expected to fuel the ongoing global extinction crisis and conservation efforts should be aimed at interconnecting isolated habitat patches.}, annote = {-argument over whether smaller, connected patches will fare better or worse than one population - develops a simple model to explore when fragmentation may be bad...strongly depends on autocorrelation between patches - includes role of environmental variability and in particular catasatophes Findings: -too small of patches are bad -disperal between patchs can reduce effect of fragmentation}, author = {Reed, David H.}, doi = {10.1017/S1367943004001313}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reed - 2004 - Extinction risk in fragmented habitats.pdf:pdf}, isbn = {1367-9430}, issn = {1367-9430}, journal = {Animal Conservation}, number = {2}, pages = {181--191}, pmid = {3087}, title = {{Extinction risk in fragmented habitats}}, url = {http://www.blackwell-synergy.com/doi/abs/10.1017/S1367943004001313}, volume = {7}, year = {2004} } @article{Poff2016, abstract = {The world's rivers are regulated by about 58,000 large dams (more than 15 m high) that provide water supplies for municipalities and irrigation, allow downstream navigation, and enable hydropower production ( 1 ). New dams are widely seen as sources of green energy. An estimated 75{\%} of the world's potential hydropower capacity is unexploited ( 2 ), and some 3700 new dams are currently proposed in developing economies ( 3 , 4 ). But dams also cause substantial and often unacknowledged environmental damage. Recent research affords insight into how dams might be strategically operated to partially restore some lost ecosystem functions and services.}, annote = {NULL}, author = {Poff, N. LeRoy and Schmidt, John C. and Kumar, A. and Zarfl, C. and Winemiller, K. O. and Poff, N. L. and Arthington, A. H. and Kennedy, T. A. and Naiman, R. J. and Olden, J. D. and Kiernan, J. D. and Pittock, J. and Hartmann, J. and Estrin, J. and Jager, H. I. and Poff, N. L.}, doi = {10.1126/science.aah4926}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Poff et al. - 2016 - How dams can go with the flow.pdf:pdf}, issn = {0036-8075}, journal = {Science}, number = {6304}, pages = {161--1100}, pmid = {27609876}, title = {{How dams can go with the flow}}, volume = {353}, year = {2016} } @article{OLeary2016, abstract = {The UN's globally adopted Convention on Biological Diversity coverage target for marine protected areas (MPAs) is ≥10{\%} by 2020. In 2014 the World Parks Congress recommended increasing this to ≥30{\%}. We reviewed 144 studies to assess whether the UN target is adequate to achieve, maximise or optimise six environmental and/or socio-economic objectives. Results consistently indicate that protecting several tens-of-percent of the sea is required to meet goals (average 37{\%}, median 35{\%}, modal group 21–30{\%}), greatly exceeding the 2.18{\%} currently protected and the 10{\%} target. The objectives we examined were met in 3{\%} of studies with ≤10{\%} MPA coverage, 44{\%} with ≤30{\%} coverage and 81{\%} with more than half the sea protected. The UN's 10{\%} target appears insufficient to protect biodiversity, preserve ecosystem services and achieve socio-economic priorities. As MPA coverages generated from theoretical studies inherently depend on scenario(s) considered, our findings do not represent explicit recommendations but rather provide perspective on policy goals. This article is protected by copyright. All rights reserved}, annote = {- should the question be what fraction of the ocean should be protected? Or what fraction should be protected given we are smart about where to put MPAs (like coastal hotspot as opposed to middle of the ocean)?}, author = {O'Leary, Bethan C. and Winther-Janson, Marit and Bainbridge, John M. and Aitken, Jemma and Hawkins, Julie P. and Roberts, Callum M.}, doi = {10.1111/conl.12247}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/O'Leary et al. - 2016 - Effective Coverage Targets for Ocean Protection.pdf:pdf}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {CBD,Conservation planning,Conservation targets,International policy,Marine protected areas}, number = {0}, pages = {1--6}, title = {{Effective Coverage Targets for Ocean Protection}}, volume = {00}, year = {2016} } @article{Barnes2016a, abstract = {SignificanceUnderstanding how social dynamics drive outcomes in environmental systems is critical to advancing global sustainability. We link comprehensive data on fishers information-sharing networks and observed fishing behaviors to demonstrate that social networks are tied to actions that can directly impact ecological health. Specifically, we find evidence that the propensity for individuals to share information primarily with others most similar to themselves creates segregated networks that impede the diffusion of sustainable behaviors--behaviors that could have mitigated the incidental catch of over 46,000 sharks in a single commercial fishery between 2008 and 2012. Our results suggest having a better understanding of social structures and bolstering effective communication across segregated networks has the potential to contribute toward more sustainable environmental outcomes. Social networks can profoundly affect human behavior, which is the primary force driving environmental change. However, empirical evidence linking microlevel social interactions to large-scale environmental outcomes has remained scarce. Here, we leverage comprehensive data on information-sharing networks among large-scale commercial tuna fishers to examine how social networks relate to shark bycatch, a global environmental issue. We demonstrate that the tendency for fishers to primarily share information within their ethnic group creates segregated networks that are strongly correlated with shark bycatch. However, some fishers share information across ethnic lines, and examinations of their bycatch rates show that network contacts are more strongly related to fishing behaviors than ethnicity. Our findings indicate that social networks are tied to actions that can directly impact marine ecosystems, and that biases toward within-group ties may impede the diffusion of sustainable behaviors. Importantly, our analysis suggests that enhanced communication channels across segregated fisher groups could have prevented the incidental catch of over 46,000 sharks between 2008 and 2012 in a single commercial fishery.}, annote = {- lack of mechanisms -NOAA have trackers on each boat Emperor penguin Uncertainty in different models (ecological and social) - even more when you combine these together When can you be predictive given high levels of uncertainty?}, author = {Barnes, Michele L. and Lynham, John and Kalberg, Kolter and Leung, PingSun}, doi = {10.1073/pnas.1523245113}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barnes et al. - 2016 - Social networks and environmental outcomes.pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {23}, pages = {6466--6471}, title = {{Social networks and environmental outcomes}}, volume = {113}, year = {2016} } @article{Rhodes2011, abstract = {Estimating temporal trends in spatially structured populations has a critical role to play in understanding regional changes in biological populations and developing management strategies. Designing effective monitoring programmes to estimate these trends requires important decisions to be made about how to allocate sampling effort among spatial replicates (i.e. number of sites) and temporal replicates (i.e. how often to survey) to minimise uncertainty in trend estimates. In particular, the optimal mix of spatial and temporal replicates is likely to depend upon the spatial and temporal correlations in population dynamics. Although there has been considerable interest in the ecological literature on understanding spatial and temporal correlations in species' population dynamics, little attention has been paid to its consequences for monitoring design. We address this issue using model-based survey design to identify the optimal allocation of sampling effort among spatial and temporal replicates for estimating population trends under different levels of spatial and temporal correlation. Based on linear trends, we show that how we should allocate sampling effort among spatial and temporal replicates depends crucially on the spatial and temporal correlations in population dynamics, environmental variation, observation error and the spatial variation in temporal trends. When spatial correlation is low and temporal correlation is high, the best option is likely to be to sample many sites infrequently, particularly when observation error and/or spatial variation in temporal trends are high. When spatial correlation is high and temporal correlation is low, the best option is likely to be to sample few sites frequently, particularly when observation error and/or spatial variation in temporal trends are low. When abundances are spatially independent, it is always preferable to maximise spatial replication. This provides important insights into how spatio-temporal monitoring programmes should be designed to estimate temporal trends in spatially structured populations.}, annote = {- explain importance of autocorrelation in determining if a monitoring program should focus on longer time series or more spatial sites for monitoring}, author = {Rhodes, Jonathan R. and Jonzen, Niclas}, doi = {10.1111/j.1600-0587.2011.06370.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rhodes, Jonzen - 2011 - Monitoring temporal trends in spatially structured populations how should sampling effort be allocated between s.pdf:pdf}, isbn = {0906-7590}, issn = {09067590}, journal = {Ecography}, number = {6}, pages = {1040--1048}, title = {{Monitoring temporal trends in spatially structured populations: how should sampling effort be allocated between space and time?}}, volume = {34}, year = {2011} } @article{Gerrodette1987, abstract = {A power analysis allows estimation of teh probability of detecting upward or downward trends in abundance using linear regression, given number of samples and estimates of sample variability and rate of change. Alternatively, the minimum number or precision of samples required to detect trends with a given degree of confidence can be computed. The results are applicable to an experimental situation in which samples are taken at regular intervals in time or space. The effects of linear and exponential change and of having sample variability be a function of abundance are investigated. Results are summarized graphically and, as an example, applied to the monitoring of the California sea otter population with aerial surveys.}, annote = {-does a nice job of explaining type I (alpha), II (beta), and power (1-beta) -looks at simple linear and exponetial models -as expected power inceases with strong trends, with more samples, and as variance decreases -also presents example of sea otters and how long of a management monitoring program would likely be needed based on some small experimentts (also examines sampling frequency)}, author = {Gerrodette, Tim}, doi = {10.2307/1939220}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gerrodette - 1987 - A power analysis for detecting trends.pdf:pdf}, isbn = {00129658}, issn = {00129658}, journal = {Ecology}, keywords = {experimental design,linear regression,power analysis,trends}, number = {5}, pages = {1364--1372}, pmid = {6467}, title = {{A power analysis for detecting trends}}, url = {http://www.jstor.org/stable/10.2307/1939220}, volume = {68}, year = {1987} } @book{Rabalais2003, abstract = {"When it rains, it pours"--or so a motorist caught in a sudden storm mnlight think while sliding into another vehicle. It is not merely the reduced visibility and the frenetic behavior of d'rvers in the rain that foster such mishaps; thesweets also are slicker just allfer the ramin begins to tfal. Why? Because the, oil and grease that are dripped, spewed. or otherwise imadvertently deposited by mi-otor vehicles onto roadways largest s and redu coo rdiniat on a nun fim are armon, tlhe first materials to, be lifted off by the rain, thereby 'literally lubricatisng the surface. Nor do mnatters end with making life miserable for rnotorists. The oil and g(rease washed off roads will most likely run into storm sewers and he dischargd into the nearest body of water From theire, the oily mnateridals often are Carried to the sea, where they c4an cause a host of environmerental problems.}, annote = {-argue that land based sources are poorly understood - Risks of disturbing mussel beds with cleanup activity after oil spill -not consensus at this time on whether to remove mussel beds or to let them recover natually}, author = {Rabalais, Nancy}, booktitle = {Issues in Science and Technology}, doi = {10.17226/10388}, isbn = {0309084385}, issn = {07485492}, number = {1}, pages = {74--78}, title = {{Oil in the Sea}}, volume = {20}, year = {2003} } @article{Seavy2007, abstract = {The ability to detect trends in population abundance is of obvious interest to wildlife managers. In recent years, the probability of detecting defined population trends has been the most common method of assessing monitoring programs. Such analyses require many assumptions, including a model for population change and a model for variance. To demonstrate potential effects of these assumptions on power analysis results, we present data for Red-tailed Tropicbirds (Phaethon rubricauda) from Tern Island, Hawaii. Depending on our assumptions, the power to detect a 50{\%} decline over 10 years varied from 80{\%} to 100{\%}. We argue that monitoring standards based upon the ability to detect population trends should be applied cautiously. As a complementary approach, we propose that monitoring standards should emphasize attributes of sampling design that increase precision (e.g., randomization, bias, and detection probability). By using standards of precision, managers can focus on the sources of variation that can be minimized. A sampling design approach to monitoring standards provides a useful complement to standards of statistical power to detect annual trends.}, annote = {- look at simple models of a bird species in which they have long term data for and then simulate trends from those models - with these simulations they are able to estimate the power to detect trends in abundance}, author = {Seavy, Nathaniel E. and Reynolds, Michelle H.}, doi = {10.1016/j.biocon.2007.08.007}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Seavy, Reynolds - 2007 - Is statistical power to detect trends a good assessment of population monitoring.pdf:pdf}, isbn = {ISSN: 0006-3207}, issn = {00063207}, journal = {Biological Conservation}, keywords = {Ecological significance,Indicator species,Monitoring standards,Phaethon rubricauda,Red-tailed Tropicbird,Sampling design,Seabird conservation}, number = {1-2}, pages = {187--191}, title = {{Is statistical power to detect trends a good assessment of population monitoring?}}, volume = {140}, year = {2007} } @article{McDonald-Madden2010, abstract = {The gross under-resourcing of conservation endeavours has placed an increasing emphasis on spending accountability. Increased accountability has led to monitoring forming a central element of conservation programs. Although there is little doubt that information obtained from monitoring can improve management of biodiversity, the cost (in time and/or money) of gaining this knowledge is rarely considered when making decisions about allocation of resources to monitoring. We present a simple framework allowing managers and policy advisors to make decisions about when to invest in monitoring to improve management. ?? 2010 Elsevier Ltd.}, author = {McDonald-Madden, Eve and Baxter, Peter W J and Fuller, Richard A. and Martin, Tara G. and Game, Edward T. and Montambault, Jensen and Possingham, Hugh P.}, doi = {10.1016/j.tree.2010.07.002}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McDonald-Madden et al. - 2010 - Monitoring does not always count.pdf:pdf}, isbn = {0169-5347}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {10}, pages = {547--550}, pmid = {20727614}, title = {{Monitoring does not always count}}, volume = {25}, year = {2010} } @article{Ramseur2012, annote = {For a complete list see the USCG Oil Spill Compendium at https://homeport.uscg.mil (click on “Investigations”).}, author = {Ramseur, Jonathan L}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ramseur - 2012 - Oil Spills in U . S . Coastal Waters Background and Governance.pdf:pdf}, journal = {CRS Report for Congress}, pages = {1--28}, title = {{Oil Spills in U . S . Coastal Waters : Background and Governance}}, year = {2012} } @article{Porszt2012, abstract = {Although there are many indicators of endangerment (i.e., whether populations or species meet criteria that justify conservation action), their reliability has rarely been tested. Such indicators may fail to identify that a population or species meets criteria for conservation action (false negative) or may incorrectly show that such criteria have been met (false positive). To quantify the rate of both types of error for 20 commonly used indicators of declining abundance (threat indicators), we used receiver operating characteristic curves derived from historical (1938-2007) data for 18 sockeye salmon (Oncorhynchus nerka) populations in the Fraser River, British Columbia, Canada. We retrospectively determined each population's yearly status (reflected by change in abundance over time) on the basis of each indicator. We then compared that population's status in a given year with the status in subsequent years (determined by the magnitude of decline in abundance across those years). For each sockeye population, we calculated how often each indicator of past status matched subsequent status. No single threat indicator provided error-free estimates of status, but indicators that reflected the extent (i.e., magnitude) of past decline in abundance (through comparison of current abundance with some historical baseline abundance) tended to better reflect status in subsequent years than the rate of decline over the previous 3 generations (a widely used indicator). We recommend that when possible, the reliability of various threat indicators be evaluated with empirical analyses before such indicators are used to determine the need for conservation action. These indicators should include estimates from the entire data set to take into account a historical baseline.}, annote = {-use longterm data on 18 populations of sockeye salmon to determine how well different metrics of populatin decline perform -make argumetn that you should use all available data, not just most recent 3 generations}, author = {Porszt, Erin J. and Peterman, Randall M. and Dulvy, Nicholas K. and Cooper, Andrew B. and Irvine, James R.}, doi = {10.1111/j.1523-1739.2012.01882.x}, isbn = {1523-1739}, issn = {08888892}, journal = {Conservation Biology}, keywords = {COSEWIC,IUCN,Receiver operating characteristic (ROC),Sockeye salmon,Threat indicators}, number = {5}, pages = {894--904}, pmid = {22741815}, title = {{Reliability of Indicators of Decline in Abundance}}, volume = {26}, year = {2012} } @article{DEon-Eggertson2015, abstract = {Assessments of extinction risk based on population declines are widely used, yet scientists have little quantitative understanding of their reliability. Incorrectly classifying whether a population is declining or not can lead to inappropriate conservation actions or management measures, with potentially profound societal costs. Here we evaluate key causes of misclassification of decline status and assess the reliability of 20 decline metrics using a stochastic model to simulate time series of population abundance of sockeye salmon (Oncorhynchus nerka). We show that between-year variability in population productivity (process variation) and, to a lesser extent, variability in abundance estimates (observation error) are important causes of unreliable identification of population status. We found that using all available data, rather than just the most recent three generations, consistently improved the reliability of risk assessments. The approach outlined here can improve understanding of the reliability of risk assessments, thereby reducing concerns that may impede their use for exploited taxa such as marine fishes. This article is protected by copyright. All rights reserved.}, annote = {-simulate population dynamics of salmon to identify how well indicators of population change do in different scenarios of population variability, autocorrelation, etc...}, author = {D'Eon-Eggertson, Faye and Dulvy, Nicholas K. and Peterman, Randall M.}, doi = {10.1111/conl.12123}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/D'Eon-Eggertson, Dulvy, Peterman - 2015 - Reliable Identification of Declining Populations in an Uncertain World.pdf:pdf}, isbn = {1755-263X}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Decline indicators,Error rates,Extinction-risk assessment,IUCN,Monte Carlo simulation,Observation error,Process variation}, number = {2}, pages = {86--96}, title = {{Reliable Identification of Declining Populations in an Uncertain World}}, volume = {8}, year = {2015} } @article{Wilson2011, abstract = {Classifying species according to their risk of extinction is a common practice and underpins much conservation activity. The reliability of such classifications rests on the accuracy of threat categorizations, but very little is known about the magnitude and types of errors that might be expected. The process of risk classification involves combining information from many sources, and understanding the quality of each source is critical to evaluating the overall status of the species. One common criterion used to classify extinction risk is a decline in abundance. Because abundance is a direct measure of conservation status, counts of individuals are generally the preferred method of evaluating whether populations are declining. Using the thresholds from criterion A of the International Union for Conservation of Nature (IUCN) Red List (critically endangered, decline in abundance of {\textgreater}80{\%} over 10 years or 3 generations; endangered, decline in abundance of 50-80{\%}; vulnerable, decline in abundance of 30-50{\%}; least concern or near threatened, decline in abundance of 0-30{\%}), we assessed 3 methods used to detect declines solely from estimates of abundance: use of just 2 estimates of abundance; use of linear regression on a time series of abundance; and use of state-space models on a time series of abundance. We generated simulation data from empirical estimates of the typical variability in abundance and assessed the 3 methods for classification errors. The estimates of the proportion of falsely detected declines for linear regression and the state-space models were low (maximum 3-14{\%}), but 33-75{\%} of small declines (30-50{\%} over 15 years) were not detected. Ignoring uncertainty in estimates of abundance (with just 2 estimates of abundance) allowed more power to detect small declines (95{\%}), but there was a high percentage (50{\%}) of false detections. For all 3 methods, the proportion of declines estimated to be {\textgreater}80{\%} was higher than the true proportion. Use of abundance data to detect species at risk of extinction may either fail to detect initial declines in abundance or have a high error rate.}, annote = {- use simulatino methods to look at reliability of various IUCN criteria -point out that linear regression (as opposed to state space models) ignores uncertainty in estimates of abundance -simulate using stochastic Gompertz model}, author = {Wilson, Howard B. and Kendall, Bruce E. and Possingham, Hugh P.}, doi = {10.1111/j.1523-1739.2011.01671.x}, isbn = {1523-1739 (Electronic)$\backslash$r0888-8892 (Linking)}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Declinaci??n poblacional,IUCN,Lista roja,Modelo estado-espacio,Population decline,Red list,Series de tiempo,State-space model,Time series,Variabilidad,Variability}, number = {4}, pages = {747--757}, pmid = {21480994}, title = {{Variability in Population Abundance and the Classification of Extinction Risk}}, volume = {25}, year = {2011} } @article{Legg2006, annote = {type I - prob of rejecting a true null hypothesis (alpha =0.05) type II - prob of not rejecting a false null hypothesis power (1-beta) = prob of rejecting null hypothesis when it is false This article briefly discusses the need to have been monitoring and survey design. They focus on power and how it can be increased. They stress that if adequate power cannot be met, it may be inappropriate to conduct an experiment or monitor as it may imply a false sense of security that something is actively being done.}, author = {Legg, Colin J and Nagy, Laszlo}, doi = {10.1016/j.jenvman.2005.04.016}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Legg, Nagy - 2006 - Why most conservation monitoring is, but need not be, a waste of time.pdf:pdf}, journal = {Journal of Environmental Management}, keywords = {1,conservation management,maintain the status quo,management are either to,monitoring,objectives of monitoring,or to manipulate the,power analysis,statistical design,system to,the aims of conservation}, pages = {194--199}, title = {{Why most conservation monitoring is, but need not be, a waste of time}}, volume = {78}, year = {2006} } @article{Makridakis2009, annote = {ubiased estimator only means that average error is zero}, author = {Makridakis, Spyros and Taleb, Nassim}, doi = {10.1016/j.ijforecast.2009.05.013}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Makridakis, Taleb - 2009 - Decision making and planning under low levels of predictability.pdf:pdf}, issn = {0169-2070}, journal = {International Journal of Forecasting}, keywords = {accuracy,forecasting,judgmental predictions,low level predictability,non-normal forecasting errors,uncertainty}, number = {4}, pages = {716--733}, publisher = {Elsevier B.V.}, title = {{Decision making and planning under low levels of predictability}}, url = {http://dx.doi.org/10.1016/j.ijforecast.2009.05.013}, volume = {25}, year = {2009} } @article{Cohen1992, abstract = {One possible reason for the continued neglect of statistical power analysis in research in the behavioral sciences is the inaccessibility of or difficulty with the standard material. A convenient, although not comprehensive, presentation of required sample sizes is provided here. Effect-size indexes and conventional values for these are given for operationally defined small, medium, and large effects. The sample sizes necessary for .80 power to detect effects at these levels are tabled for eight standard statistical tests: (a) the difference between independent means, (b) the significance of a product-moment correlation, (c) the difference between independent rs, (d) the sign test, (e) the difference between independent proportions, (f) chi-square tests for goodness of fit and contingency tables, (g) one-way analysis of variance, and (h) the significance of a multiple or multiple partial correlation.}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Cohen, Jacob}, doi = {10.1037/0033-2909.112.1.155}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cohen - 1992 - A power primer.pdf:pdf}, isbn = {1-55798-958-3}, issn = {0033-2909}, journal = {Psychological Bulletin}, keywords = {statistical power analysis {\&} effect size indexes {\&}}, number = {1}, pages = {155--159}, pmid = {19565683}, title = {{A power primer}}, url = {http://doi.apa.org/getdoi.cfm?doi=10.1037/0033-2909.112.1.155}, volume = {112}, year = {1992} } @article{Rueda-Cediel2015, annote = {They studied how simulated matrix models with varoius sources of error, stochasticity, and time series lengths would perform in estimating projected population declines - number of assumptions in population model, need to either relax assumptions or use real data - found that time series length did not have a major role after 10-15 years of sampling QUestions: - do percent decline estimations lead to over or under protection? And by how much?}, author = {Rueda-Cediel, Pamela and Anderson, Kurt E and Regan, Tracey J and Franklin, Janet and Regan, M}, doi = {10.1371/journal.pone.0132255}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rueda-Cediel et al. - 2015 - Combined influences of model choice, data quality, and data quantity when estimating population trends.pdf:pdf}, journal = {PLoSONE}, number = {7}, pages = {e0132255}, title = {{Combined influences of model choice, data quality, and data quantity when estimating population trends}}, volume = {10}, year = {2015} } @article{Magurran2010, annote = {- simulate scalar and matrix pop models of a snail species to investigate IUCN criteria effectiveness - did not find that time series length was all that important after only 10-15 years of data was collected (however they assime simple life histories with short generational times and uncorrelated noise)}, author = {Magurran, Anne E and Baillie, Stephen R and Buckland, Stephen T and Dick, Jan Mcp and Elston, David A and Scott, E Marian and Smith, Rognvald I and Somerfield, Paul J and Watt, Allan D}, doi = {10.1016/j.tree.2010.06.016}, journal = {Trends in Ecology and Evolution}, pages = {574--582}, title = {{Long-term datasets in biodiversity research and monitoring : assessing change in ecological communities through time}}, volume = {25}, year = {2010} } @article{Johnson2015, abstract = {* ‘Will my study answer my research question?' is the most fundamental question a researcher can ask when designing a study, yet when phrased in statistical terms – ‘What is the power of my study?' or ‘How precise will my parameter estimate be?' – few researchers in ecology and evolution (EE) try to answer it, despite the detrimental consequences of performing under- or over-powered research. We suggest that this reluctance is due in large part to the unsuitability of simple methods of power analysis (broadly defined as any attempt to quantify prospectively the ‘informativeness' of a study) for the complex models commonly used in EE research. With the aim of encouraging the use of power analysis, we present simulation from generalized linear mixed models (GLMMs) as a flexible and accessible approach to power analysis that can account for random effects, overdispersion and diverse response distributions. * We illustrate the benefits of simulation-based power analysis in two research scenarios: estimating the precision of a survey to estimate tick burdens on grouse chicks and estimating the power of a trial to compare the efficacy of insecticide-treated nets in malaria mosquito control. We provide a freely available R function, sim.glmm, for simulating from GLMMs. * Analysis of simulated data revealed that the effects of accounting for realistic levels of random effects and overdispersion on power and precision estimates were substantial, with correspondingly severe implications for study design in the form of up to fivefold increases in sampling effort. We also show the utility of simulations for identifying scenarios where GLMM-fitting methods can perform poorly. * These results illustrate the inadequacy of standard analytical power analysis methods and the flexibility of simulation-based power analysis for GLMMs. The wider use of these methods should contribute to improving the quality of study design in EE.}, annote = {power - probability of rejecting the null when it is indeed false (1 - typeII error rate)}, author = {Johnson, Paul CD and Barry, Sarah JE and Ferguson, Heather M and M{\"{u}}ller, Pie}, doi = {10.1111/2041-210X.12306}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Johnson et al. - 2015 - Power analysis for generalized linear mixed models in ecology and evolution.pdf:pdf}, isbn = {2041-210X}, issn = {2041210X}, journal = {Methods in Ecology and Evolution}, keywords = {Experimental design,Generalized linear mixed model,Long-lasting insecticidal net,Overdispersion,Precision,Random effects,Sample size,Simulation}, number = {2}, pages = {133--142}, pmid = {25893088}, title = {{Power analysis for generalized linear mixed models in ecology and evolution}}, volume = {6}, year = {2015} } @article{Levin2008, annote = {engineering resilience- rate at which system returns to equilbrium ecological resilience - amount of change or disruption required to move system from one state to another robustness - ability of system to recover}, author = {Levin, Simon A and Lubchenco, Jane}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levin, Lubchenco - 2008 - Marine Ecosystem-based Management.pdf:pdf}, journal = {BioScience}, keywords = {complex adaptive systems,ecosystem management,resilience,robustness,scale}, number = {1}, pages = {1--7}, title = {{Marine Ecosystem-based Management}}, volume = {58}, year = {2008} } @article{Lynham2017, annote = {- this paper explores how unfavorable regimes can be locked in by positive feedback created by the stakeholder participation process - if costs are high for stakeholders you will only here extreme views represented, this is well supported by more general models and political science -provide example of how less people now believe in government in the US - reference papers that lloked at public perceptions of MPA establishment (e.g. people often thought more of oean was protected than seen in reality) - MPAs with weak support, but low variance in support, may be more likely to be implemented than the high variance scenario - 2 examples: -- otter-kelp dynamics in Pacific -- Gulf of Maine lobster fishery recommendations to reduce particpation costs: 1) decnetralize decision making, embrace new technologies, engage all stakeholders, improve planning documents, encourage diagloue}, author = {Lynham, J. and Halpern, B.S. and Blenckner, T. and Essington, T. and Estes, J. and Hunsicker, M. and Kappel, C. and Salomon, A.K. and Scarborough, C. and Selkoe, K.A. and Stier, A.}, doi = {10.1016/j.marpol.2016.11.011}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lynham et al. - 2017 - Costly stakeholder participation creates inertia in marine ecosystems.pdf:pdf}, issn = {0308597X}, journal = {Marine Policy}, keywords = {Critical transition,Hysteresis,Non-linear,Regime shifts,Restoration ecology,Stakeholder engagement,Stakeholder participation,Threshold,Tipping points}, number = {October 2015}, pages = {122--129}, publisher = {Elsevier}, title = {{Costly stakeholder participation creates inertia in marine ecosystems}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0308597X16307199}, volume = {76}, year = {2017} } @article{Smith2010, abstract = {The creation of marine reserves is often controversial. For decisionmakers, trying to find compromises, an understanding of the timing, magnitude, and incidence of the costs of a reserve is critical. Understanding the costs, in turn, requires consideration of not just the direct financial costs but also the opportunity costs associated with reserves. We use a discrete choice model of commercial fishermen's behavior to examine both the short-run and long-run opportunity costs of marine reserves. Our results can help policymakers recognize the factors influencing commercial fishermen's responses to reserve proposals. More generally, we highlight the potential drivers behind the political economy of marine reserves.}, annote = {- argue that you must include opportunity costs of fisherman to determine if they are likely to accept marine reserves - alternative careers need to be available, need to have healthy fish stock, distance from port to fishing area should be short to increase acceptance of marine reserves}, author = {Smith, Martin D and Lynham, John and Sanchirico, James N and Wilson, James a}, doi = {10.1073/pnas.0907365107}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith et al. - 2010 - Political economy of marine reserves understanding the role of opportunity costs.pdf:pdf}, isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {43}, pages = {18300--18305}, pmid = {20133732}, title = {{Political economy of marine reserves: understanding the role of opportunity costs}}, volume = {107}, year = {2010} } @article{White2013, abstract = {Implementation of no-take marine reserves is typically followed by monitoring to ensure that a reserve meets its intended goal, such as increasing the abundance of fished species. The factors affecting whether abundance will increase within a reserve are well characterized; however, those results are based on long-term equilibria of population models. Here we use age-structured models of a generic fish population to analyze the short-term transient response. We show that it may take decades for a fished population to reach postreserve equilibrium. In the meantime, short-term transient dynamics dominate. During the transient phase, population abundance could either remain unchanged, decrease, or exhibit single-generation oscillations, regardless of the eventual long-term result. Such transient dynamics are longer and more oscillatory for populations with heavier fishing, older ages at maturity, lower natural mortality rates, and lower larval connectivity. We provide metrics based on demographic data to describe the important characteristics of these postreserve transient dynamics.}, annote = {-need to look at transient dynamics as they may dominate for decades - longer and more oscillarotry responses for pops that experience heavier fishing, have old age of maturitiy, low natural mortality rates, and lower larval connectivity - look at open (recruitment only from outside reserve) vs closed population (no recruitment from other populations) notes from Botsford lecture: -many measures of transient dynamics - use models to simulate population of rockfish being fished and then for fishing to be set to 0 - responses more evident for fished age classes, when maturity was later, and for populations previously exposed to high levels of fishing -stochastic transient responses??}, author = {White, J. Wilson and Botsford, Louis W. and Hastings, Alan and Baskett, Marissa L. and Kaplan, David M. and Barnett, Lewis A K}, doi = {10.1111/j.1755-263X.2012.00295.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2013 - Transient responses of fished populations to marine reserve establishment.pdf:pdf}, isbn = {1755-263X}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Age structure,Linear population model,Marine reserves,Overfishing,Transient dynamics}, number = {3}, pages = {180--191}, title = {{Transient responses of fished populations to marine reserve establishment}}, volume = {6}, year = {2013} } @article{Harvell2009, annote = {- short review of how host characteristics may determine host-pathogen interactions in face of climate change - provide examples of warming and disease for California abalones, east coast osysters (pathogen range shift), coral reefs in Caribbean (weaker seasonal pattern in disease now) - do pathogen distrubtions change b/c of change in growth rates, transmission, virulence, or host immunity? -talk a lot about animal movements where animals no longer migrate which can increase disease risk (e.g. longest distance migrating Monarch butterflies had lowest disease risk) -would Yang and Rudolf approach be useful for pathogen work? how do different parasite species on a single host respond differently over time? -integrating models across scales (pika model and steve snowmelt model)}, author = {Harvell, Drew and Altizer, Sonia and Cattadori, Isabella M and Harrington, Laura and Weil, Ernesto}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Harvell et al. - 2009 - Climate Change and Wildlife Diseases When Does the Host Matter the Most.pdf:pdf}, journal = {Ecology}, number = {4}, pages = {912--920}, title = {{Climate Change and Wildlife Diseases: When Does the Host Matter the Most?}}, volume = {90}, year = {2009} } @article{Poloczanska2013, abstract = {Past meta-analyses of the response of marine organisms to climate change have examined a limited range of locations(1,2), taxonomic groups(2-4) and/or biological responses(5,6). This has precluded a robust overview of the effect of climate change in the global ocean. Here, we synthesized all available studies of the consistency of marine ecological observations with expectations under climate change. This yielded a meta-database of 1,735 marine biological responses for which either regional or global climate change was considered as a driver. Included were instances of marine taxa responding as expected, in a manner inconsistent with expectations, and taxa demonstrating no response. From this database, 81-83{\%} of all observations for distribution, phenology, community composition, abundance, demography and calcification across taxa and ocean basins were consistent with the expected impacts of climate change. Of the species responding to climate change, rates of distribution shifts were, on average, consistent with those required to track ocean surface temperature changes. Conversely, we did not find a relationship between regional shifts in spring phenology and the seasonality of temperature. Rates of observed shifts in species' distributions and phenology are comparable to, or greater, than those for terrestrial systems.}, annote = {- looked at large number of responses by marine organims to climate change including distribution, phenology, abundance, community change, calcification, and demography - range shifts were order of magnitude faster compared to terrestrial species -phenology advanced for marine species, especially for phytoplankton}, author = {Poloczanska, E S and Brown, C J and Sydeman, W J and Kiessling, W and Schoeman, D S and Moore, P J and Brander, K and Bruno, J F and Buckley, L B and Burrows, M T and Duarte, C M and Halpern, B S and Holding, J and Kappel, C V and O'Connor, M I and Pandolfi, J M and Parmesan, C and Schwing, F and Thompson, S A and Richardson, A J}, doi = {Doi 10.1038/Nclimate1958}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Poloczanska et al. - 2013 - Global imprint of climate change on marine life.pdf:pdf}, isbn = {1758-678X}, issn = {1758-678X}, journal = {Nature Climate Change}, keywords = {range shifts change impacts ecosystems attribution}, number = {August}, pages = {919--925}, title = {{Global imprint of climate change on marine life}}, url = {internal-pdf://209.126.227.87/Poloczanska-2013-Global imprint of cl.pdf{\%}5Cn{\%}3CGo to ISI{\%}3E://WOS:000326818800020 http://www.nature.com/nclimate/journal/v3/n10/pdf/nclimate1958.pdf}, volume = {3}, year = {2013} } @article{Lauck1998, abstract = {Overexploitation of marine fisheries remains a serious problem worldwide, even for many fisheries that have been intensively managed by coastal nations. Many factors have contributed to these system failures, Here we discuss the implications of persistent, irreducible scientific uncertainty pertaining to marine ecosystems. When combined with typical levels of uncontrollability of catches and incidental mortality, this uncertainty probably implies that traditional approaches to fisheries management will be persistently unsuccessful. We propose the use of large-scale protected areas (marine reserves) as major components of future management programs, Protected areas can serve as a hedge against inevitable management limitations, thus greatly enhancing the long-term sustainable exploitation of fishery resources. Marine reserves would also provide an escape from the need of ever more detailed and expensive stock assessments and would be invaluable in the rehabilitation of depleted stocks.}, annote = {-using simple model and empirical examples to argue for the use of MPAs as - discuss how many uncertainties make fisheries predictions difficult: environmental, measurement - view need do do bet hedging in fisheries - use logistic (Ricker) model to examine uncertain harvests - refer to Novaczek (1995) that lists eight advantages of MPAs}, author = {Lauck, T and Clark, C W and Mangel, M and Munro, G R}, doi = {10.2307/2641364}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lauck et al. - 1998 - Implementing the precautionary principle in fisheries management through marine reserves.pdf:pdf}, isbn = {1051-0761}, issn = {1051-0761}, journal = {Ecological Applications}, keywords = {bet hedging,controlling overexploitation,diversification,fisheries,irreducible scientific uncertainty,marine protected areas,marine reserves,precautionary principle in fisheries,risk aversion}, number = {1}, pages = {S72--S78}, pmid = {2704792949163754128}, title = {{Implementing the precautionary principle in fisheries management through marine reserves}}, volume = {8}, year = {1998} } @article{Kuhnert2010, abstract = {Expert knowledge in ecology is gaining momentum as a tool for conservation decision-making where data are lacking. Yet, little information is available to help a researcher decide whether expert opinion is useful for their model, how an elicitation should be conducted, what the most relevant method for elicitation is and how this can be translated into prior distributions for analysis in a Bayesian model. In this study, we provide guidance in using expert knowledge in a transparent and credible manner to inform ecological models and ultimately natural resource and conservation decision-making. We illustrate the decisions faced when considering the use of expert knowledge in a model with the help of two real ecological case studies. These examples are explored further to examine the impact of expert knowledge through ‘priors' in Bayesian modeling and specifically how to minimize potential bias. Finally, we make recommendations on the use of expert opinion in ecology. We believe if expert knowledge is elicited and incorporated into ecological models with the same level of rigour provided in the collection and use of empirical data, expert knowledge can increase the precision of models and facilitate informed decision-making in a cost-effective manner.}, annote = {- this paper lays out how to elicient expert knowledge and then use in in a Bayesian framework, the prior in from the expert knowledge -Bayesina modeling involves prior, data on parameters through likelihood, a model of underlying prrocess, and posteriror estimates - summarize eight different ways to obtain expert information (probability, frequency, interval, distribution) - point out important of different bias (overconfidence, representativness, anchoring, misundersntading of conditional probabilities, hindsight bias, law of small numbers) -look at two exaples: livestock grazing and gillnet fisheries}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Kuhnert, Petra M. and Martin, Tara G. and Griffiths, Shane P.}, doi = {10.1111/j.1461-0248.2010.01477.x}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kuhnert, Martin, Griffiths - 2010 - A guide to eliciting and using expert knowledge in Bayesian ecological models.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Bayesian models,Bias,Decision-making,Expert judgement,Expert opinion,Prior information}, number = {7}, pages = {900--914}, pmid = {20497209}, title = {{A guide to eliciting and using expert knowledge in Bayesian ecological models}}, volume = {13}, year = {2010} } @article{Stafford2015, abstract = {In the marine environment, humans exploit natural ecosystems for food and economic benefit. Challenging policy goals have been set to protect resources, species, communities and habitats, yet ecologists often have sparse data on interactions occurring in the system to assess policy outcomes. This paper presents a technique, loosely based on Bayesian Belief Networks, to create simple models which 1) predict whether individual species within a community will decline or increase in population size, 2) encapsulate uncertainty in the predictions in an intuitive manner and 3) require limited knowledge of the ecosystem and functional parameters required to model it. We develop our model for a UK rocky shore community, to utilise existing knowledge of species interactions for model validation purposes. However, we also test the role of expert opinion, without full scientific knowledge of species interactions, by asking non-UK based marine scientists to derive parameters for the model (non-UK scientists are not familiar with the exact communities being described and will need to extrapolate from existing knowledge in a similar manner to model a poorly studied system). We find these differ little from the parameters derived by ourselves and make little difference to the final model predictions. We also test our model against simple experimental manipulations, and find that the most important changes in community structure as a result of manipulations correspond well to the model predictions with both our, and non-UK expert parameterisation. The simplicity of the model, nature of the outputs, and the user-friendly interface makes it potentially suitable for policy, conservation and management work on multispecies interactions in a wide range of marine ecosystems.}, annote = {- this paper looks at how Bayesian Belief Networks can be used to study systems which include species interactions -show that expert opinion can be a good substitute for more detailed data and may affect the results similarly -rocky intertidal in UK}, author = {Stafford, Richard and Williams, Rachel L. and Herbert, Roger J H}, doi = {10.1016/j.ocecoaman.2015.04.013}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stafford, Williams, Herbert - 2015 - Simple, policy friendly, ecological interaction models from uncertain data and expert opinion.pdf:pdf}, isbn = {0964-5691}, issn = {09645691}, journal = {Ocean and Coastal Management}, keywords = {Bayesian belief network,Conservation,Fisheries,Marine management,Predictive model,Rocky shore,Sparse data}, pages = {88--96}, publisher = {Elsevier Ltd}, title = {{Simple, policy friendly, ecological interaction models from uncertain data and expert opinion}}, url = {http://dx.doi.org/10.1016/j.ocecoaman.2015.04.013}, volume = {118}, year = {2015} } @article{Linkov2006, abstract = {Environmental risk assessment and decision-making strategies over the last several decades have become increasingly more sophisticated, information-intensive, and complex, including such approaches as expert judgment, cost-benefit analysis, and toxicological risk assessment. One tool that has been used to support environmental decision-making is comparative risk assessment (CRA), but CRA lacks a structured method for arriving at an optimal project alternative. Multi-criteria decision analysis (MCDA) provides better-supported techniques for the comparison of project alternatives based on decision matrices, and it also provides structured methods for the incorporation of project stakeholders' opinions in the ranking of alternatives. We argue that the inherent uncertainty in our ability to predict ecosystem evolution and response to different management policies requires shifting from optimization-based management to an adaptive management paradigm. This paper brings together a multidisciplinary review of existing decision-making approaches at regulatory agencies in the United States and Europe and synthesizes state-of-the-art research in CRA, MCDA, and adaptive management methods applicable to environmental remediation and restoration projects. We propose a basic decision analytic framework that couples MCDA with adaptive management and its public participation and stakeholder value elicitation methods, and we demonstrate application of the framework to a realistic case study based on contaminated sediment management issues in the New York/New Jersey Harbor. ?? 2006 Elsevier Ltd. All rights reserved.}, annote = {- most of this paper was a bit rought to get through - mostly describe how multi-criteria decision analysis (MCDA) -also argue that inheret uncertainies in our systems require adaptive management, instead of optimization, approach - provide examples from water management in New Jersey}, author = {Linkov, I. and Satterstrom, F. K. and Kiker, G. and Batchelor, C. and Bridges, T. and Ferguson, E.}, doi = {10.1016/j.envint.2006.06.013}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Linkov et al. - 2006 - From comparative risk assessment to multi-criteria decision analysis and adaptive management Recent developments.pdf:pdf}, isbn = {0160-4120 (Print)$\backslash$n0160-4120 (Linking)}, issn = {01604120}, journal = {Environment International}, keywords = {Adaptive management,Comparative risk assessment,Decision analysis,Risk analysis,Sediments}, number = {8}, pages = {1072--1093}, pmid = {16905190}, title = {{From comparative risk assessment to multi-criteria decision analysis and adaptive management: Recent developments and applications}}, volume = {32}, year = {2006} } @article{Donlan2010, abstract = {Little is known about how specific anthropogenic hazards affect the biology of organisms. Quantifying the effect of regional hazards is particularly challenging for species such as sea turtles because they are migratory, difficult to study, long lived, and face multiple anthropogenic threats. Expert elicitation, a technique used to synthesize opinions of experts while assessing uncertainty around those views, has been in use for several decades in the social science and risk assessment sectors. We conducted an internet-based survey to quantify expert opinion on the relative magnitude of anthropogenic hazards to sea turtle populations at the regional level. Fisheries bycatch and coastal development were most often ranked as the top hazards to sea turtle species in a geographic region. Nest predation and direct take followed as the second and third greatest threats, respectively. Survey results suggest most experts believe sea turtles are threatened by multiple factors, including substantial at-sea threats such as fisheries bycatch. Resources invested by the sea turtle community, however, appear biased toward terrestrial-based impacts. Results from the survey are useful for conservation planning because they provide estimates of relative impacts of hazards on sea turtles and a measure of consensus on the magnitude of those impacts among researchers and practitioners. Our survey results also revealed patterns of expert bias, which we controlled for in our analysis. Respondents with no experience with respect to a sea turtle species tended to rank hazards affecting that sea turtle species higher than respondents with experience. A more-striking pattern was with hazard-based expertise: the more experience a respondent had with a specific hazard, the higher the respondent scored the impact of that hazard on sea turtle populations. Bias-controlled expert opinion surveys focused on threatened species and their hazards can help guide and expedite species recovery plans.}, annote = {- this paper elicitated expert opinion on threats to turtles - emphasize importance of regional scale assessments as that is where management is done - not suprisingluy, fisheries bycatch and coastal development were ranked the most important - interestingly, they found that experts with more knowledge in a particular threat (e.g. fisheries bycatch) also rated those threats as more important - less experienced respondants tended to overrank certain threats}, author = {Donlan, C. Josh and Wingfield, Dana K. and Crowder, Larry B. and Wilcox, Chris}, doi = {10.1111/j.1523-1739.2010.01541.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Donlan et al. - 2010 - Using expert opinion surveys to rank threats to endangered species A case study with sea turtles.pdf:pdf}, isbn = {1523-1739}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Conservation planning,Expert bias,Expert elicitation,Prioritization,Species recovery,Threat assessment}, number = {6}, pages = {1586--1595}, pmid = {20575987}, title = {{Using expert opinion surveys to rank threats to endangered species: A case study with sea turtles}}, volume = {24}, year = {2010} } @article{Thackeray2016, abstract = {Differences in phenological responses to climate change among species can desynchronise ecological interactions and thereby threaten ecosystem function. To assess these threats, we must quantify the relative impact of climate change on species at different trophic levels. Here, we apply a Climate Sensitivity Profile approach to 10,003 terrestrial and aquatic phenological data sets, spatially matched to temperature and precipitation data, to quantify variation in climate sensitivity. The direction, magnitude and timing of climate sensitivity varied markedly among organisms within taxonomic and trophic groups. Despite this variability, we detected systematic variation in the direction and magnitude of phenological climate sensitivity. Secondary consumers showed consistently lower climate sensitivity than other groups. We used mid-century climate change projections to estimate that the timing of phenological events could change more for primary consumers than for species in other trophic levels (6.2 versus 2.5–2.9 days earlier on average), with substantial taxonomic variation (1.1–14.8 days earlier on average).}, annote = {- use species phenology data and local measures of temperature and precipitation in the UK - primary consumers and crustacea are expected to advance their timing the most. Phytoplankton is expected to advance timing very little (a bit different then suggested in other paper) - phytoplankton also had greatest variability in phenological advancement}, author = {Thackeray, Stephen J. and Henrys, Peter A. and Hemming, Deborah and Bell, James R. and Botham, Marc S. and Burthe, Sarah and Helaouet, Pierre and Johns, David G. and Jones, Ian D. and Leech, David I. and Mackay, Eleanor B. and Massimino, Dario and Atkinson, Sian and Bacon, Philip J. and Brereton, Tom M. and Carvalho, Laurence and Clutton-Brock, Tim H. and Duck, Callan and Edwards, Martin and Elliott, J. Malcolm and Hall, Stephen J. G. and Harrington, Richard and Pearce-Higgins, James W. and H{\o}ye, Toke T. and Kruuk, Loeske E. B. and Pemberton, Josephine M. and Sparks, Tim H. and Thompson, Paul M. and White, Ian and Winfield, Ian J. and Wanless, Sarah}, doi = {10.1038/nature18608}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thackeray et al. - 2016 - Phenological sensitivity to climate across taxa and trophic levels.pdf:pdf}, isbn = {0028-0836}, issn = {0028-0836}, journal = {Nature}, number = {7611}, pages = {241--245}, pmid = {27362222}, publisher = {Nature Publishing Group}, title = {{Phenological sensitivity to climate across taxa and trophic levels}}, url = {http://www.nature.com/doifinder/10.1038/nature18608}, volume = {535}, year = {2016} } @article{Klein2013, abstract = {We present a novel method for designing marine reserves that trades off three important attributes of a conservation plan: habitat condition, habitat representation, and socioeconomic costs. We calculated habitat condition in four ways, using different human impacts as a proxy for condition: all impacts; impacts that cannot be managed with a reserve; land-based impacts; and climate change impacts. We demonstrate our approach in California, where three important tradeoffs emerged. First, reserve systems that have a high chance of protecting good condition habitats cost fishers less than 3.1{\%} of their income. Second, cost to fishers can be reduced by 1/2–2/3 by triaging less than 1/3 of habitats. Finally, increasing the probability of protecting good condition habitats from 50{\%} to 99{\%} costs fishers an additional 1.7{\%} of their income, with roughly 0.3{\%} added costs for each additional 10{\%} confidence. Knowing exactly what the cost of these tradeoffs are informs discussion and potential compromise among stakeholders involved in protected area planning worldwide.}, annote = {- use Marxan type model to all for several important MPA planning components: habitat condition, habitat representation, and socioeconomic costs - apply model to California where several tradeoffs emerged - include human impacats that can not be properly handled with marine reserves - protected good habitat required loss in income for fishermen, but these lossess could be small}, author = {Klein, Carissa J. and Tulloch, Vivitskaia J. and Halpern, Benjamin S. and Selkoe, Kimberly A. and Watts, Matthew E. and Steinback, Charles and Scholz, Astrid and Possingham, Hugh P.}, doi = {10.1111/conl.12005}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Klein et al. - 2013 - Tradeoffs in marine reserve design Habitat condition, representation, and socioeconomic costs.pdf:pdf}, isbn = {1755-263X}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Climate change,Conservation planning,Cumulative human impact,Land-sea planning,Marine protected area,Marxan,Spatial conservation prioritization}, number = {5}, pages = {324--332}, title = {{Tradeoffs in marine reserve design: Habitat condition, representation, and socioeconomic costs}}, volume = {6}, year = {2013} } @article{Ibanez2010, abstract = {As a consequence of warming temperatures around the world, spring and autumn phenologies have been shifting, with corresponding changes in the length of the growing season. Our understanding of the spatial and interspecific variation of these changes, however, is limited. Not all species are responding similarly, and there is significant spatial variation in responses even within species. This spatial and interspecific variation complicates efforts to predict phenological responses to ongoing climate change, but must be incorporated in order to build reliable forecasts. Here, we use a long-term dataset (1953-2005) of plant phenological events in spring (flowering and leaf out) and autumn (leaf colouring and leaf fall) throughout Japan and South Korea to build forecasts that account for these sources of variability. Specifically, we used hierarchical models to incorporate the spatial variability in phenological responses to temperature to then forecast species' overall and site-specific responses to global warming. We found that for most species, spring phenology is advancing and autumn phenology is getting later, with the timing of events changing more quickly in autumn compared with the spring. Temporal trends and phenological responses to temperature in East Asia contrasted with results from comparable studies in Europe, where spring events are changing more rapidly than are autumn events. Our results emphasize the need to study multiple species at many sites to understand and forecast regional changes in phenology.}, annote = {- one of few studies to use longterm and spatially extensive dataset of phenology in plants - the spatial aspect (i.e. microclimate) helped resolve some of the discrepencies between sites - generally find early spring timing and later end of autumn---lengthing of the growing season - phenology of marine organims?}, author = {Ib{\'{a}}{\~{n}}ez, In{\'{e}}s and Primack, Richard B and Miller-Rushing, Abraham J and Ellwood, Elizabeth and Higuchi, Hiroyoshi and Lee, Sang Don and Kobori, Hiromi and Silander, John A}, doi = {10.1098/rstb.2010.0120}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ib{\'{a}}{\~{n}}ez et al. - 2010 - Forecasting phenology under global warming.pdf:pdf}, isbn = {1471-2970 (Electronic)$\backslash$r0962-8436 (Linking)}, issn = {1471-2970}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {Climate Change,Ecosystem,Japan,Models, Biological,Plant Development,Plant Leaves,Plant Leaves: physiology,Regression Analysis,Seasons}, number = {1555}, pages = {3247--60}, pmid = {20819816}, title = {{Forecasting phenology under global warming.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2981942{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {365}, year = {2010} } @article{Heeren, author = {Heeren, Alexander and Karns, Gabriel and Bruskotter, Jeremy and Toman, Eric and Wilson, Robyn and Szarek, Harmony}, doi = {10.1111/cobi.12838.This}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Heeren et al. - Unknown - Expert Judgment and Uncertainty Regarding the Protection of Imperiled Species.pdf:pdf}, journal = {Conservation Biology}, keywords = {accepted for publication and,and the version of,as doi,but has not been,differences between this version,pagination and proofreading process,please cite this article,record,this article has been,through the copyediting,typesetting,undergone full peer review,which may lead to}, title = {{Expert Judgment and Uncertainty Regarding the Protection of Imperiled Species}} } @article{McClanahan2002, abstract = {We review the evidence for multiple ecological states and the factors that create ecological resilience in coral reef ecosystems. There are natural differences among benthic communities along gradients of water temperature, light, nutrients, and organic matter associated with upwelling-downwelling and onshore-offshore systems.}, annote = {- multiple synergistic disturbances are often important}, archivePrefix = {arXiv}, arxivId = {381-390}, author = {McClanahan, Tim and Polunin, Nicolas and Done, Terry}, doi = {Artn 18}, eprint = {381-390}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McClanahan, Polunin, Done - 2002 - Ecological statres and the resilience of coral reefs.pdf:pdf}, isbn = {1195-5449 U6 - ctx{\_}ver=Z39.88-2004{\&}ctx{\_}enc=info{\%}3Aofi{\%}2Fenc{\%}3AUTF-8{\&}rfr{\_}id=info:sid/summon.serialssolutions.com{\&}rft{\_}val{\_}fmt=info:ofi/fmt:kev:mtx:journal{\&}rft.genre=article{\&}rft.atitle=Ecological+States+and+the+Resilience+of+Coral+Reefs{\&}rft.jtitle=Conservati}, issn = {17083087}, journal = {Conservation Ecology}, keywords = {benthic communities,coral reef ecosystems,ecological resilience}, number = {2}, pages = {1--28}, pmid = {39}, title = {{Ecological statres and the resilience of coral reefs}}, url = {http://www.consecol.org/vol6/iss2/art18}, volume = {6}, year = {2002} } @article{Chades2016, annote = {What types of approaches are common? What tools should I learn? What are the interesting future directions?}, author = {Chad{\`{e}}s, Iadine and Nicol, Sam and Rout, Tracy M. and P{\'{e}}ron, Martin and Dujardin, Yann and Pichancourt, Jean-Baptiste and Hastings, Alan and Hauser, Cindy E.}, doi = {10.1007/s12080-016-0313-0}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chad{\`{e}}s et al. - 2016 - Optimization methods to solve adaptive management problems.pdf:pdf}, issn = {1874-1738}, journal = {Theoretical Ecology}, keywords = {Adaptive management,Markov decision process,MDP,Pa,adaptive management,hidden markov models,markov decision,mdp,natural resource,of information,partially observable markov decision,pomdp,process,stochastic dynamic programming,value}, publisher = {Theoretical Ecology}, title = {{Optimization methods to solve adaptive management problems}}, url = {http://link.springer.com/10.1007/s12080-016-0313-0}, year = {2016} } @article{Post2008, abstract = {In highly seasonal environments, offspring production by vertebrates is timed to coincide with the annual peak of resource availability. For herbivores, this resource peak is represented by the annual onset and progression of the plant growth season. As plant phenology advances in response to climatic warming, there is potential for development of a mismatch between the peak of resource demands by reproducing herbivores and the peak of resource availability. For migratory herbivores, such as caribou, development of a trophic mismatch is particularly likely because the timing of their seasonal migration to summer ranges, where calves are born, is cued by changes in day length, while onset of the plant-growing season on the same ranges is cued by local temperatures. Using data collected since 1993 on timing of calving by caribou and timing of plant growth in West Greenland, we document the consequences for reproductive success of a developing trophic mismatch between caribou and their forage plants. As mean spring temperatures at our study site have risen by more than 4 degrees C, caribou have not kept pace with advancement of the plant-growing season on their calving range. As a consequence, offspring mortality has risen and offspring production has dropped fourfold.}, author = {Post, Eric and Forchhammer, Mads C and Adams, L.G. and Singer, F.J. and Dale, B.W. and Albon, S.D. and Langvatn, R. and Both, C. and Visser, M. and Both, C. and Bouwhuis, S. and Lessells, C.M. and Visser, M. and B{\o}ving, P.S. and Post, E. and Caughley, G. and Caughley, G. and Caughley, J. and Clutton-Brock, T.H. and Durant, J.M. and Hjermann, D.{\O}. and Anker-Nilssen, T. and Beaugrand, G. and Mysterud, A. and Pettorelli, N. and Stenseth, N.C. and Edwards, M. and Richardson, A.J. and Forchhammer, M.C. and Post, E. and Stenseth, N.C. and Boertmann, D. and Forchhammer, M.C. and Post, E. and Berg, T.B.G. and H{\o}ye, T.T. and Schmidt, N.-M. and Gunn, A. and Skogland, T. and H{\o}ye, T.T. and Post, E. and Meltofte, H. and Schmidt, N.M. and Forchhammer, M.C. and Klein, D.R. and Leader-Williams, N. and Lincoln, G.A. and Short, R.V. and Maxwell, B. and Miller, F.L. and Gunn, A. and Molau, U. and Palmquist, E. and Lundberg, P. and Post, E. and Post, E. and Post, E. and Post, E. and Forchhammer, M.C. and Post, E. and Forchhammer, M.C. and Post, E. and Klein, D.R. and Post, E. and Forchhammer, M.C. and Stenseth, N.C. and Callaghan, T.V. and Post, E. and B{\o}ving, P.S. and Pedersen, C. and MacArthur, M.A. and Rachlow, J.L. and Bowyer, R.T. and Robbins, C.T. and Skogland, T. and Stevenson, I.R. and Bryant, D.M. and Thing, H. and Visser, M.E. and Holleman, L.J.M. and Visser, M.E. and Noordwijk, A.J. Van and Tinbergen, J.M. and Lessells, C.M. and Walther, G.-R. and Post, E. and Convey, P. and Menzel, A. and Parmesan, C. and Beebee, T.J.C. and Fromentin, J.-M. and Guldberg, O.H. and Bairlein, F. and Whitten, K.R. and Garner, G.W. and Mauer, F.J. and Harris, R.B. and Winder, M. and Schindler, D.E.}, doi = {10.1098/rstb.2007.2207}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Post et al. - 2008 - Climate change reduces reproductive success of an Arctic herbivore through trophic mismatch.pdf:pdf}, isbn = {0962-8436}, issn = {0962-8436}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {10,1098,2007,2008,2016,2207,2369,2375,363,b,doi,nloaded from http,on august 31,org,phil,published online 15 november,r,royalsocietypublishing,rstb,soc,trans}, number = {1501}, pages = {2369--75}, pmid = {18006410}, title = {{Climate change reduces reproductive success of an Arctic herbivore through trophic mismatch.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18006410{\%}5Cnhttp://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC2606787}, volume = {363}, year = {2008} } @article{Munroe2015, abstract = {Marine diseases are a strong selective force that can have important economic and ecological consequences. Larval dispersal patterns, selective mortality and individual growth rates can modulate metapopulation responses to disease pressure. Here, we use a modeling framework that includes distinct populations, connected via larval transport, with varying disease selection pressure and connectivity to examine how these dynamics enhance or inhibit the evolu-tion of disease resistance in metapopulations. Our system, oysters and MSX disease, is one in which disease resistance is highly and demonstrably heritable. Simulations show that under con-ditions of population isolation (i.e. local retention of larvae) and strong disease selection, popula-tions rapidly evolve genetic disease resistance. Varying the patterns of larval dispersal alone dou-bles the time for evolution of disease resistance. Spatially varying disease in the absence of larval dispersal leaves some populations unable to respond to the disease, whereas adding larval disper-sal slows the response of populations under strong selection and speeds the response in popula-tions under low selection when fitness is based on relatively limited genetic structure (‘juvenile fitness' in our simulations). Under spatially variable disease pressure, larval dispersal generates a fourfold greater variance in fitness outcomes across the dispersal patterns tested. In a meta -population, populations experiencing lower selection pressure will tend to slow the development of other, more heavily selected populations. This suggests that conservation efforts aimed at improving overall metapopulation resistance in the face of marine diseases should target those populations under modest or high disease pressure, rather than protecting those experiencing low selective pressure.}, author = {Munroe, Daphne M. and Powell, Eric N. and Ford, Susan E. and Hofmann, Eileen E. and Klinck, John M.}, doi = {10.3354/meps11349}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Munroe et al. - 2015 - Outcomes of asymmetric selection pressure and larval dispersal on evolution of disease resistance A metapopulatio.pdf:pdf}, issn = {01718630}, journal = {Marine Ecology Progress Series}, keywords = {Connectivity,Disease,Evolution,Genetic adaptation,Larval dispersal,Metapopulation dynamics,Oyster,Resistance,Structured population model}, pages = {221--239}, title = {{Outcomes of asymmetric selection pressure and larval dispersal on evolution of disease resistance: A metapopulation modeling study with oysters}}, volume = {531}, year = {2015} } @article{Gunderson2016, abstract = {Activity budgets influence the expression of life history traits as well as population dynamics. For ectotherms, a major constraint on activity is environmental temperature. Nonetheless, we currently lack a comprehensive conceptual framework for understanding thermal constraints on activity, which hinders our ability to rigorously apply activity data to answer ecological and evolutionary questions. Here, we integrate multiple aspects of temperature-dependent activity into a single unified framework that has general applicability. We also provide examples of the implementation of this framework to address fundamental questions in ecology relating to climate change vulnerability and species' distributions using empirical data from a tropical lizard.}, author = {Gunderson, Alex R. and Leal, Manuel}, doi = {10.1111/ele.12552}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gunderson, Leal - 2016 - A conceptual framework for understanding thermal constraints on ectotherm activity with implications for predic.pdf:pdf}, isbn = {1461-0248}, issn = {14610248}, journal = {Ecology Letters}, keywords = {Activity,Anolis,Behaviour,Ectotherm,Global change,Physiology,Temperature}, number = {2}, pages = {111--120}, pmid = {26647860}, title = {{A conceptual framework for understanding thermal constraints on ectotherm activity with implications for predicting responses to global change}}, volume = {19}, year = {2016} } @article{Easterling2000, annote = {- investigate climate data to look at temperature extremes, extreme precipitation, droughts and flooding, tropical storms, societal impacts - argue max temps will increase - fewer frost days - more heavy rain - more hat and cold waves likely - potentially more storms}, author = {Easterling, D. R.}, doi = {10.1126/science.289.5487.2068}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Easterling - 2000 - Climate Extremes Observations, Modeling, and Impacts.pdf:pdf}, isbn = {0036-8075}, issn = {00368075}, journal = {Science}, number = {5487}, pages = {2068--2074}, pmid = {11000103}, title = {{Climate Extremes: Observations, Modeling, and Impacts}}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.289.5487.2068}, volume = {289}, year = {2000} } @article{Essington2016, author = {Essington, Timothy E. and Ciannelli, Lorenzo and Heppell, Selina S. and Levin, Phillip S. and McClanahan, Timothy R. and Micheli, Fiorenza and Plag{\'{a}}nyi, {\'{E}}va E. and van Putten, Ingrid E.}, doi = {10.1007/s10021-016-0073-0}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Essington et al. - 2016 - Empiricism and Modeling for Marine Fisheries Advancing an Interdisciplinary Science.pdf:pdf}, issn = {1432-9840}, journal = {Ecosystems}, keywords = {ciplinarity,empiri-,global change,interdis-,marine fisheries,modeling,sustainabiity}, title = {{Empiricism and Modeling for Marine Fisheries: Advancing an Interdisciplinary Science}}, url = {http://link.springer.com/10.1007/s10021-016-0073-0}, year = {2016} } @article{Wernberg2013, abstract = {Extreme climatic events, such as heat waves, are predicted to increase in frequency and magnitude as a consequence of global warming but their ecological effects are poorly understood, particularly in marine ecosystems(1-3). In early 2011, the marine ecosystems along the west coast of Australia-a global hotspot of biodiversity and endemism(4,5)-experienced the highest-magnitude warming event on record. Sea temperatures soared to unprecedented levels and warming anomalies of 2-4 degrees C persisted for more than ten weeks along {\textgreater}2,000 km of coastline. We show that biodiversity patterns of temperate seaweeds, sessile invertebrates and demersal fish were significantly different after the warming event, which led to a reduction in the abundance of habitat-forming seaweeds and a subsequent shift in community structure towards a depauperate state and a tropicalization of fish communities. We conclude that extreme climatic events are key drivers of biodiversity patterns and that the frequency and intensity of such episodes have major implications for predictive models of species distribution and ecosystem structure, which are largely based on gradual warming trends.}, annote = {-this paper provides a nice example how an unusually warm summer produced warmer waters off of Australia, this then afffected the species composition in the area -point out need to study extreme events, not simply -warmer water, tropical species, were found in the warmed areas, looked at this with tropicalizaton index before and afrter the heat wave....some of this may also be because of a warmer than average winter -of two sites, community responses only occred in the warm, not coller region}, author = {Wernberg, T and Smale, D A and Tuya, F and Thomsen, M S and Langlois, T J and de Bettignies, T and Bennett, S and Rousseaux, C S}, doi = {10.1038/nclimate1627}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wernberg et al. - 2013 - An extreme climatic event alters marine ecosystem structure in a global biodiversity hotspot.pdf:pdf}, isbn = {1758-678X}, issn = {1758-678X}, journal = {Nature Climate Change}, keywords = {ocean temperature western-australia reef fishes pa}, number = {1}, pages = {78--82}, publisher = {Nature Publishing Group}, title = {{An extreme climatic event alters marine ecosystem structure in a global biodiversity hotspot}}, volume = {3}, year = {2013} } @article{Burgess2014, abstract = {Demographic connectivity is a fundamental process influencing the dynamics and persistence of spatially structured populations. Consequently, quantifying connectivity is essential for properly designing networks of protected areas so that they achieve their core ecological objective of maintaining population persistence. Recently, many empirical studies in marine systems have provided essential, and historically challenging to obtain, data on patterns of larval dispersal and export from marine protected areas (MPAs). Here, we review the empirical studies that have directly quantified the origins and destinations of individual larvae and assess those studies' relevance to the theory of population persistence and MPA design objectives. We found that empirical studies often do not measure or present quantities that are relevant to assessing population persistence, even though most studies were motivated or contextualized by MPA applications. Persistence of spatial populations, like nonspatial populations, depends on replacement, whether individuals reproduce enough in their lifetime to replace themselves. In spatial populations, one needs to account for the effect of larval dispersal on future recruitment back to the local population through local retention and other connectivity pathways. The most commonly reported descriptor of larval dispersal was the fraction of recruitment from local origin (self-recruitment). Self-recruitment does not inform persistence-based MPA design because it is a fraction of those arriving, not a fraction of those leaving (local retention), so contains no information on replacement. Some studies presented connectivity matrices, which can inform assessments of persistence with additional knowledge of survival and fecundity after recruitment. Some studies collected data in addition to larval dispersal that could inform assessments of population persistence but which were not presented in that way. We describe how three pieces of empirical information are needed to fully describe population persistence in a network of MPAs: (1) lifetime fecundity, (2) the proportion of larvae that are locally retained (or the full connectivity matrix), and (3) survival rate after recruitment. We conclude by linking theory and data to provide detailed guidance to empiricists and practitioners on field sampling design and data presentation that better informs the MPA objective of population persistence.}, author = {Burgess, Scott C. and Nickols, Kerry J. and Griesemer, Chris D. and Barnett, Lewis A K and Dedrick, Allison G. and Satterthwaite, Erin V. and Yamane, Lauren and Morgan, Steven G. and White, J. Wilson and Botsford, Louis W.}, doi = {10.1890/13-0710.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Burgess et al. - 2014 - Beyond connectivity How empirical methods can quantify population persistence to improve marine protected-area d.pdf:pdf}, isbn = {1051-0761}, issn = {10510761}, journal = {Ecological Applications}, keywords = {Larval dispersal,Local retention,Marine reserves,Self-recruitment}, number = {2}, pages = {257--270}, pmid = {24689139}, title = {{Beyond connectivity: How empirical methods can quantify population persistence to improve marine protected-area design}}, volume = {24}, year = {2014} } @article{Bauch2016, annote = {- is this the approach I had thought of when MPAs may make people complacent? - is MPA media coverage a bad cue for how protected our oceans actually are? -science litearcy and support for science funding Discussion: - do shifting baselines matter - spatial structure of conseravtions and non conseevationists - MPAs, cues {\#} Points for discussion with QuEST class - discuss early warning signals in figure 2 - how do their results line up with what we foiund in class?}, author = {Bauch, Chris T. and Sigdel, Ram and Pharaon, Joe and Anand, Madhur}, doi = {10.1073/pnas.1604978113}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bauch et al. - 2016 - Early warning signals of regime shifts in coupled human–environment systems.pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, pages = {201604978}, pmid = {27815533}, title = {{Early warning signals of regime shifts in coupled human–environment systems}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604978113}, year = {2016} } @article{Lafferty2002, annote = {- suggest that rare species should be less suceptiple to host specific disease agent as the host pop is so small -diseases are important in conservation when there are changes in host susceptibility, immune systems are constly to maintan, other multiple stressors -habitat fragmentation may increase density and increase edge effects -Hess 1994 explored how researve corridors could increase diseasee risk -reserves would decrease disease risk, if reserve protected predator that then kept prey density down}, author = {Lafferty, Kevin D. and Gerber, Leah R}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lafferty, Gerber - 2002 - Medicine of Intersection Conservation Biology the and Conservation Theory Epidemiology for.pdf:pdf}, journal = {Conservation Biology}, number = {3}, pages = {593--604}, title = {{Medicine of Intersection Conservation Biology : the and Conservation Theory Epidemiology for}}, volume = {16}, year = {2002} } @article{Dulvy2003, abstract = {Human impacts on the world's oceans have been substantial, leading to concerns about the extinction of marine taxa. We have compiled 133 local, regional and global extinctions of marine populations. There is typically a 53-year lag between the last sighting of an organism and the reported date of the extinction at whatever scale this has occurred. Most disappearances (80{\%}) were detected using indirect historical comparative methods, which suggests that marine extinctions may have been underestimated because of low-detection power. Exploitation caused most marine losses at various scales (55{\%}), followed closely by habitat loss (37{\%}), while the remainder were linked to invasive species, climate change, pollution and disease. Several perceptions concerning the vulnerability of marine organisms appear to be too general and insufficiently conservative. Marine species cannot be considered less vulnerable on the basis of biological attributes such as high fecundity or large-scale dispersal characteristics. For commercially exploited species, it is often argued that economic extinction of exploited populations will occur before biological extinction, but this is not the case for non-target species caught in multispecies fisheries or species with high commercial value, especially if this value increases as species become rare. The perceived high potential for recovery, high variability and low extinction vulnerability of fish populations have been invoked to avoid listing commercial species of fishes under international threat criteria. However, we need to learn more about recovery, which may be hampered by negative population growth at small population sizes (Allee effect or depensation) or ecosystem shifts, as well as about spatial dynamics and connectivity of subpopulations before we can truly understand the nature of responses to severe depletions. The evidence suggests that fish populations do not fluctuate more than those of mammals, birds and butterflies, and that fishes may exhibit vulnerability similar to mammals, birds and butterflies. There is an urgent need for improved methods of detecting marine extinctions at various spatial scales, and for predicting the vulnerability of species.}, author = {Dulvy, Nicholas K and Sadovy, Yvonne and Reynolds, John D}, doi = {10.1046/j.1467-2979.2003.00105.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dulvy, Sadovy, Reynolds - 2003 - Extinction vulnerability in marine populations.pdf:pdf}, isbn = {1467-2960}, issn = {1467-2960}, journal = {Fish and Fisheries}, keywords = {Red List,biodiversity,climate-change,community structure,conservation,coral-reef fish,detection,diadema-antillarum,el-nino,evolutionary transitions,fisheries,great-barrier-reef,life-history,long-term changes,oil-spill,recovery,risk,valdez}, number = {1}, pages = {25--64}, title = {{Extinction vulnerability in marine populations}}, volume = {4}, year = {2003} } @article{Havell2002, annote = {- there is a new similar review in Annual Reviews.. - this review examines how climate change may affect disease risk in both terrestrial and marine biota - they explain various scenarios in which climate change could alter host pathogen dynamics (e.g. change pathogen growth rate, phenology of interactions, susceptibility of hosts, host life cycle, generation time, range site - argue that predictions are hard based on paucity of basline disease data and the nonlnearities in both disease and climate - some diseases (like chytrid) may be limited as they require cool and moist condiitons for spread 4 objectives moving forward: 1) collect basline data 2) effects of multuple climatic variables on disease 3) forecast epidemics using climat evariables 4) evaluate role of evolution}, author = {Havell, C. Drew and Mitchell, Charles E. and Ward, Jessica R. and Altizer, Sonia and Dobson, Andrew P. and Ostfeld, Richard S. and Samuel, Michael D.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Havell et al. - 2002 - Climate warming and disease risks for terrestrial and marine biota.pdf:pdf}, journal = {Science}, number = {June}, pages = {2158--2162}, title = {{Climate warming and disease risks for terrestrial and marine biota}}, volume = {296}, year = {2002} } @article{Kough2015, annote = {- study looked at a important virus in Caribbean lobsters - they used a particle tracking model to see how the disease may be spread - they found that if the virus spread via larvae, instead of by itself, it would spread much more quickly and throughtout the Caribbean - it would be interesting if there was vetical transmission of the disease}, author = {Kough, Andrew S and Paris, Claire B and Behringer, Donald C and Butler, Mark J}, doi = {10.1093/ices}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kough et al. - 2015 - Modelling the spread and connectivity of waterborne marine pathogens - the case of PaV1 in the Caribbean.pdf:pdf}, journal = {ICES Journal of Marine Science}, keywords = {disease,lobster,panulirus argus,physical oceanography,virus}, number = {Supplement 1}, pages = {i139--i146}, title = {{Modelling the spread and connectivity of waterborne marine pathogens - the case of PaV1 in the Caribbean}}, volume = {72}, year = {2015} } @article{Doney2012, abstract = {In marine ecosystems, rising atmospheric CO2 and climate change are associated with concurrent shifts in temperature, circulation, stratification, nutrient input, oxygen content, and ocean acidification, with potentially wide-ranging biological effects. Population-level shifts are occurring because of physiological intolerance to new environments, altered dispersal patterns, and changes in species interactions. Together with local climate-driven invasion and extinction, these processes result in altered community structure and diversity, including possible emergence of novel ecosystems. Impacts are particularly striking for the poles and the tropics, because of the sensitivity of polar ecosystems to sea-ice retreat and poleward species migrations as well as the sensitivity of coral-algal symbiosis to minor increases in temperature. Midlatitude upwelling systems, like the California Current, exhibit strong linkages between climate and species distributions, phenology, and demography. Aggregated effects may modify energy and material flows as well as biogeochemical cycles, eventually impacting the overall ecosystem functioning and services upon which people and societies depend.}, annote = {-need to know ENSO, PDO, and North pacific Gyre Oscillation - This review looks at the various ways climate change afffects marine ecosystems via indidivual, population, community, and through ecosystem levels -they then provide three case study examples: polar regions, California upwelling system, and coral reefs - point out the rising C02and climate change will increase ocean temperatures and acidity, they will also change stratification, sea level, decreased sea ice, and alter pattern of ocean circulation and precipitation - direct and indirect effects affect organims and combine with other stressors like fertilzer runoff, invaisvive species, habitat loss and explotation -i important to remeber patterns arre not uniform and interact with ENSO or NAO Polar Systems - reduction of sea ice may increase light availability and increase phytoplankton production -krill have declined in Antarctica by order of magnitude since 1950 -several declines in large mammals in Antactrica Coral Reefs - expel zooxanthellae (symbiotic dinoflagellates) at hgher temperatures, death when this becomes extremes California upwelling -strongly affected by ENSO, PDO and North Pacific Gyre Oscllation}, author = {Doney, S.C. and Ruckelshaus, M. and {Emmett Duffy}, J. and Barry, J.P. and Chan, F. and English, C.A. and Galindo, H.M. and Grebmeier, J.M. and Hollowed, A.B. and Knowlton, N. and Polovina, J. and Rabalais, N.N. and Sydeman, W.J. and Talley, L.D.}, doi = {10.1146/annurev-marine-041911-111611}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Doney et al. - 2012 - Climate Change Impacts on Marine Ecosystems.pdf:pdf}, isbn = {1941-1405$\backslash$r1941-0611}, issn = {1941-1405}, journal = {Annual Review of Marine Science}, keywords = {diversity,food webs,hypoxia,trophic structure}, number = {1}, pages = {11--37}, pmid = {22457967}, title = {{Climate Change Impacts on Marine Ecosystems}}, volume = {4}, year = {2012} } @article{Fernandes2005, abstract = {The Great Barrier Reef Marine Park, an area almost the size of Japan, has a new network of no-take areas that significantly improves the protection of biodiversity. The new marine park zoning implements, in a quantitative manner, many of the theoretical design principles discussed in the literature. For example, the new network of no-take areas has at least 20{\%} protection per "bioregion," minimum levels of protection for all known habitats and special or unique features, and minimum sizes for no-take areas of at least 10 or 20 km across at the smallest diameter. Overall, more than 33{\%} of the Great Barrier Reef Marine Park is now in no-take areas (previously 4.5{\%}). The steps taken leading to this outcome were to clarify to the interested public why the existing level of protection was inadequate; detail the conservation objectives of establishing new no-take areas; work with relevant and independent experts to define, and contribute to, the best scientific process to deliver on the objectives; describe the biodiversity (e.g., map bioregions); define operational principles needed to achieve the objectives; invite community input on all of the above; gather and layer the data gathered in round-table discussions; report the degree of achievement of principles for various options of no-take areas; and determine how to address negative impacts. Some of the key success factors in this case have global relevance and include focusing initial communication on the problem to be addressed; applying the precautionary principle; using independent experts; facilitating input to decision making; conducting extensive and participatory consultation; having an existing marine park that encompassed much of the ecosystem; having legislative power under federal law; developing high-level support; ensuring agency priority and ownership; and being able to address the issue of displaced fishers.}, annote = {- paper mostly describes how the GBR non take reserve system was established. 20{\%} of each bioregion is protected and 33{\%} of GBR is protected ovaerall -stress need for clear objectives and clear plan of action. Also need buy in and help from lots of different groups}, author = {Fernandes, Leanne and Day, Jon and Lewis, Adam and Slegers, Suzanne and Kerrigan, Brigid and Breen, Dan and Cameron, Darren and Jago, Belinda and Hall, James and Lowe, Dave and Innes, James and Tanzer, John and Chadwick, Virginia and Thompson, Leanne and Gorman, Kerrie and Simmons, Mark and Barnett, Bryony and Sampson, Kirsti and De'ath, Glenn and Mapstone, Bruce and Marsh, Helene and Possingham, Hugh and Ball, Ian and Ward, Trevor and Dobbs, Kirstin and Aumend, James and Slater, Deb and Stapleton, Kate}, doi = {10.1111/j.1523-1739.2005.00302.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fernandes et al. - 2005 - Establishing representative no-take areas in the great barrier reef Large-scale implementation of theory on ma.pdf:pdf}, isbn = {1523-1739}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Biophysical operational principles,Cultural operational principles,Economic operational principles,Reserve-design software,Social operational principles}, number = {6}, pages = {1733--1744}, title = {{Establishing representative no-take areas in the great barrier reef: Large-scale implementation of theory on marine protected areas}}, volume = {19}, year = {2005} } @techreport{, annote = {-MLPA (had six broad goals) in 1999 required assessment and further planning of MPAs -63 MPAs in 1999, now 124 MPAs and 15 additional special closures -CDFW is MPA enforcement agency -argue 10 year reviews are based on scientific findings (pg viii) -6 large objectives of MLPA (preserive biodiversity, protect populations, improve access to areas, protect natural hertigae, ensure clear objectives for MPAs, manage MPAs as a network) -many factors affect California waters: El Nino, chemical pollution, ocean acidification, habitat loss, invasion of exotic species and the harvest of marine resources, also climate change -various types of MPAs: state marine reserves, state marine conservation area, state marine park, and state marine recreational management area pg 35: emphasziee connnections betweeen MPA management and fisheries, water quality, and climate change, marine debris invaseive species Notes from discussion: - people pushed back against percent of coastline rules, better to use spacing and size guidelines -can randomly generate tornado plots (Loo's thoughts) - agree that there is not a lot of thought on if California actually truely thinks about network effects}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2016 - California Master Life Protection Act Master Plan for Marine Protected Areas.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2016 - California Master Life Protection Act Master Plan for Marine Protected Areas(2).pdf:pdf}, institution = {California Department of Fish and Wildlife}, pages = {75}, title = {{California Master Life Protection Act Master Plan for Marine Protected Areas}}, year = {2016} } @article{Snyder2014, abstract = {There is growing awareness that fluctuations in larval flux (connectivity) depress the long-run growth of marine metapopulations, but by how much is unclear. Here, we explore how reproductive schedule and larval behavior affect how much connectivity fluctuations depress growth. We combine larval dispersal simulations from the Florida Keys with theoretical results to calculate the effect of fluctuations on bicolor damselfish (Stegastes partitus). We find that fluctuations depress growth only slightly (∼2{\%}), but the effect would be much stronger for an organism that spawned only part of the year. Larval behavior can also matter, as vertical migration allows larvae to become entrained in eddies. Eddies synchronize connectivity fluctuations, further decreasing growth. However, here, they also divide the Keys into largely independently fluctuating regions, mitigating the effects of local synchrony. Therefore, in situations where connectivity fluctuations matter, the presence of independently fluctuating regions due to larval behavior may be important.}, annote = {- use detailed larval disperal simulations (particle tracking models) to create monthly transition matrices for hypothetical popualtion}, author = {Snyder, Robin E and Paris, Claire B and Vaz, Ana C}, doi = {10.1086/677925}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Snyder, Paris, Vaz - 2014 - How much do marine connectivity fluctuations matter.pdf:pdf}, isbn = {1537-5323 (Electronic)$\backslash$r0003-0147 (Linking)}, issn = {1537-5323}, journal = {The American naturalist}, keywords = {connectivity,larval behavior,larval dispersal,lation dynamics,mesoscale eddies,metapopu-,stochasticity}, number = {4}, pages = {523--30}, pmid = {25226187}, title = {{How much do marine connectivity fluctuations matter?}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25226187}, volume = {184}, year = {2014} } @article{Levin2000, abstract = {Uniting frameworks used by Hamilton and May (1977), Levin et al. (1984) and Ezoe (1998), we show that the problem of the evolution of seed size - or of any other single dispersal-determining trait - can, under certain conditions, be understood as a constrained optimization problem. We find a function, F, whose maxima represent convergence stable strategies - evolutionary attractors towards which selection will drive populations (given sufficient diversity of types, either initially or generated through mutation). This function has a nice interpretation as the product of competitive ability and fecundity (both squared) and a functional describing the spread of the dispersal kernel. Using ideas pioneered by Dan Cohen and the theory of adaptive dynamics, we explore the consequences for the evolution of dispersal and seed size in populations, focusing on examples in metapopulations, with some comments on more general spatial models.}, author = {Levin, Simon A. and Muller-Landau, Helene C.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levin, Muller-Landau - 2000 - The evolution of dispersal and seed size in plant communities.pdf:pdf}, issn = {15220613}, journal = {Evolutionary Ecology Research}, keywords = {Adaptive dynamics,Evolutionarily stable strategy,Seed dispersal,Seed size}, number = {4}, pages = {409--435}, title = {{The evolution of dispersal and seed size in plant communities}}, volume = {2}, year = {2000} } @article{White2013a, abstract = {In addition to fostering biodiversity goals, marine protected area (MPA) implementation has economic consequences for both commercial and recreational fisheries. During the implementation of the State of California (USA) Marine Life Protection Act (MLPA), which mandates the creation of an MPA network in California's state waters, the stakeholders and policymakers utilized a pair of economic analyses that addressed these considerations. One was a comparative, static assessment of short-term, " worst case" potential socioeconomic impacts to important fisheries based on surveys of local fishermen. This analysis made no assumptions about fishery management outside of MPAs, assumed no spillover of fish from MPAs into fished areas or reallocation of fishing effort, and estimated the maximum potential dollar-value economic impacts over a short time scale. The other was a dynamic, bioeconomic assessment of the changes in spatial distribution of biomass and catch, based on published biological parameter values, oceanographic models of larval connectivity, and a range of possible levels of fishing. This analysis explicitly accounted for fish population dynamics, spillover, fisher movement, and fishery management outside of the MPAs, but was limited to long-term, equilibrium-based results because of a lack of baseline abundance data. Both evaluation methods were novel in their spatial resolution and their use directly in an MPA design process, rather than after implementation. The two methods produced broadly similar (at a regional spatial scale) evaluations of the likely effects of proposed MPAs on fisheries, at least when the bioeconomic model assumed fishery management was conservative. Our experience with these analyses in the MLPA Initiative process led to several suggestions for future MPA design efforts: (i) since the change in fish biomass inside MPAs partly depends on fisheries management outside of them, it is useful to integrate or coordinate conventional fishery management and MPA planning efforts; (ii) integrate modeling assessments early into MPA design, as part of a post-implementation adaptive management approach; and (iii) integrate empirical fishery data into bioeconomic models in order to improve representations of human behavior and short-term forecasts of changes in fished populations. {\textcopyright} 2012 Elsevier Ltd.}, author = {White, J. Wilson and Scholz, Astrid J. and Rassweiler, Andrew and Steinback, Charles and Botsford, Louis W. and Kruse, Sarah and Costello, Christopher and Mitarai, Satoshi and Siegel, David A. and Drake, Patrick T. and Edwards, Christopher A.}, doi = {10.1016/j.ocecoaman.2012.06.006}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2013 - A comparison of approaches used for economic analysis in marine protected area network planning in California.pdf:pdf}, isbn = {9109624066}, issn = {09645691}, journal = {Ocean and Coastal Management}, pages = {77--89}, publisher = {Elsevier Ltd}, title = {{A comparison of approaches used for economic analysis in marine protected area network planning in California}}, url = {http://dx.doi.org/10.1016/j.ocecoaman.2012.06.006}, volume = {74}, year = {2013} } @article{Apaloo1997, abstract = {In game-theoretic or strategic models of species evolution, the phenotype of individual organisms in a population are regarded as alternate strategies for playing a competitive game. The evolutionary outcome is predicted to conform to the “solution” of that game. The most usual solution}, author = {Apaloo, J}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Apaloo - 1997 - Revisiting Strategic Models of Evolution The Concept of Neighborhood Invader Strategies.pdf:pdf}, journal = {Theoretical population biology}, pages = {71--77}, title = {{Revisiting Strategic Models of Evolution: The Concept of Neighborhood Invader Strategies}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0040580997913186{\%}5Cnpapers3://publication/uuid/920760F8-CED7-4060-85C6-ADAF8B897EBE}, volume = {77}, year = {1997} } @techreport{Foundation2016, annote = {- repeat that on average populations of vertebrate species have declined by 58{\%} - examine 14,152 populations of 3706 species -LPI calculates the rate of changef or each species for each year and the caluclates average across all species - report looks at state of planet, various contributing factors, and what we can do in the future -various indices: living planet index, IUCN Red List, and others -only have threat status for 1/3 of reported populations (or species?) -database includes information on threats (habitat loss, overexplotation, pollution, invasive speices, disease, and climate change) - break up index for different regions (e.g. terrestiral vs marine) -freshwater systems have seen largest population decline -6170 pops (birds,mammals, reptles, and fish) in marine analysis -make a wrong statement about MSY - there was previous Living Blue Planet Report Database info (pg 40) - more info in technical report - my questions: -what data is included? How is it averaged? - how important are particular species to calculations? -what happens if you look at only long term monitoring data? Not data collection specifically set up for declining species?}, author = {Foundation, World Wildlife}, isbn = {9782940529407}, title = {{Living Planet Report 2016 - Risk and resilience in a new era}}, year = {2016} } @article{Starfield1997, abstract = {I contrast 2 views of modeling: the model as a representation of "truth" and the model as a problem-solving tool. Examples are given of how, in the latter case, the objective drives the design of small, simple models that focus relentlessly on the problem to be solved. A number of applications for small, fo- cused models are offered. I stress the need for wildlife professionals to develop the skills for constructing and using such models on a regular basis; I end with ideas about how to create a modeling culture in con- servation and resource management organizations}, annote = {- discusses various misconceptions about models - advocates that models be developed to answer particular questions (e.g. how often do you need to census?) - three steps for good decision making: 1) know what objective you are trying to achieve, 2) how well does a strategy perform to achieve objective, and 3) how do we then rank different strategies}, author = {Starfield, Anthony}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Starfield - 1997 - A pragmatic approach to modeling for wildlife management.pdf:pdf}, journal = {The Journal of Wildlife Management}, keywords = {decision analysis,ecosystems,management,modeling,populations,problem solving,simulation,strategy}, number = {2}, pages = {261--270}, title = {{A pragmatic approach to modeling for wildlife management}}, volume = {61}, year = {1997} } @article{Wood2008, abstract = {Current global marine protection targets aim to protect 10-30{\%} of marine habitats within the next 3 - 5 years. However, these targets were adopted without prior assessment of their achievability. Moreover, ability to monitor progress towards such targets has been constrained by a lack of robust data on marine protected areas. Here we present the results of the first explicitly marine-focused, global assessment of protected areas in relation to global marine protection targets. Approximately 2.35 million km2, 0.65{\%} of the world's oceans and 1.6{\%} of the total marine area within Exclusive Economic Zones, are currently protected. Only 0.08{\%} of the world's oceans, and 0.2{\%} of the total marine area under national jurisdiction is no-take. The global distribution of protected areas is both uneven and unrepresentative at multiple scales, and only half of the world's marine protected areas are part of a coherent network. Since 1984 the spatial extent of marine area protected globally has grown at an annual rate of 4.6{\%}, at which even the most modest target is unlikely to be met for at least several decades rather than within the coming decade. These results validate concerns over the relevance and utility of broad conservation targets. However, given the low level of protection for marine ecosystems, a more immediate global concern is the need for a rapid increase in marine protected area coverage. In this case, the process of comparing targets to their expected achievement dates may help to mobilize support for the policy shifts and increased resources needed to improve the current level of marine protection.}, annote = {This paper lays out the first assessment of the implementation of MPAs around the world. It does not address the ecological or economic effects of these MPAs -They study the growth in number and overall areas of marine protected areas over time to show we will not reach our goals for many decades - To my surprise, they show that 56{\%} of MPAs are connected within 10-20km of at least one other MPA. Almost alll MPAs are connected to less then 10 other MPAs (is this enough of an insurance policy?) - most MPAs appear to large or small based on sizing guidelines - There are many more MPAs in tropical waters compared to temperate waters - They point out that a lot of the total MPA area is contained within a handful of mega-MPAs Could you compare different sets of marine reserve networks? Are any good replicates for one another?}, archivePrefix = {arXiv}, arxivId = {401-410}, author = {Wood, Louisa J. and Fish, Lucy and Laughren, Josh and Pauly, Daniel}, doi = {10.1017/S003060530800046X}, eprint = {401-410}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wood et al. - 2008 - Assessing progress towards global marine protection targets shortfalls in information and action.pdf:pdf}, isbn = {0030-6053}, issn = {0030-6053}, journal = {Oryx}, keywords = {conservation target,international policy,marine}, number = {03}, pages = {340--351}, title = {{Assessing progress towards global marine protection targets: shortfalls in information and action}}, url = {http://journals.cambridge.org/action/displayFulltext?type=1{\&}fid=1937368{\&}jid=ORX{\&}volumeId=42{\&}issueId=03{\&}aid=1937360{\&}newWindow=Y}, volume = {42}, year = {2008} } @article{Branch2010, annote = {- the paper assessing the idea of fishing down marine food webs, which was proposed b/c the mean trophic level appeared to be decreasing in many systems -they assessed what different fishing scenarios would do to mean trophic level for various ecosystem based models -they also looked at how mean trophic level changed for major ecosystems around the world. They find that mean trophic level was strongly dependent on just a couple of species. They found that increases in lower trophic levels, as opposed to decreased higher trophic levels, leads to what looks like fishing down food webs -they stress that MTL is not a good metric and abundance as well as spatial heterogeneity should be taken into account. -they also found that MTL was not correlated with abundance from more scientific surveys often}, author = {Branch, Trevor A. and Watson, Reg and Fulton, Elizabeth A. and Jennings, Simon and McGilliard, Carey R. and Pablico, Grace T. and Ricard, Daniel and Tracey, Sean R.}, doi = {10.1038/nature09528}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Branch et al. - 2010 - The trophic fingerprint of marine fisheries.pdf:pdf}, isbn = {0028-0836}, issn = {0028-0836}, journal = {Nature}, number = {7322}, pages = {431--435}, pmid = {21085178}, publisher = {Nature Publishing Group}, title = {{The trophic fingerprint of marine fisheries}}, url = {http://www.nature.com/doifinder/10.1038/nature09528}, volume = {468}, year = {2010} } @article{Moffitt2013, abstract = {Marine protected areas are being monitored to determine whether they increase abundance of fished populations, with responses often expected within a few years. Evaluations typically compare abundance inside versus outside or after versus before implementation, but the temporal and spatial scales over which these measures can reflect marine protected area success are untested. We modeled the response of fished populations for a range of marine protected area sizes, fishing intensities, larval dispersal distances, and adult movement ranges. Our results, which can inform experimental design and interpretation of monitoring, show that the spatial and temporal scale of population responses to marine protected areas will be determined by simple relationships between marine protected area size, larval and adult movement distances, and generation time, in addition to the effects of exploitation rate. The largest effects of marine protected areas should be expected with ‘outside' samples located at least 2 dispersal units from the edge, and after 2 generations have passed since establishment. In general, monitoring studies over time (after versus before) should provide better assessment of marine protected area success than monitoring over space (inside versus outside), but understanding of the limitations of each type of measurement is key. Because it may take many years for marine protected area effects to be fully realized, we strongly caution against judgment of marine protected area effectiveness at inappropriately short time frames. }, annote = {- detection of effect of MPAs depends on: - use model to show importance of MPA size, larval and adult movement distances, generation time, and effects of exploitation -stress importance of waiting at least two generations and looking at "outside" area two dispersal distances area from MPA to not sample spillover effect and allow proper comparision}, author = {Moffitt, Elizabeth A. and White, J. Wilson and Botsford, Louis W.}, doi = {10.3354/meps10425}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moffitt, White, Botsford - 2013 - Accurate assessment of marine protected area success depends on metric and spatiotemporal scale of mon.pdf:pdf}, issn = {01718630}, journal = {Marine Ecology Progress Series}, keywords = {Ecosystem-based management,Fisheries,Larval dispersal,Marine reserve,Monitoring,Movement,Population dynamics,Transient dynamics}, pages = {17--28}, title = {{Accurate assessment of marine protected area success depends on metric and spatiotemporal scale of monitoring}}, volume = {489}, year = {2013} } @article{Montecino2016, abstract = {Sea star wasting disease (SSWD) devastated intertidal sea star populations from Mexico to Alaska, but little detail is known about its impacts to specific subtidal species. We assessed the impacts of SSWD over 5 of the 6 basins of the transboundary US/Canadian marine ecosystem, the Salish Sea, a world-wide hotspot for temperate asteroid species diversity with a high degree of endemism. We also studied SSWD on Washington's outer coast. We analyzed data on the three most common sea star species collected by trained volunteer scuba divers, before (2006-2013) and after (2014-2015) the SSWD outbreak, as well as scientific strip transect data for 8 common asteroid species and one genus collected by scientific divers in the San Juan islands during summer 2014 and 2015. In all 5 basins and on Washington's outer coast the sunflower sea star (Pycnopodia helianthoides), the dominant species, and the giant pink sea star (Pisaster brevispinus) showed severe declines, while the leather sea star (Dermasterias imbricata) did not. Strip transect data showed increasing SSWD prevalence in P. helianthoides, mottled star (Evasterias troschelii) and Henricia sp. between May and August 2014, although the maximum prevalences varied among species. Transect counts showed severe decline of adult P. helianthoides and moderate declines of E. troschelii and Henricia sp. Rare subtidal species such as purple sea star (Pisaster ochraceus), P. brevispinus, sun star (Solaster stimpsoni) and rainbow star (Orthasterias koehleri) also seem to have declined, while counts of D. imbricata and Vermilion star (Mediaster aequalis) suggested increasing densities. Our findings are consistent with previous reports on severe P. helianthoides reductions from California to Alaska, which rises concern with respect to the conservation of this ecologically important species. These data also highlight differential susceptibility and impact of SSWD among asteroid species.}, annote = {- how important is age structure in these populations}, author = {Montecino, Diego and Eisenlord, Morgan E and Turner, Margaret and Harvell, C Drew and Yoshioka, Reyn and Pattengill-Semmens, Christy V and Gaydos, Joseph K}, doi = {10.1371/journal.pone.0163190}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Montecino et al. - 2016 - Devastating transboundary impacts of sea star wasting disease on subtidal asteroids.pdf:pdf}, issn = {1932-6203}, journal = {PLoSONE}, keywords = {Conservation,Emerging disease,Sustainability}, number = {10}, pages = {1--21}, title = {{Devastating transboundary impacts of sea star wasting disease on subtidal asteroids}}, volume = {11}, year = {2016} } @book{Conroy2012, address = {West Sussex, UK}, annote = {should probably read chapters 1,2,3,5-8, 10, appendix E Chapter 1: -many decision to make and potentially several objectives -confusion of values (or objectives) with science (data or information) -structured decision making consists of three parts: 1) specific objective in place, 2) different strategies that could meet objectives, and 3) predictive models to evalulate different strategies effect on objectives - a structured approach is needed so decision do not look arbitary -adaptive resource management extends SDM to case where outcomes of decisions are uncertain - for adaptive managment they argue that decisions have to be recurrent, models need to include information on structural uncertainty, and monitoring must be in place Chapter 2: -state problem, define objectives, paths to solve objective, define spatial and temporal bounds of problem, identify potential sticking points or problems, acknodwledge uncertianty -need clear seperation betweeen beliefs (knowledge on system) and values - need some model of how decisions may affect system state -various types of uncertainty: enviornmental, partial controlability (other random effects may affect our actions), statistical (sampling) variability, and structural uncertainty -can include uncertainty or conduct optimization that expliently seeks to avoid bad outcomes (more like robust optimization) Chapter 3: -need to distriguish between fundamental (ultimate goal) and means (sub goals to get to fundamental goal) objectives -reduce barriers to creative decision making -competing and conflicting objectives -hidden vs stranded objectives -create decision networks which go from fundmental to means objectives and then lower to actual actions that could be taken -issues with multiple objectives: common currency, conlficitng objectivese, some objectives may be more important -often need to use utility function with multiple objectives, or use one objective as constraint and to max the other Chapter 5: - basic statistical terms (probability, conditional probability, independence, complementary, law of total probability, Bayes theorem, probabibility distributions, support of distributions, expected values, utility, linear models) - given examples of all these concepts in R boxes - more advanced statistical concepts (hierarchical models for shared information and non independent samples) - make point that shared information is important for rare species or populations with little data collected) -Bayesian inference Chapter 6: -influence diagrams - common mistakes (not including all costs, not including uncertainties, defining linkage meanings) - defining node states (are things yes/no, or continuous numbers) -decision trees -solving for optimal decisions. Often it may be best to use suboptimal decision, termed satisficing decision -discuss how to use and acquire expert opinions -software available for making diagrams and estimating paramters Chapter 7 - irreducible and reducible (e.g. language or epistemoligical ) uncertainty -epistemic unceratinty can include staitical, observantional, and structural uncertainty -with uncertainty could look at expected value - alternative is termed minimax = minmize loss for worst case outcome - not usually used - could also use risk profiling --need to include risk attitudes, people may prefer certainty rather than high risk/reward scenario -other terms risk premium and risk tolerence -can calculate value of additional or better information -can try to reduce epistemic uncertainty: experimentaiton, retrospective data analysis, or through adaptive resource management -nice Bayesian updating example under adaptive management framework -single (keeping with same objectives but changing behavior) vs double-loop (altering objectives and models) forms of adaptive managment -passive vs active ARM Chapter 8 Seperate: Expert informatinon (pg. 180) -indirect vs direct approaches and quantiative vs qualitative - 4 approaches: have expert directly estimate probabilities, frequency elicitation (have someone estimate fraction of population that will surivie and use this to estimate probabilities), value elicitation (unrelated value estimatino that can be used in a distribution) , function elicitation -need to quantify uncertainty in expert judgement (ask what is the lowest, highest, most likely values, and how confident are you in the interval you created?) Chapter 10: -dolphin conservation example}, author = {Conroy, Michael J and Peterson, James T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(2).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(3).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(4).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(5).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(6).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(7).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(8).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(9).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(10).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(11).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Conroy, Peterson - 2012 - Decision Making in Natural Resource Management A Structured, Adaptive Approach(12).pdf:pdf}, isbn = {1118506200}, publisher = {John Wiley and Sons}, title = {{Decision Making in Natural Resource Management: A Structured, Adaptive Approach}}, year = {2012} } @article{Babcock2010, abstract = {Decadal-scale observations of marine reserves suggest that indirect effects on taxa that occur through cascading trophic interactions take longer to develop than direct effects on target species. Combining and analyzing a unique set of long-term time series of ecologic data in and out of fisheries closures from disparate regions, we found that the time to initial detection of direct effects on target species (+/-SE) was 5.13 +/- 1.9 years, whereas initial detection of indirect effects on other taxa, which were often trait mediated, took significantly longer (13.1 +/- 2.0 years). Most target species showed initial direct effects, but their trajectories over time were highly variable. Many target species continued to increase, some leveled off, and others decreased. Decreases were due to natural fluctuations, fishing impacts from outside reserves, or indirect effects from target species at higher trophic levels. The average duration of stable periods for direct effects was 6.2 +/- 1.2 years, even in studies of more than 15 years. For indirect effects, stable periods averaged 9.1 +/- 1.6 years, although this was not significantly different from direct effects. Populations of directly targeted species were more stable in reserves than in fished areas, suggesting increased ecologic resilience. This is an important benefit of marine reserves with respect to their function as a tool for conservation and restoration.}, annote = {- this paper examined the few cases of long term MPA examples instead of using space for time substitions - they found that organisms that had previously been fished showed signs of recovery after implementing marine reserves, species not directly by fisheries took much longer to respond to marine reserves -they looked at 6 reserves with 30 years of data and multiple populations at reserves for both inside and outside of the reserves}, archivePrefix = {arXiv}, arxivId = {753}, author = {Babcock, R C and Shears, N T and Alcala, A C and Barrett, N S and Edgar, G J and Lafferty, K D and McClanahan, T R and Russ, G R}, doi = {DOI 10.1073/pnas.0908012107}, eprint = {753}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Babcock et al. - 2010 - Decadal trends in marine reserves reveal differential rates of change in direct and indirect effects.pdf:pdf}, isbn = {0027-8424}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {community structure,ecosystems,fishing effects,interactions,lobsters jasus-edwardsii,marine protected area,new-zealand,predatory fish,protected areas,reef,sea-urchin,spiny lobsters,time lags,trophic cascade,trophic cascades}, number = {43}, pages = {18256--18261}, pmid = {20176941}, title = {{Decadal trends in marine reserves reveal differential rates of change in direct and indirect effects}}, volume = {107}, year = {2010} } @article{Williams2013, abstract = {Temporally variable conditions introduce time dependence into vital rates, and predicting the effect of this variability on population dynamics and persistence is critical for the effective management of natural populations subject to fluctuating environments. In many marine species, dispersal during the larval stage establishes links among populations and is largely determined by temporally variable fluid dynamic processes. However, the consequences of time-dependent dispersal for population persistence are largely unexplored, and so we present a model of stochastically driven dispersal to study population persistence in a temporally variable, patchy habitat. We illustrate how patterns of temporal autocorrelation, expressed as variance in stochastic population connectivity, can have counterintuitive consequences for predictions, where switching between two sets of dynamics, each of which leads to extinction, can promote metapopulation persistence. We contend that accounting for stochastic dispersal can have great relevance for understanding population persistence, in marine populations in particular and in organisms with some degree of passive dispersal in general.}, annote = {-unlike Hastings and Botsford, stochastic dispesal patterns does not require cycles in the pop connnectivity graph - use very simple metapopulation model that allows for stochastic dispersal and autocorrelations in time -discuss lots of previous work on enviornmental stochasticity in growth or reproducitive rates, but less work on dispersal patterns -negative autocorrelation in dispersal allows persistence when there normally would not be persistence (in line with what Sebastian would say)}, author = {Williams, Paul David and Hastings, Alan}, doi = {10.1086/671059}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Williams, Hastings - 2013 - Stochastic dispersal and population persistence in marine organisms.pdf:pdf}, isbn = {00030147}, issn = {1537-5323}, journal = {The American naturalist}, keywords = {Animal Distribution,Animals,Aquatic Organisms,Biological,Ecosystem,Larva,Models,Population Dynamics}, number = {2}, pages = {271--82}, pmid = {23852360}, title = {{Stochastic dispersal and population persistence in marine organisms.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23852360}, volume = {182}, year = {2013} } @article{Kearney2014, abstract = {The magnificence of the Great Barrier Reef and its worthiness of extraordinary efforts to protect it from whatever threats may arise are unquestioned. Yet almost four decades after the establishment of the Great Barrier Reef Marine Park, Australia's most expensive and intensely researched Marine Protected Area, the health of the Reef is reported to be declining alarmingly. The management of the suite of threats to the health of the reef has clearly been inadequate, even though there have been several notable successes. It is argued that the failure to prioritise correctly all major threats to the reef, coupled with the exaggeration of the benefits of calling the park a protected area and zoning subsets of areas as 'no-take', has distracted attention from adequately addressing the real causes of impact. Australia's marine conservation efforts have been dominated by commitment to a National Representative System of Marine Protected Areas. In so doing, Australia has displaced the internationally accepted primary priority for pursuing effective protection of marine environments with inadequately critical adherence to the principle of having more and bigger marine parks. The continuing decline in the health of the Great Barrier Reef and other Australian coastal areas confirms the limitations of current area management for combating threats to marine ecosystems. There is great need for more critical evaluation of how marine environments can be protected effectively and managed efficiently.}, annote = {-argue that expansion of marine parks in Australia has happened without critical evalulation or planning -management shortcomings they argue 1) failure to investigate all causes and impacts and to prioritize them appropriatly 2) need to recongnize difference b/w terretrial and marine environmentts - this misses what the primary threats are in marine setting. To much focus on fishing, not enough on poullution and climate change 4) bad evaluations of the impacts of fishing and the benefits of closing areas 5) inapprorpiiate adaptive management -argue that naming of marine protected areas is important -80{\%} of tourism happens in just 7{\%} of GBR -fishing benefits have not materlized as they had been predicted to}, author = {Kearney, Bob and Farebrother, Graham}, doi = {10.1016/B978-0-12-800214-8.00007-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kearney, Farebrother - 2014 - Inadequate Evaluation and Management of Threats in Australia's Marine Parks, Including the Great Barrier R.pdf:pdf}, isbn = {0065-2881}, issn = {00652881}, journal = {Advances in Marine Biology}, keywords = {Adaptive marine management,Australian marine conservation strategy,Evidence-based marine conservation,Great Barrier Reef Management,Poorly justified restriction of fishing in MPAs,Uncritical science used to underpin marine policy}, pages = {253--288}, pmid = {25358302}, title = {{Inadequate Evaluation and Management of Threats in Australia's Marine Parks, Including the Great Barrier Reef, Misdirect Marine Conservation}}, url = {http://dx.doi.org/10.1016/B978-0-12-800214-8.00007-4}, volume = {69}, year = {2014} } @article{White2010a, abstract = {Variability in larval supply introduces uncertainty into the management$\backslash$nof marine fisheries. This variability can confound short-term population$\backslash$nprojections of both traditional and spatially explicit models of fishery$\backslash$nproductivity. A potential remedy is the use of physical oceanographic$\backslash$nvariables, such as an upwelling index or the Pacific Decadal$\backslash$nOscillation, as proxies for recruitment year class strength. We describe$\backslash$na method for incorporating proxy information into population models for$\backslash$nfishery management. Our model of a conventional fishery (using kelp$\backslash$nrockfish as an example) suggested that proxies were effective in$\backslash$npredicting actual larval survival if there was a strong correlation$\backslash$nbetween the proxy and larval survival (r {\textgreater} 0.8), when recruitment was$\backslash$nhighly variable. Model outputs were most useful when used to hindcast$\backslash$nrather than forecast the population trajectory. A spatial extension of$\backslash$nthe model for marine protected areas (MPAs) confirmed those results and$\backslash$nrevealed that 1) larval dispersal distances did not affect the utility$\backslash$nof the proxy, and 2) adult home range size influenced whether before:$\backslash$nafter or inside: outside biomass ratios provided a more effective metric$\backslash$nof MPA success. We found that proxies greatly improved model projections$\backslash$nover short time scales, but that projections beyond the time needed for$\backslash$nrecruits to enter the fishery were less effective. This work provides an$\backslash$nexample of how information about environmental variability affecting$\backslash$nrecruitment can be incorporated into fishery models to improve$\backslash$nmanagement.}, annote = {- develop simple non spatial and spatial models that incorporate variability in larval survival. They look at how environmental parameters (e.g. PDO) can improve predictions in these models as larval variability correlates well with these types of enviromental factors (the correlation needs to be relatively strong, p{\textgreater}0.8) -point out that it is well know that environmental factors affect larval transport and survival -on short time scales, variability drowns out signal making MPA evaluation difficult}, author = {White, J. Wilson and Rogers-Bennett, Laura}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White, Rogers-Bennett - 2010 - Incorporating physical oceanographic proxies of recruitment into population models to improve fishery and.pdf:pdf}, isbn = {9109624066}, issn = {05753317}, journal = {California Cooperative Oceanic Fisheries Investigations Reports}, pages = {128--149}, title = {{Incorporating physical oceanographic proxies of recruitment into population models to improve fishery and marine protected area management}}, volume = {51}, year = {2010} } @book{Bacaer2011, annote = {Chapter 1: -begins by discussed Fibonacci (Leonardo of Pisa) and rabbit problem -work was not picked up by others -Daniel Bernoilli look at geometric growth Chapter 2: Edmond Halley -used tables created by others to study ortality and births -created an early life table -also worked on insurance problems Chapter 3: Euler and geometric growth -calculated pop growth for london and for human pop growth after the flood Chapter 4: Daniel Bernoulli and smallbox (1760) -invesitaged if inoculatin of small pox was a good idea -shortly after Daniel's work was less imoprtant as Edward Jenner inveted the compox to human vaccination Chapter 5: Malthus and obstacles to geometric growth -argued that population growth would be faster than what hmans could produce for subsistence -strong inflience on Charles Darwin Chapter 6: Verhulst and logistic equation (1838) Chapter 7 - extinction of familty names Chapter 8 - Mendel Chapter 9: Galton, Watson, and extinction Chapter 9: Lotka and stable pop theory -devlopmet of Lotka's equation -writes book Elements of Physical Biology Chapter 13: Lotka-Volterra - Lotka found that checmical reaction models applied to species would indicate that species could cycle -Volterra became interested in work that showed increased number of sharks in catch during world war I when fishing effort was reduced Chapter 16: McKendrick and Kermack (1926-1927) -McKendrick studied medicine and mathematics and often worked in the field -in 1926 he wrote article on "Applications of mathematics to medical problems" -Kermck started in organic chemisty but became completely blind after a lab explosion -Kermack and McKendrick publish SIR model in 1927 --find defintion of R0 and min threshold for pop density --apply model to Bombay plague data --devloped more complicated versions of this model Chapter 26: Contemporay problems -imporant disease issues: AIDS, Ebola, West Nile, SARS, bird flu, chikungunya, HINI influenze -resistence is also a large problem -management of fish populations}, author = {Baca{\"{e}}r, Nicolas}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Baca{\"{e}}r - 2011 - A Short History of Mathematical Population Dynamics.pdf:pdf}, isbn = {9780857291141}, title = {{A Short History of Mathematical Population Dynamics}}, year = {2011} } @article{Kaplan2005, annote = {- this paper looked more interesting than I originally thought. They simply looked at how important variable spacing (as opposed to all reserves being equally spaced) was to various objeccitves -essentially found that variable spacing created minor effects ocmpared to uniform distributions of reserves}, author = {Kaplan, David M. and Botsford, Louis W.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kaplan, Botsford - 2005 - Effects of variability in spacing of coastal marine reserves on fisheries yield and sustainability.pdf:pdf}, isbn = {0027100901730}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, pages = {905--912}, title = {{Effects of variability in spacing of coastal marine reserves on fisheries yield and sustainability}}, volume = {62}, year = {2005} } @article{Watson2012, abstract = {The probability of dispersal from one habitat patch to another is a key quantity in our efforts to understand and predict the dynamics of natural populations. Unfortunately, an often overlooked property of this potential connectivity is that it may change with time. In the marine realm, transient landscape features, such as mesoscale eddies and alongshore jets, produce potential connectivity that is highly variable in time. We assess the impact of this temporal variability by comparing simulations of nearshore metapopulation dynamics when potential connectivity is constant through time (i.e., when it is deterministic) and when it varies in time (i.e., when it is stochastic). We use mathematical analysis to reach general conclusions and realistic biophysical modeling to determine the actual magnitude of these changes for a specific system: nearshore marine species in the Southern California Bight. We find that in general the temporal variability of potential connectivity affects two important quantities: metapopulation growth rates when the species is rare and equilibrium abundances. Our biophysical models reveal that stochastic outcomes are almost always lower than their deterministic counterparts, sometimes by up to 40{\%}. This has implications for how we use spatial information, such as connectivity, to manage nearshore (and other) systems.}, author = {Watson, James R and Kendall, Bruce E and Siegel, David a and Mitarai, Satoshi}, doi = {10.1086/665992}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Watson et al. - 2012 - Changing seascapes, stochastic connectivity, and marine metapopulation dynamics.pdf:pdf}, isbn = {00030147}, issn = {1537-5323}, journal = {The American naturalist}, keywords = {Animals,Animals, Newborn,Ecosystem,Fishes,Models, Biological,Population Dynamics,Stochastic Processes}, number = {1}, pages = {99--112}, pmid = {22673654}, title = {{Changing seascapes, stochastic connectivity, and marine metapopulation dynamics.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22673654}, volume = {180}, year = {2012} } @book{Keeling2007, address = {Princeton, New Jersey}, annote = {Interesting notes: Chapter 2 -compares epi models to metapop where each host is a patch -references Kermack and McKendrink (1927) as first studying simple SIR models -frequency dependent is mass-action whereas density dependent is psueo mass-action -gamma would be recovery rate and 1/gamma would be average infectious period -simple SIR model has been essential for: 1) threshold phenomen - which gives min number of S needed for disease to spread...which then gives you R0 = transmission rate/ average infectious period 2) epidemic burnout (number of S declines during epidemic) -discusses other simple models like those with demogrpahy, mortality, and just SI models -discuss parameterization Chapter 3 - host heterogeneties Chapter 4 - multi pathogen/ multi host models Chpater 5 - temporally forced models Chapter 6 - stochastic dynamics Chapter 7 - spatial models Chapter 8 - controlling infectious diseases}, author = {Keeling, Mattt J. and Rohani, Pejman}, edition = {1}, pages = {366}, publisher = {Princeton University Press}, title = {{Modeling Infectious Diseases in Humans and Animals}}, year = {2007} } @article{Wagner2007, abstract = {We consider the optimal spacing between marine reserves for maximising the viability of a species occupying a reserve network. The closer the networks are placed together, the higher the probability of colonisation of an empty reserve by an occupied reserve, thus increasing population viability. However, the closer the networks are placed together, the higher the probability that a catastrophe will cause extinction of the species in both reserves, thus decreasing population viability. Using a simple discrete-time Markov chain model for the presence or absence of the species in each reserve we determine the distance between the two reserves which provides the optimal trade-off between these processes, resulting in maximum viability of the species. ?? 2006 Elsevier B.V. All rights reserved.}, annote = {-use simple MPA model to detemine distance between patches and what different uncertainty frameworks would predict Results -provide bounds are spacing betweeen reserves -find similar answer to Botsford et al that spacing should be the average dispersal distance -not surprising uncertainty says reserves should be closer together, but it depends -many other factors may matter -current guidelines recommend based on dispersal distance from 10-20 km}, archivePrefix = {arXiv}, arxivId = {math/0309255}, author = {Wagner, L. D. and Ross, J. V. and Possingham, H. P.}, doi = {10.1016/j.ecolmodel.2006.07.030}, eprint = {0309255}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wagner, Ross, Possingham - 2007 - Catastrophe management and inter-reserve distance for marine reserve networks.pdf:pdf}, isbn = {0304-3800}, issn = {03043800}, journal = {Ecological Modelling}, keywords = {Catastrophes,Extinction,Marine reserves,Metapopulation model}, number = {1}, pages = {82--88}, primaryClass = {math}, title = {{Catastrophe management and inter-reserve distance for marine reserve networks}}, volume = {201}, year = {2007} } @article{May2004, abstract = {In the physical sciences, mathematical theory and experimental investigation have always marched together. Mathematics has been less intrusive in the life sciences, possibly because they have until recently been largely descriptive, lacking the invariance principles and fundamental natural constants of physics. Increasingly in recent decades, however, mathematics has become pervasive in biology, taking many different forms: statistics in experimental design; pattern seeking in bioinformatics; models in evolution, ecology, and epidemiology; and much else. I offer an opinionated overview of such uses--and abuses.}, annote = {-discusses path in how science happens and how math enter each stage -a lot of modelers now have little grounding in math - provides examples, like overly-complicated models in HIV, where math was used poorly could you lkook at number of equations, or math density, in papers in different disiplines over time}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {May, Robert M}, doi = {10.1126/science.1094442}, eprint = {arXiv:1011.1669v3}, isbn = {1095-9203 (Electronic)$\backslash$n0036-8075 (Linking)}, issn = {1095-9203}, journal = {Science}, keywords = {Allergy and Immunology,Biological,Biological Science Disciplines,Computational Biology,Computer Simulation,Creutzfeldt-Jakob Syndrome,Creutzfeldt-Jakob Syndrome: prevention {\&} control,Ecology,Evolution,Genetics,HIV Infections,HIV Infections: epidemiology,HIV Infections: immunology,HIV Infections: transmission,Humans,Mathematics,Models,Nonlinear Dynamics,Population,Statistical,Statistics as Topic}, number = {5659}, pages = {790--793}, pmid = {14764866}, title = {{Uses and abuses of mathematics in biology.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/14764866}, volume = {303}, year = {2004} } @book{Lewis2016, address = {Switzerland}, annote = {- some have argued to manage invasive species like we do natural disasters as the are difficult to predict and can cause massive damage... argue you need stochastic models -two central questions: what makes an invader more likely to invade? And what about a community makes it more invadable? -argue for importance of long distance dispersal, stochastiity in initial invasion, and explicent spatial process..also deal with risk management and optimization Chapter 1: introduction -several classic examples: rats and cats on oceanic islands, Muskrat in Eastern Europe (classic work by Skellum), Japanese Beetle in North America, Gray squirrels in UK that have nearly exterpated the red squirrel, a jellyfish psecies in the black sea, gypsy moth in NOrth Americs (it exhibited patchy spread unlike other species), Meeting: Chapter 2: -stages: introduction, establishent, spred, and impact - clain that 10{\%} of introductions actually establish -argue that stochasticity in models of large populations is not important -discrete vs continuous models -single species population model (density dependence, Allee effects) -two species models -HOolling funcatinos -discrete time models -discuss "invasivness" of different species depending on their biology -pg. 54 on dispersal kernels Chapter 3:}, author = {Lewis, Mark A. and Petrovskii, Sergei V. and Potts, Jonathan R.}, booktitle = {Book}, doi = {10.1007/978-3-319-32043-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lewis, Petrovskii, Potts - 2016 - The Mathematics Behind Biological Invasions.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lewis, Petrovskii, Potts - 2016 - The Mathematics Behind Biological Invasions(2).pdf:pdf}, isbn = {978-3-319-32042-7}, pages = {362}, publisher = {Springer International Publishing}, title = {{The Mathematics Behind Biological Invasions}}, year = {2016} } @article{SchreiberSJ2010, abstract = {It is an ecological truism that population persistence depends on$\backslash$na population�s growth rate when rare.$\backslash$n$\backslash$nTo understand the interplay between temporal correlations, spatial$\backslash$nheterogeneity and dispersal on per-$\backslash$n$\backslash$nsistence, an analytic approximation for this growth rate is derived$\backslash$nfor partially mixing populations.$\backslash$n$\backslash$nPartial mixing has two effects on population growth. In the absence$\backslash$nof temporal correlations in relative$\backslash$n$\backslash$nfitness, greater movement to patches with, on average, higher relative$\backslash$nfitness increases population growth$\backslash$n$\backslash$nrates. In the absence of spatial heterogeneity in the average relative$\backslash$nfitnesses, lower dispersal rates$\backslash$n$\backslash$nenhance population growth when temporal autocorrelations of relative$\backslash$nfitness within a patch exceed$\backslash$n$\backslash$ntemporal cross-correlations in relative fitness between patches. This$\backslash$napproximation implies that$\backslash$n$\backslash$nmetapopulations whose expected fitness in every patch is less than$\backslash$n1 can persist if there are positive tem-$\backslash$n$\backslash$nporal autocorrelations in relative fitness, sufficiently weak spatial$\backslash$ncorrelations and the population$\backslash$n$\backslash$ndisperses at intermediate rates. It also implies that movement into$\backslash$nlower quality habitats increases the$\backslash$n$\backslash$npopulation growth rate whenever the net temporal variation in per$\backslash$ncapita growth rates is sufficiently$\backslash$n$\backslash$nlarger than the difference in the means of these per capita growth$\backslash$nrates. Moreover, temporal autocorrela-$\backslash$n$\backslash$ntions, whether they be negative or positive, can enhance population$\backslash$ngrowth for optimal dispersal$\backslash$n$\backslash$nstrategies.}, author = {Schreiber, Sebastian J.}, doi = {10.1098/rspb.2009.2006}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Schreiber - 2010 - Interactive effects of temporal correlations, spatial heterogeneity and dispersal on population persistence.pdf:pdf}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {metapopulation persistence,spatial heterogeneity}, number = {NA}, pages = {1907--1914}, title = {{Interactive effects of temporal correlations, spatial heterogeneity and dispersal on population persistence}}, url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2009.2006}, volume = {277}, year = {2010} } @book{Botsford2014, abstract = {California responded to concerns about overfishing in the 1990s by implementing a network of marine protected areas (MPAs) through two science-based decision-making processes. The first process focused on the Channel Islands, and the second addressed California's entire coastline, pursuant to the state's Marine Life Protection Act (MLPA). We review the interaction between science and policy in both processes, and lessons learned. For the Channel Islands, scientists controversially recommended setting aside 30-50{\%} of coastline to protect marine ecosystems. For the MLPA, MPAs were intended to be ecologically connected in a network, so design guidelines included minimum size and maximum spacing of MPAs (based roughly on fish movement rates), an approach that also implicitly specified a minimum fraction of the coastline to be protected. As MPA science developed during the California processes, spatial population models were constructed to quantify how MPAs were affected by adult fish movement and larval dispersal, i.e., how population persistence within MPA networks depended on fishing outside the MPAs, and how fishery yields could either increase or decrease with MPA implementation, depending on fishery management. These newer quantitative methods added to, but did not supplant, the initial rule-of-thumb guidelines. In the future, similar spatial population models will allow more comprehensive evaluation of the integrated effects of MPAs and conventional fisheries management. By 2011, California had implemented 132 MPAs covering more than 15{\%} of its coastline, and now stands on the threshold of the most challenging step in this effort: monitoring and adaptive management to ensure ecosystem sustainability.}, annote = {- dicusses past management failure sin california and large Santa Barbara oil spill in 1969 -two steps in california: channel islands MPAs and then the rest of the state - identified and tried to have replicates of bioregions protected -all state wide networks have been implemented recently except for the San Fran Bay network -need to include fishery effects on MPAs and MPA effects on fisheries - - the California MPA system was very expensive to implment in the end}, author = {Botsford, Louis W. and White, J. Wilson and Carr, Mark H. and Caselle, Jennifer E.}, booktitle = {Advances in Marine Biology}, doi = {10.1016/B978-0-12-800214-8.00006-2}, edition = {1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botsford et al. - 2014 - Marine Protected Area Networks in California, USA.pdf:pdf}, isbn = {9780128002148}, issn = {00652881}, keywords = {California,Channel Islands,MPA,Planning,Population models,Process,Science}, pages = {205--251}, pmid = {25358301}, publisher = {Elsevier Ltd.}, title = {{Marine Protected Area Networks in California, USA}}, url = {http://dx.doi.org/10.1016/B978-0-12-800214-8.00006-2}, volume = {69}, year = {2014} } @article{Mangel1993, annote = {-develop model to compute extintion properties in populiation experiecning catastophes, compare results to MacArthur-WIlson which has no catastrophes -present reviews of huge dieoffs that are attributed to some catastrophe Truman Young: rate of catastophes around 0.02-0.06 per year for large mammals -catasophes bound extinction times in MW theoreitcal framework}, author = {Mangel, Marc and Tier, Charles}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mangel, Tier - 1993 - Dynamics of metapopulations with demographic stochasticity and environmental catastrophes.pdf:pdf}, journal = {Theoretical Population Biology}, pages = {1--31}, title = {{Dynamics of metapopulations with demographic stochasticity and environmental catastrophes}}, volume = {44}, year = {1993} } @misc{Fretwell1970, abstract = {Fretwell S "Say that in Algebra" Current Contents {\#}8, p.8, February 25, 1991}, author = {Fretwell, Stephen. D.}, booktitle = {Acta Biotheoretica}, pages = {16--36}, title = {{Say that in algebra}}, volume = {19}, year = {1970} } @article{Worm2009, annote = {- looked at 10 large ecosystems to see what ecosystem models and stock assessments said about explotation - 166 stock assessments done around world, overfishing of 35{\%} of stocks - you can look at explotation rates of at biomass compared to B{\_}MSY -also assessed research trawl surveys -increasing number of collapsed stocks over time (14{\%} of stocks assessed were collaped in 2007) -have table of different management strategies: closed areas, gear restrictions, total allowable catch reduced, and catch shares were the most important - how do you actually recover a stock? depends on magnitude of previous decline, loss of biodviersity, life histories, spieces interactions , and climate}, author = {Worm, B. and Hilborn, R. and Baum, J. K. and Branch, T. A. and Collie, J. S. and Costello, C. and Fogarty, M. J. and Fulton, E. A. and Hutchings, J. A. and Jennings, S. and Jensen, O. P. and Lotze, H. K. and Mace, P. M. and McClanahan, T. R. and Minto, C. and Palumbi, S. R. and Parma, A. M. and Ricard, D. and Rosenberg, A. A. and Watson, R. and Zeller, D.}, doi = {10.1126/science.1173146}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Worm et al. - 2009 - Rebuilding Global Fisheries.pdf:pdf}, isbn = {0036-8075}, issn = {0036-8075}, journal = {Science}, number = {5940}, pages = {578--585}, pmid = {19644114}, title = {{Rebuilding Global Fisheries}}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.1173146}, volume = {325}, year = {2009} } @book{Taleb2007, abstract = {Part one - Umberto Eco's antilibrary, or how we seek validation -- Part two - We just can't predict -- Part three - Thos gray swans of extremistan -- Part four - The end.}, annote = {http://andrewgelman.com/2007/04/09/nassim{\_}talebs{\_}t/ Overall, I enjoyed reading Taleb's, The Black Swan. It put a lot of my current research and thoughts into a broad framework. Taleb discussed several aspects of Black Swan, or rare and impactful events: health, finances, and in nature. He spends a lot of effort pushing back on people (especially financial analysts) who do not take rare events in account. He splits his thoughts into two main views: Mediocristan and Extremistan (page 36) The book is not very technical, but he occasionally dives into some probability theory. Since the book has been published he has apparently published several papers on the same topic. He certainly tended to get a bit repetitive and sometimes arrogant, but overall it was still a good read.  There are a number of specific comments I highlighted in the book: pg. 14: shares view that taxi drivers and more educated people can predict to same ability, but taxi cab drivers don't pretend to know how to predict pg. 27: discusses difference between scalable and non scalable professions. For example, a dentist is not scalable b/c it requires time, same with jobs paid by the hour. However, this type of work is also pretty predictable. You can get a steady stream of customers. Conversely, a writer or scientist is driven by “Black Swan” events that lead to lots of success pg. 45: positive black swans take a long time to show there effects while negative black swans can have near instantaneous effects pg. 53: often people separate work from personal lives. e.g. statisticians who cannot answer statistical questions not phrased as statistical questions pg. 57: discusses Popper and falsifiability  pg 61: argues that frequency of earthquakes has not changed much but our ability to handle these events has changed a lot pg. 86: difficulty of working in science b/c an average day involves discovering nothing, which is important but still discouraging. A watch repairman may still fix watches each day pg. 94: if you engage in such black swan work, it is best to be part of a group pg. 146: physchology work on which fields whose experts are really experts true for: livestock judges, chess master, mathematicians, accountants.. no experts for: stockbrokers, clinical psychologists, college admissions officers, intelligence analysts... pg. 147: discusses evolutionary biologist Robert Trivers pg. 179: Discusses Lorenz and chaos theory pg. 183: rails against idea of tenured faculty as they shouldn't be ultimate owners of knowledge pg. 184: argues that optimization is a form of sterile modeling  pg. 204: to take advantage of rare positive events, you need to increase the serendipity around you should also use a barbell strategy in life - be hyper conservative na dhyperagreesive  have 85 percent in safe investments and 15 percent in black swan possibilities  how does this relate to scientific research as well? Spend 15 percent of effort on crazy ideas perhaps? have to take advtange of opportunities all the time to hope one pays off pg 234: begins discusses power law distributions, 80/20 rule,  pg. 257: Galileo wrote: The great book of Nature lies ever open before our eyes and the true philosophy is written in  it{\ldots} But we cannot read it unless we have first learned the language and the characters in which it is written{\ldots} It is written in mathematical language and the characters and triangles, circles, and other geometric figures. pg 267: discusses difficulty in predicting in different directions of time. For example, it is very difficult to calculate the shape of an ice cube after it has melted pg. 315: makes argument that large (or more complex) organisms should be hurt more by large shocks  pg. 316: discusses the larger species density on smaller islands as evidence that Mother Nature does not like too much connectivity and globalization Need redundancy to deal with black swans pg 335: note about papers in last couple of years in scientific journals pg. 350: “ the more remote the event, the less we can get empirical data (assuming generously that the future will resemble the past) and the more we need to rely on theory pg. 355: “ there is no reliable way to compute small probabilities" pg. 362: “The modelers' respond to black swan ideas: “We know all that. Nothing is perfect. The assumptions are reasonable. The assumptions don't matter. The assumptions are conservation. You can't prove the assumptions are wrong. WE're only doing what everybody else does. The decision-maker has to be better off with us than without us. The models aren't totally useless. You have to the best you can with the data. You have to make assumptions in order to make progress. You have to give the models the benefit of the doubt. What's the harm?" pg. 365: four quadrants of payoffs - can use most statistics in one or two quadrants comfortably  pg. 368: discusses how science is not set of to appreciate negative results. The incentives are not there. You need to strive to be the next Darwin or something pg. 370: how to deal with the black swan quadrant avoid optimization, learn to love redundancy  pg. 374: 10 principles for a black swan robust socieity let fragile things break early when they are small no socialization of losses and privatization of gains don't let someone with incentive bonus operative nuclear plant - they will cut corners and take risks pg. 397: power law explanation}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Taleb, Nassim Nicholas}, booktitle = {Penguin Books Ltd}, doi = {10.5465/AMP.2011.61020810}, eprint = {arXiv:1011.1669v3}, isbn = {1400063515 9781400063512 9780713999952}, issn = {1075-2730}, keywords = {Forecasting,Uncertainty (Information theory) -- Social aspects}, number = {November 2008}, pages = {72--78}, pmid = {71833470}, title = {{The black swan : the impact of the highly improbable}}, year = {2007} } @book{Hilborn2014, abstract = {No issue in marine conservation and management seems to have generated as much interest, and controversy as marine protected areas (MPAs). In the past 30 years, a substantial scientific literature on the subject has developed, international agreements have set targets for proportion of the sea to be protected, and hundreds of millions of dollars have been spent on research and advocacy for MPA establishment. While the objectives of MPAs are diverse, few studies evaluate the success of MPAs against stated objectives. It is clear that well-enforced MPAs will protect enough fish from exploitation that within reserves abundance increases, fish live to be larger, and measures of diversity are higher. What is much more poorly understood is the impacts of reserve establishment on areas outside reserves. Theory suggests that when stocks are seriously overfished outside reserves, the yield and abundance outside the reserves may be increased by spillover from the reserve. When stocks are not overexploited, reserve establishment will likely decrease the total yield. The chapters in this volume explore a broad set of case studies of MPAs, their objectives and their outcomes.}, annote = {argues that MPAs are mostly focused on biodiversity first theoretical work on closures was by Beaverton and HOolt 1957 Four conclusions from 2003 special issues effects on yield within reserve is same as increasing size limit effect of yield is same as decreased mortality need low movement for conservation, need intermediate adult movement for successful fishery management - could MPAs be bad for large roaming species longer dispersal means more coastline in reserves  -models would say that fisheries yields only go up for previously heavily fished species}, author = {Hilborn, Ray}, booktitle = {Advances in Marine Biology}, doi = {10.1016/B978-0-12-800214-8.00001-3}, edition = {1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hilborn - 2014 - Introduction to Marine Managed Areas.pdf:pdf}, isbn = {9780128002148}, issn = {00652881}, keywords = {Closed areas,Fisheries management,MPAs,Marine protected areas,Marine reserves,Spatially explicit management}, pages = {1--13}, pmid = {25358296}, publisher = {Elsevier Ltd.}, title = {{Introduction to Marine Managed Areas}}, url = {http://dx.doi.org/10.1016/B978-0-12-800214-8.00001-3}, volume = {69}, year = {2014} } @article{Game2008a, abstract = {It is thought that recovery of marine habitats from uncontrollable disturbance may be faster in marine reserves than in unprotected habitats. But which marine habitats should be protected, those areas at greatest risk or those at least risk? We first defined this problem mathematically for 2 alternate conservation objectives. We then analytically solved this problem for both objectives and determined under which conditions each of the different protection strategies was optimal. If the conservation objective was to maximize the chance of having at least 1 healthy site, then the best strategy was protection of the site at lowest risk. On the other hand, if the goal was to maximize the expected number of healthy sites, the optimal strategy was more complex. If protected sites were likely to spend a significant amount of time in a degraded state, then it was best to protect low-risk sites. Alternatively, if most areas were generally healthy then, counterintuitively, it was best to protect sites at higher risk. We applied these strategies to a situation of cyclone disturbance of coral reefs on Australia's Great Barrier Reef. With regard to the risk of cyclone disturbance, the optimal reef to protect differed dramatically, depending on the expected speed of reef recovery of both protected and unprotected reefs. An adequate consideration of risk is fundamental to all conservation actions and can indicate surprising routes to conservation success.}, annote = {- find that marine reserve location depends strongly on disturbancs risk and speed of recover for reefs in and outside of reserves -there is higher resilience following disturbances for corals -two objectives: 1) select reserves sites to max the expected number of healthy sites 2) max prob that at least one healthy site is present at all times -time spent recovering from disturbance is 1/r, where r is resilience of site and 1/d is time until next disturabce where d is annual probability of distruabnce at site -looked at 2 potenetial reserve sites for coral reef setip, also looked at n reef model -appy model to cycolone data on reefs in GBR -a number of simplifications: cyclones caused binary effect, disturbance prob. oes not change with time, potential positive effects of cycloones You should probably not protect the weakest sites if there is a lot of disturbances present. Instead you should invest in low-risk sites. If most reefs are relatively health, it was better to protect higher-risk sites}, author = {Game, Edward T. and McDonald-Madden, Eve and Puotinen, Marji L. and Possingham, Hugh P.}, doi = {10.1111/j.1523-1739.2008.01037.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Game et al. - 2008 - Should we protect the strong or the weak Risk, resilience, and the selection of marine protected areas.pdf:pdf}, isbn = {1523-1739}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Catastrophes,Coral reefs,Cyclones,Habitat disturbance,Marine reserves,Reserve selection}, number = {6}, pages = {1619--1629}, pmid = {18759769}, title = {{Should we protect the strong or the weak? Risk, resilience, and the selection of marine protected areas}}, volume = {22}, year = {2008} } @article{Mcgilliard2011, annote = {- in face of uncetainty, past work has argued that marine reserves lower probability of extinction and decreases variability in catches -past work has not include explicent spatial structure, density dependence in mortality, consideration of smaller spatial scales -examine different types of catastophes in their model - spatial structure of the population is key -model is 100 patch linear metapop with larvae and adults, larval dispersal, --- the MPA is always 20{\%} of the coastline -local catastophes hurt if pops were centered in one area, surprisngly this was also the result for the global catatrophe (this is b/c of local density dependen mortality) -argue you must distiguish role of uncertainty compared to determinstic skeleton -marine reserves are not always an insurance factor against catastophes - reserves were 20{\%} of coastline, but always as one large reserve in the middle}, author = {McGilliard, Carey R and Punt, Andr{\'{e}} E and Hilborn, Ray}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McGilliard, Punt, Hilborn - 2011 - Spatial structure induced by marine reserves shapes population responses to catastrophes in mathemati.pdf:pdf}, journal = {Ecological Applications}, keywords = {1998,2003,2006,allison et al,catastrophes,catastrophic events,e,extinction threshold,fisheries management,g,halpern et al,lauck et al,mangel 2000,marine,no-take marine reserve,population dynamics,protected areas,spatial modeling,total allowable catch,two common,uncertainties}, number = {4}, pages = {1399--1409}, title = {{Spatial structure induced by marine reserves shapes population responses to catastrophes in mathematical models}}, volume = {21}, year = {2011} } @article{Aber1997, annote = {-begins by discussing disbelif and distrust of modeling by most people. Unfortuantly, few people would say they are a modeler and a field biologist -suggests several things that increase the use and effectiveness of models in ecology: -model strucuture (fully display and explain it), parameterization, model validation (need a case study at least), sensitivity analysis (of parameters and comparing to null, or statistical models), prediction (only after previous steps have been made), make models freely accessible after paper is published2}, author = {Aber, John D}, journal = {Bulletin of the Ecological Society of America}, number = {3}, pages = {232--233}, title = {{Why don't we believe the models ?}}, volume = {78}, year = {1997} } @article{Paine1966, abstract = {It is suggested that local animal species diversity is related to the number of predators in the system and their efficiency in preventing single species from monopolizing some important, limiting, requisite. In the marine rocky intertidal this requisite usually is space. Where predators capable of preventing monopolies are missing, or are experimentally removed, the systems become less diverse. On a local scale, no relationship between latitude (10⚬ to 49⚬ N.) and diversity was found. On a geographic scale, an increased stability of annual production may lead to an increased capacity for systems to support higher-level carnivores. Hence tropical, or other, ecosystems are more diverse, and are characterized by disproportionately more carnivores.}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Paine, Robert T.}, doi = {10.1086/282400}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Paine - 1966 - Food web complexity and species diversity.pdf:pdf}, isbn = {00030147}, issn = {0003-0147}, journal = {The American Naturalist}, number = {910}, pages = {65--75}, pmid = {19425949}, title = {{Food web complexity and species diversity}}, url = {http://www.jstor.org/stable/2459379{\%}5Cnhttp://www.journals.uchicago.edu/doi/10.1086/282400}, volume = {100}, year = {1966} } @article{Halpern2006, abstract = {Ecosystems and the species and communities within them are highly complex systems that defy predictions with any degree of certainty. Managing and conserving these systems in the face of uncertainty remains a daunting challenge, particularly with respect to developing networks of marine reserves. Here we review several modelling frameworks that explicitly acknowledge and incorporate uncertainty, and then use these methods to evaluate reserve spacing rules given increasing levels of uncertainty about larval dispersal distances. Our approach finds similar spacing rules as have been proposed elsewhere - roughly 20-200 km - but highlights several advantages provided by uncertainty modelling over more traditional approaches to developing these estimates. In particular, we argue that uncertainty modelling can allow for (1) an evaluation of the risk associated with any decision based on the assumed uncertainty; (2) a method for quantifying the costs and benefits of reducing uncertainty; and (3) a useful tool for communicating to stakeholders the challenges in managing highly uncertain systems. We also argue that incorporating rather than avoiding uncertainty will increase the chances of successfully achieving conservation and management goals.}, annote = {-paper is really an attempt to introduce decision theory and probabilistic risk assessment into the study of ecological systesms -stress that you need to know where the uncertainty stems from -under severe unceertainty it may not be possible to parameterize probability distributoins --have to move to worst/best case scenarios or using information gap theory -info gap theory - evaluate robustness of decisiosns when only best guesses for parameters are available and then choose the more robust answers instead -use simple MPA model to detemine distance between patches and what different uncertainty frameworks would predict Results -provide bounds are spacing betweeen reserves -find similar answer to Botsford et al that spacing should be the average dispersal distance -not surprising uncertainty says reserves should be closer together, but it depends -many other factors may matter -current guidelines recommend based on dispersal distance from 10-20 km}, author = {Halpern, Benjamin S. and Regan, Helen M. and Possingham, Hugh P. and McCarthy, Michael A.}, doi = {10.1111/j.1461-0248.2005.00827.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Halpern et al. - 2006 - Accounting for uncertainty in marine reserve design.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Dispersal,Marine protected areas,Marine reserves,Metapopulation model,Reserve networks,Spacing,Uncertainty}, number = {1}, pages = {2--11}, pmid = {16958861}, title = {{Accounting for uncertainty in marine reserve design}}, volume = {9}, year = {2006} } @article{Baskett2014, abstract = {Community-level resilience depends on the interaction between multiple populations that vary in individual responses to disturbance. For example, in tropical reefs, some corals can survive higher stress (resistance) while others exhibit faster recovery (engineering resilience) following disturbances such as thermal stress. While each type will negatively affect the other through competition, each might also benefit the other by reducing the potential for an additional competitor such as macroalgae to invade after a disturbance. To determine how community composition affects ecological resilience, we modeled coral-macroalgae interactions given either a resistant coral, a resilient coral, or both together. Having both coral types (i.e., response diversity) can lead to observable enhanced ecological resilience if (1) the resilient coral is not a superior competitor and (2) disturbance levels are high enough such that the resilient coral would collapse when considered alone. This enhanced resilience occurs through competitor-enabled rescue where each coral increases the potential for the other to recover from disturbance through external recruitment, such that both corals benefit from the presence of each other in terms of total cover and resilience. Therefore, conservation management aimed at protecting resilience under global change requires consideration of both diversity and connectivity between sites experiencing differential disturbance.}, author = {Baskett, Marissa L and Fabina, Nicholas S and Gross, Kevin}, doi = {10.1086/676643}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Baskett, Fabina, Gross - 2014 - Response diversity can increase ecological resilience to disturbance in coral reefs.pdf:pdf}, isbn = {0003-0147}, issn = {1537-5323}, journal = {The American naturalist}, keywords = {Animals,Anthozoa,Anthozoa: growth {\&} development,Coral Reefs,Ecosystem,Environment,Herbivory,Models,Seaweed,Seaweed: growth {\&} development,Theoretical}, number = {2}, pages = {E16--31}, pmid = {25058289}, title = {{Response diversity can increase ecological resilience to disturbance in coral reefs.}}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84904796376{\&}partnerID=tZOtx3y1}, volume = {184}, year = {2014} } @article{Powell2015, abstract = {Disease effects on host population dynamics and the transmission of pathogens between hosts are two important challenges for understanding how epizootics wax and wane and how disease influences host population dynamics. For the management of marine shellfish resources, marine diseases pose additional challenges in early intervention after the appearance of disease, management of the diseased population to limit a decline in host abundance, and application of measures to restrain that decline once it occurs. Mathematical models provide one approach for quantifying these effects and addressing the competing goals of managing the diseased population versus managing the disease. The majority of models for molluscan diseases fall into three categories distinguished by these competing goals. (1) Models that consider disease effects on the host population tend to focus on pathogen proliferation within the host. Many of the well-known molluscan diseases are pandemic, in that they routinely reach high prevalence rapidly over large geographic expanses, are characterized by transmission that does not depend upon a local source, and exert a significant influence on host population dynamics. Models focused on disease proliferation examine the influence of environmental change on host population metrics and provide a basis to better manage diseased stocks. Such models are readily adapted to questions of fishery management and habitat restoration. (2) Transmission models are designed to understand the mechanisms triggering epizootics, identify factors impeding epizootic development, and evaluate controls on the rate of disease spread over the host's range. Transmission models have been used extensively to study terrestrial diseases, yet little attention has been given to their potential for understanding the epidemiology of marine molluscan diseases. For management of diseases of wild stocks, transmission models open up a range of options, including the application of area management, manipulation of host abundance, and use of scavengers and filter feeders to limit the concentration of infective particles. (3) The details of host population processes and pathogen transmission dynamics are blended in models that evaluate the effects of natural selection and/or genetic modification in developing disease resistance in the host population. Application of gene-based models to marine diseases is only now beginning and represents a promising approach that may provide a mechanistic basis for managing marine diseases and their host populations. Overall disease models remain both uncommon and underutilized in addressing the needs for managing molluscan diseases and their host populations.}, annote = {-a few classes of models have been developed 1) how pathogen proliferating within host 2) transmission models - what triggers the epizootic development and 3) a combindation of the two types -argue you need hydroynamic models to include free particle transmission models -they don't examine statistical models in this review -contact b/w individuals not major factor (more about environment), infection load is important, salinity matters a lot -details an get complex including energy budgets -some detail on genetics and disease resistence -most management models only have a disease mortality term, nothing more specific -point out that MPAs could harbor disease susceptuble individuals that could seed other areas and prevent resistance -few transmission models (that focus on SI type stuff) have been developed except for hydrodnmaic models or theoretically assumed transmisson processes}, author = {Powell, Eric N. and Hofmann, Eileen E.}, doi = {10.1016/j.jip.2015.07.017}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Powell, Hofmann - 2015 - Models of marine molluscan diseases Trends and challenges.pdf:pdf}, isbn = {0022-2011}, issn = {10960805}, journal = {Journal of Invertebrate Pathology}, keywords = {Gene-based models,Marine disease management models,Marine disease models,Marine disease transmission models,Pathogen proliferation models}, pages = {212--225}, pmid = {26239016}, publisher = {Elsevier Inc.}, title = {{Models of marine molluscan diseases: Trends and challenges}}, url = {http://dx.doi.org/10.1016/j.jip.2015.07.017}, volume = {131}, year = {2015} } @article{Lin2012, archivePrefix = {arXiv}, arxivId = {NIHMS150003}, author = {Lin, George Guan-hua and Scott, Jeffrey G}, doi = {10.1016/j.pestbp.2011.02.012.Investigations}, eprint = {NIHMS150003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lin, Scott - 2012 - NIH Public Access.pdf:pdf}, isbn = {8585348585}, issn = {15378276}, keywords = {cyp6d1 transcription,hr96,musca domestica,phenobarbital induction,pyrethroid resistance}, number = {2}, pages = {130--134}, pmid = {1000000221}, title = {{NIH Public Access}}, volume = {100}, year = {2012} } @article{Mangel1994, annote = {-begin by discusses role of catastrophes -past work has shown importance of including catastrophic mortality in PVA analyses -often difficult to deal with catastophes mathematically Facts people should know: 1) Lewontin and COhen result (but they dont reference it 2) easy to calculate persitence in catastophe models (can calculate mean time and variance in time to extinction) 3) something with MacArthur WIlson 1967 4( Extinction times are approx exponentially distrubuted ...therefore extinctions are likely -discuss how multuple, smaller resrves may be better}, author = {Mangel, Marc and Tier, Charles}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mangel, Tier - 1994 - Four facts every conservation biologist should know about persistence.pdf:pdf}, journal = {Ecology}, number = {3}, pages = {607--614}, title = {{Four facts every conservation biologist should know about persistence}}, volume = {75}, year = {1994} } @article{Schreiber2012, abstract = {Understanding under what conditions populations, whether they be plants, animals or viral particles, persist is an issue of theoretical and practical importance in population biology. Both biotic interactions and environmental fluctuations are key factors that can facilitate or disrupt persistence. One approach to examining the interplay between these deterministic and stochastic forces is the construction and analysis of stochastic difference equations X t+1 = F(X t, $\xi$ t+1), where X t $\epsilon$ R $\kappa$ represents the state of the populations and $\xi$ 1, $\xi$ 2,... is a sequence of random variables representing environmental stochasticity. In the analysis of these stochastic models, many theoretical population biologists are interested in whether the models are bounded and persistent. Here, boundedness asserts that asymptotically X t tends to remain in compact sets. In contrast, persistence requires that X t tends to be 'repelled' by some 'extinction set' S 0 ⊂ R $\kappa$. Here, results on both of these proprieties are reviewed for single species, multiple species and structured population models. The results are illustrated with applications to stochastic versions of the Hassell and Ricker single species models, Ricker, Beverton-Holt, lottery models of competition, and lottery models of rock-paper-scissor games. A variety of conjectures and suggestions for future research are presented. {\textcopyright} 2012 Copyright Taylor and Francis Group, LLC.}, archivePrefix = {arXiv}, arxivId = {arXiv:1109.5967v1}, author = {Schreiber, Sebastian J.}, doi = {10.1080/10236198.2011.628662}, eprint = {arXiv:1109.5967v1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Schreiber - 2012 - Persistence for stochastic difference equations a mini-review.pdf:pdf}, issn = {1023-6198}, journal = {Journal of Difference Equations and Applications}, keywords = {and discrete-time markov processes,applications of markov chains,general,general state spaces,on,population dynamics,stochastic difference equations}, number = {8}, pages = {1381--1403}, title = {{Persistence for stochastic difference equations: a mini-review}}, volume = {18}, year = {2012} } @article{Mangel2000, abstract = {The case for marine reserves is strengthening, and both deterministic and stochastic calculations show that fisheries management using reserves may achieve harvests comparable with management without reserves. Thus, depending upon the metric used, reserves need not disadvantage harvest. Reserves provide a buffer that increases the chances of sustainability of the stock, and thus the fishery. In this paper, I develop methods (deterministic and stochastic) that allow one to determine how much habitat needs to be set aside as reserve, once societal decisions concerning the goals of reserves are made. The answer to the question: “how much habitat needs to be allocated to reserves” is not a simple single number. Rather, it is a procedure that can be employed once biological, operational and social information are provided. The methods also apply to reserves used to aid stock recovery.}, annote = {-allows harvest to be stochastic (all this is is additional mortality on the stock caused by whatever) -shows that reserve fraction has to increase with an increased coefficient of varaiatino of U(t) (once you get above some level of variability, you must use marine reserves)}, author = {Mangel, Marc}, doi = {10.1046/j.1461-0248.2000.00104.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mangel - 2000 - On the fraction of habitat allocated to marine reserves.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Marine protected areas,Marine reserves,Sustainable fisheries}, number = {1}, pages = {15--22}, pmid = {111}, title = {{On the fraction of habitat allocated to marine reserves}}, volume = {3}, year = {2000} } @article{Sokolow2009, abstract = {Coral reefs are experiencing devastating mortality due, in part, to emerging disease. Despite this growing problem, the long-term consequences of infectious disease in marine ecosystems remain poorly understood, and the application of epidemiological models to marine disease systems represents a research priority for managing resources in the world's oceans. Metapopulation models may provide a framework for modelling coral population dynamics at the regional scale, and we use this approach to investigate the effects of infectious disease. The model presented here incorporates a susceptible-infected or 'S-I' disease into a system of patchily distributed, dynamic coral hosts, and highlights some basic differences that set many marine disease systems apart from their terrestrial counterparts. The model predicts several possible long-term outcomes of disease introduction, and suggests that the consequences of disease may vary considerably among different pathogens and regions. Due to the long time-scales for coral dynamics, epizootics are expected to be prolonged with recovery slow at the regional scale. Our model results show how infectious disease can substantially alter host metapopulation dynamics, with some non-linear relationships which are likely to affect the response of these systems to management and environmental change. For example, higher rates of coral colonization can have variable consequences for host population occupancy (i.e. coral cover) when infectious disease is considered, and chronic diseases with long-lived pathogens pose the highest risks for regional coral extinction. Synthesis and applications. We present a tractable epidemiological model within a metapopulation framework and compare the model output with empirical data for a white plague type II (WPII) outbreak among coral of the upper Florida Keys. We conclude that this model fits well with the spatial and temporal patterns of WPII over a decade. Despite terrestrial2013marine differences, many patterns derived from our model are consistent with epidemiological principles. Thus, the careful application of these principles within the context of marine management may be a promising research frontier. Although we focus on coral disease, the methods and results may apply to other marine metapopulations.}, annote = {-discuss how models have to be different for marine systems (e.g. in the water column) and pathogens may be sensitive to enviriomental conditiosn -apply framework to white plague type II which affects hard corals in Caribbean -use SI model with proportion of patches infected with Levins style metapop setup (could you make this model explicent?) -discuss how connecticity can be bad or good for disease management -stochastic variability is important}, author = {Sokolow, Susanne H. and Foley, Patrick and Foley, Janet E. and Hastings, Alan and Richardson, Laurie L.}, doi = {10.1111/j.1365-2664.2009.01649.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sokolow et al. - 2009 - Disease dynamics in marine metapopulations Modelling infectious diseases on coral reefs.pdf:pdf}, isbn = {1365-2664}, issn = {00218901}, journal = {Journal of Applied Ecology}, keywords = {Coral conservation,Coral health,Disease management,Emerging infectious disease,Epidemiology,Marine ecology,Model,Simulation}, number = {3}, pages = {621--631}, title = {{Disease dynamics in marine metapopulations: Modelling infectious diseases on coral reefs}}, volume = {46}, year = {2009} } @article{Hastings2016, author = {Hastings, Alan}, doi = {10.1073/pnas.1604974113}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 2016 - Timescales and the management of ecological systems.pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, pages = {201604974}, title = {{Timescales and the management of ecological systems}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1604974113}, year = {2016} } @article{BalD.V.andRao1984, author = {{Bal, D. V. and Rao}, K. V.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bal, D. V. and Rao - 1984 - Marine fisheries.pdf:pdf}, pages = {457}, title = {{Marine fisheries}}, year = {1984} } @book{Lande2003, abstract = {This chapter discusses a number of issues related to measuring poverty over time. It highlights some of the key normative decisions that have to be taken, in particular, the role of compensation over time (whether poverty spells can be compensated for by non-poverty spells); the issue of the discount rate (whether each spell should be given an equal weight); and the issue of the role of persistence (whether repeated spells should be given a higher weight). It offers a number of plausible poverty measures, each with different assumptions regarding these key issues, and shows how these insights can be used to construct a forward-looking measure of vulnerability. The chapter applies a number of these measures to data from rural Ethiopia, and shows that while correlations are high, there would still be considerable differences in ranking households by poverty according to different measures, especially those that have different views on the role of compensation}, annote = {-discuss old Pimm papers on amount of varviabilty in populations -population sizes in sequaetional years are not indepenedent -determinstic part of dynamics would be incrrease or decrease in pop size, also detemrinsitic cycles -confident that most population fluctuations are stochastic and not the result of noisy cycles or chaos -have demographic stoch, environ stoch, and sampling error -classify random catastropehs as extreme form of ES (Shaffer 1987)}, archivePrefix = {arXiv}, arxivId = {arXiv:cond-mat/0402594v3}, author = {Lande, Russell and Engen, Steinar and Saether, Bert-Erik}, doi = {10.1093/acprof}, eprint = {0402594v3}, isbn = {9780199682676}, issn = {0873626X}, keywords = {Olfaction,Olfactory experience,Representationalism,Subjectivism}, number = {38}, pages = {45--66}, pmid = {16683413}, primaryClass = {arXiv:cond-mat}, publisher = {Oxford University Press}, title = {{Stochastic Population Dynamics in Ecology and Conservation}}, volume = {6}, year = {2003} } @article{Lawson2015, abstract = {Species' responses to environmental changes such as global warming are affected not only by trends in mean conditions, but also by natural and human-induced environmental fluctuations. Methods are needed to predict how such environmental variation affects ecological and evolutionary processes, in order to design effective strategies to conserve biodiversity under global change. Here, we review recent theoretical and empirical studies to assess: (1) how populations respond to changes in environmental variance, and (2) how environmental variance affects population responses to changes in mean conditions. Contrary to frequent claims, empirical studies show that increases in environmental variance can increase as well as decrease long-term population growth rates. Moreover, environmental variance can alter and even reverse the effects of changes in the mean environment, such that even if environmental variance remains constant, omitting it from population models compromises their ability to predict species' responses to changes in mean conditions. Drawing on theory relating these effects of environmental variance to the curvatures of population growth responses to the environment, we outline how species' traits such as phylogenetic history and body mass could be used to predict their responses to global change under future environmental variability.}, annote = {-discsuss past work on environmental variability in both theory and empirical context -most studies have concluded effect of environmetanl variance on stochastic growth rate to be weak -climate studies think changes in th emean ar emore important -discuss changes in means, variances, and mean-temperature interactions}, author = {Lawson, Callum R. and Vindenes, Yngvild and Bailey, Liam and van de Pol, Martijn}, doi = {10.1111/ele.12437}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lawson et al. - 2015 - Environmental variation and population responses to global change.pdf:pdf}, isbn = {1461-0248}, issn = {14610248}, journal = {Ecology Letters}, keywords = {Climate change,Climate fluctuations,Climate variation,Demographic rates,Extreme events,Functional type,Global warming,Stochastic growth rate,Temperature variation,Thermal performance}, number = {7}, pages = {724--736}, pmid = {25900148}, title = {{Environmental variation and population responses to global change}}, volume = {18}, year = {2015} } @article{Maynard2016, abstract = {To forecast marine disease outbreaks as oceans warm requires new environmental surveillance tools. We describe an iterative process for developing these tools that combines research, development and deployment for suitable systems. The first step is to identify candidate host–pathogen systems. The 24 candidate systems we identified include sponges, corals, oysters, crustaceans, sea stars, fishes and sea grasses (among others). To illustrate the other steps, we present a case study of epizootic shell disease (ESD) in the American lobster. Increasing prevalence of ESD is a contributing factor to lobster fishery collapse in southern New England (SNE), raising concerns that disease prevalence will increase in the northern Gulf of Maine under climate change. The lowest maximum bottom temperature associated with ESD prevalence in SNE is 12°C. Our seasonal outlook for 2015 and long-term projections show bottom temperatures greater than or equal to 12°C may occur in this and coming years in the coastal bays of Maine. The tools presented will allow managers to target efforts to monitor the effects of ESD on fishery sustainability and will be iteratively refined. The approach and case example highlight that temperature-based surveillance tools can inform research, monitoring and management of emerging and continuing marine disease threats.}, annote = {-give example of monitoring and projecting forward has already been done for coral bleaching, why not do it for others? --"temperature-based survellance tools" -identified 24 host pathogen systems that are sensitive to temperature, and therefore possible for modeling --Vibrio, MSX, oyster disease, black band dissease in stony tropical corals, eelgrass wasting disease (Zoestra), American lobster) -need data on temperature peferomance curve of host pathogen system, temperature in spatial and temporal context}, author = {Maynard, Jeffrey and Hooidonk, Ruben Van and Harvell, C Drew and Eakin, C Mark and Liu, Gang and Willis, Bette L and Williams, Gareth J and Groner, Maya L and Dobson, Andrew and Heron, Scott F and Glenn, Robert and Reardon, Kathleen and Shields, Jeffrey D}, doi = {10.1098/rstb.2015.0208}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Maynard et al. - 2016 - Improving marine disease surveillance through sea temperature monitoring, outlooks and projections.pdf:pdf}, isbn = {0962-8436}, issn = {14712970}, journal = {Philosophical Transactions of the Royal Society of London B}, number = {1689}, pages = {20150208}, title = {{Improving marine disease surveillance through sea temperature monitoring, outlooks and projections}}, volume = {371}, year = {2016} } @article{Cowen2009, abstract = {Connectivity, or the exchange of individuals among marine populations, is a central topic in marine ecology. For most benthic marine species with com-plex life cycles, this exchange occurs primarily during the pelagic larval stage. The small size of larvae coupled with the vast and complex fluid environment they occupy hamper our ability to quantify dispersal and connectivity. Ev-idence from direct and indirect approaches using geochemical and genetic techniques suggests that populations range from fully open to fully closed. Understanding the biophysical processes that contribute to observed disper-sal patterns requires integrated interdisciplinary approaches that incorporate high-resolution biophysical modeling and empirical data. Further, differen-tial postsettlement survival of larvae may add complexity to measurements of connectivity. The degree to which populations self recruit or receive subsidy from other populations has consequences for a number of fundamental eco-logical processes that affect population regulation and persistence. Finally, a full understanding of population connectivity has important applications for management and conservation.}, author = {Cowen, Robert K and Sponaugle, Su}, doi = {10.1146/annurev.marine.010908.163757}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cowen, Sponaugle - 2009 - Larval Dispersal and Marine Population Connectivity.pdf:pdf}, isbn = {1941-1405 978-0-8243-4501-3}, issn = {1941-1405}, journal = {Annu. Rev. Mar. Sci}, keywords = {biophysical modeling,complex life cycles,larval transport,metapopulation,population dynamics,self recruitment}, pages = {443--66}, pmid = {21141044}, title = {{Larval Dispersal and Marine Population Connectivity}}, url = {www.annualreviews.org}, volume = {1}, year = {2009} } @article{Reed2016, abstract = {Many ecological processes play out over longer time scales and larger spatial scales than can be studied in a traditional 2–4-year grant cycle. Uncertainties in future funding hinder efforts to implement comprehensive research programs that integrate coupled time series observations of physical variables and ecological responses, manipulative experiments and synthetic analyses over the long term. Such research is essential for advancing our understanding of ecological responses associated with climate change, and the physical and biological processes that control them. This need is perhaps greatest for ecosystems that display highly dynamic and spatially complex patterns that are difficult to explain with short-term, small-scale studies. Such is the case for kelp forest ecosystems, which often show tremendous spatial and temporal variability in resource supply, consumer control and physical disturbance across spatial scales of metres to hundreds of kilometres and temporal scales of hours to decades. Here we present four examples from the Santa Barbara Coastal Long-term Ecological Research project that demonstrate the value of a broad temporal and spatial perspective in understanding the causes and ecological consequences of short-term local dynamics of giant kelp forests of California, USA. }, annote = {-point out difficulty in doing longterm, spatially broad work with current institutions -also cite Reed et al 2011 on wave disturbance being majhor control of primary productivity -argue that coastal reefs and coastal zones more generally fluctuate a lot - kelp foresrts especiially fluctuate as they dont handle disturbances well but can in fact respond to disturbances quickl therefter -NPP and macroalgal biomass collected over 10 years, argue that disturbances before growing season overwhelm both bottom up and top down processes -{\textgreater} could increase scale using landsat images}, author = {Reed, Daniel C. and Rassweiler, Andrew R. and Miller, Robert J. and Page, Henry M. and Holbrook, Sally J.}, doi = {10.1071/MF14158}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reed et al. - 2016 - The value of a broad temporal and spatial perspective in understanding dynamics of kelp forest ecosystems.pdf:pdf}, issn = {13231650}, journal = {Marine and Freshwater Research}, keywords = {climate change,community structure and dynamics,human impacts,long-term ecological research,marine protected areas,net primary production,stable isotopes,trophic relationships}, number = {1}, pages = {14--24}, title = {{The value of a broad temporal and spatial perspective in understanding dynamics of kelp forest ecosystems}}, volume = {67}, year = {2016} } @article{Gerber2014a, abstract = {Effective spatial management in the ocean requires a network of conservation areas that are connected by larval and adult dispersal. We propose a conceptual framework for including the likely impacts of a changing climate on marine connectivity, and synthesize information on the relationships between changing ocean temperature and acidification, connectivity and conservation tools. Our framework relies on concepts of functional connectivity, which depends on an organism's biological and behavioral responses to the physical environment, and structural connectivity, which describes changes in the physical and spatial structure of the environment that affect connectivity and movement. Our review confirms that ocean climate change likely reduces potential dispersal distance and therefore functional connectivity. Structural connectivity in the ocean will inevitably change with the spatial arrangement of biogenic habitats resulting from disturbance as well as enhanced growth and mortality due to climate change. Climate change will also likely reduce the spatial scale of connectivity, suggesting that we will need more closely spaced protected areas.}, annote = {-discuss how climate change affects physilogy and fitness -discussion of looking at more than one variable at a time -discuss connectivity via functional (niological) and structural (abiotic facotrs) connecvity -For reserve design need to consider mean larval dispersal distance (why just mean?) -with variability is disp distances, reserve spacing is less important then reserve size (Kaplan 2006) -need to capture adequate fraction of larvae -argue connectivity will be reduced in warmer, more acidic oceans}, author = {Gerber, Leah R and {Del Mark Mancha-Cisneros}, Maria and O'Connor, Mary and Selig, Elizabeth R}, doi = {10.1890/ES13-00336.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gerber et al. - 2014 - Climate change impacts on connectivity in the ocean Implications for conservation.pdf:pdf}, isbn = {2150-8925}, issn = {2150-8925}, journal = {Ecosphere}, keywords = {climate change,connectivity,dispersal,marine reserves,marine spatial planning,ocean acidification}, number = {3}, pages = {1--18}, title = {{Climate change impacts on connectivity in the ocean: Implications for conservation}}, volume = {5}, year = {2014} } @article{McDonald-Madden2011, abstract = {Research on the allocation of resources to manage threatened species typically assumes that the state of the system is completely observable; for example whether a species is present or not. The majority of this research has converged on modeling problems as Markov decision processes (MDP), which give an optimal strategy driven by the current state of the system being managed. However, the presence of threatened species in an area can be uncertain. Typically, resource allocation among multiple conservation areas has been based on the biggest expected benefit (return on investment) but fails to incorporate the risk of imperfect detection. We provide the first decision-making framework for confronting the trade-off between information and return on investment, and we illustrate the approach for populations of the Sumatran tiger (Panthera tigris sumatrae) in Kerinci Seblat National Park. The problem is posed as a partially observable Markov decision process (POMDP), which extends MDP to incorporate incomplete detection and allows decisions based on our confidence in particular states. POMDP has previously been used for making optimal management decisions for a single population of a threatened species. We extend this work by investigating two populations, enabling us to explore the importance of variation in expected return on investment between populations on how we should act. We compare the performance of optimal strategies derived assuming complete (MDP) and incomplete (POMDP) observability. We find that uncertainty about the presence of a species affects how we should act. Further, we show that assuming full knowledge of a species presence will deliver poorer strategic outcomes than if uncertainty about a species status is explicitly considered. MDP solutions perform up to 90{\%} worse than the POMDP for highly cryptic species, and they only converge in performance when we are certain of observing the species during management: an unlikely scenario for many threatened species. This study illustrates an approach to allocating limited resources to threatened species where the conservation status of the species in different areas is uncertain. The results highlight the importance of including partial observability in future models of optimal species management when the species of concern is cryptic in nature.}, annote = {- this paper examines how partially observable markov chain models can be used to manage rare species - they compare POMCM to standard MC models to see when detection is important - they use sumatran tiger example to explore which of two areas you should conduct censuses, manage, and spend resources on - begin by setting up obectives, ations, and model definitions}, author = {McDonald-Madden, Eve and Chad{\`{e}}s, Iadine and McCarthy, Michael A. and Linkie, Matthew and Possingham, Hugh P.}, doi = {10.1890/09-2075.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McDonald-Madden et al. - 2011 - Allocating conservation resources between areas where persistence of a species is uncertain.pdf:pdf}, isbn = {1051-0761}, issn = {10510761}, journal = {Ecological Applications}, keywords = {Decision theory,Detectability,Partially observable Markov decision process,Poaching,Return on investment,Sumatran tiger,Surveying,Threatened species management}, number = {3}, pages = {844--858}, pmid = {21639049}, title = {{Allocating conservation resources between areas where persistence of a species is uncertain}}, volume = {21}, year = {2011} } @article{Yokomizo2014, abstract = {Many species are threatened by human activity through processes such as habitat modification, water management, hunting, and introduction of invasive species. These anthropogenic threats must be mitigated as efficiently as possible because both time and money available for mitigation are limited. For example, it is essential to address the type and degree of uncertainties present to derive effective management strategies for managed populations. Decision science provides the tools required to produce effective management strategies that can maximize or minimize the desired objective(s) based on imperfect knowledge, taking into account stochasticity. Of particular importance are questions such as how much of available budgets should be invested in reducing uncertainty and which uncertainties should be reduced. In such instances, decision science can help select efficient environmental management actions that may be subject to stochasticity and imperfect knowledge. Here, we review the use of decision science in environmental management to demonstrate the utility of the decision science framework. Our points are illustrated using examples from the literature. We conclude that collaboration between theoreticians and practitioners is crucial to maximize the benefits of decision science's rational approach to dealing with uncertainty.}, annote = {- you have stochasticity in a system and imperfect knowledge about that system}, author = {Yokomizo, Hiroyuki and Coutts, Shaun R. and Possingham, Hugh P.}, doi = {10.1007/s10144-013-0421-2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yokomizo, Coutts, Possingham - 2014 - Decision science for effective management of populations subject to stochasticity and imperfect kn.pdf:pdf}, isbn = {1438-3896}, issn = {14383896}, journal = {Population Ecology}, keywords = {Adaptive management,Information-gap decision theory,Monitoring,Stochastic dynamic programming,Uncertainty,Value of information analysis}, number = {1}, pages = {41--53}, title = {{Decision science for effective management of populations subject to stochasticity and imperfect knowledge}}, volume = {56}, year = {2014} } @article{Hastings2003a, abstract = {We compare and contrast the design of networks of marine reserves for two different, commonly stated goals: (1) maintaining high yield in fisheries and (2) conserving biodiversity, in an idealized setting using simple models. The models describe larval dispersal over a system of evenly spaced reserves of equal size, assuming sedentary adults. We initially demonstrate that, since populations in reserve systems can be sustained either by covering a minimal fraction of the coast with small reserves or by covering a smaller fraction of the coast with few large reserves, cost considerations dictate that the conservation goal would be best met by reserves as large as practically possible. In contrast, the fisheries goal of maximizing yield requires maximizing larval export outside of reserves, which we show means that reserves should be as small as practically possible. Meeting the fisheries goal is ultimately more costly because it suggests a larger area of the coastline should be in reserves, but it also improves on conservation goals by enhancing sustainability for species dispersing longer distances.}, annote = {-results say that for consevation it is best to have one large reserve where as for fisheries it is best to have many small reserves (to export larvae out of reserves to fished areas) -my hypothesis would be a single large reserve would not be the result given disturbances}, author = {Hastings, Alan and Botsford, Louis W}, doi = {10.1890/1051-0761(2003)013[0065:CDOMRF]2.0.CO;2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Botsford - 2003 - Comparing designs of marine reserves for fisheries and for biodiversity.pdf:pdf}, issn = {10510761}, journal = {Ecological Applications}, keywords = {biodiversity,conservation,dispersal,fisheries,marine reserves,models.}, number = {1}, pages = {S65--S70}, title = {{Comparing designs of marine reserves for fisheries and for biodiversity}}, volume = {13}, year = {2003} } @article{Mellin2016, abstract = {With marine biodiversity declining globally at accelerating rates, maximising the effectiveness of conservation has become a key goal for local, national and international regulators. Marine protected areas (MPAs) have been widely advocated for conserving and managing marine biodiversity yet, despite extensive research, their benefits for conserving non-target species and wider ecosystem functions remain unclear. Here, we demonstrate that MPAs can increase the resilience of coral reef communities to natural disturbances, including coral bleaching, coral diseases, Acanthaster planci outbreaks and storms. Using a 20-year time series from Australia's Great Barrier Reef, we show that within MPAs, (1) reef community composition was 21–38{\%} more stable; (2) the magnitude of disturbance impacts was 30{\%} lower and (3) subsequent recovery was 20{\%} faster that in adjacent unprotected habitats. Our results demonstrate that MPAs can increase the resilience of marine communities to natural disturbance possibly through herbivory, trophic cascades and portfolio effects.}, annote = {-comparing corals in and outside of MPAs and evaluated their responses to bleaching, diseases, and storms -20 year data set of GBR -could use this type of model in Fabina's framework for more specifics (and reprlicates with each MPA or not MPA)}, author = {Mellin, Camille and {Aaron Macneil}, M. and Cheal, Alistair J. and Emslie, Michael J. and {Julian Caley}, M.}, doi = {10.1111/ele.12598}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mellin et al. - 2016 - Marine protected areas increase resilience among coral reef communities.pdf:pdf}, isbn = {1461-0248}, issn = {14610248}, journal = {Ecology Letters}, keywords = {Acanthaster planci,Benthos,Biodiversity,Bleaching,Crown-of-thorns starfish,Cyclone,Disturbance,Fish,Great Barrier Reef,Marine reserves}, number = {6}, pages = {629--637}, pmid = {27038889}, title = {{Marine protected areas increase resilience among coral reef communities}}, volume = {19}, year = {2016} } @article{Hewson2014, abstract = {Populations of at least 20 asteroid species on the Northeast Pacific Coast have recently experienced an extensive outbreak of sea-star (asteroid) wasting disease (SSWD). The disease leads to behavioral changes, lesions, loss of turgor, limb autotomy, and death characterized by rapid degradation ("melting"). Here, we present evidence from experimental challenge studies and field observations that link the mass mortalities to a densovirus (Parvoviridae). Virus-sized material (i.e., {\textless}0.2 $\mu$m) from symptomatic tissues that was inoculated into asymptomatic asteroids consistently resulted in SSWD signs whereas animals receiving heat-killed (i.e., control) virus-sized inoculum remained asymptomatic. Viral metagenomic investigations revealed the sea star-associated densovirus (SSaDV) as the most likely candidate virus associated with tissues from symptomatic asteroids. Quantification of SSaDV during transmission trials indicated that progression of SSWD paralleled increased SSaDV load. In field surveys, SSaDV loads were more abundant in symptomatic than in asymptomatic asteroids. SSaDV could be detected in plankton, sediments and in nonasteroid echinoderms, providing a possible mechanism for viral spread. SSaDV was detected in museum specimens of asteroids from 1942, suggesting that it has been present on the North American Pacific Coast for at least 72 y. SSaDV is therefore the most promising candidate disease agent responsible for asteroid mass mortality.}, annote = {-hypothesis of wasting disease include storms, temp, starvation, pathogens -early evidence showed that wasting disease appearing to be contagious (aqriums that did not use UV to sterlize water had seastar dieoffs) -team could not identify any microbes on tissues, so they proposed viruses -also seee it can be transmitted for symptomatic individuals to those susceptible -identified densovirus genome through metagenotmics (similar viruses found for sea urchins and other echinoderms) -then looked and viral load and prevalence in the field -having wasting disease was associated with virus load, being from southern location, starfish size -dont need host-suceptiple contact, can be in water coloum -why didn't virus cause large outbreaks in the past? -how much does density matter?}, author = {Hewson, Ian and Button, Jason B and Gudenkauf, Brent M and Miner, Benjamin and Newton, Alisa L and Gaydos, Joseph K and Wynne, Janna and Groves, Cathy L and Hendler, Gordon and Murray, Michael and Fradkin, Steven and Breitbart, Mya and Fahsbender, Elizabeth and Lafferty, Kevin D and Kilpatrick, A Marm and Miner, C Melissa and Raimondi, Peter and Lahner, Lesanna and Friedman, Carolyn S and Daniels, Stephen and Haulena, Martin and Marliave, Jeffrey and Burge, Colleen A and Eisenlord, Morgan E and Harvell, C Drew}, doi = {10.1073/pnas.1416625111}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hewson et al. - 2014 - Densovirus associated with sea-star wasting disease and mass mortality.pdf:pdf}, isbn = {1091-6490 (Electronic)$\backslash$r0027-8424 (Linking)}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {Animals,Conservation of Natural Resources,Conservation of Natural Resources: methods,DNA, Viral,DNA, Viral: genetics,DNA, Viral: isolation {\&} purification,Densovirus,Densovirus: genetics,Densovirus: physiology,Environmental Monitoring,Environmental Monitoring: methods,Gene Expression Regulation, Viral,Geography,Geologic Sediments,Geologic Sediments: virology,Host-Pathogen Interactions,Metagenome,Metagenome: genetics,North America,Pacific Ocean,Phylogeny,Plankton,Plankton: virology,Population Density,Population Dynamics,Reverse Transcriptase Polymerase Chain Reaction,Seawater,Seawater: virology,Species Specificity,Starfish,Starfish: classification,Starfish: genetics,Starfish: virology,Viral Proteins,Viral Proteins: genetics}, number = {48}, pages = {17278--83}, pmid = {25404293}, title = {{Densovirus associated with sea-star wasting disease and mass mortality.}}, url = {http://www.pnas.org/cgi/content/long/111/48/17278}, volume = {111}, year = {2014} } @article{Groner2016, abstract = {Infectious marine diseases can decimate populations and are increasing among some taxa due to global change and our increasing reliance on marine environments. Marine diseases become emergencies when significant ecological, economic or social impacts occur. We can prepare for and manage these emergencies through improved surveillance, and the development and iterative refinement of approaches to mitigate disease and its impacts. Improving surveillance requires fast, accurate diagnoses, forecasting disease risk and real-time monitoring of disease-promoting environmental conditions. Diversifying impact mitigation involves increasing host resilience to disease, reducing pathogen abundance and managing environmental factors that facilitate disease. Disease surveillance and mitigation can be adaptive if informed by research advances and catalysed by communication among observers, researchers and decision-makers using information-sharing platforms. Recent increases in the awareness of the threats posed by marine diseases may lead to policy frameworks that facilitate the responses and management that marine disease emergencies require.}, annote = {-stress importance of moditoring environmental variables relvant to organims (the right scale) and to create predictive models from these}, author = {Groner, Maya L and Maynard, Jeffrey and Breyta, Rachel and Carnegie, Ryan B and Dobson, Andy and Friedman, Carolyn S and Froelich, Brett and Garren, Melissa and Gulland, Frances M D and Heron, Scott F and Noble, Rachel T and Revie, Crawford W and Shields, Jeffrey D and Vanderstichel, Rapha{\"{e}}l and Weil, Ernesto and Wyllie-Echeverria, Sandy and Harvell, C Drew}, doi = {10.1098/rstb.2015.0364}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Groner et al. - 2016 - Managing marine disease emergencies in an era of rapid change.pdf:pdf}, issn = {1471-2970}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {ecology,epidemiology,health and disease and}, number = {1689}, pmid = {26880835}, title = {{Managing marine disease emergencies in an era of rapid change.}}, url = {http://rstb.royalsocietypublishing.org/content/371/1689/20150364.abstract}, volume = {371}, year = {2016} } @article{Lamb2016, abstract = {Marine protected areas can prevent over-exploitation, but their effect on marine diseases is less clear. We examined how marine reserves can reduce diseases affecting reef-building corals following acute and chronic disturbances. One year after a severe tropical cyclone, corals inside reserves had sevenfold lower levels of disease than those in non-reserves. Similarly, disease prevalence was threefold lower on reserve reefs following chronic exposure to terrestrial run-off from a degraded river catchment, when exposure duration was below the long-term site average. Examination of 35 predictor variables indicated that lower levels of derelict fishing line and injured corals inside reserves were correlated with lower levels of coral disease in both case studies, signifying that successful disease mitigation occurs when activities that damage reefs are restricted. Conversely, reserves were ineffective in moderating disease when sites were exposed to higher than average levels of run-off, demonstrating that reductions in water quality undermine resilience afforded by reserve protection. In addition to implementing protected areas, we highlight that disease management efforts should also target improving water quality and limiting anthropogenic activities that cause injury.}, annote = {- found that corals in reserves had lower levels of disease following a tropical cyclone - stresss that effect of marine reserves depends on if disease is density dependent or driven by environment}, author = {Lamb, Joleah B. and Wenger, Amelia S. and Devlin, Michelle J. and Ceccarelli, Daniela M. and Williamson, David H. and Willis, Bette L.}, doi = {10.1098/rstb.2015.0210}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lamb et al. - 2016 - Reserves as tools for alleviating impacts of marine disease.pdf:pdf}, issn = {0962-8436}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {ecology,environmental science}, number = {1689}, pages = {20150210}, pmid = {26880842}, title = {{Reserves as tools for alleviating impacts of marine disease}}, url = {http://rstb.royalsocietypublishing.org/lookup/doi/10.1098/rstb.2015.0210}, volume = {371}, year = {2016} } @article{Botsford2001, abstract = {Marine reserves hold promise for maintaining biodiversity and sustainable fishery management, but studies supporting them have not addressed a crucial aspect of sustainability: the reduction in viability of populations with planktonic larvae dispersing along a coastal habitat with noncontiguous marine reserves. We show how sustainability depends on the fraction of natural larval settlement (FNLS) remaining after reserves are implemented, which in turn depends on reserve configuration and larval dispersal distance. Sustainability requires FNLS to be greater than an empirically determined minimum, Maintaining an adequate value for all species requires either a large, unlikely fraction ({\textgreater} 35{\%}) of coastline in reserves, or reserves that are larger than the mean larval dispersal distance of the target species. FNLS is greater for species dispersing shorter distances, which implies reserves can lead to: (1) changes in community composition and (2) genetic selection fur shorter dispersal distance. Dependence of sustainability on dispersal distance is a new source of uncertainty.}, author = {Botsford, L. W. and Hastings, A. and Gaines, S. D.}, doi = {10.1046/j.1461-0248.2001.00208.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botsford, Hastings, Gaines - 2001 - Dependence of sustainability on the configuration of marine reserves and larval dispersal distance.pdf:pdf}, isbn = {1461-023X}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Dispersal,Fisheries,Marine reserves,Sustainability,Uncertainty}, number = {2}, pages = {144--150}, pmid = {99}, title = {{Dependence of sustainability on the configuration of marine reserves and larval dispersal distance}}, volume = {4}, year = {2001} } @article{Neubert2003, abstract = {Advocates of no-take marine reserves emphasize their conservation benefits. Critics counter that reserves would decrease fisheries yield. Analysis of a spatially explicit harvesting model, however, shows that no-take marine reserves are always part of an optimal harvest designed to maximize yield. The optimal harvest generates a spatial source–sink structure with source populations placed in reserves. The sizes and locations of the optimal reserves depend on a dimensionless length parameter. For small values of this parameter, the maximum yield is obtained by placing a large reserve in the centre of the habitat. For large values of this parameter, the optimal harvesting strategy is a spatial ‘chattering control' with infinite sequences of reserves alternating with areas of intense fishing. Such a chattering strategy would be impossible to actually implement, but in these cases an approximate yet practicable policy, utilizing a small number of reserves, can be constructed.}, annote = {-shows that optimal harvest strategy would have to include a marine reserve somewhere -ignores stage structure and assumes 1d space}, author = {Neubert, Michael G.}, doi = {10.1046/j.1461-0248.2003.00493.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Neubert - 2003 - Marine reserves and optimal harvesting.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Bioeconomics,Fisheries,Marine protected areas,Marine reserves,Maximum principle,Maximum sustainable yield,Optimal control theory,Source-sink}, number = {9}, pages = {843--849}, title = {{Marine reserves and optimal harvesting}}, volume = {6}, year = {2003} } @article{Lafferty2016, annote = {- just an introduction to theme issue on marine dieseases}, author = {Lafferty, Kevin D and Hofmann, Eileen E}, doi = {10.1098/rstb.2015.0200}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lafferty, Hofmann - 2016 - Marine disease impacts, diagnosis, forecasting, management and policy.pdf:pdf}, isbn = {0000000175}, issn = {0962-8436}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {disease and epidemiology,ecology,environmental science,health and}, pages = {20150200}, title = {{Marine disease impacts, diagnosis, forecasting, management and policy}}, volume = {371}, year = {2016} } @article{White2014a, abstract = {Marine reserve design often involves a tradeoff between meeting$\backslash$nconservation goals (persistence of fished populations) and minimizing$\backslash$neconomic costs (lost fishing grounds). Optimization tools such as Marxan$\backslash$nnavigate that tradeoff by finding reserve configurations that minimize$\backslash$neconomic costs while protecting some minimum fraction of fish habitat.$\backslash$nHowever, typical Marxan implementations do not account for patterns of$\backslash$nlarval connectivity among reserves, a factor known to be the key to$\backslash$npopulation dynamics. We show how connectivity information$\backslash$n(self-recruitment and network centrality) can be incorporated into the$\backslash$noptimization. We then used a spatially explicit population model to$\backslash$ncompare the performance of reserves designed using habitat information$\backslash$nalone or including connectivity. Incorporating connectivity information$\backslash$nimproved reserve performance for some species but not others. We$\backslash$nconclude that including connectivity information can improve reserve$\backslash$ndesign algorithms, but it is essential to evaluate species' population$\backslash$ndynamics to determine which species will benefit from a given reserve$\backslash$nnetwork.}, annote = {- want to bring together dynamic modeling and static optimization in planning marine reserves - simulated population dynamics after Marxan identified reserve locations - connecticity informatiaon improved performance of reserves for three of five species White et al. (2013) link static and dynamic approaches of reserve design. They found that including connectivity was important in designing reserves... - Need dynamic models to include connectivity and explicently examine population dynamics}, author = {White, Wilson J. and Schroeger, Julianna and Drake, Patrick T. and Edwards, Christopher A.}, doi = {10.1111/conl.12097}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2014 - The Value of Larval Connectivity Information in the Static Optimization of Marine Reserve Design.pdf:pdf}, isbn = {9109624066}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {Larval connectivity,Marine protected area,Marine reserve,Marxan,Reserve design}, number = {6}, pages = {533--544}, title = {{The Value of Larval Connectivity Information in the Static Optimization of Marine Reserve Design}}, volume = {7}, year = {2014} } @article{Hastings2006, abstract = {There is a need for better description and heuristic understanding of the sustainability of populations connected over space by a dispersing stage, both for management purposes and to increase our basic knowledge of the dynamics of these populations. We show that persistence of such a population of connected subpopulations depends on whether the sum of the reproductive gains through all possible closed, between-patch reproductive paths through multiple generations, relative to the shortfall in self-persistence in each path, exceeds unity plus extra terms, which only appear if there are four or more patches. These extra terms have the heuristic explanation that they avoid double counting of reproductive paths that arise with four or more patches because there can be nonoverlapping subnetworks. Thus only those patterns of reproduction and connectivity which eventually lead to descendants returning to the patch from which they originate contribute to persistence. This result provides the basis for evaluating connectivity and habitat heterogeneity to understand reserve design, the effects of human fragmentation, the collapse of marine fisheries, and other conservation issues.}, annote = {- want to use R0 or replacement, instead of largest eigenvalue. Cannot use largest eignevalue in spatially heterogenous population -argue understanindg of pop persistence is limited to 1) single, well mixed, nonspatial populations and 2) idealized systems of spatially distrubuted populations without habitat heterogeneity (same issue as in my pika paper) -look at cases where smaller networks are not persistent but larger networks can be}, author = {Hastings, Alan and Botsford, Louis W}, doi = {10.1073/pnas.0506651103}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Botsford - 2006 - Persistence of spatial populations depends on returning home.pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Animals,Conservation of Natural Resources,Ecosystem,Environment,Models,Population Density,Population Dynamics,Reproduction,Theoretical}, number = {15}, pages = {6067--6072}, pmid = {16608913}, title = {{Persistence of spatial populations depends on returning home}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1458697{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {103}, year = {2006} } @article{White2010, annote = {-argue that to account for MPA success or failure you must look at fishery management outside the MPA -argue you must use profit, not yield, as a currency for evaluating fishery strategies -argue that major factors of uncertainty are about connectivity b/w subpopulations and lack of info regarding conditions under which marine populations will become unsustainable (focus of this and past papers) -focus on lifetime egg production (or eggs per recruit) - fishing will truncate size structure of pops -most uncertaint that is accounted for is usually with respect to biological parameters}, author = {White, J Wilson and Botsford, Louis W and Moffitt, Elizabeth a and Fischer, Douglas T}, doi = {10.1890/09-0962.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2010 - Decision analysis for designing marine protected areas for multiple species with uncertain fishery status.pdf:pdf}, isbn = {1051–0761}, issn = {1051-0761}, journal = {Ecological Applications}, keywords = {california,decision analysis,decision support,fishery stock status,fishery yield,marine protected area,metapopulation persistence,mpa,overfishing,spatially explicit population model,usa}, number = {6}, pages = {1523--1541}, pmid = {20945757}, title = {{Decision analysis for designing marine protected areas for multiple species with uncertain fishery status}}, volume = {20}, year = {2010} } @article{Brown2015, abstract = {Marine reserves are widely used to manage for the potentially conflicting objectives of conserving biodiversity and improving fisheries. The fisheries and conservation benefits of alternative reserve designs would ideally be assessed using dynamic models, which consider spillover of fish and larvae to fished areas, and the displacement of fishers to unprotected sites. In practice, however, decisions about the location of marine reserves generally rely on cheaper and faster static models. Static models analyze only spatial patterns in habitats, and typically assume fisheries profits are reduced by the amount that was generated in areas designated as reserves. To help determine the benefits of developing dynamic fisheries models, we assessed how well static models estimate costs of reserve systems to fisheries and how outcomes from reserves designed using either static or dynamic models differ. We tested these questions in two case studies, the network of marine protected areas in southern California, USA and the proposed Tun Mustapha Marine Park in Malaysia. Static models could either under or over-estimate the cost of reserve plans to fisheries, depending on the relative importance of fisher movement and larval dispersal dynamics. Despite the inaccuracy of static models for estimating costs, reserves designed using static models were similar to those designed with dynamic models if fisheries were well managed; or larval dispersal networks were simple. If larval networks were complex or there was overfishing, dynamic models generated substantially different reserve networks from static models, which improved conservation outcomes by up to 10{\%} and fishing profits by up 20{\%}. The time-scale of management was also important, because only dynamic models accounted for larval dispersal, so could find reserves that maximized the long-term benefits of larval spillover. Our case studies provide quantitative support for the assertion that static models can be useful for planning marine reserves for short-term objectives in well managed fisheries, but are not reliable for evaluating the relative costs of reserves to fisheries.}, annote = {-static models do an okay job if fisheries are well managed and larval disperasal networks are simple, otherwise need dynamics models -dynamic models better at looking spillover effects in long term Mumby et al 2011 on climate change -cannot simply run models to equilbrium in stochastic setting -objective function was to maximize profit while each coral reef habitat type was represented in marine reserves at a cetain amount -use a greedy algorithem for one study site and a genetic search algorithem for the other site -use dynamic model to generate ``best-case" scenario and see if static model can perform similarly Dynamic models should have to be used when stochasticity is involved. Static approaches cannot account for varibility in patch connectivity or productivity...}, author = {Brown, Christopher J and White, Crow and Beger, Maria and Grantham, Hedley S and Halpern, Benjamin S and Klein, Carissa J and Mumby, Peter J and Tulloch, Vivitskaia J D and Ruckelshaus, Mary and Possingham, Hugh P}, doi = {10.1890/ES14-00429.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brown et al. - 2015 - Fisheries and biodiversity benefits of using static versus dynamic models for designing marine reserve networks.pdf:pdf}, isbn = {2150-8925}, issn = {2150-8925}, journal = {Ecosphere}, keywords = {conservation planning,fishery behavior,marine protected area,model complexity,spatial population}, number = {10}, pages = {art182}, title = {{Fisheries and biodiversity benefits of using static versus dynamic models for designing marine reserve networks}}, url = {http://dx.doi.org/10.1890/ES14-00429.1{\%}5Cnhttp://www.esajournals.org/doi/pdf/10.1890/ES14-00429.1}, volume = {6}, year = {2015} } @article{Eisenlord2016, abstract = {Over 20 species of asteroids were devastated by a sea star wasting disease (SSWD) epizootic, linked to a densovirus, from Mexico to Alaska in 2013 and 2014. For Pisaster ochraceus from the San Juan Islands, South Puget Sound and Washington outer coast, time-series monitoring showed rapid disease spread, high mortality rates in 2014, and continuing levels of wasting in the survivors in 2015. Peak prevalence of disease at 16 sites ranged to 100{\%}, with an overall mean of 61{\%}. Analysis of longitudinal data showed disease risk was correlated with both size and temperature and resulted in shifts in population size structure; adult populations fell to one quarter of pre-outbreak abundances. In laboratory experiments, time between development of disease signs and death was influenced by temperature in adults but not juveniles and adult mortality was 18{\%} higher in the 19 degrees C treatment compared to the lower temperature treatments. While larger ochre stars developed disease signs sooner than juveniles, diseased juveniles died more quickly than diseased adults. Unusual 2-3 degrees C warm temperature anomalies were coincident with the summer 2014 mortalities. We suggest these warm waters could have increased the disease progression and mortality rates of SSWD in Washington State.}, annote = {- age and spatial structure included Why did it shift from local, single species outbreaks decades ago to a large, multi-species outbreak? Could a model help explian this}, author = {Eisenlord, M E and Groner, M L and Yoshioka, R M and Elliott, J and Maynard, J and Fradkin, S and Turner, M and Pyne, K and Rivlin, N and van Hooidonk, R and Harvell, C D}, doi = {10.1098/rstb.2015.0212}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eisenlord et al. - 2016 - Ochre star mortality during the 2014 wasting disease epizootic role of population size structure and temperatu.pdf:pdf}, isbn = {1471-2970 (Electronic)$\backslash$r0962-8436 (Linking)}, issn = {14712970 09628436}, journal = {Philos Trans R Soc Lond B Biol Sci}, keywords = {ecology,epidemiology,health and disease and}, number = {1689}, pmid = {26880844}, title = {{Ochre star mortality during the 2014 wasting disease epizootic: role of population size structure and temperature}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26880844}, volume = {371}, year = {2016} } @techreport{Ehler2010, address = {Paris}, annote = {-which ecosystem services conflict with one another how does marine spatial planning fit in cntext of SDGs? -many factors that may make an area ecologically important: iniqueness, special importance for certain life histories, endagered species, productivity, diversity, naturalness -need information spatial and temporal on ecological, abiotic, and human factors --argues that not much work really includes human aspects in marine spatial planning -three categories of goals: ecology, economy, society and culture}, author = {Ehler, Charles and Douvere, Fanny}, booktitle = {IOC Manual and Guides}, doi = {Intergovernmental Oceanographic Commission and Man and the Biosphere Programme}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ehler, Douvere - 2010 - Marine Spatial Planning A step-by-step approach toward ecosystem-based management.pdf:pdf}, institution = {Intergovernmental Oceanographic Commission of Man and the Biosphere Programme. UNESCO}, isbn = {8439378807}, keywords = {environmental management,guides,marine ecosystems,marine environment}, number = {2}, pages = {1--7}, title = {{Marine Spatial Planning: A step-by-step approach toward ecosystem-based management}}, volume = {13}, year = {2010} } @article{White2011, annote = {-argue importance of replacement rate and how this varies in a metapop context -need reserve to be larger than average larval dispersal in order to retain neccessary fraction of larvve Fishery yield -show graph explaining that context will detemrine if you can tell diff between inside and outside reserves -provide citations on reviews of marine reserve networks -argues that empirical studies focus on single reserves and modeling studies look at networks mostly}, author = {White, Wilson J. and Botsford, Louis W and Baskett, Marissa L. and Barnett, Lewis A.K. and Barr, R Jeffrey and Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2011 - Linking models with monitoring data for assessing performance of no-take marine reserves.pdf:pdf}, journal = {Frontiers in Ecology and the Environment}, number = {7}, pages = {390--399}, title = {{Linking models with monitoring data for assessing performance of no-take marine reserves}}, volume = {9}, year = {2011} } @article{Cigliano2016, abstract = {Despite advances in marine conservation research, policy, and management, human activities continue to negatively affect marine species, habitats, and ecosystems, and the people who rely on them for needed resources. This begs the question: What is preventing us from being more effective in conserving marine species, habitats, and ecosystems? Answering this requires us to identify gaps in marine conservation efforts and develop a consensus on how best to target our efforts. One way to do this is to conduct research prioritization exercises. The questions discussed here were identified during a series of workshops designed to establish a list of important questions that need to be answered to advance marine conservation. We deemed these particular questions to be in a separate class than those considered in the associated paper “Seventy-One Important Questions for the Conservation of Marine Biodiversity” (Parsons et al. 2014). These questions were put into a separate category because they were identified as areas of ecological, social, and economic research that include external drivers or required sizable paradigm shifts to address. Here we describe and discuss these "Kraken in the aquarium" questions—the marine equivalent of “the elephant in the room” questions—in four sections: human nature, meeting our responsibilities, entrenched interests, and corporate driven policy. Within each section, we address multiple questions by identifying the issues and offering examples of ways forward where possible. This paper is intended to start a dialogue about these difficult questions that loom over marine conservation research and management. It is becoming increasingly important that the conservation practitioner community engages in these discussions and develops solutions in order for our work to be fully effective.}, author = {Cigliano, John A. and Bauer, Amy and Draheim, Megan M. and Foley, Melissa M. and Lundquist, Carolyn J. and McCarthy, Julie-Beth and Patterson, Katheryn W. and Wright, Andrew J. and Parsons, E. C. M.}, doi = {10.3389/fmars.2016.00174}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cigliano et al. - 2016 - The Kraken in the Aquarium Questions that Urgently Need to be Addressed in Order to Advance Marine Conservation.pdf:pdf}, issn = {2296-7745}, journal = {Frontiers in Marine Science}, keywords = {Marine Biodiversity,Research agenda,Research questions,horizon scanning,marine conservation,policy,priority setting}, number = {September}, pages = {174}, title = {{The Kraken in the Aquarium: Questions that Urgently Need to be Addressed in Order to Advance Marine Conservation}}, url = {http://journal.frontiersin.org/article/10.3389/fmars.2016.00174}, volume = {3}, year = {2016} } @article{Mumby2011, abstract = {Rising sea temperatures cause mass coral bleaching and threaten reefs worldwide. We show how maps of variations in thermal stress can be used to help manage reefs for climate change. We map proxies of chronic and acute thermal stress and develop evidence-based hypotheses for the future response of corals to each stress regime. We then incorporate spatially realistic predictions of larval connectivity among reefs of the Bahamas and apply novel reserve design algorithms to create reserve networks for a changing climate. We show that scales of larval dispersal are large enough to connect reefs from desirable thermal stress regimes into a reserve network. Critically, we find that reserve designs differ according to the anticipated scope for phenotypic and genetic adaptation in corals, which remains uncertain. Attempts to provide a complete reserve design that hedged against different evolutionary outcomes achieved limited success, which emphasises the importance of considering the scope for adaptation explicitly. Nonetheless, 15{\%} of reserve locations were selected under all evolutionary scenarios, making them a high priority for early designation. Our approach allows new insights into coral holobiont adaptation to be integrated directly into an adaptive approach to management.}, annote = {-include thermal stress variability among sites and larval dispersal in a Marxan model -in Marxan cost function (which is usually just fishing losses cost) they ncluded connectivity metric into cost function- seems a bit adhoc -different areas in Bahamas had different thermal tolerences as indicated by how corals respondeed after the large 1998 bleaching event -examined scenarios assuming corals would or would be able to keep up with warming - diff reserve networks emerged for either (did not seem to make a big different) -discuss challenge of incorprating connectivity into reserve design -what happens if you include herbivory, fishing, and hurricanes? The results about patch connectivity and heteregentiy (coral reef resilience) remind me of the work on pikas They show that depending on what types of coral reefs who try to have connectivity between, you will get different reserve design.s}, author = {Mumby, Peter J. and Elliott, Ian A. and Eakin, C. Mark and Skirving, William and Paris, Claire B. and Edwards, Helen J. and Enr{\'{i}}quez, Susana and Iglesias-Prieto, Roberto and Cherubin, Laurent M. and Stevens, Jamie R.}, doi = {10.1111/j.1461-0248.2010.01562.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mumby et al. - 2011 - Reserve design for uncertain responses of coral reefs to climate change.pdf:pdf}, isbn = {1461-0248}, issn = {14610248}, journal = {Ecology Letters}, keywords = {Acclimation,Adaptation,Algorithm,Connectivity,Conservation,Coral,Marine reserve}, number = {2}, pages = {132--140}, pmid = {21105980}, title = {{Reserve design for uncertain responses of coral reefs to climate change}}, volume = {14}, year = {2011} } @article{Cabral2016, annote = {-argue you need to account for uncertainty in tradeoffs between diferent objectives -two case studies: mangroves and shrump aquacuture vs nursery habitat for fish 2) consevation of fish and uield in MPA -use Ricker model for fish case study and study effect of using MPA -they allowed carryinug capacity to fluctuate given uniform noise -optimal solution (MSY) becomes suboptimal when you account for uncertainties -use many tools from decision analysis (tradeoff plots)}, author = {Cabral, Reniel and Halpern, Benjamin S and Costello, Christopher and Gaines, Steven D.}, doi = {10.1007/s11548-012-0737-y}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cabral et al. - 2016 - Unexpected management choices when accounting for uncertainty in ecosystem service tradeoff analyses.pdf:pdf}, isbn = {1044071060}, journal = {Conservation Letters}, pages = {5030}, title = {{Unexpected management choices when accounting for uncertainty in ecosystem service tradeoff analyses}}, year = {2016} } @article{Boag1981, abstract = {Survival of Darwin's finches through a drought on Daphne Major Island was nonrandom. Large birds, especially males with large beaks, survived best because they were able to crack the large and hard seeds that predominated in the drought. Selection intensities, calculated by O'Donald's method, are the highest yet recorded for a vertebrate population.}, author = {Boag, Peter T and Grant, Peter R}, doi = {10.1126/science.214.4516.82}, isbn = {00368075}, issn = {1095-9203}, journal = {Science}, keywords = {natural selection}, number = {4516}, pages = {82--85}, pmid = {1025}, title = {{Intense Natural Selection in a Population of Darwin's Finches (Geospizinae) in the Gal{\'{a}}pagos}}, url = {http://www.sciencemag.org/content/214/4516/82.abstract}, volume = {214}, year = {1981} } @article{Allison1998, annote = {-develop model to compute extintion properties in populiation experiecning catastophes, compare results to MacArthur-WIlson which has no catastrophes -present reviews of huge dieoffs that are attributed to some catastrophe Truman Young: rate of catastophes around 0.02-0.06 per year for large mammals -catasophes bound extinction times in MW theoreitcal framework}, author = {Allison, Gary W and Lubchenco, Jane and Carr, Mark H and Applications, Source Ecological and Ecosystem, Supplement}, doi = {10.2307/2641365}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Allison et al. - 1998 - Marine reserves are neccessary but not sufficient for marine conservation.pdf:pdf}, isbn = {1051-0761}, issn = {10510761}, journal = {Ecological Applications}, keywords = {biodiversity}, number = {1}, pages = {79--92}, pmid = {69}, title = {{Marine reserves are neccessary but not sufficient for marine conservation}}, volume = {8}, year = {1998} } @article{Marshall2013, annote = {-interviewed buisnesses dependent on great barrier reef after a severe tropical cycline -vulnerability: system's exposure, sensitivity and adaptive capacticty -people lacked adaptive capccity for dealing with event -past work indcates larger businesses had more capactiy to deal with fluctuating conditions and were more open to taking risks}, author = {Marshall, Nadine A and Tobin, Renae C and Marshall, Paul A and Gooch, Margaret and Hobday, Alistair J}, doi = {10.1007/s10021-013-9651-6}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Marshall et al. - 2013 - Social vulnerability of marine resource users to extreme weather events.pdf:pdf}, journal = {Ecosystems}, keywords = {adaptive capacity social resilience,fishing,resource,socio-ecological system,tourism}, pages = {797--809}, title = {{Social vulnerability of marine resource users to extreme weather events}}, volume = {16}, year = {2013} } @article{Fulton2015, annote = {-paper reviews varoiius modeling approaches of MPAs and when they arelikely to fail or succeed (e.g. static reservve design will fail for mobile species or those affected by climate change) -distiguish between models (abstract, simplied description of nature) and counterfactual (what would or happened if sequence of events was different) -fucus on dynamic models in this reserve and leave out static approaches -break up models into conceptual, tactical, strategic: depends on questions of interest and data availability -impossible to maximize generaity, precision, and realism}, author = {Fulton, Elizabeth A and Bax, Nicholas J and Bustamante, Rodrigo H and Dambacher, Jeffrey M and Dichmont, Catherine and Dunstan, Piers K and Hayes, R and Hobday, Alistair J and Pitcher, Roland and Punt, E and Savina-rolland, Marie and Smith, Anthony D M and Smith, C and Fulton, Elizabeth A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fulton et al. - 2015 - Modelling marine protected areas - insights and hurdles.pdf:pdf}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {environmental science}, number = {20140278}, title = {{Modelling marine protected areas - insights and hurdles}}, volume = {380}, year = {2015} } @article{Stelzenmuller2013, abstract = {Marine planners use spatial data to assess planning options. They need analytical approaches, methods, applications and practical software tools to enable assessment of the relationships between human uses and ecosystem components. Here the results of a two-stage process, aimed at developing practical and GIS-based tools for direct use by planners, are presented. First, some available tools for use in the early stages of plan development were reviewed; for example, to identify interaction between activities to reduce potential conflicts or assist in zone delineation, methods to facilitate a risk assessment of the cumulative effect of human pressures and tools offering decision support. Second, a stakeholder workshop was organised to identify routine marine planning tasks and the technical tools required to support those tasks. From the 39 practical tools reviewed, mostly published in peer-reviewed literature between 1998 and 2009, the majority have been applied in the marine environment in Europe, USA and Australia. It was observed that many of the tools are designed to be used by scientists, programmers or strategic planners with only a few that could be used by case officers (regulators). Together with the results of the stakeholder workshop a suite of prototype tools were developed that offer utility to marine planners. Thus the developed tools provide a solid basis for future development as they are a result of a transparent and participatory process.}, author = {Stelzenm{\"{u}}ller, Vanessa and Lee, Janette and South, Andy and Foden, Jo and Rogers, Stuart I.}, doi = {10.1016/j.marpol.2012.05.038}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stelzenm{\"{u}}ller et al. - 2013 - Practical tools to support marine spatial planning A review and some prototype tools.pdf:pdf}, isbn = {0308-597X}, issn = {0308597X}, journal = {Marine Policy}, keywords = {GIS,Impact,Marine planning,Pressure,Tools}, pages = {214--227}, title = {{Practical tools to support marine spatial planning: A review and some prototype tools}}, volume = {38}, year = {2013} } @article{Geritz1997, abstract = {We present a formal framework for modeling evolutionary dynamics with special emphasis on the generation of diversity through branching of the evolutionary toe. Fitness is defined as the long term growth rate which is influenced by the biotic environment leading to an ever-changing adaptive landscape. Evolution can be described as a dynamics in a space with variable number of dimensions corresponding to the number of different types present. The dynamics within a subspace is governed by the local fitness gradient. Entering a higher dimensional subspace is possible only at a particular type of attractors where the population undergoes evolutionary branching.}, author = {Geritz, Stefan and Metz, J. and Kisdi, {\'{E}}va and Mesz{\'{e}}na, G{\'{e}}za}, doi = {10.1103/PhysRevLett.78.2024}, isbn = {0031-9007}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {10}, pages = {2024--2027}, pmid = {5809}, title = {{Dynamics of Adaptation and Evolutionary Branching}}, volume = {78}, year = {1997} } @article{Game2008, annote = {-present details of how they extend Allison et al 2003 paper by allowing for heterogeneties in how different spatial areas will respond to catastophes -modify existing work in MARXAN -include econmomics by looking at cost of maintaing reef per unit area and the possible loss of fishing from closing such an area -doont allow for bleaching thresholds to change in the future -use climate change models to predict water temps in 2100 -Do we have better downscaling methods now? -timing horizon is important in this problem RESUTS -including risk of catasophes changed results a lot -discuss other risks (cyclones, disease, algal blooms, and hypoxis, ilegal fishing?) -As Marissa pointed out this paper doesn't actually deal with any population dynamics (or genetics) -What does MARXAN usually allow or assume?}, author = {Game, Edward T. and Watts, Matthew E. and Wooldridge, Scott and Possingham, Hugh P.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Game et al. - 2008 - Planning for Persistence in Marine Reserves - A Question of Catastrophic Importance.pdf:pdf}, journal = {Ecological Applications}, keywords = {associated mortality can,catastrophes,coral bleaching,coral bleaching events and,ecosystems they encompass,great barrier reef,marine reserves,marx an,of persistence,probability,reserve selection,the true effectiveness of}, number = {3}, pages = {670--680}, title = {{Planning for Persistence in Marine Reserves - A Question of Catastrophic Importance}}, volume = {18}, year = {2008} } @article{Huntly1986, annote = {-pikas spent about 5.15 min/hr foraging through the summer}, author = {Huntly, Nancy J and Smith, Andrew T and Ivins, Barbara L}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Huntly, Smith, Ivins - 1986 - Foraging behavior of the pika (emph{\{}Ochotona princeps{\}}), with comparisons of grazing versus haying.pdf:pdf}, journal = {Journal of Mammalogy}, number = {1}, pages = {139--148}, title = {{Foraging behavior of the pika ($\backslash$emph{\{}Ochotona princeps{\}}), with comparisons of grazing versus haying}}, volume = {67}, year = {1986} } @article{Smith2011, abstract = {1. Growing recognition of the importance of climate extremes as drivers of contemporary and future ecological dynamics has led to increasing interest in studying these locally and globally important phenomena. 2. Many ecological studies examining the impacts of what are deemed climate extremes, such as heat waves and severe drought, do not provide a definition of extremity, either from a statistical context based on the long-term climatic record or from the perspective of the response of the system – are the effects extreme (unusual or profound) in comparison to normal variability? 3. A synthetic definition of an extreme climatic event (ECE) is proposed that includes ‘extremeness' in both the driver and the response: an ECE is as an episode or occurrence in which a statistically rare or unusual climatic period alters ecosystem structure and/or function well outside the bounds of what is considered typical or normal variability. This definition is accompanied by a mechanistic framework based on the concept that extreme response thresholds associated with significant community change and altered ecosystem function must be crossed in order for an ECE to occur. 4. Synthesis. A definition and mechanistic framework for ECEs is used to identify priorities for future research that will enable ecologists to more fully assess the ecological consequences of climate extremes for ecosystem structure and function today and in a future world where their frequency and intensity are expected to increase.}, annote = {-can you do a formal analysis of respones to rare events? -this review focuses on rare climatic events -defines difference b.w rare cliatic event and systems response to rare event -extrmem climataic events may include long peridos of recovery, hysteresis, or persistent state changes -provides a couple of examples, like rainfall shelters in an experiment and another example of just a particurly bad year -need a plot of frequency of events over time (hurricanes, oil spills, climatic events, invasions, etc..)}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Smith, Melinda D.}, doi = {10.1111/j.1365-2745.2011.01798.x}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith - 2011 - An ecological perspective on extreme climatic events A synthetic definition and framework to guide future research.pdf:pdf}, isbn = {1365-2745}, issn = {00220477}, journal = {Journal of Ecology}, keywords = {Climate change,Drought,Ecosystem sensitivity,Extreme events,Extreme weather,Global change,Heat wave,Plant-climate interactions,State change,Thresholds}, number = {3}, pages = {656--663}, pmid = {25246403}, title = {{An ecological perspective on extreme climatic events: A synthetic definition and framework to guide future research}}, volume = {99}, year = {2011} } @article{Diez2012, abstract = {Extreme climatic events (ECEs) – such as unusual heat waves, hurricanes, floods, and droughts – can dramatically affect ecological and evolutionary processes, and these events are projected to become more frequent and more intense with ongoing climate change. However, the implications of ECEs for biological invasions remain poorly understood. Using concepts and empirical evidence from invasion ecology, we identify mechanisms by which ECEs may influence the invasion process, from initial introduction through establishment and spread. We summarize how ECEs can enhance invasions by promoting the transport of propagules into new regions, by decreasing the resistance of native communities to establishment, and also sometimes by putting existing non-native species at a competitive disadvantage. Finally, we outline priority research areas and management approaches for anticipating future risks of unwanted invasions following ECEs. Given predicted increases in both ECE occurrence and rates of species introduction...}, author = {Diez, Jeffrey M. and D'Antonio, Carla M. and Dukes, Jeffrey S. and Grosholz, Edwin D. and Olden, Julian D. and Sorte, Cascade J B and Blumenthal, Dana M. and Bradley, Bethany A. and Early, Regan and Ib{\'{a}}{\~{n}}ez, In{\'{e}}s and Jones, Sierra J. and Lawler, Joshua J. and Miller, Luke P.}, doi = {10.1890/110137}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Diez et al. - 2012 - Will extreme climatic events facilitate biological invasions.pdf:pdf}, isbn = {i1540-9295-10-5-249}, issn = {15409295}, journal = {Frontiers in Ecology and the Environment}, number = {5}, pages = {249--257}, title = {{Will extreme climatic events facilitate biological invasions?}}, volume = {10}, year = {2012} } @techreport{Loffoley2008, address = {Washington, D.C.}, author = {Loffoley, Dan and White, Alan T. and Kilarski, Stacey and Gleason, Mary and Smith, Scott and Llewellyn, Ghislaine and Day, John and Hillary, Annie and Weddell, Victoria and Pee, Daphine}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Loffoley et al. - 2008 - Establishing resilient marine protected area networks — making it happen.pdf:pdf}, institution = {IUCN World Commission on Protected Areas (IUCN-WCPA)}, isbn = {9782831710907}, pages = {118}, title = {{Establishing resilient marine protected area networks — making it happen}}, year = {2008} } @article{Smith1984a, author = {Smith, Andrew T. and Ivins, Barbara L.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Ivins - 1984 - Spatial relationships and social organization in adult pikas - a facultatively monogaous mammal.pdf:pdf}, journal = {Zeitschrift fur Tierpsychologie}, pages = {289--308}, title = {{Spatial relationships and social organization in adult pikas - a facultatively monogaous mammal}}, volume = {66}, year = {1984} } @article{Wilkening2011, abstract = {The American pika (Ochotona princeps) inhabits talus slopes on isolated mountaintops in the Great Basin, where the species is susceptible to localized extirpations. Previous studies from the region related pika extirpations to proxies for climate and habitat quality, or to relatively short datasets on microclimate. This study extends previous research by modeling extirpation using new data from microclimates and microhabitats, and by including data on the vegetation available to individual pikas. We re-surveyed 25 sites historically occupied by pikas, and collected microclimatic and vegetative-cover data from each site. Sites of pika extirpation experienced higher summer temperatures and higher frequency of extremely warm days during 2005-2007 than did sites of pika persistence. Several aspects of vegetative cover also differed between persistence and extirpation sites, and relative forb cover was positively related to pika persistence. Evaluation of competing models within an information-theoretic framework suggests strong support for recent mean summer temperature as the primary driver of extirpations in this dataset. In agreement with other modeling efforts, this result supports the hypothesis that extirpation results from chronic heat stress during the summer months when pikas must gather and store food for the winter. In contrast with previous studies, we found less support for the hypothesis that extirpation results from acute cold stress during the winter months, possibly due to several differences in analytical methods. {\textcopyright} 2010 Elsevier Ltd and INQUA.}, author = {Wilkening, Jennifer L. and Ray, Chris and Beever, Erik A. and Brussard, Peter F.}, doi = {10.1016/j.quaint.2010.05.004}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wilkening et al. - 2011 - Modeling contemporary range retraction in Great Basin pikas (emph{\{}Ochotona princeps{\}}) using data on microclima.pdf:pdf}, isbn = {1040-6182}, issn = {10406182}, journal = {Quaternary International}, number = {1-2}, pages = {77--88}, publisher = {Elsevier Ltd and INQUA}, title = {{Modeling contemporary range retraction in Great Basin pikas ($\backslash$emph{\{}Ochotona princeps{\}}) using data on microclimate and microhabitat}}, url = {http://dx.doi.org/10.1016/j.quaint.2010.05.004}, volume = {235}, year = {2011} } @techreport{Assessment2005, abstract = {The Arctic is now experiencing some of the most rapid and severe climate change on earth. Over the next 100 years, climate change is expected to accelerate, contributing to major physical, ecological, social, and economic changes, many of which have already begun. Changes in arctic climate will also affect the rest of the world through increased global warming and rising sea levels. Arctic Climate Impact Assessment was prepared by an international team of over 300 scientists, experts, and knowledgeable members of indigenous communities. The report has been thoroughly researched, is fully referenced, and provides the first comprehensive evaluation of arctic climate change, changes in ultraviolet radiation and their impacts for the region and for the world. It is illustrated in full color throughout. The results provided the scientific foundations for the ACIA synthesis report - Impacts of a Warming Arctic - published by Cambridge University Press in 2004.}, author = {ACIA}, booktitle = {Cambridge University Press}, isbn = {0521865093}, pages = {1046}, title = {{Arctic Climate Impact Assessment - Scientific Report}}, year = {2005} } @article{Garcia-Carreras2013, abstract = {Population dynamics are affected by changes in both the mean and standard deviation of climate, e.g., changes in average temperature are likely to affect populations, but so are changes in the strength of year-to-year temperature variability. The impacts of increases in average temperature are extensively researched, while the impacts of changes in climate variability are less studied. Is the greater attention given to changes in mean environment justified? To help answer this question we developed a simple population model, explicitly linked to an environmental process. We used the model to compare the sensitivities of a population's long-term stochastic growth rate, a measure of fitness, to changes in the mean and standard deviation of the environment. Results are interpreted in light of a comparative analysis of the relative magnitudes of change in means and standard deviations of biologically relevant climate variables in the United States. Results show that changes in the variability of the environment can be more important for many populations. Changes in mean conditions are likely to have a greater impact than changes in variability on populations far from their ideal environment, for example, populations near species range boundaries and potentially of conservation concern. Populations near range centres and close to their ideal environment are more likely to be affected by changes in variability. Among pest and insect disease vectors, as well as species of commercial value, populations likely to be of greatest economic and public health significance are those near species range centers, living in a near-ideal environment for the species. Observed changes in the variability of climate variables may benefit these populations.}, annote = {-study an unstructred environemental and examine how changes in mean and variability of environmental factor affect long term stochastic growth rate -specific response functino (typically skewed and peaked) is important -it is not the same to look at stochastic growth rate sensitive to variance in vital rates compared to variance in environmental parameters}, author = {Garc{\'{i}}a-Carreras, Bernardo and Reuman, Daniel C.}, doi = {10.1371/journal.pone.0063974}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Garc{\'{i}}a-Carreras, Reuman - 2013 - Are Changes in the Mean or Variability of Climate Signals More Important for Long-Term Stochastic Grow.pdf:pdf}, issn = {19326203}, journal = {PLoS ONE}, number = {5}, pmid = {23691131}, title = {{Are Changes in the Mean or Variability of Climate Signals More Important for Long-Term Stochastic Growth Rate?}}, volume = {8}, year = {2013} } @article{Dearing1997, annote = {25{\%} of haypile decomposes over winter "The initial magnitude of the haypile, together with the proportion of leftovers, suggests that pikas are profligate hayers, gathering far more than they are able to consume during most years" What fraction of haypile weight is actually edible food?}, author = {Dearing, M. Denise}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dearing - 1997 - The function of haypiles of pikas.pdf:pdf}, journal = {Journal of Mammalogy}, keywords = {1965,broadbrooks,cache,food hoarding,haypiles,is a small herbivore,known for its un-,lagomor-,ochotona princeps,pha,pika,the pika,usual haying behavior}, number = {4}, pages = {1156--1163}, title = {{The function of haypiles of pikas}}, volume = {78}, year = {1997} } @article{Allison2003, annote = {This was a very interesting paper that discussed marine catastophes and marine researves in general ,but focused on oil spills and hurricanes given the data available. They developed a simple tool to estimate the additional amount of area that should be put aside in marine reserves if you want to account for rare events. There are a lot of extensions that oculd be made on this paper -it depends if you look at average vs worst years for analyses -discuss fact that extremes may change in the future -need to deal with multiple, interacting factors - argue we need better data on disturbances to make specific predictions - balance between disturbance size and dispersal ratio - can I look at the ratio between these two...}, author = {Allison, Gary W. and Gaines, Steven D. and Lubchenco, Jane and Possingham, Hugh P.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Allison et al. - 2003 - Ensuring Persistence of Marine Reserves- Catastrophes Require Adopting an Insurance Factor.pdf:pdf}, journal = {Ecological Applications}, keywords = {disturbance,hurricane,marine reserves,oil spill,rare events}, number = {1}, pages = {S8--S24}, title = {{Ensuring Persistence of Marine Reserves- Catastrophes Require Adopting an Insurance Factor}}, volume = {13}, year = {2003} } @article{Gaines2010, abstract = {Marine protected areas (MPAs) that exclude fishing have been shown repeatedly to enhance the abundance, size, and diversity of species. These benefits, however, mean little to most marine species, because individual protected areas typically are small. To meet the larger-scale conservation challenges facing ocean ecosystems, several nations are expanding the benefits of individual protected areas by building networks of protected areas. Doing so successfully requires a detailed understanding of the ecological and physical characteristics of ocean ecosystems and the responses of humans to spatial closures. There has been enormous scientific interest in these topics, and frameworks for the design of MPA networks for meeting conservation and fishery management goals are emerging. Persistent in the literature is the perception of an inherent tradeoff between achieving conservation and fishery goals. Through a synthetic analysis across these conservation and bioeconomic studies, we construct guidelines for MPA network design that reduce or eliminate this tradeoff. We present size, spacing, location, and configuration guidelines for designing networks that simultaneously can enhance biological conservation and reduce fishery costs or even increase fishery yields and profits. Indeed, in some settings, a well-designed MPA network is critical to the optimal harvest strategy. When reserves benefit fisheries, the optimal area in reserves is moderately large (mode ≈30{\%}). Assessing network design principals is limited currently by the absence of empirical data from large-scale networks. Emerging networks will soon rectify this constraint.}, annote = {-argue you need networks to represent and replicate many different habitats -need replication to deal with disasters$\backslash$ -scales of larvae movement determine connectence and persistence where adult movement distance will determine success of reserves -does too much connectance bad in context of disturbance or invasive species? -location and size of reserves in network is obviously important -there is not always a tradeoff between fisheries and conservation, depends on the species Oustanding question they posed: -what rules of thumb can we develop if species respond differently -how willl differential respones affect community dynamics? can we empirically evaluate how networks are doing? Move beyond theoretical level.}, author = {Gaines, Steven D and White, Crow and Carr, Mark H and Palumbi, Stephen R}, doi = {10.1073/pnas.0906473107}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gaines et al. - 2010 - Designing marine reserve networks for both conservation and fisheries management.pdf:pdf}, isbn = {0027-8424}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {Animals,Biodiversity,Biomass,Conservation of Natural Resources,Conservation of Natural Resources: economics,Conservation of Natural Resources: methods,Ecosystem,Fisheries,Fisheries: economics,Fishes,Fishes: growth {\&} development,Larva,Larva: growth {\&} development,Marine Biology,Marine Biology: organization {\&} administration,Population Dynamics}, number = {43}, pages = {18286--93}, pmid = {20200311}, title = {{Designing marine reserve networks for both conservation and fisheries management}}, volume = {107}, year = {2010} } @article{Parsons2014, abstract = {The ocean provides food, economic activity, and cultural value for a large proportion of humanity. Our knowledge of marine ecosystems lags behind that of terrestrial ecosystems, limiting effective protection of marine resources. We describe the outcome of 2 workshops in 2011 and 2012 to establish a list of important questions, which, if answered, would substantially improve our ability to conserve and manage the world's marine resources. Participants included individuals from academia, government, and nongovernment organizations with broad experience across disciplines, marine ecosystems, and countries that vary in levels of development. Contributors from the fields of science, conservation, industry, and government submitted questions to our workshops, which we distilled into a list of priority research questions. Through this process, we identified 71 key questions. We grouped these into 8 subject categories, each pertaining to a broad component of marine conservation: fisheries, climate change, other anthropogenic threats, ecosystems, marine citizenship, policy, societal and cultural considerations, and scientific enterprise. Our questions address many issues that are specific to marine conservation, and will serve as a road map to funders and researchers to develop programs that can greatly benefit marine conservation. Setenta y Un Preguntas Importantes para la Conservaci{\'{o}}n de la Biodiversidad Marina.}, annote = {this review explains some of the most important questions that need to be solved to move forward in marine conservation biology Questions I particurly liked: -when do no take zones benefit fisheries -prevelence of evolutionary effects in fishing -role of tails of diftribution with global climate change -changing frequency, magnitutde, and intensity of disturbances? -questions related to how science itself operates Questions an online research derby could get at: 19, 30, 35, 42, 44, 71}, author = {Parsons, E. C M and Favaro, Brett and Aguirre, A. Alonso and Bauer, Amy L. and Blight, Louise K. and Cigliano, John A. and Coleman, Melinda A. and C??t??, Isabelle M. and Draheim, Megan and Fletcher, Stephen and Foley, Melissa M. and Jefferson, Rebecca and Jones, Miranda C. and Kelaher, Brendan P. and Lundquist, Carolyn J. and Mccarthy, Julie Beth and Nelson, Anne and Patterson, Katheryn and Walsh, Leslie and Wright, Andrew J. and Sutherland, William J.}, doi = {10.1111/cobi.12303}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Parsons et al. - 2014 - Seventy-one important questions for the conservation of marine biodiversity.pdf:pdf}, isbn = {1523-1739}, issn = {15231739}, journal = {Conservation Biology}, keywords = {Horizon scanning,Marine biodiversity,Policy,Priority setting,Research agenda,Research questions}, number = {5}, pages = {1206--1214}, pmid = {24779474}, title = {{Seventy-one important questions for the conservation of marine biodiversity}}, volume = {28}, year = {2014} } @article{Mcnamara2016, annote = {-paper strives to include bet hedging and adaptive plastiity in the same formal framework}, author = {Mcnamara, John M and Dall, Sasha R X and Hammerstein, Peter and Leimar, Olof}, doi = {10.1111/ele.12663}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mcnamara et al. - 2016 - Detection vs Selection Integration of Genetic, Epigenetic and Environmental Cues in Fluctuating Environments.pdf:pdf}, issn = {1461023X}, keywords = {1267,1276,19,2016,adaptive development,bet hedging,ecology letters,habitat tracking,maternal effects,plasticity,reaction norm,transgenerational effects}, pages = {1--53}, title = {{Detection vs Selection: Integration of Genetic, Epigenetic and Environmental Cues in Fluctuating Environments}}, year = {2016} } @article{Urban, author = {Urban, Mark C and Bocedi, Greta and Hendry, Andrew P. and Mihoub, Jean-Baptiste and Pe'er, Guy and Singer, Alexander and Bridle, Jon R and Crozier, Lisa G and {De Meester}, Luc and Godsoe, William and Gonzalez, Andrew and Hellmann, Jessica J and Holt, Robert D and Huth, Andreas and Johst, Karin and Krug, C.B. and Leadley, Paul and Palmer, S.C.F and Pantel, J.H and Schmitz, A. and Zollner, P. A. and Travis, J.M.J.}, doi = {10.1126/science.aad8466}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Urban et al. - Unknown - Improving the forecast for biodiversity under climate change.pdf:pdf}, issn = {0036-8075}, journal = {Science}, pages = {in revision}, title = {{Improving the forecast for biodiversity under climate change}} } @article{Gleason2013, abstract = {The State of California recently planned and is implementing a network of marine protected areas (MPAs) in state waters as mandated by the Marine Life Protection Act (MLPA). A public-private partnership (the MLPA Initiative) completed four regional public MPA planning processes characterized by robust stakeholder contributions and the incorporation of best readily available science. Prior to enactment of the MLPA in 1999, less than 3{\%} of California state waters were in MPAs, and most of those MPAs were small and lacked clear objectives. By 2013, approximately 16{\%} of state waters will be in 124 MPAs that represent and replicate most marine and estuarine habitats and are designed to be ecologically-connected. The redesigned statewide network of MPAs improves marine ecosystem protection in California, advanced the science and practice of designing MPA networks, and increased the awareness and capacity of stakeholders, scientists and decision-makers for marine spatial planning. The public planning effort took almost seven years and significant financial investment (approximately {\$}19.5 million in private charitable foundation funds and {\$}18.5 million in public funds). Not all stakeholders were pleased with the outcomes and the planning processes faced many challenges. While the design of the MPA network aimed to meet science and feasibility guidelines, final decisions on MPAs in each region reflected tradeoffs needed to garner public acceptance and support for implementation. The MLPA Initiative offers some key lessons about implementing policy through a public planning process. While California is developing mechanisms for assessing effectiveness of the MPA network in coming years, including establishing a MPA Monitoring Enterprise and a process for periodic review and adaptive management of MPAs, significant challenges remain for effective implementation. ?? 2012 Elsevier Ltd.}, annote = {-MPAs cover and replicate most habitat types -explicent goal to have connectivty betweeen resrves even though they were decided on locally -how do MPAs and fisheries planning interact with one another -stressed involvement of many stakeholders being involved}, author = {Gleason, Mary and Fox, Evan and Ashcraft, Susan and Vasques, Jason and Whiteman, Elizabeth and Serpa, Paulo and Saarman, Emily and Caldwell, Meg and Frimodig, Adam and Miller-Henson, Melissa and Kirlin, John and Ota, Becky and Pope, Elizabeth and Weber, Mike and Wiseman, Ken}, doi = {10.1016/j.ocecoaman.2012.08.013}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gleason et al. - 2013 - Designing a network of marine protected areas in California Achievements, costs, lessons learned, and challenges.pdf:pdf}, isbn = {0964-5691}, issn = {09645691}, journal = {Ocean and Coastal Management}, pages = {90--101}, title = {{Designing a network of marine protected areas in California: Achievements, costs, lessons learned, and challenges ahead}}, volume = {74}, year = {2013} } @article{Baskett2015, abstract = {Here we review the population, community, and evolutionary consequences of marine reserves. Responses at each level depend on the tendency of fisheries to target larger body sizes and the tendency for greater reserve protection with less movement within and across populations. The primary population response to reserves is survival to greater ages and sizes plus increases in the population size for harvested species, with greater response to reserves that are large relative to species' movement rates. The primary community response to reserves is an increase in total biomass and diversity, with the potential for trophic cascades and altered spatial patterning of metacommunities. The primary evolutionary response to reserves is increased genetic diversity, with the theoretical potential for protection against fisheries-induced evolution and selection for reduced movement. The potential for the combined outcome of these responses to buffer marine populations and communities against temporal environmental he...}, annote = {=MPAs different than terrestrial resrves b/c of explicient consideration of fishing as well -discuss various ecological and evolutionary effects of reserves -after intense harvesting, there is a filling in of older age classes -stochasticity and transiet dynamics interact on short time scale to increase time needed for MPA to be effective -discuss spillover effects that is theoretically possible, hard to do before and after studies. Therefore models can be helpful -**argue that MPAs can help buffer from uncertainty and envirionmental variability** -MPAs would increase species of target or those of bycatch. If a species is not fished, it is unlikely to change with MPA establishment -argue that largest species should be most helped by MPAs? But what if largest also move the most? -discuss many metrics of stability and how they scale with diversity -not consistent whether or not MPAs decrease variability in biomass and rather or not there is creased resistance to disturbance -potential consequence of MPAs is increased genetic diversity -connections to fisheries induced evolution -slection againast dispersal could happen Questions: -What would happen if you model california researves seperately and together? -MPAs and envrionmental stochasticity??? -what are all possible types of ecosystem based management? -comparing different marine networks?}, author = {Baskett, Marissa L. and Barnett, Lewis A.K.}, doi = {10.1146/annurev-ecolsys-112414-054424}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Baskett, Barnett - 2015 - The Ecological and Evolutionary Consequences of Marine Reserves.pdf:pdf}, isbn = {1543-592X 1545-2069}, issn = {1543-592X}, journal = {Annual Review of Ecology, Evolution, and Systematics}, keywords = {community stability,fisheries-induced evolution,marine protected areas,marine reserve network,size-selective fisheries,spillover}, number = {1}, pages = {49--73}, title = {{The Ecological and Evolutionary Consequences of Marine Reserves}}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-ecolsys-112414-054424}, volume = {46}, year = {2015} } @article{Pau2011, abstract = {Forecasting how species and ecosystems will respond to climate change has been a major aim of ecology in recent years. Much of this research has focused on phenology – the timing of life-history events. Phenology has well-demonstrated links to climate, from genetic to landscape scales; yet our ability to explain and predict variation in phenology across species, habitats and time remains poor. Here, we outline how merging approaches from ecology, climate science and evolutionary biology can advance research on phenological responses to climate variability. Using insight into seasonal and interannual climate variability combined with niche theory and community phylogenetics, we develop a predictive approach for species' reponses to changing climate. Our approach predicts that species occupying higher latitudes or the early growing season should be most sensitive to climate and have the most phylogenetically conserved phenologies. We further predict that temperate species will respond to climate change by shifting in time, while tropical species will respond by shifting space, or by evolving. Although we focus here on plant phenology, our approach is broadly applicable to ecological research of plant responses to climate variability.}, annote = {-species at hugh lats or with early growing seasons should be most sensitve to climate -predict that temperate spcies should respond by shifting in time while tropical species should respond by shifting in space or evolving -comm eco has tended to focus on species interactions and trophic mismatachs -climate focused work had looked at long term time series -depending on the scale you use, you detemrine diff factors which you think are important -discuss variability and how plants living in more variabile environments should be more plastic to abiotic facotrs -they also predict that species living in dramatically changing seasons would be less sensitive to climate -should have faster rates of evolution for species respondignt to photoperioud compared to temp or preceop}, author = {Pau, Stephanie and Wolkovich, Elizabeth M. and Cook, Benjamin I. and Davies, T. Jonathan and Kraft, Nathan J B and Bolmgren, Kjell and Betancourt, Julio L. and Cleland, Elsa E.}, doi = {10.1111/j.1365-2486.2011.02515.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pau et al. - 2011 - Predicting phenology by integrating ecology, evolution and climate science.pdf:pdf}, isbn = {1365-2486}, issn = {13541013}, journal = {Global Change Biology}, keywords = {Environmental filtering,Growing-degree day models,Niche conservatism,Photoperiod,Temperature sensitivity,Temporal niche}, number = {12}, pages = {3633--3643}, pmid = {20113363331}, title = {{Predicting phenology by integrating ecology, evolution and climate science}}, volume = {17}, year = {2011} } @article{Peacock1997, abstract = {A combination of direct (mark-resight) and indirect genetic methods were tued to investigate natal dispersal patterns and genetic population structure in a population of North American pikas, Ochotona princeps. Pikas are small lagomorphs found in talus habitat of alpine areas throughout western North America. Adult pikas are individually territorial and rarely disperse. I used multilocus DNA fingerprinting to identify the parents ofjuvenile animait The settlement pattern of markedjuveniles and the pattern of relatedness of pikas across the study site was then examined within the study area. Although juveniles born at the study site exhibited a philopatric settlement pattern, an isolation-by-distance analysis did not reveal clusters of highly related individuals within the population. The Fn mim{\^{}}t* suggests little genetic differentiation between populations 2 km apart, and average DNA fingerprinting band-sharing among adults was similar to values reported for outbred spedes. An average of 34{\%} of the adult population was replaced each winter by immigrants. DNA fingerprinting band-sharing analysis suggests that these immigrants had dispersed short, intermediate, and long distances. These findings differ from earlier studies which used obser- vations of marked animals only to characterize dispersal patterns. Direct observations of marked juveniles had documented a philopatric settlement pattern, little or no dispersal out of natal populations, and no direct evidence of long distance movement. Of the three major hypotheses proposed to explain the evolution of dispersal in birds and mammal{\^{}}, competition for resources, competition for mates, and inbreeding avoidance, the results of this study support a competition for resources hypothesis, where the key resource is territory. Kty words: dispersal patterns, genetic population structure, Ochotona princtps}, author = {Peacock, Mary M}, doi = {10.1093/beheco/8.3.340}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Peacock - 1997 - Determining natal dispersal patterns in a population of North American pikas ( emph{\{}Ochotona princeps{\}}) using direct ma.pdf:pdf}, isbn = {1045-2249}, issn = {1045-2249}, journal = {Behavioral Ecology}, number = {3}, pages = {340--350}, pmid = {1812}, title = {{Determining natal dispersal patterns in a population of North American pikas ( $\backslash$emph{\{}Ochotona princeps{\}}) using direct mark-resight and indirect genetic methods}}, volume = {8}, year = {1997} } @article{Johansson2015, abstract = {The timing of biological events (phenology) is an important aspect of both a species' life cycle and how it interacts with other species and its environment. Patterns of phenological change have been given much scientific attention, particularly recently in relation to climate change. For pairs of interacting species, if their rates of phenological change differ, then this may lead to asynchrony between them and disruption of their ecological interactions. However it is often difficult to interpret differential rates of phenological change and to predict their ecological and evolutionary consequences. We review theoretical results regarding this topic, with special emphasis on those arising from life history theory, evolutionary game theory and population dynamic models. Much ecological research on phenological change builds upon the concept of match/mismatch, so we start by putting forward a simple but general model that captures essential elements of this concept. We then systematically compare the predictions of this baseline model with expectations from theory in which additional ecological mechanisms and features of species life cycles are taken into account. We discuss the ways in which the fitness consequences of interspecific phenological asynchrony may be weak, strong, or idiosyncratic. We discuss theory showing that synchrony is not necessarily an expected evolutionary outcome, and how population densities are not necessarily maximized by adaptation, and the implications of these findings. By bringing together theoretical developments regarding the eco-evolutionary consequences of phenological asynchrony, we provide an overview of available alternative hypotheses for interpreting empirical patterns as well as the starting point for the next generation of theory in this field.}, annote = {-have a simple basline model and gradually add on more and more complications including: sensitity of interactino strength to asynchrony, density dependence, frequency dependence, interactinos with several species, spatial heterogeneity, environmental fluctuations, sensitivty of fitness to vital rates, life history tradeoffs, connected life stages , - focused on biotic interactions (as opposed to seasonal environmental factors) Cushing 1969 - match/mismatch hypothesis Facators that influence eco-evo dynamics of phenological asynchrony:}, author = {Johansson, Jacob and Kristensen, Nadiah P. and Nilsson, Jan {\AA}ke and Jonz{\'{e}}n, Niclas}, doi = {10.1111/oik.01909}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Johansson et al. - 2015 - The eco-evolutionary consequences of interspecific phenological asynchrony - a theoretical perspective.pdf:pdf}, isbn = {1600-0706}, issn = {16000706}, journal = {Oikos}, number = {1}, pages = {102--112}, title = {{The eco-evolutionary consequences of interspecific phenological asynchrony - a theoretical perspective}}, volume = {124}, year = {2015} } @article{Levis2016, abstract = {Many biologists are asking whether environmentally initiated phenotypic change (i.e., 'phenotypic plasticity') precedes, and even facilitates, evolutionary adaptation. However, this 'plasticity-first' hypothesis remains controversial, primarily because comprehensive tests from natural populations are generally lacking. We briefly describe the plasticity-first hypothesis and present much-needed key criteria to allow tests in diverse, natural systems. Furthermore, we offer a framework for how these criteria can be evaluated and discuss examples where the plasticity-first hypothesis has been investigated in natural populations. Our goal is to provide a means by which the role of plasticity in adaptive evolution can be assessed. Phenotypic plasticity has long been proposed to precede and possibly facilitate adaptive evolution.This 'plasticity-first hypothesis' is controversial because skeptics argue that it lacks compelling evidence from natural populations.A chief difficulty with demonstrating plasticity-first evolution in natural populations is that, once a trait has evolved, its evolution cannot be studied in situ. To get around this difficulty, researchers can study extant lineages that act as ancestral-proxies to the lineage possessing the focal trait.Using such an approach, key criteria of the plasticity-first hypothesis can be evaluated using a relatively simple experimental design.Applying these criteria to various systems, the plasticity-first hypothesis has some empirical support. However, more studies are needed to conclusively determine the role of plasticity in adaptive evolution.}, annote = {what to provdie clear criteria for testing whether plasticity led evolution has occured in natural pops 1. the focal trait will have been environmentally induced originally 2. cryptic genetic variation will be exposed in natural habitat 3. focal trait will later undeergo evolutionary change (change of reaction norm intercept or slope) 4.}, author = {Levis, Nicholas A. and Pfennig, David W.}, doi = {10.1016/j.tree.2016.03.012}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levis, Pfennig - 2016 - Evaluating 'Plasticity-First' Evolution in Nature Key Criteria and Empirical Approaches.pdf:pdf}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {7}, pages = {563--574}, pmid = {27067134}, publisher = {Elsevier Ltd}, title = {{Evaluating 'Plasticity-First' Evolution in Nature: Key Criteria and Empirical Approaches}}, url = {http://dx.doi.org/10.1016/j.tree.2016.03.012}, volume = {31}, year = {2016} } @article{Ferriere2013, abstract = {Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause 'evolutionary suicide'. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called 'evolutionary trapping'. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.}, annote = {-move around from optimization thinkiing and think about selection in frequency dependent setting E3 diagrams - ecology, evo, environment Quantative genetics best for questions of: If you take AD view, when environment changes, the evo attractor may eventually collide with a non viable region Can you use criticacl slowing down metrics to detect evolutionary suicide in the field?}, author = {Ferriere, Regis and Legendre, St{\'{e}}phane}, doi = {10.1098/rstb.2012.0081}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ferriere, Legendre - 2013 - Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory.pdf:pdf}, isbn = {0962-8436}, issn = {0962-8436}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {Adaptation,Biological,Biological Evolution,Competitive Behavior,Ecosystem,Extinction,Genetic,Genetic Fitness,Genetic Variation,Genetics,Models,Phenotype,Population,Population Density,Population Dynamics,Population: methods,Selection}, number = {1610}, pages = {20120081--20120081}, pmid = {23209163}, title = {{Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3538448{\&}tool=pmcentrez{\&}rendertype=abstract{\%}5Cnhttp://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.2012.0081}, volume = {368}, year = {2013} } @article{Johansson2015a, abstract = {The timing of biological events (phenology) is an important aspect of both a species' life cycle and how it interacts with other species and its environment. Patterns of phenological change have been given much scientific attention, particularly recently in relation to climate change. For pairs of interacting species, if their rates of phenological change differ, then this may lead to asynchrony between them and disruption of their ecological interactions. However it is often difficult to interpret differential rates of phenological change and to predict their ecological and evolutionary consequences. We review theoretical results regarding this topic, with special emphasis on those arising from life history theory, evolutionary game theory and population dynamic models. Much ecological research on phenological change builds upon the concept of match/mismatch, so we start by putting forward a simple but general model that captures essential elements of this concept. We then systematically compare the predictions of this baseline model with expectations from theory in which additional ecological mechanisms and features of species life cycles are taken into account. We discuss the ways in which the fitness consequences of interspecific phenological asynchrony may be weak, strong, or idiosyncratic. We discuss theory showing that synchrony is not necessarily an expected evolutionary outcome, and how population densities are not neces- sarily maximized by adaptation, and the implications of these findings. By bringing together theoretical developments regarding the eco-evolutionary consequences of phenological asynchrony, we provide an overview of available alternative hypotheses for interpreting empirical patterns as well as the starting point for the next generation of theory in this field.}, author = {Johansson, Jacob and Nilsson, Jan-{\AA}ke and Jonz{\'{e}}n, Niclas}, doi = {10.1111/oik.02077}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Johansson, Nilsson, Jonz{\'{e}}n - 2015 - Phenological change and ecological interactions An introduction.pdf:pdf}, isbn = {1600-0706}, issn = {16000706}, journal = {Oikos}, number = {1}, pages = {1--3}, title = {{Phenological change and ecological interactions: An introduction}}, volume = {124}, year = {2015} } @techreport{COSEWIC2011, abstract = {This small rabbit-relative is a Beringian relict that is restricted to talus slopes in alpine areas in northern west British Columbia, Yukon, and Northwest Territories. This region comprises over half the global range of this species, and is witnessing climate-driven shifts in habitat, temperature, and precipitation at faster rates than elsewhere in Canada. A demonstrated sensitivity to climate variability, coupled with poor dispersal ability and the naturally fragmented nature of its populations, heightens the vulnerability of this small mammal to climate change. The species is well-studied in a very limited portion of its range, but baseline information on population trends at the range level, and a clear understanding of the extent and severity of climate impacts to this species and its habitat in the coming decades is limited. However, the best available information suggests that this species may be particularly sensitive to a changing climate, including concomitant increases in precipitation variability, leading to reductions in habitat availability. The potential of negative impacts of climate change to the persistence of this species over the long term is substantial.}, address = {Ottawa}, annote = {importantly, they calculate density as per ha of talus, not simply for the whole study site}, author = {COSEWIC}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/COSEWIC - 2011 - COSEWIC assessment and status report on the Collared Pika (Ochotona collaris) in Canada.pdf:pdf}, institution = {Committee on the Status of Endangered Wildlife in Canada}, isbn = {978-1-100-20220-4}, pages = {50}, title = {{COSEWIC assessment and status report on the Collared Pika (Ochotona collaris) in Canada}}, url = {www.registrelep-sararegistry.gc.ca/default{\_}e.cfm{\%}5Cnhttp://www.cosewic.gc.ca}, year = {2011} } @article{Barrio2013, abstract = {Interspecific interactions often determine the structure and stability of biotic communities. In low-productivity and highly seasonal environments such as the alpine tundra, most interactions occur during a short, snow-free period. The strength and direction of these interactions are likely to be determined by the availability of resources, particularly among species of the same ecological guild. Understanding how species interact in such environments can provide insights into the conditions that facilitate their coexistence. We determined the potential for interspecific interactions among 3 resident medium-sized mammalian herbivores inhabiting the alpine tundra and investigated how they share available space and resources. Overlap in their respective activity areas indicated that these species were aggregated at a landscape scale, but other mechanisms allowed their coexistence at a finer scale. Their distributions were primarily associated with shorter distances to heterospecifics and, secondly, with habitat features related to shelter and escape from predation. Our results suggest that these species can (and do) coexist by partitioning their ecological niches. Competition is likely not a major factor in structuring these communities; in turn, facilitative mechanisms may allow co-occurrence of these sympatric herbivores in seasonal, low productivity environments.}, annote = {-during one month they censured (location) all three species by observing various sign -paper is good example of how ranges overlap, but there is local spatial segregation occuring -provide information on what determines pika locations -paper is important in discussing why we only consider pikas -mnake point that pikas harvest relatively late in season compared to other herbivores in the area}, author = {Barrio, Isabel C. and Hik, David S.}, doi = {10.2980/20-3-3595}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barrio, Hik - 2013 - Good Neighbours Determinants of Aggregation and Segregation among Alpine Herbivores.pdf:pdf}, isbn = {1195-6860}, issn = {1195-6860}, journal = {Ecoscience}, keywords = {alpine tundra,coexistence,facilitation,interspecific interactions,medium-sized mammals}, number = {3}, pages = {276--282}, title = {{Good Neighbours? Determinants of Aggregation and Segregation among Alpine Herbivores}}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84896820313{\&}partnerID=tZOtx3y1}, volume = {20}, year = {2013} } @article{Giroud2012, abstract = {This book summarises the newest information on seasonal adaptation in animals. Topics include animal hibernation, daily torpor, thermoregulation, heat production, metabolic depression, biochemical adaptations, neurophysiology and energy balance. The contributors to this book present interdisciplinary research at multiple levels ranging from the molecular to the ecophysiological, as well as evolutionary approaches. The chapters of this book provide original data not published elsewhere, which makes it the most up-to-date, comprehensive source of information on these fields. The book's subchapters correspond to presentations given at the 14th International Hibernation Symposium in August 2012 in Austria. This is a very successful series of symposia (held every four years since 1959) that attracts leading researchers in the field. Like the past symposia, this meeting – and consequently the book – is aimed not only at hibernation but at covering the full range of animal adaptations to seasonal environments. For the next four years, this book will serve as the cutting-edge reference work for graduate students and scientists active in this field of physiology and ecology..}, author = {Giroud, Sylvain and Turbill, Christopher and Ruf, Thomas}, doi = {10.1007/978-3-642-28678-0}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Giroud, Turbill, Ruf - 2012 - Living in a Seasonal World.pdf:pdf}, isbn = {978-3-642-28677-3}, journal = {Animals}, pages = {481--491}, pmid = {11598878}, title = {{Living in a Seasonal World}}, url = {http://www.springerlink.com/index/10.1007/978-3-642-28678-0}, year = {2012} } @article{Sheriff2011, abstract = {Ecologists need an empirical understanding of physiological and behavioural adjustments that animals can make in response to seasonal and long-term variations in environmental conditions. Because many species experience trade-offs between timing and duration of one seasonal event versus another and because interacting species may also shift phenologies at different rates, it is possible that, in aggregate, phenological shifts could result in mismatches that disrupt ecological communities. We investigated the timing of seasonal events over 14 years in two Arctic ground squirrel populations living 20 km apart in Northern Alaska. At Atigun River, snow melt occurred 27 days earlier and snow cover began 17 days later than at Toolik Lake. This spatial differential was reflected in significant variation in the timing of most seasonal events in ground squirrels living at the two sites. Although reproductive males ended seasonal torpor on the same date at both sites, Atigun males emerged from hibernation 9 days earlier and entered hibernation 5 days later than Toolik males. Atigun females emerged and bred 13 days earlier and entered hibernation 9 days earlier than those at Toolik. We propose that this variation in phenology over a small spatial scale is likely generated by plasticity of physiological mechanisms that may also provide individuals the ability to respond to variation in environmental conditions over time.}, annote = {-main point is that there are tradeoffs in multiple timing traits, cannot simply look at one phenological measure -at Toolik Lake, snow happens earlier in autuomn and melts four weeks later than the Atigun River -this snowfall has been correlated with plant abundance -look at hiberating ground squirrel species in Alaska have soi8l temperature information and snow cover}, author = {Sheriff, Michael J and Kenagy, G Jim and Richter, Melanie and Lee, Trixie and T{\o}ien, Oivind and Kohl, Franziska and Buck, C Loren and Barnes, Brian M}, doi = {10.1098/rspb.2010.2482}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sheriff et al. - 2011 - Phenological variation in annual timing of hibernation and breeding in nearby populations of Arctic ground squir.pdf:pdf}, isbn = {0962-8452}, issn = {0962-8452}, journal = {Proc. R. Soc. Lond. B}, keywords = {arctic,climate,local phenological variation,phenotypic flexibility,urocitellus parryii}, number = {1716}, pages = {2369--2375}, pmid = {21177687}, title = {{Phenological variation in annual timing of hibernation and breeding in nearby populations of Arctic ground squirrels.}}, volume = {278}, year = {2011} } @article{Parvinen2005, abstract = {The great majority of species that lived on this earth have gone extinct. These extinctions are often explained by invoking changes in the environment, to which the species has been unable to adapt. Evolutionary suicide is an alternative explanation to such extinctions. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist. In this paper different models, where evolutionary suicide occurs are discussed, and the theory behind the phenomenon is reviewed.}, annote = {-evolutionary suicide, also called dawinian extinciton and evolution to extinction -need specific bifurcation to cause evo suicide variations include deterministic evo suicice, mutationally stochastic evo suicide and demographuacll stocahsti evo suicicde AD -assume resident has reached attractor, introduce mutant, and look at fitness evo suicide - starting with viable strategy, evo can move e.g. larger trait values give advantage over compeitors (asymmetric compeition) but it results in decreased fecundity or survival -evolutonary suicide implies there is more than one attractor, going against what AD usually assumes -can only move from one attractor to another near bifuractions point, otherwise a mutant should reside in same attractor as resident -could have evo suicide even in frequency-independent scenario -can imagine situation where evo branching occurs but one branch goes extinct (evo of dispersal, asymmetric comp, and evo of cannibalism) EXAMPLES ofevo suicide -asymmetric competition, chemostat with inflow of poison, evo of dispersal in metapop model,}, author = {Parvinen, Kalle}, doi = {10.1007/s10441-005-2531-5}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Parvinen - 2005 - Evolutionary suicide.pdf:pdf}, isbn = {0001-5342 (Print)}, issn = {0001-5342}, journal = {Acta biotheoretica}, number = {3}, pages = {241--264}, pmid = {16329010}, title = {{Evolutionary suicide.}}, volume = {53}, year = {2005} } @article{Neuhaus1999, author = {Neuhaus, Peter and Bennett, Ron and Hubbs, Anne}, doi = {10.1139/z99-052}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Neuhaus, Bennett, Hubbs - 1999 - Effects of a late snowstorm and rain on survival and reproductive success in Columbian ground squirrels.pdf:pdf}, issn = {0008-4301}, journal = {Canadian Journal of Zoology}, number = {6}, pages = {879--884}, title = {{Effects of a late snowstorm and rain on survival and reproductive success in Columbian ground squirrels ( Spermophilus columbianus )}}, url = {http://www.nrcresearchpress.com/doi/abs/10.1139/z99-052}, volume = {77}, year = {1999} } @article{Lane2011, author = {Lane, J E and Kruuk, L E B and Charmantier, A and Murie, J O and Coltman, D W and Buoro, M and Raveh, S and Dobson, F S}, doi = {10.1111/j.1420-9101.2011.02334.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lane et al. - 2011 - A quantitative genetic analysis of hibernation emergence date in a wild population of Columbian ground squirrels.pdf:pdf}, keywords = {additive genetic variation}, pages = {1949--1959}, title = {{A quantitative genetic analysis of hibernation emergence date in a wild population of Columbian ground squirrels}}, volume = {24}, year = {2011} } @article{Zhang2011, annote = {-mostly juust provide maps of what is happenin with climate accross Canada, need to access the raw data}, author = {Zhang, X. and Brown, R. and Vincent, L. and Skinner, W. and Feng, Y. and Mekis, E.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Zhang et al. - 2011 - Canadian climate trends, 1950-2007.pdf:pdf}, isbn = {9781100186801}, journal = {Canadian Biodiversity: Ecosystem Status and Trends 2010, Technical Thematic Report No. 5}, pages = {iv + 21p}, title = {{Canadian climate trends, 1950-2007}}, url = {http://www.biodivcanada.ca/default.asp?lang=En{\&}n=137E1147-0}, year = {2011} } @incollection{Lane, annote = {plastiicity is individual level phenomena, not change in mean trait of a population -argues that no studies to date have quantified reaction norms for hibernation traits -{\textgreater} would allow you to see if populations in more stocahstic environments had greater plasticity -discusses animal model as it allows you to account for maternal effects -discusses Ozgul et al paper more}, author = {Lane, Jeffrey E}, doi = {10.1007/978-3-642-28678-0}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lane - Unknown - Evolutionary Ecology of Mammalian Hibernation Phenology.pdf:pdf}, isbn = {9783642286780}, pages = {51--61}, title = {{Evolutionary Ecology of Mammalian Hibernation Phenology}} } @article{Morrison2009, annote = {-timing of haypile inititation is function of vegetaion mautrity and moisture content (Smith 1974, 1990) -haying should probably be delayed for juveniles and females -collect data on timing and rate of haypile collection -don't provide raw data -look at total summer mass of haypiles, see if this is enough for winter based on consumption rates}, author = {Morrison, Shawn F. and Pelchat, Graeme and Donahue, Aaron and Hik, David S.}, doi = {10.1007/s00442-008-l}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Morrison et al. - 2009 - Influence of food hoarding behavior on the over-winter survival of pikas in strongly seasonal envrionments.pdf:pdf}, isbn = {0044200811868}, issn = {00298549}, journal = {Oecologia}, keywords = {adult pikas began haying,age and sex,alpine,an,annual haypile initiation was,classification tree,enced by age and,lagomorph,ochotona collaris,strongly influ-,year,yukon}, number = {1}, pages = {107--116}, pmid = {18975012}, title = {{Influence of food hoarding behavior on the over-winter survival of pikas in strongly seasonal envrionments}}, volume = {157}, year = {2009} } @article{Berteaux2006, annote = {-discuss statistical versus mechanistic predictions -argue that you need to study energetics to mechanistically get at phenology changes and climate -argue that multiple trophic levels are useful as plants are more directly tied to CC unlike animal dynamics. Suggest using NDVI for this. Could we use NDVI for pika site?}, author = {Berteaux, D and Humphries, M M and Krebs, C J and Lima, M and McAdam, A G and Pettorelli, N and R{\'{e}}ale, D and Saitoh, T and Tkadlec, E and Weladji, R B and Stenseth, N Chr}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Berteaux et al. - 2006 - Constraints to projecting the effects of climate change on mammals.pdf:pdf}, journal = {Climate Research}, keywords = {cause-effect relationships,climate change,ecology,forecasting,mammals,models,of the publisher,permitted without written consent,prediction,resale or republication not,scientific projection,time series}, pages = {151--158}, title = {{Constraints to projecting the effects of climate change on mammals}}, volume = {32}, year = {2006} } @article{McIntire2002, abstract = {1We measured leaf births, leaf deaths and leaf length of three alpine perennial species, Kobresia myosuroides, Erigeron humilis and Oxytropis nigrescens, from sites with different grazing histories (strong or weak) in response to two levels of current season grazing (present or absent) by collared pikas (Ochotona collaris), a small lagomorph, in the south-west Yukon. 2All three species appeared to tolerate the removal of 58201361{\%} of summer leaf production under natural conditions. Grazing history, which was defined by the location of plants located either {\textless} 2 m or {\textgreater} 6 m from boulderfields with a history of occupation by pikas, was the most significant factor determining shifts in leaf births and leaf deaths following herbivory. 3The only detectable influence of current season herbivory for any measured species was a reduction of leaf length of Kobresia. 4A comparison of historically grazed with historically ungrazed plants indicated several changes in leaf demography and morphology. Kobresia leaves were generally shorter and had higher rates of production of new leaves. Oxytropis had higher rates of new leaf production. Erigeron had fewer leaf births throughout the summer, but showed a large and highly significant delay in the timing of leaf senescence. 5These responses can be largely understood as strategies to avoid the predictable intensive late season foraging that is characteristic of pikas. Morphological mechanisms allow these species to tolerate and, more importantly for the herbivore, persist under heavy and chronic grazing."}, author = {McIntire, Eliot J B and Hik, David S.}, doi = {10.1046/j.1365-2745.2001.00672.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McIntire, Hik - 2002 - Grazing history versus current grazing Leaf demography and compensatory growth of three alpine plants in response.pdf:pdf}, isbn = {0022-0477}, issn = {00220477}, journal = {Journal of Ecology}, keywords = {Alpine meadows,Collared pika,Erigeron humilis,Grazing history,Herbivory gradient,Kobresia myosuroides,Ochotona collaris,Oxytropis nigrescens}, number = {2}, pages = {348--359}, title = {{Grazing history versus current grazing: Leaf demography and compensatory growth of three alpine plants in response to a native herbivore (Ochotona collaris)}}, volume = {90}, year = {2002} } @article{McIntire2005, abstract = {We studied an alpine herbivory gradient established by collared pikas, a small central place foraging lagomorph, to examine the effects of multiple grazing levels on above-ground live biomass (AGB) and species richness (SR) in alpine tundra. The effects of within-season (four sampling periods), multi-season (across three summers) and longer-term dynamics (inferred from spatial location of vegetation with respect to pika haypiles) were examined. Along the grazing gradient, we found support for and against hypotheses that propose biphasic, increasing, or decreasing responses to herbivory, both in terms of AGB and SR. Our results suggest that plant-herbivore predictability is still weak. To further examine the impact of herbivory, we experimentally removed pikas using mesh exclosures placed at increasing distance from the edge of talus occupied by pikas. AGB after the second consecutive year of herbivore exclusion increased by 125{\%} compared to control plots in highly grazed areas adjacent to talus ({\textless}1 m). In more lightly grazed sites at distances 1-6 m from talus, AGB increased by more than 40{\%} after pikas were removed. No differences were observed in the ungrazed sites {\textgreater}6 m from talus. AGB was highest in meadow patches previously grazed by pikas compared to those with little grazing history, but this response was only observed after two seasons following release from herbivory. Grazed sites at distances of 1-6 m had the highest SR. These results indicate that multi-year measurements of growth are particularly relevant in ecosystems dominated by long-lived perennials in regions where productivity is low. Infrequent herbivore vacancies may provide local short-term release from pika grazing, thereby contributing to the persistence of productive, highly palatable vegetation.}, annote = {-looked at above ground biomasss and speies compsitiion of plants in response to pika foraging -look at within season and between year dynamics -plants in area with history ofgrazing can grow much more when grazing is stopped}, author = {McIntire, Eliot J B and Hik, David S.}, doi = {10.1007/s00442-005-0127-z}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McIntire, Hik - 2005 - Influences of chronic and current season grazing by collared pikas on above-ground biomass and species richness i.pdf:pdf}, isbn = {0044200501}, issn = {00298549}, journal = {Oecologia}, keywords = {Grazing history,Herbivory,Net above-ground primary production,Ochotona collaris,Yukon}, number = {2}, pages = {288--297}, pmid = {15959819}, title = {{Influences of chronic and current season grazing by collared pikas on above-ground biomass and species richness in subarctic alpine meadows}}, volume = {145}, year = {2005} } @article{Morrison2007, abstract = {1. Demographic analysis is essential in order to determine which factors, such as survival, fertility and other life-history characteristics, have the greatest influence on a population's rate of growth (lambda). 2. We used life-table response experiments (LTREs) to assess the relative importance of survival and fertility rates for an alpine lagomorph, the collared pika Ochotona collaris, using 12 years (1995-2006) of census data. The LTRE analysis was repeated for each of three subpopulations within the main study site that were defined by aspect (east, west and south). 3. Across the entire study site, the survival and fertility of adults contributed 35.6 and 43.5{\%}, respectively, to the variance observed in the projected population growth rate, V(lambda), whereas juvenile survival contributed 20.9{\%}. Adult survival and fertility contributed approximately equal amounts for each subpopulation when considered separately, although their rank order varied spatially. 4. Adult survival across the entire site was positively correlated to the Pacific Decadal Oscillation (PDO) with a time lag of 1 year, and was uncorrelated to adult density. The PDO was negatively correlated to the timing of spring snowmelt at our site, implicating the importance of earlier spring conditions and plant phenology on the subsequent winter survival of adults and therefore, population growth. 5. When subpopulations were analysed separately, survivals and fertilities were variously correlated to lagged PDO and adult densities, but the patterns varied spatially. Therefore, the mechanisms underlying V(lambda) can vary substantially over relatively short distances.}, annote = {with higher PDO, should have earlier snow free day of the year For pooled pop, results differed slightly for subpops -adult female surival correlated to PDO with 1 year lag, and surival was not correlated with density -fertility negatively correlated to density -juv surival not correlated with density or PDO -the three aspects appear to represent relatively distinct sub populations that are not connected snowmelt depends on slope aspect freeze thaw events likely to be important have individual tagged animals, sexed, and aged as juveniles (YOY) or adults --capture juveniles after they disperse}, author = {Morrison, Shawn F. and Hik, David S.}, doi = {10.1111/j.1365-2656.2007.01276.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Morrison, Hik - 2007 - Demographic analysis of a declining pika Ochotona collaris population Linking survival to broad-scale climate pat.pdf:pdf}, isbn = {0021-8790}, issn = {00218790}, journal = {Journal of Animal Ecology}, keywords = {Collared pika,Fertility,Life-table response experiment,Pacific Decadal Oscillation,Snowmelt}, number = {5}, pages = {899--907}, pmid = {17714268}, title = {{Demographic analysis of a declining pika Ochotona collaris population: Linking survival to broad-scale climate patterns via spring snowmelt patterns}}, volume = {76}, year = {2007} } @article{Moore2002, abstract = {The relatively short length of most instrumental climate records restricts the study of climate variability1,2, and it is therefore essential to extend the record into the past with the help of proxy data. Only since the late 1940s have atmospheric data been available3 that are sufficient in quality and spatial resolution to identify the dominant patterns of climate variability, such as the Pacific North America pattern4,5 and the Pacific Decadal Oscil- lation6. Here we present a 301-year snow accumulation record from an ice core at a height of 5,340 m above sea level—from Mount Logan, in northwestern North America. This record shows features that are closely linked with the Pacific North America pattern for the period of instrumental data availability. Our record extends back in time to cover the period from the closing stages of the Little Ice Age to the warmest decade in the past millennium7. We find a positive, accelerating trend in snow accumulation after the middle of the nineteenth century. This trend is paralleled by a warming over northwestern North America which has been associated with secular changes in both the Pacific North America pattern and the Pacific Decadal Oscillation.}, annote = {-snow accumulation has increased over last 300 years}, author = {Moore, G W K and Holdsworth, G and Alverson, K}, doi = {10.1038/nature01229}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moore, Holdsworth, Alverson - 2002 - Climate change in the North Pacific region over the past three centuries.pdf:pdf}, isbn = {0028-0836}, issn = {0028-0836}, journal = {Nature}, number = {2001}, pages = {401--403}, pmid = {12459737}, title = {{Climate change in the North Pacific region over the past three centuries}}, volume = {420}, year = {2002} } @article{Danby2011, abstract = {Repeat measurements from long-term plots provide precise data for studying plant community change. In 2010, we visited a remote location in Yukon, Canada, where a detailed survey of alpine tundra communities was conducted in 1968. Plant community composition was resurveyed on the same four slopes using the same methods as the original study. Species richness and diversity increased significantly over the 42 years and non-metric multidimensional scaling indicated that community composition had also changed significantly. However, the direction and magnitude of change varied with aspect. Dominant species were not replaced or eliminated but, instead, declined in relative importance. Fine-scale changes in vegetation were evident from repeat photography and dendro-ecological analysis of erect shrubs, supporting the community-level analysis. The period of study corresponds to a mean annual temperature increase of 2 degrees C, suggesting that climate warming has influenced these changes.}, author = {Danby, Ryan K. and Koh, Saewan and Hik, David S. and Price, Larry W.}, doi = {10.1007/s13280-011-0172-2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Danby et al. - 2011 - Four decades of plant community change in the alpine tundra of southwest Yukon, Canada.pdf:pdf}, isbn = {0044-7447}, issn = {00447447}, journal = {Ambio}, keywords = {Arctic-alpine,Climate change,Community ecology,Tundra,Yukon}, number = {6}, pages = {660--671}, pmid = {21954728}, title = {{Four decades of plant community change in the alpine tundra of southwest Yukon, Canada}}, volume = {40}, year = {2011} } @article{Johansson2012, abstract = {Phenology is an important part of life history that is gaining increased attention because of recent climate change. We use game theory to model phenological adaptation in migratory birds that compete for territories at their breeding grounds. We investigate how the evolutionarily stable strategy (ESS) for the timing of arrival is affected by changes in the onset of spring, the timing of the resource peak, and the season length. We compare the ESS mean arrival date with the environmental optimum, that is, the mean arrival date that maximizes fitness in the absence of competition. When competition is strong, the ESS mean arrival date responds less than the environmental optimum to shifts in the resource peak but more to changes in the onset of spring. Increased season length may not necessarily affect the environmental optimum but can still advance the ESS mean arrival date. Conversely, shifting a narrow resource distribution may change the environmental optimum without affecting the ESS mean arrival date. The ESS mean arrival date and the environmental optimum may even shift in different directions. Hence, treating phenology as an evolutionary game rather than an optimization problem fundamentally changes what we predict to be an adaptive response to environmental changes.}, annote = {-what happens when climate change could affect multiple selective pressures? -bird reproction that depends on resource abundance and on territory counts -nicely compare evolutionary outcomes of game theory model and density independent cases -use unimodal curve for reproductive output -territory quality descreases over the seaon -examine how arrival timing (which has mean and a variance) evolves over time --the arrival interval is just some set amount of time for which birds arrive - therby it is not really a funciton valued trait -what happens when you allow for plasticity?}, author = {Johansson, Jacob and Jonz{\'{e}}n, Niclas}, doi = {10.1086/664624}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Johansson, Jonz{\'{e}}n - 2012 - Effects of territory competition and climate change on timing of arrival to breeding grounds a game-theory a.pdf:pdf}, isbn = {1537-5323 (Electronic)$\backslash$r0003-0147 (Linking)}, issn = {1537-5323}, journal = {The American Naturalist}, keywords = {Animal Migration,Animals,Birds,Birds: physiology,Climate Change,Game Theory,Models,Reproduction,Seasons,Theoretical}, number = {4}, pages = {463--74}, pmid = {22437176}, title = {{Effects of territory competition and climate change on timing of arrival to breeding grounds: a game-theory approach.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22437176}, volume = {179}, year = {2012} } @article{Reed2013, abstract = {Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-$\alpha$-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 {\AA} for the interface backbone atoms) increased from 21{\%} with default Glide SP settings to 58{\%} with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63{\%} success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40{\%} of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.}, annote = {-find no affect of phenological mismatch on population growth. Why? --have relaxed competition i.e. densty dependence helped buffe population growth}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Reed, Thomas E. and Gr{\o}tan, Vidar' and Jenouvrier, Stephanie and S{\ae}ther, B-E and Visser, Marcel E}, doi = {10.1017/CBO9781107415324.004}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reed et al. - 2013 - Population growth in a wild bird is buffered against phenological mismatch.pdf:pdf}, isbn = {9788578110796}, issn = {1098-6596}, journal = {Science}, keywords = {icle}, pages = {488--491}, pmid = {25246403}, title = {{Population growth in a wild bird is buffered against phenological mismatch}}, volume = {340}, year = {2013} } @article{Forsman2014, abstract = {Much research has been devoted to identify the conditions under which selection favours flexible individuals or genotypes that are able to modify their growth, development and behaviour in response to environmental cues, to unravel the mechanisms of plasticity and to explore its influence on patterns of diversity among individuals, populations and species. The consequences of developmental plasticity and phenotypic flexibility for the performance and ecological success of populations and species have attracted a comparatively limited but currently growing interest. Here, I re-emphasize that an increased understanding of the roles of plasticity in these contexts requires a 'whole organism' (rather than 'single trait') approach, taking into consideration that organisms are integrated complex phenotypes. I further argue that plasticity and genetic polymorphism should be analysed and discussed within a common framework. I summarize predictions from theory on how phenotypic variation stemming from developmental plasticity and phenotypic flexibility may affect different aspects of population-level performance. I argue that it is important to distinguish between effects associated with greater interindividual phenotypic variation resulting from plasticity, and effects mediated by variation among individuals in the capacity to express plasticity and flexibility as such. Finally, I claim that rigorous testing of predictions requires methods that allow for quantifying and comparing whole organism plasticity, as well as the ability to experimentally manipulate the level of and capacity for developmental plasticity and phenotypic flexibility independent of genetic variation.Heredity advance online publication, 8 October 2014; doi:10.1038/hdy.2014.92.}, annote = {-argues for whole organism, rather than single trait studies of plasticity}, author = {Forsman, A}, doi = {10.1038/hdy.2014.92}, isbn = {doi:10.1038/hdy.2014.92}, issn = {1365-2540}, journal = {Heredity}, number = {August}, pages = {1--9}, pmid = {25293873}, publisher = {Nature Publishing Group}, title = {{Rethinking phenotypic plasticity and its consequences for individuals, populations and species.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25293873}, volume = {115}, year = {2014} } @article{Scheffer2015, abstract = {Ecological resilience is the ability of a system to persist in the face of per- turbations. Although resilience has been a highly influential concept, its interpretation has remained largely qualitative. Here we describe an emerg- ing family of methods for quantifying resilience on the basis of observations. A first set of methods is based on the phenomenon of critical slowing down, which implies that recovery upon small perturbations becomes slower as a system approaches a tipping point. Such slowing down can be measured experimentally but may also be indirectly inferred from changes in natu- ral fluctuations and spatial patterns. A second group of methods aims to characterize the resilience of alternative states in probabilistic terms based on large numbers of observations as in long time series or satellite images. These generic approaches to measuring resilience complement the system- specific knowledge needed to infer the effects of environmental change on the resilience of complex systems.}, annote = {-resilience could mean rate of return after perturbation or the size of basins of attraction -start with idea that system is gnerally at som eequilbrium -talk about a number of different terms and how things get complicated very quickly when these ideas are applied to real systems -look at various methods for detecting resilience near equilbrium points (critical slowing down) or far away from equilibrium (flickering- visiting different basins stochastically) -discuss spatial extensions -discuss when systems may be experiencing periodic or chaotic dynamics -End with practical advice for actually examining these ideas with data (GDPP for this work?) --need to remove other trends (seasonal or increases/decreases) Class notes: -Turing morphogenesis and spatial patterns}, author = {Scheffer, Marten and Carpenter, Stephen R and Dakos, Vasilis and van Nes, Egbert}, doi = {10.1146/annurev-ecolsys-112414-054242}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Scheffer et al. - 2015 - Generic Indicators of Ecological Resilience.pdf:pdf}, isbn = {10.1146/annurev-ecolsys-112414-054242}, issn = {1543-592X}, journal = {Annual Review of Ecology, Evolution, and Systematics}, keywords = {alternative stable states,big data,critical transitions,early warning signals,resilience,resilience,tipping point,critical transitions,earl,tipping point}, pages = {145--167}, title = {{Generic Indicators of Ecological Resilience}}, volume = {46}, year = {2015} } @article{Chevin2010, abstract = {We study the dynamics of evolutionary recovery after an abrupt environmental shift in a density-regulated population with evolving plasticity. Maladaptation to the new environment initially causes the population to decline, until adaptive phenotypic plasticity and genetic evolution restore positive population growth rate. We assume that selection on a quantitative trait is density-independent and that the initial cost of plasticity is much lower than the benefit of the initial plastic response. The initial partially adaptive plasticity reduces the effective magnitude of the environmental shift, whereas evolution of plasticity increases the rate of adaptation. Both effects greatly facilitate population persistence. In contrast, density dependence of population growth always hinders persistence. With theta-logistic population regulation, a lower value of theta produces a faster initial population decline and a higher extinction risk.}, annote = {-models how plasticity and subsequaent evolution of plasticity allows pop to recover from abrupt environmental shift -this model explicently includes demography to see how plasticity can help a population -show conditions for how plasticity can increase rate of evolution towards new optimum}, author = {Chevin, Luis Miguel and Lande, Russell}, doi = {10.1111/j.1558-5646.2009.00875.x}, isbn = {1558-5646 (Electronic)$\backslash$n0014-3820 (Linking)}, issn = {00143820}, journal = {Evolution}, keywords = {Abrupt environmental shift,Adaptation,Density dependence,Extinction,Phenotypic plasticity,Quantitative genetics}, number = {4}, pages = {1143--1150}, pmid = {19863583}, title = {{When do adaptive plasticity and genetic evolution prevent extinction of a density-regulated population?}}, volume = {64}, year = {2010} } @article{Charmantier2014, abstract = {There are multiple observations around the globe showing that in many avian species, both the timing of migration and breeding have advanced, due to warmer springs. Here, we review the literature to disentangle the actions of evolutionary changes in response to selection induced by climate change versus changes due to individual plasticity, that is, the capacity of an individual to adjust its phenology to environmental variables. Within the abundant literature on climate change effects on bird phenology, only a small fraction of studies are based on individual data, yet individual data are required to quantify the relative importance of plastic versus evolutionary responses. While plasticity seems common and often adaptive, no study so far has provided direct evidence for an evolutionary response of bird phenology to current climate change. This assessment leads us to notice the alarming lack of tests for microevolutionary changes in bird phenology in response to climate change, in contrast with the abundant claims on this issue. In short, at present we cannot draw reliable conclusions on the processes underlying the observed patterns of advanced phenology in birds. Rapid improvements in techniques for gathering and analysing individual data offer exciting possibilities that should encourage research activity to fill this knowledge gap.}, annote = {-discuss conditions when plasticity will help or when it can hapen adaptation (by non adaptive plasticity - Ghalambor et al 2007) -for "adaptive plasticty" you also need measures of fitness over time}, author = {Charmantier, Anne and Gienapp, Phillip}, doi = {10.1111/eva.12126}, isbn = {1752-4571}, issn = {17524563}, journal = {Evolutionary Applications}, keywords = {Bird,Climate change,Evolution,Phenology,Phenotypic plasticity,Selection,Timing of breeding,Timing of migration}, number = {1}, pages = {15--28}, pmid = {24454545}, title = {{Climate change and timing of avian breeding and migration: Evolutionary versus plastic changes}}, volume = {7}, year = {2014} } @article{Ripa2013, abstract = {The evolution of natural organisms is ultimately driven by the invasion and possible fixation of mutant alleles. The invasion process is highly stochastic, however, and the probability of success is generally low, even for advantageous alleles. Additionally, all organisms live in a stochastic environment, which may have a large influence on what alleles are favorable, but also contributes to the uncertainty of the invasion process. We calculate the invasion probability of a beneficial, mutant allele in a monomorphic, large population subject to stochastic environmental fluctuations, taking into account density- and frequency-dependent selection, stochastic population dynamics and temporal autocorrelation of the environment. We treat both discrete and continuous time population dynamics, and allow for overlapping generations in the continuous time case. The results can be generalized to diploid, sexually reproducing organisms embedded in communities of interacting species. We further use these results to derive an extended canonical equation of adaptive dynamics, predicting the rate of evolutionary change of a heritable trait on long evolutionary time scales.}, author = {Ripa, J{\"{o}}rgen and Dieckmann, Ulf}, doi = {10.1111/evo.12046}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ripa, Dieckmann - 2013 - Mutant invasions and adaptive dynamics in variable environments.pdf:pdf}, isbn = {1558-5646}, issn = {00143820}, journal = {Evolution}, keywords = {Adaptation,Fitness,Mutations,Population biology,Population genetics,Selection-natural}, number = {5}, pages = {1279--1290}, pmid = {23617908}, title = {{Mutant invasions and adaptive dynamics in variable environments}}, volume = {67}, year = {2013} } @article{Williams2014, abstract = {The production of offspring by vertebrates is often timed to coincide with the annual peak in resource availability. However, capital breeders can extend the energetic benefits of a resource pulse by storing food or fat, thus relaxing the need for synchrony between energy supply and demand. Food-hoarding red squirrels (Tamiasciurus hudsonicus) breeding in the boreal forest are reliant on cones from a masting conifer for their nutrition, yet lactation is typically completed before the annual crop of cones is available for consumption such that peaks in energy supply and demand are not synchronized. We investigated the phenological response of red squirrels to annual variation in environmental conditions over a 20-year span and examined how intra- and inter-annual variation in the timing of reproduction affected offspring recruitment. Reproductive phenology was strongly affected by past resource availability with offspring born earlier in years following large cone crops, presumably because this affected the amount of capital available for reproduction. Early breeders had higher offspring survival and were more likely to renest following early litter loss when population density was high, perhaps because late-born offspring are less competitive in obtaining a territory when vacancies are limited. Early breeders were also more likely to renest after successfully weaning their first litter, but renesting predominantly occurred during mast years. Because of their increased propensity to renest and the higher survival rates of their offspring, early breeders contribute more recruits to the population but the advantage of early breeding depends on population density and resource availability.}, author = {Williams, Cory T. and Lane, Jeffrey E. and Humphries, Murray M. and McAdam, Andrew G. and Boutin, Stan}, doi = {10.1007/s00442-013-2826-1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Williams et al. - 2014 - Reproductive phenology of a food-hoarding mast-seed consumer Resource- and density-dependent benefits of early.pdf:pdf}, isbn = {0029-8549}, issn = {00298549}, journal = {Oecologia}, keywords = {Density dependence,Hoarding,Mast seeding,North American red squirrel,Phenology}, number = {3}, pages = {777--788}, pmid = {24241530}, title = {{Reproductive phenology of a food-hoarding mast-seed consumer: Resource- and density-dependent benefits of early breeding in red squirrels}}, volume = {174}, year = {2014} } @article{Day2005, annote = {-gives brief background on theoretical ecology and theoretical evolution (just pop gen and game theory) -goes on to desribe four approaches in eco-evo dynamics modeling (single locus theory, quant gen, game theory, adaptive dynamics) -Pop gen could be combined with ecology by recongizing that per capita production per individual was equivalent to absolute fitness Quan gen -developed at same time but focused on many genes, each with small effect -{\textgreater} allows you to assume normal distribution and you only have to keep track of mean and var - Game theory -ususally seperates timescale by assuming pop is at equilbrium when mutant introduced -invasion fitness of rare mutant has also been callyed "fitness generating function" and "fitness G-function" -Nash equilbrium def -mutant invades, sweeps through to fixation, an then another mutant can invade -little work focused on dynamics before an ESS occured -not all ESSs are attainable -can include sexual dynamics (though these do not usually include freq depend selection) -CSS vs ESS Adaptive dynamics -feels it is a subset of game theory -a focus of AD has been on evolutionary branching -three important developments by AD --that branching points may be common phenomena --diversification at branching points --canonical equation (including stochasticity)}, author = {Day, Troy}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Day - 2005 - Modeling the ecological context of evolutionary change d{\'{e}}j{\`{a}} vu or something new.pdf:pdf}, isbn = {0120884593}, journal = {Ecological Paradigms Lost: Routes to Theory Change}, pages = {273--309}, title = {{Modeling the ecological context of evolutionary change: d{\'{e}}j{\`{a}} vu or something new?}}, year = {2005} } @article{Boutin2014, abstract = {Phenotypic plasticity and microevolution are the two primary means by which organisms respond adaptively to local conditions. While these mechanisms are not mutually exclusive, their relative magnitudes will influence both the rate of, and ability to sustain, phenotypic responses to climate change. We review accounts of recent phenotypic changes in wild mammal populations with the purpose of critically evaluating the following: (i) whether climate change has been identified as the causal mechanism producing the observed change; (ii) whether the change is adaptive; and (iii) the relative influences of evolution and/or phenotypic plasticity underlying the change. The available data for mammals are scant. We found twelve studies that report changes in phenology, body weight or litter size. In all cases, the observed response was primarily due to plasticity. Only one study (of advancing parturition dates in American red squirrels) provided convincing evidence of contemporary evolution. Subsequently, however, climate change has been shown to not be the causal mechanism underlying this shift. We also summarize studies that have shown evolutionary potential (i.e. the trait is heritable and/or under selection) in traits with putative associations with climate change and discuss future directions that need to be undertaken before a conclusive demonstration of plastic or evolutionary responses to climate change in wild mammals can be made.}, annote = {-report on 12 studies of mammals that observed phenological changes -could you use "animal model" for bimini or pia stuff? How many study sites have data that could be used in this framework to assess plasticity?}, author = {Boutin, Stan and Lane, Jeffrey E.}, doi = {10.1111/eva.12121}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Boutin, Lane - 2014 - Climate change and mammals Evolutionary versus plastic responses.pdf:pdf}, isbn = {1752-4571}, issn = {17524563}, journal = {Evolutionary Applications}, keywords = {Adaptation,Climate change,Contemporary evolution,Ecological genetics,Natural selection,Phenotypic plasticity,Quantitative genetics}, number = {1}, pages = {29--41}, pmid = {24454546}, title = {{Climate change and mammals: Evolutionary versus plastic responses}}, volume = {7}, year = {2014} } @article{Husby2010, abstract = {Phenotypic plasticity is an important mechanism via which populations can respond to changing environmental conditions, but we know very little about how natural populations vary with respect to plasticity. Here we use random-regression animal models to understand the multivariate phenotypic and genetic patterns of plasticity variation in two key life-history traits, laying date and clutch size, using data from long-term studies of great tits in The Netherlands (Hoge Veluwe [HV]) and UK (Wytham Woods [WW]). We show that, while population-level responses of laying date and clutch size to temperature were similar in the two populations, between-individual variation in plasticity differed markedly. Both populations showed significant variation in phenotypic plasticity (IxE) for laying date, but IxE was significantly higher in HV than in WW. There were no significant genotype-by-environment interactions (GxE) for laying date, yet differences in GxE were marginally nonsignificant between HV and WW. For clutch size, we only found significant IxE and GxE in WW but no significant difference between populations. From a multivariate perspective, plasticity in laying date was not correlated with plasticity in clutch size in either population. Our results suggest that generalizations about the form and cause of any response to changing environmental conditions across populations may be difficult.}, annote = {-GxE means genetic basis to variation in plasticity -{\textgreater} plasticity is heritable versus IxE = phenotypic plasticity}, author = {Husby, Arild and Nussey, Dan H. and Visser, Marcel E. and Wilson, Alastair J. and Sheldon, Ben C. and Kruuk, Loeske E B}, doi = {10.1111/j.1558-5646.2010.00991.x}, isbn = {1558-5646}, issn = {00143820}, journal = {Evolution}, keywords = {Animal model,Climate change,Genotype environment interaction,Heritability,Multivariate,Phenotypic plasticity,Random regression}, number = {8}, pages = {2221--2237}, pmid = {20298465}, title = {{Contrasting patterns of phenotypic plasticity in reproductive traits in two great tit (Parus major) populations}}, volume = {64}, year = {2010} } @article{Blackwood2012, abstract = {Coral resilience is important for withstanding ecological disturbances as well as anthropogenic changes to the environment. However, the last several decades have demonstrated a decline in resilience that has often resulted in phase shifts to a degraded coral-depleted state with high levels of algal abundance. A major defining issue in current research is to identify when and how it is possible to reverse these phase shifts allowing for the ecosystem to escape coral depletion and maintain coral-based ecosystem services. We extend an analytic model to focus on the effects of over-harvesting of herbivorous reef fish in the Caribbean by explicitly including grazer dynamics which introduces feedbacks between habitat and grazer abundance posing constraints on management options excluded in previous studies. This allows us to develop ecosystem-based management recommendations for two distinct scenarios of coral reef recovery: The first follows significant habitat damage in response to a large disturbance and the second maintains reef structure but has suffered from events such as coral bleaching. We identify critical fishing effort levels to allow for coral recovery and demonstrate that regions exhibiting severe damage to reef structure have little resilience implying that fishing reductions should be coupled with other restoration methods. Regions that are coral-depleted but maintain reef structure allow for recovery given sufficiently small levels of fishing mortality. However, we demonstrate the difference in recovery time in response to varying levels of control efforts on fishing. {\textcopyright} 2010 The Author(s).}, annote = {-optimal control for this type of model? -looks at parrotfish dynamics and stochastic perturbations from hurricanes - both cause you to switch to ASS by different methods}, author = {Blackwood, Julie C. and Hastings, Alan and Mumby, Peter J.}, doi = {10.1007/s12080-010-0102-0}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Blackwood, Hastings, Mumby - 2012 - The effect of fishing on hysteresis in Caribbean coral reefs.pdf:pdf}, isbn = {1874-1738}, issn = {18741738}, journal = {Theoretical Ecology}, keywords = {Coral reefs,Hysteresis,Phase shifts,Resilience}, number = {1}, pages = {105--114}, title = {{The effect of fishing on hysteresis in Caribbean coral reefs}}, volume = {5}, year = {2012} } @article{Kefi2016, annote = {- Class discussion: -main example of shallow lakes - different feedbacks for two different altenative stable states -scale dependent feedbacks -restoration efforts -positive interactions and evolution (evolution and innovations cause shift to alternative stable states) -time scale on hysteresis diagrams}, author = {Kefi, Sonia and Holmgren, Milena and Scheffer, Marten}, doi = {10.1111/1365-2435.12601}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kefi, Holmgren, Scheffer - 2016 - When can positive interactions cause alternative stable states in ecosystems.pdf:pdf}, journal = {Functional Ecology}, pages = {88--97}, title = {{When can positive interactions cause alternative stable states in ecosystems ?}}, volume = {30}, year = {2016} } @article{Chisholm2015, abstract = {Nutrient enrichment of native grasslands can promote invasion by exotic plant species, leading to reduced biodiversity and altered ecosystem function. Empirical evidence suggests that positive feedbacks may make such transitions difficult to reverse. We developed a mathematical model of grassland dynamics in which one group of species (native) is a better competitor for nitrogen (N) and another group (exotic) is a better competitor for light. We parameterized the model for a grassland community and reproduced observed transitions from a native- to an exotic-dominated state under N loading. Within known bounds of parameter values, both smooth and hysteretic transitions are plausible. The model also predicts that N loading alone is insufficient to achieve a transition to an exotic-dominated state on a timescale relevant to grassland management (a few decades), and that therefore some other disturbance (e.g., fire suppression or heaving grazing) must be present to accelerate it. The model predicts that to restore a grassland to a native-dominated state after N inputs have been reduced, fire and carbon supplements would be most effective. Further field research in N-enriched invaded grasslands is required to establish the strengths of positive feedbacks and, in turn, the consequences of anthropogenic modification of grasslands worldwide.}, annote = {exotic-resident grassland system set of differential equations where the exotic is a bettter compeitiorir for light but the resident is a better compeitor for nitrogen -find that eleviated nutrient inpits can cause a flip in system state but not a relevant imescale for management -explored different management regimes, only fire could bring system back to native state -simulate system with nutriet puleses, causes shift to alternative stable state. Takes a long time to return to another stae What are alternative hypotheses to apparent hystereis? Class discussion: -4 different equilbium -bifurcation diagrams show salternative stable states (one species dominating or even coexist - three colors)}, author = {Chisholm, Ryan A. and Menge, Duncan N L and Fung, Tak and Williams, Nicholas S G and Levin, Simon A.}, doi = {10.1007/s12080-015-0258-8}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chisholm et al. - 2015 - The potential for alternative stable states in nutrient-enriched invaded grasslands.pdf:pdf}, isbn = {1208001502588}, issn = {18741746}, journal = {Theoretical Ecology}, keywords = {Alternative stable states,Bistability,Grasslands,Hysteresis,Invasion,Nutrient enrichment}, number = {4}, pages = {399--417}, title = {{The potential for alternative stable states in nutrient-enriched invaded grasslands}}, volume = {8}, year = {2015} } @article{Ratajczak2014, abstract = {1. This review synthesizes evidence that altered fire frequency drives discontinuous ecosystem transitions from mesic grasslands to shrublands or woodlands in the Central Great Plains, USA. 2. Long-term fire manipulations reveal that grassland to shrubland transitions are triggered when fire-free intervals increase from 1–3 years to ≥ 3–8 years, and longer fire returns (˜10 years or more) result in transitions to woodlands. Grazing and soil properties alter these fire thresholds. 3. Grassland to shrubland transitions are abrupt and exhibit nonlinear relationships between driver and state variables. Transitions to shrublands and woodlands exhibit hysteresis, where reintroducing frequent fires does not reverse transitions in management-relevant time-scales (decades). 4. Nonlinear transitions and hysteresis emerge because grasses generate positive feedbacks with fire that create strong demographic barriers for shrub and tree establishment. Fire-free intervals allow shrubs and trees to reach a size sufficient to survive fire, reproduce and disrupt the fire feedback loop through competition. 5. Synthesis. Mesic grasslands, shrublands and woodlands constitute self-reinforcing states (alternative attractors) separated by critical fire frequency thresholds. Even without major shifts in climate, altered fire frequency can produce dramatic state changes, highlighting the importance of fire for predicting future ecosystem states. Local management should focus on prevention of unwanted transitions rather than post hoc restoration.}, annote = {-when rare fire events are made more infrequent, grasslands turn into shrublands -they have estimats of pre and post settlement fire events -present tri stability system of grassland, shrub land, and woodlands --each state has various self reinforcing mechanims which causes hysteresis Discussion: -fire return time - look at proportion of landscape burned and how often -burning more frequently won't help bring system back to grasslands}, author = {Ratajczak, Zak and Nippert, Jesse B. and Briggs, John M. and Blair, John M.}, doi = {10.1111/1365-2745.12311}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ratajczak et al. - 2014 - Fire dynamics distinguish grasslands, shrublands and woodlands as alternative attractors in the central great.pdf:pdf}, isbn = {0022-0477}, issn = {13652745}, journal = {Journal of Ecology}, keywords = {Alternative stable states,Bi-stability,Bush encroachment,Critical transitions,Plant population and community dynamics,Positive feedbacks,Resilience,Restoration,Stability,Tallgrass prairie,Tipping points,Woody encroachment}, number = {6}, pages = {1374--1385}, title = {{Fire dynamics distinguish grasslands, shrublands and woodlands as alternative attractors in the central great plains of North America}}, volume = {102}, year = {2014} } @article{Gienapp2013, abstract = {Populations need to adapt to sustained climate change, which requires micro-evolutionary change in the long term. A key question is how the rate of this micro-evolutionary change compares with the rate of environmental change, given that theoretically there is a 'critical rate of environmental change' beyond which increased maladaptation leads to population extinction. Here, we parametrize two closely related models to predict this critical rate using data from a long-term study of great tits (Parus major). We used stochastic dynamic programming to predict changes in optimal breeding time under three different climate scenarios. Using these results we parametrized two theoretical models to predict critical rates. Results from both models agreed qualitatively in that even 'mild' rates of climate change would be close to these critical rates with respect to great tit breeding time, while for scenarios close to the upper limit of IPCC climate projections the calculated critical rates would be clearly exceeded with possible consequences for population persistence. We therefore tentatively conclude that micro-evolution, together with plasticity, would rescue only the population from mild rates of climate change, although the models make many simplifying assumptions that remain to be tested.}, author = {Gienapp, Phillip and Lof, Marjolein and Reed, Thomas E and McNamara, John and Verhulst, Simon and Visser, Marcel E}, doi = {10.1098/rstb.2012.0289}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gienapp et al. - 2013 - Predicting demographically sustainable rates of adaptation can great tit breeding time keep pace with climate ch.pdf:pdf}, isbn = {1471-2970}, issn = {1471-2970}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {Adaptation,Animals,Biological,Biological Evolution,Breeding,Climate Change,Female,Forecasting,Genetic Fitness,Models,Ovum,Ovum: physiology,Passeriformes,Passeriformes: genetics,Passeriformes: physiology,Phenotype,Population Dynamics,Seasons,Temperature,Time Factors}, number = {1610}, pages = {20120289}, pmid = {23209174}, title = {{Predicting demographically sustainable rates of adaptation: can great tit breeding time keep pace with climate change?}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3538459{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {368}, year = {2013} } @article{Berteaux2004, abstract = {Adaptations to the cold and to short growing seasons characterize arctic life, but climate in the Arctic is warming at an unprecedented rate. Will plant and animal populations of the Arctic be able to cope with these drastic changes in environmental conditions? Here we explore the potential contribution of evolution by natural selection to the current response of populations to climate change. We focus on the spring phenology of populations because it is highly responsive to climate change and easy to document across a wide range of species. We show that evolution can be fast and can occur at the time scale of a few decades. We present an example of reproductive phenological change associated with climate change (North American red squirrels in the Yukon), where a detailed analysis of quantitative genetic parameters demonstrates contemporary evolution. We answer a series of frequently asked questions that should help biologists less familiar with evolutionary theory and quantitative genetic methods to think about the role of evolution in current responses of ecological systems to climate change. Our conclusion is that evolution by natural selection is a pertinent force to consider even at the time scale of contemporary climate changes. However, all species may not be equal in their capacity to benefit from contemporary evolution.}, annote = {-natural selection ultimately acts on physiology and behavior -focus on Arctic systems -go through a very structured guide of phenology evolution first -to predict how phenology may change in face of CC you need to know magnitude of phenotypic plasticity and the speed at which the population can evolve -Discuss advancement of reproduction for NA req squirrels in the Yukon from 1989-2002 --were able to seperate effects of plasticity and evolution by studying same females over multiple years --62{\%} of advancement in date was due to plasticity -expect that fitness should stay the same over time if plasticity and gen. change are sufficient Discuss four general questions: 1) What are the main factors affecting ability of a species to evolve quickly? Genetic variability -note that plasticity can help a pop deal with change as plasticity probably evolved for that reason -*Adaptive phenotypic plasticity may weaken or increase selection -e.g. plasticty allowed partirtuion date to move forward, which weakened intensity of selection on partrition date, and thus decreased evolutionary response of partrtiion date -discuss role of maternal effects as cross generational plasticity 2) is there more or less gen. variation in northern (or pop. under more variable) environments? 3) species gen. length important? yes 4) what selective pressures will occur under CC? 5) we need long term datat sets to predict and measure evoluionaty change --Need data on indviduals over many years with relationships known between them to seperate effects of plasticity and genetic change}, author = {Berteaux, Dominique and R{\'{e}}ale, Denis and McAdam, Andrew G and Boutin, Stan and Reale, D}, doi = {10.1093/icb/44.2.140}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Berteaux et al. - 2004 - Keeping pace with fast climate change can arctic life count on evolution.pdf:pdf}, isbn = {1540-7063}, issn = {1540-7063}, journal = {Integrative and comparative biology}, number = {2}, pages = {140--51}, pmid = {21680494}, title = {{Keeping pace with fast climate change: can arctic life count on evolution?}}, volume = {44}, year = {2004} } @article{Baskett2012, abstract = {This paper presents an overview of how mechanistic knowledge of organism-environment interactions, including biomechanical interactions of heat, mass and momentum transfer, can be integrated into basic theoretical population biology through mechanistic functional responses that quantitatively describe how organisms respond to their physical environment. Integrating such functional responses into simple community and microevolutionary models allows scaling up of the organism-level understanding from biomechanics both ecologically and temporally. For community models, Holling-type functional responses for predator-prey interactions provide a classic example of the functional response affecting qualitative model dynamics, and recent efforts are expanding analogous models to incorporate environmental influences such as temperature. For evolutionary models, mechanistic functional responses dependent on the environment can serve as fitness functions in both quantitative genetic and game theoretic frameworks, especially those concerning function-valued traits. I present a novel comparison of a mechanistic fitness function based on thermal performance curves to a commonly used generic fitness function, which quantitatively differ in their predictions for response to environmental change. A variety of examples illustrate how mechanistic functional responses enhance model connections to biologically relevant traits and processes as well as environmental conditions and therefore have the potential to link theoretical and empirical studies. Sensitivity analysis of such models can provide biologically relevant insight into which parameters and processes are important to community and evolutionary responses to environmental change such as climate change, which can inform conservation management aimed at protecting response capacity. Overall, the distillation of detailed knowledge or organism-environment interactions into mechanistic functional responses in simple population biology models provides a framework for integrating biomechanics and ecology that allows both tractability and generality.}, author = {Baskett, M. L.}, doi = {10.1242/jeb.059022}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Baskett - 2012 - Integrating mechanistic organism-environment interactions into the basic theory of community and evolutionary ecology.pdf:pdf}, isbn = {00220949 (ISSN)}, issn = {0022-0949}, journal = {Journal of Experimental Biology}, keywords = {fitness function,functional response,game theory,mechanistic models,quantitative genetics,species interactions}, number = {6}, pages = {948--961}, pmid = {22357588}, title = {{Integrating mechanistic organism-environment interactions into the basic theory of community and evolutionary ecology}}, volume = {215}, year = {2012} } @article{Chevin2010a, abstract = {Many species are experiencing sustained environmental change mainly due to human activities. The unusual rate and extent of anthropogenic alterations of the environment may exceed the capacity of developmental, genetic, and demographic mechanisms that populations have evolved to deal with environmental change. To begin to understand the limits to population persistence, we present a simple evolutionary model for the critical rate of environmental change beyond which a population must decline and go extinct. We use this model to highlight the major determinants of extinction risk in a changing environment, and identify research needs for improved predictions based on projected changes in environmental variables. Two key parameters relating the environment to population biology have not yet received sufficient attention. Phenotypic plasticity, the direct influence of environment on the development of individual phenotypes, is increasingly considered an important component of phenotypic change in the wild and should be incorporated in models of population persistence. Environmental sensitivity of selection, the change in the optimum phenotype with the environment, still crucially needs empirical assessment. We use environmental tolerance curves and other examples of ecological and evolutionary responses to climate change to illustrate how these mechanistic approaches can be developed for predictive purposes.}, annote = {-call for more mechanistic models in studying effects of CC -extends previous model of evoution under changing conditions but includes plasticity and an explicit envrionemental driver -different from Chevin and Lande who looked at abrupt change -argue that more work has to be done on long lived organisms or those that live in seasonal environments, to determine costs of plasticicty -they use model in which only optimumum mean phenotype changes, the curve remains the same though -bring up point that plasticity itself can evolve}, author = {Chevin, Luis Miguel and Lande, Russell and Mace, Georgina M.}, doi = {10.1371/journal.pbio.1000357}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chevin, Lande, Mace - 2010 - Adaptation, plasticity, and extinction in a changing environment Towards a predictive theory.pdf:pdf}, isbn = {1545-7885 (Electronic)$\backslash$n1544-9173 (Linking)}, issn = {15449173}, journal = {PLoS Biology}, number = {4}, pmid = {20463950}, title = {{Adaptation, plasticity, and extinction in a changing environment: Towards a predictive theory}}, volume = {8}, year = {2010} } @article{Metzger2014, annote = {Maybe I should use vocabulary from this paper?}, author = {Villard, Marc-Andr{\'{e}} and Metzger, Jen Paul}, doi = {10.1111/1365-2664.12190}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Villard, Metzger - 2014 - Beyond the fragmentation debate a conceptual model to predict when habitat configuration really matters.pdf:pdf}, journal = {Journal of Applied Ecology}, pages = {309--318}, title = {{Beyond the fragmentation debate: a conceptual model to predict when habitat configuration really matters}}, volume = {51}, year = {2014} } @article{Reed2011, abstract = {Abstract:G{\c{C}}{\'{e}}Climate change affects individual organisms by altering development, physiology, behavior, and fitness, and populations by altering genetic and phenotypic composition, vital rates, and dynamics. We sought to clarify how selection, phenotypic plasticity, and demography are linked in the context of climate change. On the basis of theory and results of recent empirical studies of plants and animals, we believe the ecological and evolutionary issues relevant to population persistence as climate changes are the rate, type, magnitude, and spatial pattern of climate-induced abiotic and biotic change; generation time and life history of the organism; extent and type of phenotypic plasticity; amount and distribution of adaptive genetic variation across space and time; dispersal potential; and size and connectivity of subpopulations. An understanding of limits to plasticity and evolutionary potential across traits, populations, and species and feedbacks between adaptive and demographic responses is lacking. Integrated knowledge of coupled ecological and evolutionary mechanisms will increase understanding of the resilience and probabilities of persistence of populations and speciesResumen:G{\c{C}}{\'{e}}El cambio clim+{\'{i}}tico afecta a organismos individuales alterando su desarrollo, fisiolog+¡a, comportamiento y adaptabilidad y a las poblaciones alterando la composici+¦n gen+¬tica y fenot+¡pica, las tasas vitales y su din+{\'{i}}mica. Buscamos clarificar c+¦mo est+{\'{i}}n ligadas la selecci+¦n, la plasticidad fenot+¡pica y la demograf+¡a en el contexto del cambio clim+{\'{i}}tico. Con base en la teor+¡a y los resultados de estudios emp+¡ricos recientes de plantas y animales, creemos que la tasa, tipo, magnitud y patr+¦n espacial del cambio abi+¦tico y bi+¦tico inducido por el clima; el tiempo generacional y la historia de vida del organismo; la extensi+¦n y tipo de plasticidad fenot+¡pica; la cantidad y distribuci+¦n de la variaci+¦n gen+¬tica adaptativa en espacio y tiempo; el potencial de dispersi+¦n; y el tama+¦o y la conectividad de subpoblaciones son los aspectos ecol+¦gicos y evolutivos relevantes para la persistencia de las poblaciones a medida que cambia el clima. Se carece de entendimiento de los l+¡mites de la plasticidad y potencial evolutivo de caracteres, y las retroalimentaciones entre respuestas adaptativas y demogr+{\'{i}}ficas. El conocimiento integral de mecanismos ecol+¦gicos y evolutivos acoplados incrementar+{\'{i}} el entendimiento de la resiliencia y de las probabilidades de persistencia de las poblaciones y especies}, annote = {Define a number of useful terms related to evo. under climate change: adaptive surface, lag, lag load -CC can change peak height and location on adaptive landscape -to track changes in environment, species can have adaptive evolution (changes in gene frequencies) and adaptive phenotypic plasticity -pops in more variable environments experience fluctuating selection (Easterling et al 2000) - plasticity would be facored in this case -need mechanistic models to predict future responses to climate change (Holt 1990) --example of long term data on Great Tits in Netherlands - measured strength of directional selection and noticed earlier data of egg laying based on food resources -discuss importance of selection on multiple correlated traits and how that alters dynamics --point oout that under CC there should be strong selection for timinig of events, physiological toleraces, diet preferences, and disease reisistance Bradshaw and Holzapfel (2008) argue timing of traits will be under strongest selection Phenotypic plasticity -squirrels in Yukon have responded to earlier cone production mostly through plasticity as opposed to genetic adaptation -plasticity has limits though (DeWitt et al 1998) -plasticity not well studied in wild populations -reactions norms are functional relations that desribe how traits change as a result of plasticity when the environment changes -reaction norm incepts and slopes can be heritable -fluctuating conditions promotes evolution of plasticity (Svanback et al 2009) -plasticity can of course be costly -adaptive plasticity will reduce demographic effect of strong selection (Chevin et al 2010) Summary: This paper is a broad overview of how evolution, plasticity, and demography are inheritantly linked. Understanding the interactions between them is crucial for predicting and responding to species' responses to climate change. They stress that in a changing environment, species will always lag behind some phenotypic optimum. They also point out that climate change can alter these fitness landscapes in several ways including optimum locations or the elevation of the fitness surface. They discuss notion that species living in variable environments should probably have a higher propensity for phenotypic plasticity. They stres that when selection acts on several traits or if there are correlations among traits, the rate of evolition will be slower.}, author = {Reed, Thomas E. and Schindler, Daniel E. and Waples, Robin S.}, doi = {10.1111/j.1523-1739.2010.01552.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reed, Schindler, Waples - 2011 - Interacting effects of phenotypic plasticity and evolution on population persistence in a changing clim.pdf:pdf}, isbn = {1523-1739}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Adaptation,Climate projections,Ecological and evolutionary dynamics,Extinction,Phenotypic plasticity}, number = {1}, pages = {56--63}, pmid = {20646016}, title = {{Interacting effects of phenotypic plasticity and evolution on population persistence in a changing climate}}, volume = {25}, year = {2011} } @article{Merila2014, abstract = {Many studies have recorded phenotypic changes in natural populations and attributed them to climate change. However, controversy and uncertainty has arisen around three levels of inference in such studies. First, it has proven difficult to conclusively distinguish whether phenotypic changes are genetically based or the result of phenotypic plasticity. Second, whether or not the change is adaptive is usually assumed rather than tested. Third, inferences that climate change is the specific causal agent have rarely involved the testing - and exclusion - of other potential drivers. We here review the various ways in which the above inferences have been attempted, and evaluate the strength of support that each approach can provide. This methodological assessment sets the stage for 11 accompanying review articles that attempt comprehensive syntheses of what is currently known - and not known - about responses to climate change in a variety of taxa and in theory. Summarizing and relying on the results of these reviews, we arrive at the conclusion that evidence for genetic adaptation to climate change has been found in some systems, but is still relatively scarce. Most importantly, it is clear that more studies are needed - and these must employ better inferential methods - before general conclusions can be drawn. Overall, we hope that the present paper and special issue provide inspiration for future research and guidelines on best practices for its execution.}, annote = {Table 2 sums up the rest of the review papers in the special issue -It is difficult to infer genetic vs plastic, adaptive versus nonadaptive responses, and specific environmental drivers -this paper lays out past work on these questions and compares various approaches -Many difficulties associated with identifiying genetic changes in a pop due to CC Kopp and Matuszeqski (2014) theoreitcal approaches to modeling evo under CC -do not feel plasticity should be the null model -to infer plasticity you can you animals models, common gardens, experiments, spop responses, or measures of inidvidual palsticity}, author = {Meril{\"{a}}, Juha and Hendry, Andrew P.}, doi = {10.1111/eva.12137}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Meril{\"{a}}, Hendry - 2014 - Climate change, adaptation, and phenotypic plasticity The problem and the evidence.pdf:pdf}, isbn = {1752-4571}, issn = {17524563}, journal = {Evolutionary Applications}, keywords = {Environmental change,Evolution,Genetics,Global change,Individual plasticity,Natural selection}, number = {1}, pages = {1--14}, pmid = {24454544}, title = {{Climate change, adaptation, and phenotypic plasticity: The problem and the evidence}}, volume = {7}, year = {2014} } @article{Reale2003, abstract = {Climate change is predicted to be most severe in northern regions and there has been much interest in to what extent organisms can cope with these changes through phenotypic plasticity or microevolutionary processes. A red squirrel population in the southwest Yukon, Canada, faced with increasing spring temperatures and food supply has advanced the timing of breeding by 18 days over the last 10 years (6 days per generation). Longitudinal analysis of females breeding in multiple years suggests that much of this change in parturition date can be explained by a plastic response to increased food abundance (3.7 days per generation). Significant changes in breeding values (0.8 days per generation), were in concordance with predictions from the breeder's equation (0.6 days per generation), and indicated that an evolutionary response to strong selection favouring earlier breeders also contributed to the observed advancement of this heritable trait. The timing of breeding in this population of squirrels, therefore, has advanced as a result of both phenotypic changes within generations, and genetic changes among generations in response to a rapidly changing environment.}, author = {R{\'{e}}ale, Denis and McAdam, Andrew G and Boutin, Stan and Berteaux, Dominique}, doi = {10.1098/rspb.2002.2224}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/R{\'{e}}ale et al. - 2003 - Genetic and plastic responses of a northern mammal to climate change.pdf:pdf}, isbn = {0962-8452}, issn = {0962-8452}, journal = {Proceedings. Biological sciences / The Royal Society}, keywords = {breeding values,evolution,phenotypic plasticity,selection,tamiasciurus hudsonicus}, number = {1515}, pages = {591--596}, pmid = {12769458}, title = {{Genetic and plastic responses of a northern mammal to climate change.}}, volume = {270}, year = {2003} } @article{Price2003, abstract = {Models of population divergence and speciation are often based on the assumption that differences between populations are due to genetic factors, and that phenotypic change is due to natural selection. It is equally plausible that some of the differences among populations are due to phenotypic plasticity. We use the metaphor of the adaptive landscape to review the role of phenotypic plasticity in driving genetic evolution. Moderate levels of phenotypic plasticity are optimal in permitting population survival in a new environment and in bringing populations into the realm of attraction of an adaptive peak. High levels of plasticity may increase the probability of population persistence but reduce the likelihood of genetic change, because the plastic response itself places the population close to a peak. Moderate levels of plasticity arise whenever multiple traits, some of which are plastic and others not, form a composite trait involved in the adaptive response. For example, altered behaviours may drive selection on morphology and physiology. Because there is likely to be a considerable element of chance in which behaviours become established, behavioural change followed by morphological and physiological evolution may be a potent force in driving evolution in novel directions. We assess the role of phenotypic plasticity in stimulating evolution by considering two examples from birds: (i) the evolution of red and yellow plumage coloration due to carotenoid consumption; and (ii) the evolution of foraging behaviours on islands. Phenotypic plasticity is widespread in nature and may speed up, slow down, or have little effect on evolutionary change. Moderate levels of plasticity may often facilitate genetic evolution but careful analyses of individual cases are needed to ascertain whether plasticity has been essential or merely incidental to population differentiation.}, annote = {"If individuals can attain high fitness in the new environment as a consequence of a plastic response, it is not obvious why there should be directional selection at all, and there would then be no adaptive genetic differentiation from the source." -genetic adaptation occurs if there is a cost to plasticity or if plasticity is inadequate -Focuses on invasive species, or species inhabitating new environments -Point out that plasticity may allow initial transition -pllasticity can allow shifts to other adaptive peaks (it could be a lower peak though that you could maybe not get off of?) "The observation that plasticity is present does not, in itself, indicate if it would enhance or slow down evolution- ary progress, because this also depends on the form of the adaptive surface" -provide examples on carotenoids in birds and -foragin behaviors of animals in novel environments (behavior can change rapidly) - these behavior modifications then led to a genetic change PAPER is about how plasticity can faciliate genetic evolution}, author = {Price, Trevor D. and Qvarnstrom, A. and Irwin, Darren E. and Qvarnstr{\"{o}}m, Anna and Irwin, Darren E.}, doi = {10.1098/rspb.2003.2372}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Price et al. - 2003 - The role of phenotypic plasticity in driving genetic evolution.pdf:pdf}, isbn = {0962-8452}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {carotenoid pigments,foraging behaviour,genetic assimilation,peak shift,phenotypic plasticity}, number = {1523}, pages = {1433--1440}, pmid = {12965006}, title = {{The role of phenotypic plasticity in driving genetic evolution}}, url = {http://rspb.royalsocietypublishing.org/cgi/doi/10.1098/rspb.2003.2372}, volume = {270}, year = {2003} } @article{Bradshaw2008, abstract = {The primary nonbiological result of recent rapid climate change is warming winter temperatures, particularly at northern latitudes, leading to longer growing seasons and new seasonal exigencies and opportunities. Biological responses reflect selection due to the earlier arrival of spring, the later arrival of fall, or the increasing length of the growing season. Animals from rotifers to rodents use the high reliability of day length to time the seasonal transitions in their life histories that are crucial to fitness in temperate and polar environments: when to begin developing in the spring, when to reproduce, when to enter dormancy or when to migrate, thereby exploiting favourable temperatures and avoiding unfavourable temperatures. In documented cases of evolutionary (genetic) response to recent, rapid climate change, the role of day length (photoperiodism) ranges from causal to inhibitory; in no case has there been demonstrated a genetic shift in thermal optima or thermal tolerance. More effort should be made to explore the role of photoperiodism in genetic responses to climate change and to rule out the role of photoperiod in the timing of seasonal life histories before thermal adaptation is assumed to be the major evolutionary response to climate change.}, annote = {-discuss adaptations to changing seasonality -beleive that temp. is not a major factor, instead advancement of spring, less severe winter, or longer growing seasons have more direct effects on animals under CC -argue that at northern latutudes the major effecto f global warming is altering winter colds, not summer heats (it reduces severity of winters) -argue that most temperate and polar animals relay on day length or photoperiod -go through a number of examples: mosquitos, birds, fruit flies}, author = {Bradshaw, W. E. and Holzapfel, C. M.}, doi = {10.1111/j.1365-294X.2007.03509.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bradshaw, Holzapfel - 2008 - Genetic response to rapid climate change It's seasonal timing that matters.pdf:pdf}, isbn = {1365-294X}, issn = {09621083}, journal = {Molecular Ecology}, keywords = {Day length,Evolution,Genetic response,Global warming,Photoperiodism,Seasonal timing}, number = {1}, pages = {157--166}, pmid = {17850269}, title = {{Genetic response to rapid climate change: It's seasonal timing that matters}}, volume = {17}, year = {2008} } @article{Chevin2013, abstract = {Population persistence in a new and stressful environment can be influenced by the plastic phenotypic responses of individuals to this environment, and by the genetic evolution of plasticity itself. This process has recently been investigated theoretically, but testing the quantitative predictions in the wild is challenging because (i) there are usually not enough population replicates to deal with the stochasticity of the evolutionary process, (ii) environmental conditions are not controlled, and (iii) measuring selection and the inheritance of traits affecting fitness is difficult in natural populations. As an alternative, predictions from theory can be tested in the laboratory with controlled experiments. To illustrate the feasibility of this approach, we briefly review the literature on the experimental evolution of plasticity, and on evolutionary rescue in the laboratory, paying particular attention to differences and similarities between microbes and multicellular eukaryotes. We then highlight a set of questions that could be addressed using this framework, which would enable testing the robustness of theoretical predictions, and provide new insights into areas that have received little theoretical attention to date.}, author = {Chevin, Luis-Miguel and Gallet, Romain and Gomulkiewicz, Richard and Holt, Robert D and Fellous, Simon}, doi = {10.1098/rstb.2012.0089}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chevin et al. - 2013 - Phenotypic plasticity in evolutionary rescue experiments.pdf:pdf}, isbn = {0962-8436}, issn = {1471-2970}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {Adaptation, Physiological,Animals,Bacteria,Biological Evolution,Competitive Behavior,Environment,Extinction, Biological,Genetic Fitness,Genetic Fitness: physiology,Mutation,Phenotype,Plants,Population Density,Population Dynamics,Selection, Genetic,Stress, Physiological}, number = {1610}, pages = {20120089}, pmid = {23209170}, title = {{Phenotypic plasticity in evolutionary rescue experiments.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3538455{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {368}, year = {2013} } @article{Williams2014, abstract = {Winter is a key driver of individual performance, community composition, and ecological interactions in terrestrial habitats. Although climate change research tends to focus on performance in the growing season, climate change is also modifying winter conditions rapidly. Changes to winter temperatures, the variability of winter conditions, and winter snow cover can interact to induce cold injury, alter energy and water balance, advance or retard phenology, and modify community interactions. Species vary in their susceptibility to these winter drivers, hampering efforts to predict biological responses to climate change. Existing frameworks for predicting the impacts of climate change do not incorporate the complexity of organismal responses to winter. Here, we synthesise organismal responses to winter climate change, and use this synthesis to build a framework to predict exposure and sensitivity to negative impacts. This framework can be used to estimate the vulnerability of species to winter climate change. We describe the importance of relationships between winter conditions and performance during the growing season in determining fitness, and demonstrate how summer and winter processes are linked. Incorporating winter into current models will require concerted effort from theoreticians and empiricists, and the expansion of current growing-season studies to incorporate winter.}, annote = {-look at first or last frost timing}, author = {Williams, Caroline M. and Henry, Hugh A L and Sinclair, Brent J.}, doi = {10.1111/brv.12105}, isbn = {1464-7931}, issn = {14647931}, journal = {Biological Reviews}, keywords = {Average temperatures,Cold,Energetics,Extreme events,Freeze-thaw cycles,Frost,Hibernation,Snow,Sub-lethal impacts}, pages = {214--235}, pmid = {24720862}, title = {{Cold truths: How winter drives responses of terrestrial organisms to climate change}}, volume = {90}, year = {2014} } @article{Johanna2016, author = {Johanna, Author and Joshua, Varner and Mallory, J Horns and Westberg, Elizabeth and Ruff, James S and Wolfenberger, Katelyn and Dearing, A Beever M Denise}, doi = {10.1016/j.beproc.2016.01.009}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Johanna et al. - 2016 - Plastic Pikas Behavioral flexibility in low-elevation pikas (emph{\{}Ochotona princeps{\}}).pdf:pdf}, issn = {0376-6357}, journal = {Behavioural Processes}, keywords = {behavioural plasticity}, pages = {63--71}, publisher = {Elsevier B.V.}, title = {{Plastic Pikas: Behavioral flexibility in low-elevation pikas ($\backslash$emph{\{}Ochotona princeps{\}})}}, url = {http://dx.doi.org/10.1016/j.beproc.2016.01.009}, volume = {125}, year = {2016} } @article{Metz2016, abstract = {This paper should be read as addendum to Dieckmann et al. (J Theor Biol 241:370-389, 2006) and Parvinen et al. (J Math Biol 67: 509-533, 2013). Our goal is, using little more than high-school calculus, to (1) exhibit the form of the canonical equation of adaptive dynamics for classical life history problems, where the examples in Dieckmann et al. (J Theor Biol 241:370-389, 2006) and Parvinen et al. (J Math Biol 67: 509-533, 2013) are chosen such that they avoid a number of the problems that one gets in this most relevant of applications, (2) derive the fitness gradient occurring in the CE from simple fitness return arguments, (3) show explicitly that setting said fitness gradient equal to zero results in the classical marginal value principle from evolutionary ecology, (4) show that the latter in turn is equivalent to Pontryagin's maximum principle, a well known equivalence that however in the literature is given either ex cathedra or is proven with more advanced tools, (5) connect the classical optimisation arguments of life history theory a little better to real biology (Mendelian populations with separate sexes subject to an environmental feedback loop), (6) make a minor improvement to the form of the CE for the examples in Dieckmann et al. and Parvinen et al.}, author = {Metz, Johan A Jacob and Stankova, Katetina and Johansson, Jacob}, doi = {10.1007/s00285-015-0938-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Metz, Stankova, Johansson - 2016 - The canonical equation of adaptive dynamics for life histories from fitness-returns to selection grad.pdf:pdf}, issn = {14321416}, journal = {Journal of Mathematical Biology}, keywords = {Age-dependent resource allocation,Canonical equation of adaptive dynamics,Evolution in periodic environments,Function valued traits,Mendelian take on life history theory,Pontryagin???s maximum principle}, pages = {1125--1152}, pmid = {26586121}, title = {{The canonical equation of adaptive dynamics for life histories: from fitness-returns to selection gradients and Pontryagin???s maximum principle}}, volume = {72}, year = {2016} } @article{Visser2004, abstract = {Climate change is apparent as an advancement of spring phenology. However, there is no a priori reason to expect that all components of food chains will shift their phenology at the same rate. This differential shift will lead to mistimed reproduction in many species, including seasonally breeding birds. We argue that climate change induced mistiming in avian reproduction occurs because there is a substantial period between the moment of decision making on when to reproduce and the moment at which selection operates on this decision. Climate change is therefore likely to differentially alter the environment of decision-making and the environment of selection. We discuss the potential consequences of such mistiming, and identify a number of ways in which either individual birds or bird populations potentially can adapt to reproductive mistiming. ?? 2004 Elsevier Ltd. All rights reserved.}, author = {Visser, Marcel E. and Both, Christiaan and Lambrechts, Marcel M.}, doi = {10.1016/S0065-2504(04)35005-1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Visser, Both, Lambrechts - 2004 - Global Climate Change Leads to Mistimed Avian Reproduction.pdf:pdf}, isbn = {0120139359}, issn = {00652504}, journal = {Advances in Ecological Research}, number = {04}, pages = {89--110}, pmid = {489}, title = {{Global Climate Change Leads to Mistimed Avian Reproduction}}, volume = {35}, year = {2004} } @article{Skelly2007, abstract = {On the basis of the present knowledge of genetic variation in performance traits and species' capacity for evolutionary response, it can be concluded that evolutionary change will often occur concomitantly with changes in climate as well as other environmental changes (e.g., Grant {\&} Grant 2002; Stockwell et al. 2003; Balanya et al. 2006; Jump et al. 2006; Pelletier et al. 2007). We cannot ignore that, in many instances, adaptation is likely to mitigate the impacts predicted by models that take into account only one of the two major modalities of biotic response. Although the study of Malcolm et al. and its antecedents (e.g., Thomas et al. 2004) have likely overestimated extinction probabilities, few conservation biologists have focused on what may be the most pervasive effect of climate change: as species evolve in a changing world, genetic responses may render them forever different. Such within-species changes in biodiversity remain deserving of close study if we are to fully comprehend and accurately communicate the consequences global change.}, annote = {-argues that evolution must be included in climatic envelope models under climate change -provide examples of how qickly some organisms can respond to climate change -constraits on evolutionary response to climate change include: time lag b/w change and repsponse, lack of genetic variation (important in pikas?), and erosion of genetic variation}, author = {Skelly, David K. and Joseph, Liana N. and Possingham, Hugh P. and Freidenburg, L. Kealoha and Farrugia, Thomas J. and Kinnison, Michael T. and Hendry, Andrew P.}, doi = {10.1111/j.1523-1739.2007.00764.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Skelly et al. - 2007 - Evolutionary responses to climate change.pdf:pdf}, isbn = {0888-8892}, issn = {08888892}, journal = {Conservation Biology}, number = {5}, pages = {1353--1355}, pmid = {17883501}, title = {{Evolutionary responses to climate change}}, volume = {21}, year = {2007} } @article{Visser2005, annote = {Visser et al 2004 also an important paper -organisms are changing phenology, but how fast should they be changing in order to keep of with GCC --perhaps their food abundance would be good measure -natural seleciton should shape mechanisms that would allow predators to respond to temp similar to their food species -discusses breeding phenology of birds -state that although insects and plants are often temp sensitive, vertebrates also use photoperiod -mismatche in marine plankton communities -we have optimal period and width of the oprimal period window that may be changing}, author = {Visser, Marcel E. and Both, Christiaan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Visser, Both - 2005 - Shifts in phenology due to global climate change the need for a yardstick.pdf:pdf}, journal = {Proceedings of the Royal Society B}, keywords = {climate change,food chains,mistiming,phenology}, pages = {2561--2569}, title = {{Shifts in phenology due to global climate change: the need for a yardstick}}, volume = {272}, year = {2005} } @article{Steiner2009, abstract = {Despite the recognition of the importance of seasonal forcing in nature, remarkably few studies have theoretically explored periodically forced community dynamics. Here we employ a novel approach called "successional state dynamics" (SSD) to model a seasonally forced predator-prey system. We first generated analytical predictions of the effects of altered seasonality on species persistence and the timing of community state transitions. We then parameterized the model using a zooplankton-phytoplankton system and tested quantitative predictions using controlled experiments. In the majority of cases, timing of zooplankton and algal population peaks matched model predictions. Decreases in growing-period length delayed algal blooms, consequently delaying peaks in zooplankton abundance. Predictions of increased probability of predator extinction at low growing-period lengths were also upheld experimentally. Our results highlight the utility of the SSD modeling approach as a framework for predicting the effects of altered seasonality on the structure and dynamics of multitrophic communities.}, author = {Steiner, Christopher F and Schwaderer, Anne S and Huber, Veronika and Klausmeier, Christopher a and Litchman, Elena}, doi = {10.1890/08-2377.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Steiner et al. - 2009 - Periodically forced food-chain dynamics model predictions and experimental validation.pdf:pdf}, isbn = {0012-9658}, issn = {0012-9658}, journal = {Ecology}, keywords = {brachionus calyciflorus,chlamydomonas reinhardtii,environmental forcing,mortality,periodic,phytoplankton,predator,prey dynamics,seasonal succession,seasonality,transient dynamics}, number = {11}, pages = {3099--3107}, pmid = {19967865}, title = {{Periodically forced food-chain dynamics: model predictions and experimental validation.}}, volume = {90}, year = {2009} } @article{Gavish2012, abstract = {Habitat loss reduces species diversity, but the effect of habitat fragmentation on number of species is less clear because fragmentation generally accompanies loss of habitat. We compared four methods that aim to decouple the effects of fragmentation from the effects of habitat loss. Two methods are based on species-area relations, one on Fisher's alpha index of diversity, and one on plots of cumulative number of species detected against cumulative area sampled. We used these methods to analyze the species diversity of spiders in 2, 3.2 × 4 km agricultural landscapes in Southern Judea Lowlands, Israel. Spider diversity increased as fragmentation increased with all four methods, probably not because of the additive within-patch processes, such as edge effect and heterogeneity. The positive relation between fragmentation and species diversity might reflect that most species can disperse through the fields during the wheat-growing season. We suggest that if a given area was designated for the conservation of spiders in Southern Judea Lowlands, Israel, a set of several small patches may maximize species diversity over time.}, author = {Gavish, Yoni and Ziv, Yaron and Rosenzweig, Michael L.}, doi = {10.1111/j.1523-1739.2011.01799.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gavish, Ziv, Rosenzweig - 2012 - Decoupling Fragmentation from Habitat Loss for Spiders in Patchy Agricultural Landscapes.pdf:pdf}, isbn = {1523-1739}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Arthropods,Landscape,SLOSS,Species diversity,Species-area relation}, number = {1}, pages = {150--159}, pmid = {22136430}, title = {{Decoupling Fragmentation from Habitat Loss for Spiders in Patchy Agricultural Landscapes}}, volume = {26}, year = {2012} } @article{Stevenson2015, abstract = {The rhythm of life on earth is shaped by seasonal changes in the environment. Plants and animals show profound annual cycles in physiology, health, mor- phology, behaviour and demography in response to environmental cues. Seasonal biology impacts ecosystems and agriculture, with consequences for humans and biodiversity. Human populations show robust annual rhythms in health and well-being, and the birth month can have lasting effects that persist throughout life.This reviewemphasizestheneed fora betterunderstand- ing of seasonal biology against the backdrop of its rapidly progressing disruption through climate change, human lifestyles and other anthropogenic impact. Climate change is modifying annual rhythms to which numerous organisms have adapted, with potential consequences for industries relating to health, ecosystems and food security. Disconcertingly, human lifestyles under artificial conditions of eternal summer provide the most extreme example for disconnect from natural seasons, making humans vulnerable to increased morbidity and mortality. In this review, we intro- duce scenarios of seasonal disruption, highlight key aspects of seasonal biology and summarize frombiomedical, anthro- pological, veterinary, agricultural and environmental perspectives the recent evidence for seasonal desynchroniza- tion between environmental factors and internal rhythms. Because annual rhythms are pervasive across biological sys- tems, they provide a common framework for trans- disciplinary research.}, annote = {-what is predictive or end of winter for pikas? Frequency of storms, photoperiod, something else? -population may appear to breed asynchronously over course of year, but individuals may be highly seasonally cyclical -discuss importance of birth month -Can compare things in Northern and southern latidutdes as they have opposite day length pattterns -seasonality of many human diseases (e.g. Cholera and increased temp during El Nino) -most work on disrupted seasonality in ecological systems comes from pred-prey mismatch or plant-polinator ineractions "in fact complex networks. Therefore, a major challenge is to move beyond relatively simple, mostly pairwise ecological interactions to consider the consequences of disrupted seasonal- ity on population and community dynamics within broader, multispecies, interaction networks that include humans" -when will evolution be fast enough to keep up? -What animals hae experienced generations of changes in seasonality? E.g. chickens no longer have seasonal reproduction "There is a real need for large-scale exper- imental approaches to understand the ecosystem-level consequences of shifted or disrupted seasonal timing." -three future aims: understand internal clock, seasonal analyses in human and animal contexts, styudying seasonal disruptions in ecologcial networks, not just pairwise interactions}, author = {Stevenson, T J and Visser, M E and Arnold, W and Barrett, P and Biello, S and Dawson, A and Denlinger, D L and Dominoni, D and Ebling, F J and Elton, S and Evans, N and Ferguson, H M and Foster, R G and Hau, M and Haydon, D T and Hazlerigg, D G and Heideman, P and Hopcraft, J G C and Jonsson, N N and Kronfeld-Schor, N and Kumar, V and Lincoln, G A and Macleod, R and Martin, S A M and Martinez-Bakker, M and Nelson, R J and Reed, T and Robinson, J E and Rock, D and Schwartz, W J and Steffan-Fewenter, I and Tauber, E and Thackeray, S J and Umstatter, C and Yoshimura, T and Helm, B}, doi = {10.1098/rspb.2015.1453}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stevenson et al. - 2015 - Disrupted seasonal biology impacts health, food security and ecosystems.pdf:pdf}, isbn = {0000000273169}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {ecology,environmental science,epidemiology,health and disease and}, pages = {20151453}, pmid = {26468242}, title = {{Disrupted seasonal biology impacts health, food security and ecosystems}}, volume = {282}, year = {2015} } @article{Millar1974, author = {Millar, John C.}, doi = {10.1644/870.1.Key}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Millar - 1974 - Success of reproduction in pikas, emph{\{}Ochotona princeps{\}}.pdf:pdf}, isbn = {0953604918}, journal = {Journal of Mammalogy}, number = {3}, pages = {527--542}, title = {{Success of reproduction in pikas, $\backslash$emph{\{}Ochotona princeps{\}}}}, volume = {55}, year = {1974} } @article{Bronson2009, abstract = {Seasonal reproduction is common among mammals at all latitudes, even in the deep tropics. This paper (i) discusses the neuroendocrine pathways via which foraging conditions and predictive cues such as photoperiod enforce seasonality, (ii) considers the kinds of seasonal challenges mammals actually face in natural habitats, and (iii) uses the information thus generated to suggest how seasonal reproduction might be influenced by global climate change. Food availability and ambient temperature determine energy balance, and variation in energy balance is the ultimate cause of seasonal breeding in all mammals and the proximate cause in many. Photoperiodic cueing is common among long-lived mammals from the highest latitudes down to the mid-tropics. It is much less common in shorter lived mammals at all latitudes. An unknown predictive cue triggers reproduction in some desert and dry grassland species when it rains. The available information suggests that as our climate changes the small rodents of the world may adapt rather easily but the longer lived mammals whose reproduction is regulated by photoperiod may not do so well. A major gap in our knowledge concerns the tropics; that is where most species live and where we have the least understanding of how reproduction is regulated by environmental factors.}, annote = {-paper is more in line with general framwork on mammals that we discussed in our skype call Bradshaw and Holzapfel 2006, 2007 on annimal evolution in response to CC -high costs during reproduction times -some species have individual variation within species in how they respond to phtoperiod, this variation is heritable -argue that a low latitutdes in temperate zone, small mamals do not respond to photoperiod Marmot example where they emerge from hiberation earlier}, author = {Bronson, F H}, doi = {10.1098/rstb.2009.0140}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bronson - 2009 - Climate change and seasonal reproduction in mammals.pdf:pdf}, isbn = {0962-8436}, issn = {1471-2970}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {Adaptation, Physiological,Animals,Biological Evolution,Climate Change,Ecosystem,Feeding Behavior,Mammals,Mammals: genetics,Mammals: physiology,Reproduction,Reproduction: physiology,Seasons}, number = {1534}, pages = {3331--40}, pmid = {19833645}, title = {{Climate change and seasonal reproduction in mammals.}}, url = {http://rstb.royalsocietypublishing.org/content/364/1534/3331}, volume = {364}, year = {2009} } @article{Ludwig1978, annote = {-have fast (budworm dynamics) and slow variables (tree growth) in the system -model budworms using logistic growth to account for food supply limitations with a saturating predation term added to it (type III response) -Analysis of fast variables when slow variables are held constant --scale model using non dimensionalization --look for equilbrium points that depend on param values (show that model has 1-3 equilbria) --plot a bif. like diagram -Examine slow variables as we hold fast variables constant --look at average tree size (S) and an energy reserve (E) -When you combine results from previous two cases you see that buwdworms and trees will move in a cyclic patterns from low to high abundance -Examine set of 3 ODEs to combine fast and slow systems and use some guesses for parameter values -In the third part, they parametize their model with actual field data -discuss importance of placing 75 age tree into a single state variable and how that is wrwong Class notes: -prey switching behavior at low prey density (type III) response -equation 9 solves for equilbrium (look at intersection of curves) -fig1: if you increase R, you will eventually go to bif. point -catastophe theory - "Book: the Emperor has no clothes" - pushed too far in applications -separatrix is nonlinear extension of eigenvectors of saddle points -Fig. 4 shows bifurcation that leads to extinction -compare discrete-time simulation to 3D ODE model, cont time model not capable of multiple outbreaks}, author = {Ludwig, D. and Jones, D.D. and Holling, C.S.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ludwig, Jones, Holling - 1978 - Qualitative analysis of insect outbreak systems - the spruce budworm and forest.pdf:pdf}, journal = {Journal of Animal Ecology}, number = {1}, pages = {315--332}, title = {{Qualitative analysis of insect outbreak systems - the spruce budworm and forest}}, volume = {47}, year = {1978} } @article{Forrest2010, abstract = {Phenology affects nearly all aspects of ecology and evolution. Virtually all biological phenomena-from individual physiology to interspecific relationships to global nutrient fluxes-have annual cycles and are influenced by the timing of abiotic events. Recent years have seen a surge of interest in this topic, as an increasing number of studies document phenological responses to climate change. Much recent research has addressed the genetic controls on phenology, modelling techniques and ecosystem-level and evolutionary consequences of phenological change. To date, however, these efforts have tended to proceed independently. Here, we bring together some of these disparate lines of inquiry to clarify vocabulary, facilitate comparisons among habitat types and promote the integration of ideas and methodologies across different disciplines and scales. We discuss the relationship between phenology and life history, the distinction between organismal- and population-level perspectives on phenology and the influence of phenology on evolutionary processes, communities and ecosystems. Future work should focus on linking ecological and physiological aspects of phenology, understanding the demographic effects of phenological change and explicitly accounting for seasonality and phenology in forecasts of ecological and evolutionary responses to climate change.}, annote = {-phenology questions usually lie o pop level (e.g. advancing of dates) -diff b/w phenology and life history -breeding date is also determined by maternal condtion, which may depend on previous years -discuss some of the mechanistic basis of phenology --argue to include genetics and physiology --timing of events is mix of genes and environment (photoperiod, temp, precip, snowmelt) -Consequences of shifts in phenology of interacting species depends on interaction types -discuss importance of looking at whole phenological distributions and their various properties --end of the season timing is often more important too -discuss ecosystem processes (e.g. carbon fluxes) that may change with GCC -also discuss evolution of phenology Summary for lit review: This is a nice review paper that attempts to bring together work on genetic controls of phenology, specific modeling technuques, and the consequences of phenological change. They do a nice job at discussing the role of genetics, the envrionment, and interactions between the two in driving phenology. ....They make important points about looking at the whole distribution of phenological activity, not simply peaks or first events; this is strongly tied to ideas in AD}, author = {Forrest, Jessica and Miller-Rushing, Abraham J.}, doi = {10.1098/rstb.2010.0145}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Forrest, Miller-Rushing - 2010 - Toward a synthetic understanding of the role of phenology in ecology and evolution.pdf:pdf}, isbn = {0962-8436{\textless}p{\textgreater}}, issn = {0962-8436}, journal = {Philosophical Transactions of the Royal Society B: Biological Sciences}, keywords = {Biological Evolution,Climate,Ecosystem,Seasons,climate change,life history,natural selection,phenology,synchrony}, number = {1555}, pages = {3101--3112}, pmid = {20819806}, title = {{Toward a synthetic understanding of the role of phenology in ecology and evolution}}, volume = {365}, year = {2010} } @article{Visser2015, abstract = {Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first two decades (1980-2000) but weakened during the last decade (2001-2010). Against expectation, this pattern could not be explained by the temporal variation in the phenological mismatch with food abundance. We therefore explored an alternative hypothesis that selection on timing was affected by conditions individuals experience when arriving in spring at the breeding grounds: arriving early in cold conditions may reduce survival. First, we show that in female recruits, spring arrival date in the first breeding year correlates positively with hatch date; hence, early-hatched individuals experience colder conditions at arrival than late-hatched individuals. Second, we show that when temperatures at arrival in the recruitment year were high, early-hatched young had a higher recruitment probability than when temperatures were low. We interpret this as a potential cost of arriving early in colder years, and climate warming may have reduced this cost. We thus show that higher temperatures in the arrival year of recruits were associated with stronger selection for early reproduction in the years these birds were born. As arrival temperatures in the beginning of the study increased, but recently declined again, directional selection on timing of reproduction showed a nonlinear change. We demonstrate that environmental conditions with a lag of up to two years can alter selection on phenological traits in natural populations, something that has important implications for our understanding of how climate can alter patterns of selection in natural populations.}, author = {Visser, Marcel E. and Gienapp, Phillip and Husby, Arild and Morrisey, Michael and de la Hera, Iv{\'{a}}n and Pulido, Francisco and Both, Christiaan}, doi = {10.1371/journal.pbio.1002120}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Visser et al. - 2015 - Effects of Spring Temperatures on the Strength of Selection on Timing of Reproduction in a Long-Distance Migrator.pdf:pdf}, issn = {15457885}, journal = {PLoS Biology}, number = {4}, pages = {1--17}, pmid = {25848856}, title = {{Effects of Spring Temperatures on the Strength of Selection on Timing of Reproduction in a Long-Distance Migratory Bird}}, volume = {13}, year = {2015} } @article{Hoffmann2011, abstract = {Evolutionary adaptation can be rapid and potentially help species counter stressful conditions or realize ecological opportunities arising from climate change. The challenges are to understand when evolution will occur and to identify potential evolutionary winners as well as losers, such as species lacking adaptive capacity living near physiological limits. Evolutionary processes also need to be incorporated into management programmes designed to minimize biodiversity loss under rapid climate change. These challenges can be met through realistic models of evolutionary change linked to experimental data across a range of taxa.}, annote = {-paper reviews models or evolutionary change to GCC for various ecological scenarios -will selection pressures be stronger and fluctuate more b/c of GCC?}, author = {Hoffmann, AA and Sgr{\`{o}}, CM}, doi = {10.1038/nature09670}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hoffmann, Sgr{\`{o}} - 2011 - Climate change and evolutionary adaptation.pdf:pdf}, isbn = {0028-0836}, issn = {1476-4687}, journal = {Nature}, keywords = {Adaptation,Animals,Biodiversity,Biological Evolution,Climate Change,Climate Change: mortality,Conservation of Natural Resources,Conservation of Natural Resources: methods,Gene Flow,Phylogeny,Physiological,Physiological: genetics,Physiological: physiology}, number = {7335}, pages = {479--485}, pmid = {21350480}, title = {{Climate change and evolutionary adaptation.}}, url = {http://www.nature.com/nature/journal/v470/n7335/abs/nature09670.html}, volume = {470}, year = {2011} } @article{Roland2013, abstract = {We examined the long-term, 15-year pattern of population change in a network of 21 Rocky Mountain populations of Parnassius smintheus butterflies in response to climatic variation. We found that winter values of the broadscale climate variable, the Pacific Decadal Oscillation (PDO) index, were a strong predictor of annual population growth, much more so than were endogenous biotic factors related to population density. The relationship between PDO and population growth was nonlinear. Populations declined in years with extreme winter PDO values, when there were either extremely warm or extremely cold sea surface temperatures in the eastern Pacific relative to that in the western Pacific. Results suggest that more variable winters, and more frequent extremely cold or warm winters, will result in more frequent decline of these populations, a pattern exacerbated by the trend for increasingly variable winters seen over the past century.}, annote = {-Examined time series of butterfly pop in Colorado and found it had low growth rates in unusually hot or cold winters -climate effects may be buffered in long lived species as they can respond the next year -they look at growth rates compared to PDO and population size. PDO only mattered for the winter months. Could put a variable for different seasons and see which one matters I think it would be interesting to conduct a study like this for a number of different species}, author = {Roland, Jens and Matter, Stephen F.}, doi = {10.1890/12-0611.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Roland, Matter - 2013 - Variability in winter climate and winter extremes reduces population growth of an alpine butterfly.pdf:pdf}, isbn = {0012-9658 (Print)$\backslash$n0012-9658 (Linking)}, issn = {00129658}, journal = {Ecology}, keywords = {Alberta,Alpine habitat,Canada,Climate change,Climate extremes,Climate variability,Jumpingpound and lusk ridges,PDO,Pacific decadal oscillation,Parnassius smintheus,Population dynamics,Rocky mountain apollo butterfly}, number = {1}, pages = {190--199}, pmid = {23600253}, title = {{Variability in winter climate and winter extremes reduces population growth of an alpine butterfly}}, volume = {94}, year = {2013} } @article{Glorvigen2013, abstract = {The role of local habitat geometry (habitat area and isolation) in predicting species distribution has become an increasingly more important issue, because habitat loss and fragmentation cause species range contraction and extinction. However, it has also become clear that other factors, in particular regional factors (environmental stochasticity and regional population dynamics), should be taken into account when predicting colonisation and extinction. In a live trapping study of a mainland-island metapopulation of the root vole (Microtus oeconomus) we found extensive occupancy dynamics across 15 riparian islands, but yet an overall balance between colonisation and extinction over 4 years. The 54 live trapping surveys conducted over 13 seasons revealed imperfect detection and proxies of population density had to be included in robust design, multi-season occupancy models to achieve unbiased rate estimates. Island colonisation probability was parsimoniously predicted by the multi-annual density fluctuations of the regional mainland population and local island habitat quality, while extinction probability was predicted by island population density and the level of the recent flooding events (the latter being the main regionalized disturbance regime in the study system). Island size and isolation had no additional predictive power and thus such local geometric habitat characteristics may be overrated as predictors of vole habitat occupancy relative to measures of local habitat quality. Our results suggest also that dynamic features of the larger region and/or the metapopulation as a whole, owing to spatially correlated environmental stochasticity and/or biotic interactions, may rule the colonisation-extinction dynamics of boreal vole metapopulations. Due to high capacities for dispersal and habitat tracking voles originating from large source populations can rapidly colonise remote and small high quality habitat patches and re-establish populations that have gone extinct due to demographic (small population size) and environmental stochasticity (e.g. extreme climate events).}, author = {Glorvigen, Petter and Andreassen, Harry P. and Ims, Rolf A.}, doi = {10.1371/journal.pone.0056462}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Glorvigen, Andreassen, Ims - 2013 - Local and Regional Determinants of Colonisation-Extinction Dynamics of a Riparian Mainland-Island Ro.pdf:pdf}, isbn = {19326203 (ISSN)}, issn = {19326203}, journal = {PLoS ONE}, number = {2}, pmid = {23437137}, title = {{Local and Regional Determinants of Colonisation-Extinction Dynamics of a Riparian Mainland-Island Root Vole Metapopulation}}, volume = {8}, year = {2013} } @article{Robles2012, abstract = {Despite extensive research on the effects of habitat fragmentation, the ecological mechanisms underlying colonization and extinction processes are poorly known, but knowledge of these mechanisms is essential to understanding the distribution and persistence of populations in fragmented habitats. We examined these mechanisms through multiseason occupancy models that elucidated patch-occupancy dynamics of Middle Spotted Woodpeckers (Dendrocopos medius) in northwestern Spain. The number of occupied patches was relatively stable from 2000 to 2010 (15-24{\%} of 101 patches occupied every year) because extinction was balanced by recolonization. Larger and higher quality patches (i.e., higher density of oaks {\textgreater}37 cm dbh [diameter at breast height]) were more likely to be occupied. Habitat quality (i.e., density of large oaks) explained more variation in patch colonization and extinction than did patch size and connectivity, which were both weakly associated with probabilities of turnover. Patches of higher quality were more likely to be colonized than patches of lower quality. Populations in high-quality patches were less likely to become extinct. In addition, extinction in a patch was strongly associated with local population size but not with patch size, which means the latter may not be a good surrogate of population size in assessments of extinction probability. Our results suggest that habitat quality may be a primary driver of patch-occupancy dynamics and may increase the accuracy of models of population survival. We encourage comparisons of competing models that assess occupancy, colonization, and extinction probabilities in a single analytical framework (e.g., dynamic occupancy models) so as to shed light on the association of habitat quality and patch geometry with colonization and extinction processes in different settings and species.}, author = {Robles, Hugo and Ciudad, Carlos}, doi = {10.1111/j.1523-1739.2011.01816.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Robles, Ciudad - 2012 - Influence of Habitat Quality, Population Size, Patch Size, and Connectivity on Patch-Occupancy Dynamics of the M.pdf:pdf}, isbn = {1523-1739}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Colonization,Dendrocopos medius,Extinction,Habitat fragmentation,Persistence}, number = {2}, pages = {284--293}, pmid = {22268847}, title = {{Influence of Habitat Quality, Population Size, Patch Size, and Connectivity on Patch-Occupancy Dynamics of the Middle Spotted Woodpecker}}, volume = {26}, year = {2012} } @article{Yang2010a, abstract = {Climate change is altering the phenology of many species and the timing of their interactions with other species, but the impacts of these phenological shifts on species interactions remain unclear. Classical approaches to the study of phenology have typically documented changes in the timing of single life-history events, while phenological shifts affect many interactions over entire life histories. In this study, we suggest an approach that integrates the phenology and ontogeny of species interactions with a fitness landscape to provide a common mechanistic framework for investigating phenological shifts. We suggest that this ontogeny-phenology landscape provides a flexible method to document changes in the relative phenologies of interacting species, examine the causes of these phenological shifts, and estimate their consequences for interacting species.}, annote = {-timing and strength can vary depending on body size (which changes over time) -Present compelling reasons why ontogeny needs to be thought about in phenology studies -Follows work of Visser 2005 -Need to read Both et al 2009 (J Anim. Ecol) and Van Asch et al 2007 (glb. chang. biol) -a number of relevant citations for IIASA and my own PhD work -discuss how interaction types or at least interaction stengths can change over time due to changes in body size (or some other ontogeneic shift) -e.g. a moth larvae may heavily consume a plant but later it turns out to be the plant's pollinator as an adult -propose plotting two interacting species on phase plane to examine interaction (a trajectory through this path could indicate different interactions between the species) -difficult as you need detailed (within year) interactions information for pairs of species -could conduct experiments where you allow two species to interact but fully cross which species stages interact with one another (egg-egg, egg-larvae, egg-adult, larve-adult, larve-egg, adult-larve) -Next steps: need more detailed field data, think about multispecies interactions, evolutionary responses, and other important ecological drivers}, author = {Yang, Louie H. and Rudolf, V. H W}, doi = {10.1111/j.1461-0248.2009.01402.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yang, Rudolf - 2010 - Phenology, ontogeny and the effects of climate change on the timing of species interactions.pdf:pdf}, isbn = {1461-023X}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Climate change,Competition,Development,Global warming,Match-mismatch,Mistiming,Mutualism,Phenology,Predation,Size structure}, number = {1}, pages = {1--10}, pmid = {19930396}, title = {{Phenology, ontogeny and the effects of climate change on the timing of species interactions}}, volume = {13}, year = {2010} } @article{VanAsch2007, abstract = {Climate change has led to an advance in phenology in many species. Synchrony in phenology between different species within a food chain may be disrupted if an increase in temperature affects the phenology of the different species differently, as is the case in the winter moth egg hatch2013oak bud burst system. Operophtera brumata (winter moth) egg hatch date has advanced more than Quercus robur (pedunculate oak) bud burst date over the past two decades. Disrupted synchrony will lead to selection, and a response in phenology to this selection may lead to species genetically adapting to their changing environment. However, a prerequisite for such genetic change is that there is sufficient genetic variation and severe enough fitness consequences. So far, examples of observed genetic change have been few. Using a half-sib design, we demonstrate here that O. brumata egg-hatching reaction norm is heritable, and that genetic variation exists. Fitness consequences of even a few days difference between egg hatch and tree bud opening are severe, as we experimentally determined. Estimates of genetic variation and of fitness were then combined with a climate scenario to predict the rate and the amount of change in the eggs' response to temperature. We predict a rapid response to selection, leading to a restoration of synchrony of egg hatch with Q. robur bud opening. This study shows that in this case there is a clear potential to adapt 2013 rapidly 2013 to environmental change. The current observed asynchrony is therefore not due to a lack of genetic variation and at present it is unclear what is constraining O. brumata to adapt. This kind of model may be particularly useful in gaining insight in the predicted amount and rate of change due to environmental changes, given a certain genetic variation and selection pressure.}, author = {van Asch, Margriet and van Tienderen, Peter H. and Holleman, Leonard J M and Visser, Marcele E.}, doi = {10.1111/j.1365-2486.2007.01400.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/van Asch et al. - 2007 - Predicting adaptation of phenology in response to climate change, an insect herbivore example.pdf:pdf}, isbn = {1365-2486}, issn = {13541013}, journal = {Global Change Biology}, keywords = {Adaptation,Climate change,Egg hatch,Fitness,Genetic variation,Heritability,Operophtera brumata,Predictive model,Quercus robur,Synchrony}, number = {8}, pages = {1596--1604}, title = {{Predicting adaptation of phenology in response to climate change, an insect herbivore example}}, volume = {13}, year = {2007} } @article{Both2009, abstract = {1. Climate change has been shown to affect the phenology of many organisms, but interestingly these shifts are often unequal across trophic levels, causing a mismatch between the phenology of organisms and their food. 2. We consider two alternative hypotheses: consumers are constrained to adjust sufficiently to the lower trophic level, or prey species react more strongly than their predators to reduce predation. We discuss both hypotheses with our analyses of changes in phenology across four trophic levels: tree budburst, peak biomass of herbivorous caterpillars, breeding phenology of four insectivorous bird species and an avian predator. 3. In our long-term study, we show that between 1988 and 2005, budburst advanced (not significantly) with 0.17 d yr(-1), while between 1985 and 2005 both caterpillars (0.75 d year(-1)) and the hatching date of the passerine species (range for four species: 0.36-0.50 d year(-1)) have advanced, whereas raptor hatching dates showed no trend. 4. The caterpillar peak date was closely correlated with budburst date, as were the passerine hatching dates with the peak caterpillar biomass date. In all these cases, however, the slopes were significantly less than unity, showing that the response of the consumers is weaker than that of their food. This was also true for the avian predator, for which hatching dates were not correlated with the peak availability of fledgling passerines. As a result, the match between food demand and availability deteriorated over time for both the passerines and the avian predators. 5. These results could equally well be explained by consumers' insufficient responses as a consequence of constraints in adapting to climate change, or by them trying to escape predation from a higher trophic level, or both. Selection on phenology could thus be both from matches of phenology with higher and lower levels, and quantifying these can shed new light on why some organisms do adjust their phenology to climate change, while others do not.}, annote = {Summary: This is one of the few papers that has examined phenological shifts over time in mutiple trophic levels. For almost every species, phenolgoy advanced to some degree, though not always significantly. Less syncrony over time between predators and prey.}, author = {Both, Christiaan and {Van Asch}, Margriet and Bijlsma, Rob G. and {Van Den Burg}, Arnold B. and Visser, Marcel E.}, doi = {10.1111/j.1365-2656.2008.01458.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Both et al. - 2009 - Climate change and unequal phenological changes across four trophic levels Constraints or adaptations.pdf:pdf}, isbn = {1365-2656}, issn = {00218790}, journal = {Journal of Animal Ecology}, keywords = {Accipiter nisus,Breeding date,Budburst,Cyanistes caeruleus,Ficedula hypoleuca,Parus ater,Parus major,Phenology,Quercus robus,Timing}, number = {1}, pages = {73--83}, pmid = {18771506}, title = {{Climate change and unequal phenological changes across four trophic levels: Constraints or adaptations?}}, volume = {78}, year = {2009} } @article{Franken2004b, abstract = {The length of the snow-free season has a significant influence on reproduction and growth in northern alpine environments, and these life history traits may provide sensitive indicators of the responses of organisms to climate change. We examined growth rates and timing of parturition of collared pikas (Ochotona collaris) from 1995-2002 in the Ruby Range, Yukon Territory, Canada. Growth rates were best described using a Gompertz model, in which the asymptotic mass, determined from the average male and female weights, was 157 g, the growth rate constant (K) was 0.0557, and the age at inflection (I) was 18.12 days, for a birth weight of 10 g. The maximum growth rate for North American pikas (O. collaris and O. princeps) increased with latitude, with maximum growth rates being approximately one-third greater in northern populations where the snow-free season is less than three months long. The mean parturition date varied significantly among years from 3 June to 3 July, and delayed parturition was correlated with indices of high snow accumulation and, to a lesser extent, late spring snowmelt. However, parturition date did not significantly affect the subsequent over-winter survival of juveniles in this population, suggesting that pikas are able to adjust to seasonal uncertainty associated with highly variable spring conditions.}, annote = {-have growth rates estimated for individuals, use this to predict partrition times -this paper looks at timing of partrition over a series of years at a Yukon site for O. Collaris -mean date of partrition is later in year when there is more snow (an idea discussed by Smith 1978) -number of successfully weaned juveniles was 1 per female per year -discuss balance of being born too early or too later -found no over winter survival benefits of being born earlier or later (unless it affecting really young ind. before they emerged)}, author = {Franken, Renee J and Hik, David S}, doi = {10.1093/icb/44.2.186}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Franken, Hik - 2004 - Interannual variation in timing of parturition and growth of collared pikas (Ochotona collaris) in the Southwest Y.pdf:pdf}, isbn = {1540-7063 (Print) 1540-7063 (Linking)}, issn = {1540-7063}, journal = {Integrative and Comparative Biology}, number = {2}, pages = {186--93}, pmid = {21680498}, title = {{Interannual variation in timing of parturition and growth of collared pikas (Ochotona collaris) in the Southwest Yukon.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21680498}, volume = {44}, year = {2004} } @article{May1977, annote = {Outline of presentation: -May 1977 figures of ASS versus more modern figures -terminology (ASS, hysteresis, regime shifts, catastophe, ...) -discussion of paper -relation to hysteresis Grazing ecosystems: -focus on vegetation with constant herbivore pop. -simple equation and eq. values -figure 1 (intersection, and which points are stable or not) -type II holling -fig 2 - type III holling with logistic growth -dimensionless form of the equation (which is used by Ludwig et al 1978) - get ASS for certain param values -figure 3 is from figure 2 -fig 4 -points about vegetation and management -sheep empirical example Harvesting animal pops: -often people want to harvest in order to keep a constant yield (when alpha goes to 0) -similar to previos case Insect pests: -spruce budworm in Canada on tree foliarge -use same equation as in fig 2 and also use dimensionless form (look at density of budworms instead of actual counts) -fig. 6 is when you vary resource level S after fixing P --can think about tree growth at various parts of curve, fast and slow dynamics --fig. 7 shows budworm explosions -Ludwig et al use 3d system and field data -management implications Human host-parasite systems -verbal Malaria example, will infected mosquito produce more than one additonal infected mosquito --this threshold is important -fig. 8 and schristosomiasis -management implications of reducing below threshold to the left or down}, author = {May, Robert M.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/May - 1977 - Threshold and breakpoints in ecosystems with a multiplicity of stable states.pdf:pdf}, journal = {Nature}, pages = {471--477}, title = {{Threshold and breakpoints in ecosystems with a multiplicity of stable states}}, volume = {269}, year = {1977} } @article{Visser2008, abstract = {The pivotal question in the debate on the ecological effects of climate change is whether species will be able to adapt fast enough to keep up with their changing environment. If we establish the maximal rate of adaptation, this will set an upper limit to the rate at which temperatures can increase without loss of biodiversity.The rate of adaptation will primarily be set by the rate of microevolution since (i) phenotypic plasticity alone is not sufficient as reaction norms will no longer be adaptive and hence microevolution on the reaction norm is needed, (ii) learning will be favourable to the individual but cannot be passed on to the next generations, (iii) maternal effects may play a role but, as with other forms of phenotypic plasticity, the response of offspring to the maternal cues will no longer be adaptive in a changing environment, and (iv) adaptation via immigration of individuals with genotypes adapted to warmer environments also involves microevolution as these genotypes are better adapted in terms of temperature, but not in terms of, for instance, photoperiod.Long-term studies on wild populations with individually known animals play an essential role in detecting and understanding the temporal trends in life-history traits, and to estimate the heritability of, and selection pressures on, life-history traits. However, additional measurements on other trophic levels and on the mechanisms underlying phenotypic plasticity are needed to predict the rate of microevolution, especially under changing conditions.Using this knowledge on heritability of, and selection on, life-history traits, in combination with climate scenarios, we will be able to predict the rate of adaptation for different climate scenarios. The final step is to use ecoevolutionary dynamical models to make the link to population viability and from there to biodiversity loss for those scenarios where the rate of adaptation is insufficient. {\textcopyright} 2008 The Royal Society.}, annote = {-best documented responses to CC are changes in phenology or range shifts (has also been work on changes in body size and interactions b/w species) -both genetic change and plasticity can help species adapt (change their phenotypic distribution) in response to CC -great tits have had insufficient or sufficient rates of adaptation dependiing on the specifc location -argues that plasticity is not sufficient, also need genetic change -argues that allow animals may be plastic in repsonse due to climate change, that this will not be sufficient in the face of CC. THis is because reaction norms will no longer ba adaptive due to the disruption of the corrleation between cues and changing conditions -argues that CC will affect many stages on an individuals life - need to integrate across these changes -discuss secltion of elevation or slope of reaction norms (Nusset et al 2005 on slope elevation in great tits) Summary:}, author = {Visser, M E}, doi = {10.1098/rspb.2007.0997}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Visser - 2008 - Keeping up with a warming world assessing the rate of adaptation to climate change.pdf:pdf}, isbn = {0962-8452}, issn = {09628452 (ISSN)}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {Animalia,Animals,Biological,Birds,Evolution,Intergovernmental panel on climate change,Microevolution,Pedigree,Phenotype,Scenarios,Temperature,Time Factors,adaptation,biodiversity,climate change,ecological modeling,environmental change,genotype,greenhouse effect,heritability,learning,life history,life history trait,molecular dynamics,molecular evolution,nonhuman,phenology,phenotypic plasticity,photoperiodicity,priority journal,progeny,review,temperature acclimatization,temperature profile}, number = {1635}, pages = {649--659}, pmid = {18211875}, title = {{Keeping up with a warming world; assessing the rate of adaptation to climate change}}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-38849159051{\&}partnerID=40{\&}md5=a25851cd3f9dca8267fe6339a48e5066}, volume = {275}, year = {2008} } @article{Eskola2011, abstract = {We study the evolution of an individual's reproductive strategy in a mechanistic modeling framework. We assume that the total number of juveniles one adult individual can produce is a finite constant, and we study how this number should be distributed during the season, given the types of inter-individual interactions and mortality processes included in the model. The evolution of the timing of reproduction in this modeling framework has already been studied earlier in the case of equilibrium resident dynamics, but we generalize the situation to also fluctuating population dynamics. We find that, as in the equilibrium case, the presence or absence of inter-juvenile aggression affects the functional form of the evolutionarily stable reproductive strategy. If an ESS exists, it can have an absolutely continuous part only if inter-juvenile aggression is included in the model. If inter-juvenile aggression is not included in the model, an ESS can have no continuous parts, and only Dirac measures are possible.}, annote = {-look at reproductive strategy as a funciton of age$\backslash$ -reference series of papers of evolution in stochastic environments (like Iwasa papers), however in this paper the stochastic el;ement is not an external driver, but instead a fluctuating population size -my model explicictely looks at competition for resources, not simply some -x{\^{}}2 term -if the attractor is not a point equilbrium, then long term growth rate is given by geometrix average instead}, author = {Eskola, Hanna T M and Geritz, Stefan A H and Gyllenberg, Mats}, doi = {10.1007/s11538-010-9560-1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eskola, Geritz, Gyllenberg - 2011 - On the Evolution of the Timing of Reproduction with Non-equilibrium Resident Dynamics.pdf:pdf}, issn = {00928240}, journal = {Bulletin of Mathematical Biology}, keywords = {Evolution of measure-valued traits,Evolutionarily stable strategy,Invasion analysis,Non-equilibrium dynamics,Timing of reproduction}, number = {6}, pages = {1312--1332}, pmid = {20658199}, title = {{On the Evolution of the Timing of Reproduction with Non-equilibrium Resident Dynamics}}, volume = {73}, year = {2011} } @article{Iwasa1994, abstract = {The evolutionarily stable (or ESS) emergence schedule for males of univoltine butterflies is analysed in an environment in which the female emergence schedule fluctuates stochastically between years. The ESS emergence curve, computed using the mutant invadability criterion, is shown to be the one that maximizes mean logarithmic lifetime mating success in the population in which it dominates. If males have accurate information about the female emergence schedule within each year, their emergence curve would evolve to the one predicted by a deterministic game model. The male emergence curve would then shift between years, closely following year to year changes in the female emergence pattern. If, instead, males have uncertainty about the female emergence schedule, the ESS male emergence curve becomes broader than the one predicted by the deterministic game model and will not track the between-year fluctuation of female emergence well. In a special case, we show how the between-year variation of mean emergence date, the variance of emergence date, the sexual difference in mean emergence dates (protandry) and the between-year correlation of mean emergence dates of both sexes should change with the degree of accuracy of information available to males.}, annote = {-male emergence will depend on frequency of mutants, cue availability, and female fluctuations -Iwasa et al (1983) looked at same question with field data but did not investigate environmental stochasticity or spatial heterogeneity, the latter of which was investigate by Baughman et al (1988) -males will have ESS that is the same each year, even if females fluctuate, if there is no accurate cue for them to use (if this model fit pikas well, it means they do not use any cue) -show example where female emergence is normally distributed -discuss situation when a cue is available Summary: This paper examines the ESS emergence times of males in an environment where female emergence varies between years. Male emergence time is strongly selected for as females typically only mate once. However, there is high male mortality rates per day, so it is dangerous to emerge too soon. If males had perfect information about female emergence, the maximized emergence curve would be the deterministic game model. But, when the environment varies and a cue is not perfect, the male emergence times will be broader than that of the females.}, author = {Iwasa, Yoh and Haccou, Patsy}, doi = {10.1007/BF01238255}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Iwasa, Haccou - 1994 - ESS emergence pattern of male butterflies in stochastic environments.pdf:pdf}, isbn = {0269-7653}, issn = {02697653}, journal = {Evolutionary Ecology}, keywords = {accuracy of cue,butterfly,emergence pattern,evolutionarily stable strategy,mate-finding game,mixed strategy,protandry,stochastic environment}, number = {5}, pages = {503--523}, title = {{ESS emergence pattern of male butterflies in stochastic environments}}, volume = {8}, year = {1994} } @article{Eskola2009, abstract = {In this paper, we study the evolution of the per capita rate of reproduction as a function of time in the modelling framework introduced by Eskola and Geritz [Eskola, H.T.M., Geritz, S.A.H., 2007. On the mechanistic derivation of various discrete-time population models, Bull. Math. Biol. 69, 329-346]. We assume that the total number of juveniles one adult individual can produce is a finite constant, and we study how this number should be distributed during the season, when certain interaction and mortality processes are also included in the model. If aggressive interactions between the juveniles are not included in the model, evolution is simply optimizing, and the optimal reproductive strategy is always a single Dirac ??-peak within the season. If aggressive interactions between the juveniles are included, an evolutionarily stable strategy can consist of not only one or two ??-peaks, but also of continuous reproduction during the season. Using this approach, we have also derived conditions under which the classical population dynamical models of Beverton and Holt [Beverton, R.J.H., Holt, S.J., 1957. On the dynamics of exploited fish populations. Fisheries Investigations, Ser. 219], Hassell [Hassell, M.P., 1975. Density-dependence in single-species populations. J. Animal Ecology 44, 283-295] and Ricker [Ricker, W.E., 1954. Stock and recruitment. J. Fisheries Res. Board Can. 11, 559-623] are evolutionarily stable. ?? 2008 Elsevier Inc. All rights reserved.}, annote = {-explain how results relate to Beverton holt or Ricker models -allows reproduction to be distributed over season (but is bounded over the enture season), as compared to Eskola 2007 paper -study annual species with aggressiove interactions b/w juvs and adults}, author = {Eskola, Hanna T.M.}, doi = {10.1016/j.tpb.2008.12.001}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eskola - 2009 - On the evolution of the timing of reproduction.pdf:pdf}, isbn = {0040-5809}, issn = {00405809}, journal = {Theoretical Population Biology}, keywords = {Evolution of function-valued traits,Invasion analysis,The Beverton-Holt model,The Hassell model,The Ricker model,Timing of reproduction}, number = {2-3}, pages = {98--108}, pmid = {19136020}, publisher = {Elsevier}, title = {{On the evolution of the timing of reproduction}}, url = {http://dx.doi.org/10.1016/j.tpb.2008.12.001}, volume = {75}, year = {2009} } @article{Heino2008, abstract = {Question: How are competing foragers expected to distribute their lifetime foraging effort on a gradient of resource types that differ in abundance, quality, foraging costs, and associated mortality risks? Mathematical method: Population dynamics of foragers and resources coupled with adaptive dynamics of foraging strategies based on continuous, function-valued traits. Key assumptions: We start from generalizing the classical patch-based theory of optimal foraging to continuous resource gradients following the traditional assumptions of constant renewal rates of resources, spatially homogeneous mortality risks, and of foragers that are omniscient, free to move without costs, equal, and not experiencing any saturation of intake. We then relax the restrictive assumptions of the classical model, thus accounting for nonlinear functional responses of the foragers, heterogeneous mortality risks and resource qualities, energetically costly foraging, genetic covariances constraining foraging, feedbacks between foraging and resource dynamics, and different types of competition between foragers. Results: (1) When expressed as instantaneous rates with the same units (time-1), mortality risks (d), foraging costs (c), and resource qualities (q) all influence the evolutionarily stable distribution of foraging effort through the dimensionless expression (d+c)/q; (2) functional responses that imply intake saturation may result in a subset of resources remaining entirely unused; (3) coupling foraging to resource dynamics results in a rich array of evolutionary outcomes, depending on the type of competition among foragers and the inter-play between forager and resource characteristics; and (4) genetic constraints may cause foraging effort to track the resource gradient more coarsely than classical models predict.}, author = {Heino, Mikko and Parvinen, Kalle and Dieckmann, Ulf}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Heino, Parvinen, Dieckmann - 2008 - Evolution of foraging strategies on resource gradients.pdf:pdf}, issn = {15220613}, journal = {Evolutionary Ecology Research}, keywords = {Exploitation competition,Frequency-dependent selection,Function-valued traits,Ideal free distribution,Interference competition,Optimal foraging,Resource dynamics,Resource gradient}, number = {8}, pages = {1131--1156}, title = {{Evolution of foraging strategies on resource gradients}}, volume = {10}, year = {2008} } @article{Parvinen2006, annote = {-in nonlinear reaction norm setting, plastic should simply be derivative of trait as funciton of environment}, author = {Parvinen, Kalle and Dieckmann, Ulf and Heino, Mikko}, doi = {10.1007/s00285-006-0020-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Parvinen, Dieckmann, Heino - 2006 - Function-valued adaptive dynamics and the calculus of variations.pdf:pdf}, isbn = {0-387-95223-3}, journal = {Journal of Mathematical Biology}, keywords = {adaptive dynamics,infinite-dimensional traits,or phrases,reaction norms}, pages = {1--26}, title = {{Function-valued adaptive dynamics and the calculus of variations}}, volume = {52}, year = {2006} } @article{Parmesan2006, annote = {Key points: - review focuses on long term datasets with detailed mechnisms - most responses are phenology...reveiw mismatvh lit (visseer and both 2005), also range shifts ------ -focus on long term datasets or or examples with mechinisms well worked out -most examples fous on changes in species' phenologies --discuss severall papers with data even going back to 1400 -discusss general increase in the NA growing season from NDVI estimates Sectionon mismatches -look at syncorony over time b/w pred. and prey? -discuss Visser and Both 2005 Section on range shift -discuss Beever et al 2003 on pikas -community shifts in marine systems b.c of CC Extinctions - Evolution and platicity section -need longterm ecological and genetic data --allows you to seperate plastic vs. evolutionary responses (for example a paper on red squirrels in the Arcti esimtated 62{\%} of change in breeding dates over 10 years was b/c of plasticity and 13{\%} was due to genetic change (Berteaux et al. 2004; Reale et al. 2003).}, author = {Parmesan, Camille}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Parmesan - 2006 - Ecological and evolutionary responses to recent climate change.pdf:pdf}, journal = {Annual Review of Ecology, Evolution, and Systematics}, keywords = {a review in advance,aquatic,first published online as,global warming,phenology,range shift,terrestrial,trophic}, pages = {637--669}, title = {{Ecological and evolutionary responses to recent climate change}}, volume = {37}, year = {2006} } @phdthesis{Nurmi2015, author = {Nurmi, Tuomas}, isbn = {9789512960361}, pages = {1--119}, school = {University of Turku}, title = {{Adaptive Dynamics of Resource Specialization}}, year = {2015} } @article{Jentsch2007, annote = {-paper on extreme events in ecology -define abruptness of event (magnitude/duration) -could look at rare events, standardized for lifespans to compare organims -what baseline do you use to determine rare event if the mean trend is also changing? I think you can detrend this -discuss experiments of rare events - like manipulating rainfall timing -describe their own large experiment in Germany, the EVENT experiment}, author = {Jentsch, Anke and Kreyling, J{\"{u}}rgen and Beierkuhnlein, Carl}, doi = {10.1890/1540-9295(2007)5}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Jentsch, Kreyling, Beierkuhnlein - 2007 - A new generation of climate-change experiments events, not trends.pdf:pdf}, journal = {Front Ecol Environ}, number = {7}, pages = {365--374}, title = {{A new generation of climate-change experiments: events, not trends}}, volume = {5}, year = {2007} } @article{Eskola2007, abstract = {We present a derivation of various discrete-time population models within a single unifying mechanistic context. By systematically varying the within-year patterns of reproduction and aggression between individuals we can derive various discrete-time population models. These models include classical examples such as the Ricker model, the Beverton-Holt model, the Skellam model, the Hassell model, and others. Some of these models until now lacked a good mechanistic interpretation or have been derived in a different context. By using this mechanistic approach, the model parameters can be interpreted in terms of individual behavior.}, annote = {-examine annual species (juv-adult) with different combinations of reproductive schedules (continuous, burst early, or burst late) and aggressive interactions --{\textgreater} these lead to various well known models (e.g. Ricker)}, author = {Eskola, H. T M and Geritz, S. A H}, doi = {10.1007/s11538-006-9126-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eskola, Geritz - 2007 - On the mechanistic derivation of various discrete-time population models.pdf:pdf}, isbn = {1153800691264}, issn = {00928240}, journal = {Bulletin of Mathematical Biology}, keywords = {Beverton-Holt model,Discrete-time population model,Hassell model,Ricker model,Skellam model}, number = {1}, pages = {329--346}, pmid = {16838083}, title = {{On the mechanistic derivation of various discrete-time population models}}, volume = {69}, year = {2007} } @article{Akhmetzhanov2011, abstract = {The interplay between individual adaptive life histories and populations dynamics is an important issue in ecology. In this context, we considered a seasonal consumer-resource model with nonoverlapping generations. We focused on the consumers decision-making process through which they maximize their reproductive output via a differential investment into foraging for resources or reproducing. Our model takes a semi-discrete form, and is composed of a continuous time within-season part, similar to a dynamic model of energy allocation, and of a discrete time part, depicting the between seasons reproduction and mortality processes. We showed that the optimal foraging-reproduction strategies of the consumers may be "determinate" or "indeterminate" depending on the season length. More surprisingly, it depended on the consumers population density as well, with large densities promoting indeterminacy. A bifurcation analysis showed that the long-term dynamics produced by this model were quite rich, ranging from both populations' extinction, coexistence at some season-to-season equilibrium or on (quasi)-periodic motions, to initial condition-dependent dynamics. Interestingly, we observed that any long-term sustainable situation corresponds to indeterminate consumers' strategies. Finally, a comparison with a model involving typical nonoptimal consumers highlighted the stabilizing effects of the optimal life histories of the consumers.}, annote = {-interesting applications to foraging ideas in pikas -feel there is not a lot of work connecting life history and population dynamic -semi discrtee models are more mechanistic often -look at consumers that have to decide between foraging and -no mortality during season makes some sense Summary: This paper examines how a consumer can maximize reproductive output by putting more effort towards foraging or reproduction during a season. Using a semi-discrete mechanistic model of a consumer-resource system, they examine the optimal foraging strategy, {\$}u{\_}n(t){\$}, which is allowed to vary over the course of a season. Both consumers and resources are assumed to be annual species and mortality takes place at the end of each year. They then sent up an optimal control problem to determine the optimal foraging strategy of consumers. They study both within season and long term behavior of their model. Consumer density was important as low density selected for determinate strategies.}, author = {Akhmetzhanov, Andrei R. and Grognard, Frederic and Mailleret, Ludovic}, doi = {10.1111/j.1558-5646.2011.01381.x}, issn = {00143820}, journal = {Evolution}, keywords = {Foraging-reproduction trade-off,Individual behavior,Population dynamics,Semi-discrete model}, number = {11}, pages = {3113--3125}, pmid = {22023579}, title = {{Optimal life-history strategies in seasonal consumer-resource dynamics}}, volume = {65}, year = {2011} } @article{Cai2014, abstract = {El Ni{\~{n}}o events are a prominent feature of climate variability with global climatic impacts. The 1997/98 episode, often referred to as ‘the climate event of the twentieth century'1,2, and the 1982/83 extreme El Ni{\~{n}}o3, featured a pronounced eastward extension of the west Pacific warm pool and development of atmospheric convection, and hence a huge rainfall increase, in the usually cold and dry equatorial eastern Pacific. Such a massive reorganization of atmospheric convection, which we define as an extreme El Ni{\~{n}}o, severely disrupted global weather patterns, affecting ecosystems4,5, agriculture6, tropical cyclones, drought, bushfires, floods and other extreme weather events worldwide3,7–9. Potential future changes in such extreme El Ni{\~{n}}o occurrences could have profound socio-economic consequences. Here we present climate modelling evidence for a doubling in the occurrences in the future in response to greenhouse warming.We estimate the change by aggregating results from climate models in the Coupled Model Intercomparison Project phases 3 (CMIP3; ref. 10) and 5 (CMIP5; ref. 11) multi-model databases, and a perturbed physics ensemble12. The increased frequency arises from a projected surface warming over the eastern equatorial Pacific that occurs faster than in the surrounding ocean waters13,14, facilitating more occurrences of atmospheric convection in the eastern equatorial region.}, author = {Cai, Wenju and Borlace, Simon and Lengaigne, Matthieu and van Rensch, Peter and Collins, Mat and Vecchi, Gabriel and Timmermann, Axel and Santoso, Agus and McPhaden, Michael J. and Wu, Lixin and England, Matthew H. and Wang, Guojian and Guilyardi, Eric and Jin, Fei-Fei}, doi = {10.1038/nclimate2100}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cai et al. - 2014 - Increasing frequency of extreme El Ni{\~{n}}o events due to greenhouse warming.pdf:pdf}, isbn = {1758-678X}, issn = {1758-678X}, journal = {Nature Climate Change}, number = {2}, pages = {1--6}, publisher = {Nature Publishing Group}, title = {{Increasing frequency of extreme El Ni{\~{n}}o events due to greenhouse warming}}, url = {http://www.nature.com/doifinder/10.1038/nclimate2100}, volume = {5}, year = {2014} } @article{Mcgill2007, annote = {Two reasons contrinous traits using game theory has not been applied much: 1) usually modeled using quan gen or 2) confusing erms -here continuous trait means continuos in the quan gen sense, not as funciton-valued traits History -von Neumann on two-player zero-sum games (one player's gains equals another's losses) -Nash on Nash equilbrium -Price and Maynard-Smith on ESSs Empiricaly examples of evol branches? Most early work focused on single traits for deterministic systems with stable and fast pop dyn.Extensions: -density dependence (non equilirium dynamics) -stochastic environments (Cohen 1966, Roff 1992) - look at evolutionary stable combination instead of ESS -structured populations -multiple traits (eq. points can now be saddlees instead of just attractors and repellers) -multiple species}, author = {Mcgill, Brian J and Brown, Joel S}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mcgill, Brown - 2007 - Evolutionary game theory and adaptive dynamics of continous traits.pdf:pdf}, journal = {Annual Review of Ecology, Evolution, and Systematics}, pages = {403--435}, title = {{Evolutionary game theory and adaptive dynamics of continous traits}}, volume = {38}, year = {2007} } @article{Wiegand2005, abstract = {We used a spatially explicit population model that was generalized to produce nine ecological profiles of long-lived species with stable home ranges and natal dispersal to investigate the effects of habitat loss and fragmentation on population dynamics. We simulated population dynamics in landscapes composed of three habitat types (good-quality habitat ranging from 10–25{\%}, poor-quality habitat ranging from 10– 70{\%}, and matrix). Landscape structures varied from highly fragmented to completely contiguous. The specific aims of our model were (1) to investigate under which biological circumstances the traditional approach of using two types only (habitat and matrix) failed and assess the potential impact of restoring matrix to poor- quality habitat, (2) to investigate how much of the variation in population size was explained by landscape composition alone and which key attributes of landscape structure can serve as predictors of population r esponse, and (3) to estimate the maximum fragmentation effects expressed in equivalent pure loss of good- quality habitat. Poor-quality habitat mattered most in situations when it was generally not considered (i.e., fo r metapopulations or spatially structured populations when it provides dispersal habitat). Population size increased up to 3 times after restoring matrix to poor-quality habitat. Overall, habitat amount accounted fo r 68{\%} of the variation in population size, whereas ecological profile and fragmentation accounted for approximately 13{\%} each. The maximal effect of (good-quality) habitat fragmentation was equivalent to a pure loss of up to 15{\%} of good-quality habitat, and the maximal loss of individuals resulting from maximal fragmentation reached 80{\%}. Abundant dispersal habitat and sufficiently large dispersal potential, however, r esulted in functionally connected landscapes, and maximal fragmentation had no effect at all. Our findings suggest that predicting fragmentation effects requires a good understanding of the biology and habitat use of the species in question and that the uniqueness of species and the landscapes in which they live confound simple analysis.}, annote = {-use spatially explicit simulation model to examine many different combinations of habitat loss and fragmentation -find that habitat amount is amount, not neccessarily the degree of fragmentation -obviously dispersal capability and}, author = {Wiegand, Thorsten and Revilla, Eloy and Moloney, Kirk A.}, doi = {10.1111/j.1523-1739.2005.00208.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wiegand, Revilla, Moloney - 2005 - Effects of habitat loss and fragmentation on population dynamics.pdf:pdf}, isbn = {0888-8892}, issn = {08888892}, journal = {Conservation Biology}, keywords = {Ecological profiles,Individual-based spatially explicit population mod,Landscape metrics,Landscape structure,Matrix heterogeneity,Metapopulation,Source-sink}, number = {1}, pages = {108--121}, pmid = {1176}, title = {{Effects of habitat loss and fragmentation on population dynamics}}, volume = {19}, year = {2005} } @misc{Hanski1994, abstract = {1. This paper describes a novel approach to modelling of metapopulation dynamics. The model is constructed as a generalized incidence function, which describes how the fraction of occupied habitat patches depends on patch areas and isolations. 2. The model may be fitted to presence/absence data from a metapopulation at a dynamic equilibrium between extinctions and colonizations. 3. Using the estimated parameter values, transient dynamics and the equilibrium fraction of occupied patches in any system of habitat patches can be predicted. The significance of particular habitat patches for the long-term persistence of the metapopulation, for example, can also be evaluated. 4. The model is fitted to data from three butterfly metapopulations. The model predicts well the observed minimum patch size for occupancy and the numbers of extinctions and colonizations per year (turnover rate). The results suggest that local populations of the three butterflies in patches of 1 ha, which may support of the order of 1000 adult butterflies, have an expected lifetime of 20-100 years.}, author = {Hanski, Ilkka}, booktitle = {Journal of Animal Ecology}, doi = {10.2307/5591}, isbn = {00218790}, issn = {0021-8790}, number = {1}, pages = {151--162}, pmid = {741704}, title = {{A practical model of metapopulation dynamics}}, volume = {63}, year = {1994} } @incollection{Moya-Larano2014, abstract = {One of the current challenges in evolutionary ecology is understanding the long-term persistence of contemporary-evolving predator-prey interactions across space and time. To address this, we developed an extension of a multi-locus, multi-trait eco-evolutionary individual-based model that incorporates several interacting species in explicit landscapes. We simulated eco-evolutionary dynamics of multiple species food webs with different degrees of connectance across soil-moisture islands. A broad set of parameter combinations led to the local extinction of species, but some species persisted, and this was associated with (1) high connectance and omnivory and (2) ongoing evolution, due to multi-trait genetic variability of the embedded species. Furthermore, persistence was highest at intermediate island distances, likely because of a balance between predation-induced extinction (strongest at short island distances) and the coupling of island diversity by top predators, which by travelling among islands exert global top-down control of biodiversity. In the simulations with high genetic variation, we also found widespread trait evolutionary changes indicative of eco-evolutionary dynamics. We discuss how the ever-increasing computing power and high-resolution data availability will soon allow researchers to start bridging the in vivo-in silico gap. ?? 2014 Elsevier Ltd.}, annote = {-point to Polis' work early on explaining the species interactions are embedded in larger web of dynamics difference between contemporay and rapid evolution? How does genetic variation and the strength of selection affect food web structure and dynamics? Beleive that studies of eco-evo dynamics have not paid enough attention to space They want to merge space, food webs, and evolution Use soil food webs as an example system Use program called Weaver- IBM approach of food webs that are heterogenous in space Interested in food web persistence, connectance, genetic variation, role of spatial strucute -Looked at varying level of connectivity and genetic variation in a 20 species food web where each species had 13 characteerstics - food webs eere also on four micro islands. Ran 5 simulations of each scenario Results -increased connectence (with lots of omnivory) allowed for more species to coexist - specifically it increased predator persistence but decreassed prey persistence -{\textgreater} this is a bit suprising in light of May's work. Connectance should be destabalizing? It depends on cannabalism and other feedbacks -gen var also helped persistence When predators are around population sizes of predators changes which affects seleciton pressures McCann, Hastings papers on higher connectance and strong omnivory being stabalizing Genetic variability can help stablity by allowing rapid evolution (that affects pop dyn) or by increasing connectance in the web (b/c of diversity of interactions present with high gen var) Evolution can be stabalizing or destabalizing Term "growth ratio" - not common term Intermediant distances b/w patches with predators present allow the most prey persistence Simulations are not independent from one another (have same mathematical framework) so it is tricky to do statistical analyses on this Also issue of more simulations driving now p-values - Sebastian doesn't have a huge issue with this}, author = {Moya-Larano, Jordi and Bilbao-Castro, Jose Roman and Barrionuevo, Gabriel and Ruiz-Lupion, Dolores and Casado, Leocadio G. and Montserrat, Marta and Melian, Carlos J. and Magalhaes, Sara}, booktitle = {Advances in Ecological Research}, doi = {10.1016/B978-0-12-801374-8.00003-7}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moya-Larano et al. - 2014 - Eco-evolutionary spatial dynamics. Rapid evolution and isolation explain food web persistence.pdf:pdf}, isbn = {9780128013748}, issn = {00652504}, keywords = {Animal personalities,Eco-evolutionary dynamics,Food Web Engineering,Food web stability,Food webs,Genetic variation,Multi-trophic metacommunities,Rapid evolution}, pages = {75--143}, title = {{Eco-evolutionary spatial dynamics. Rapid evolution and isolation explain food web persistence}}, volume = {50}, year = {2014} } @article{Nicholson1935, annote = {-chose to study host-parasitoid interactions as it simplifies a number of things (e.g. parasite offspring do not need to search for food) -discuss many situations (specific or general parasties and hosts, outside forces) -present case of hyperparasitism}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Nicholson, A.J. and Bailey, V.A.}, doi = {10.1007/s13398-014-0173-7.2}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nicholson, Bailey - 1935 - The balance of animal populations.pdf:pdf}, isbn = {9780874216561}, issn = {0717-6163}, journal = {Proceedings of the Zoological Society of London}, keywords = {coevolution,host,parasitoid,theoretical ecology}, mendeley-tags = {coevolution,host,parasitoid,theoretical ecology}, pages = {551--598}, pmid = {15003161}, title = {{The balance of animal populations}}, volume = {1}, year = {1935} } @article{Schoener2015, annote = {-hump-shaped curves for relationship between predation effect size and island size or competition and island size -island size always correlates with perimeter-to-area relationship -{\textgreater} any way to experimentally change this? Close beaches or something Ascending (Left hand size) of relationship -{\textgreater}they suggest that on small islands, physcial factors are harsh. Distrubances also affect them more strongly -{\textgreater} smaller island should also have higher allochthonous subsidies, which would weaken predation effects as predators switch to eating different food type Descending side of relationship -spatial heterogeneity is greater on larger islands -mutualism was stronger on smaller island}, author = {Schoener, Thomas W and Spiller, David A and Piovia-scott, Jonah}, doi = {10.1111/geb.12297}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Schoener, Spiller, Piovia-scott - 2015 - Variation in ecological interaction strength with island area theory and data from the Bahamia.pdf:pdf}, journal = {Global Ecology and Biogeography}, keywords = {ants,buttonwood,competition,interaction strength,island area,lizards,mutualism,predation,sea daisy,spiders}, pages = {1--9}, title = {{Variation in ecological interaction strength with island area : theory and data from the Bahamian archipelago}}, year = {2015} } @article{Anderson1991, annote = {-lays out history of studying disease (noting epidemics, figuring out causes, identifying microbes, -Daniel Bernouli (1760) studied smallpox Main early questions: what caused magnitude of epidemic? what caused epidemic to end? -two early hypotheses: suspetiples eventually ran out or the virulence of the infectious agent declined Dives into Kermack-McKendrick (1927) paper using more modern notation -introduces R0 concept and how Kermack-McKendrick basically understood it as well Here R0 = beta*N/v = (transmission rate)*N/(recover or death rate) -Then discusses later Kerack and McKendrick papers -Control by Mass Vaccination -Two questions: what percentage of pop needs to be vaccinated and at what age -if at birth prop needed is p{\textgreater}[1- 1/R0] -Heterogeneity is important and has been a focus more recently -different rates for different ages turns the vaccination problem in a matrix prblem Also have heterogeneity in sexual behavior (e.g AIDS - where variance in rate is much more important than mean often), space, behavior, genetic,}, author = {Anderson, Roy M.}, doi = {10.1007/s11538-006-9134-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Anderson - 1991 - Discussion The Kermack-McKendrick epidemic threshold theorem.pdf:pdf}, isbn = {1153800691}, issn = {0092-8240}, journal = {Bulletin of Mathematical Biology}, number = {1-2}, pages = {1--32}, title = {{Discussion: The Kermack-McKendrick epidemic threshold theorem}}, volume = {53}, year = {1991} } @article{Huxel2002, annote = {-reference earlier work by Huxel and McCann 1998 that looked a pulses in trophic chain Question: how to orgainms partition autochthonous and allochthonous resources? -webs that experience low to moderate allochthounous resources are more persisten -generalist communities supposifly should be more persistent than specliast systems Things that matter for persistence: -the trophic level at which resources enter matters a lot -partioning of local or pulse resources matters -amount of allochthonous resource input -strength of consumer resouce interactions Polis and Hurd (1995, 1996) - found that more than 90{\%} of prey for coastal terrestiral predators was detritvores that fed on marine inpts}, author = {Huxel, GR and McCann, K and Polis}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Huxel, McCann, Polis - 2002 - Effects of allocthonous and autocthonous resources on partitioning food web stability.pdf:pdf}, journal = {Ecological Research}, keywords = {allochthonous resources,compartmentalization,energetics,food webs,intraguild,persistence,predation,resource partitioning,spatial subsidies,trophic specialization}, pages = {419--432}, title = {{Effects of allocthonous and autocthonous resources on partitioning food web stability}}, volume = {17}, year = {2002} } @misc{Huffaker1958, abstract = {N4 - JA, not in file}, annote = {-predator and prey mites on spatial system of oranges and rubber balls -following work of Gausa by seeing if predators and prey can in fact coexist -would replace old oragnges (like a resource pulse) Looked at sytems with and without predators -Systems without predators- see oscillaitons in population size around some equilbrium pt --this result depends on the degree of food heterogeneity -System with predators Most spatial designs were insufficient to allow predators and prey to coexist Most select large enough area that populations can persist, but not small enough where local areas would be discoupled and asynchronous -{\textgreater} would hide predator-prey cycles that were occuring Believes migraiton is important for coexistence}, author = {Huffaker, C B}, booktitle = {Hilgardia}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Huffaker - 1958 - Experimental studies on predation dispersion factors and predator-prey oscillations.pdf:pdf}, isbn = {alphabetical}, number = {14}, pages = {343--383}, pmid = {3636}, title = {{Experimental studies on predation: dispersion factors and predator-prey oscillations}}, url = {http://faculty.washington.edu/kerrb/Huffaker1958.pdf}, volume = {27}, year = {1958} } @incollection{Talley2006, annote = {-related question with disease that sea otters get from domestic cats?? primary and secondary effects of connected ecosystems linkages can be classified by a number of features: directionality, feedback, temporal variation, biotic/abiotic mediation This paper focuses on feedbacks and directionality of linkages -Baja islands with their seaweed on shores are example of unidirectional flow with no feedback -The birds represent bidirectional movement without feedback (movement of nutrietns are decoupled from each other) How related is all this stuff to Chesson's work? Alan thinks it is different}, author = {Talley, DM and Huxel, GR and Holyoak, Marcel}, booktitle = {Conservatino Biology Series}, doi = {10.1017/CBO9780511754821}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Talley, Huxel, Holyoak - 2006 - Connectivity at the land-water interface.pdf:pdf}, isbn = {9780521857062}, pages = {97--129}, publisher = {Cambridge}, title = {{Connectivity at the land-water interface}}, url = {http://www.des.ucdavis.edu/faculty/holyoak/MHpubs/Talley{\_}et{\_}al{\_}connectivity{\_}book{\_}ch{\_}2006.pdf}, year = {2006} } @article{Kermack1927, abstract = {(1) A mathematical investigation has been made of the progress of an epidemic in a homogeneous population. It has been assumed that complete immunity is conferred by a single attack, and that an individual is not infective at the moment at which he receives infection. With these reservations the problem has been investigated in its most general aspects, and the following conclusions have been arrived at. (2) In general a threshold density of population is found to exist, which depends upon the infectivity, recovery and death rates peculiar to the epidemic. No epidemic can occur if the population density is below this threshold value. (3) Small increases of the infectivity rate may lead to large epidemics; also, if the population density slightly exceeds its threshold value the effect of an epidemic will be to reduce the density as far below the threshold value as initially it was above it. (4) An epidemic, in general, comes to an end, before the susceptible population has been exhausted. (5) Similar results are indicated for the case in which transmission is through an intermediate host.}, annote = {-in first paragraph they discuss a number of key assumtions (different sickness classes, constant population size, everyone is susceptible, gain immmnity after one infection) -derive equations for sustiple, infected, and recovered}, author = {Kermack, W. O. and McKendrick, a. G.}, doi = {10.1098/rspa.1927.0118}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kermack, McKendrick - 1927 - Contributions to the mathematical theory of epidemics.pdf:pdf}, issn = {0092-8240}, journal = {Proceedings of the Royal Society of London}, number = {772}, pages = {700--721}, pmid = {20475492}, title = {{Contributions to the mathematical theory of epidemics}}, volume = {115}, year = {1927} } @article{Talley2011, abstract = {Across the United States there is increasing concern about the dwindling scientific workforce and the lack of students prepared for careers in the sciences. To build future leadership in this arena, we must employ innovative approaches that generate young peoples' interest and develop their capabilities so that an increased number will pursue and be prepared for careers in scientific fields. Marine ecology is an ideal platform to engage young people in the sciences, develop their skills across multiple disciplines, and prepare them to face the complex challenges that lie ahead. In response, Ocean Discovery Institute, a non-profit organization, has developed Ocean Leaders, a model program to empower young people to become tomorrow's scientific leaders. Using evaluation data that span the 5years of the program, we asked how this model can affect participants' interest and performance in science and how it can contribute directly to the field of marine ecology. Content assessments, surveys, interviews, and tracking data reveal that 73{\%} of Ocean Leader students during this period have declared majors in science and conservation fields, scored higher on standardized science tests relative to their peers, and contributed to ecological research through 10 publications and more than 30 scientific presentations. Using a framework analogous to adaptive management strategies, key components of the program (including in-depth interactions with scientists and rigorous college readiness coursework) have been identified, resulting in an increased number of students who are interested in and ready to pursue science careers. Critical to this model is the partnership between scientists and a non-profit organization. Although this model may not easily be replicated in its entirety, aspects of this collaboration and the strategies employed can help to simultaneously advance the field of marine ecology and scientific leadership and understanding. {\textcopyright} 2011 Blackwell Verlag GmbH.}, author = {Talley, D and Goodwin, L and Ruzic, R and Fisler, S}, doi = {10.1111/j.1439-0485.2011.00468.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Talley et al. - 2011 - Marine ecology as a framework for preparing the next generation of scientific leaders.pdf:pdf}, isbn = {01739565 (ISSN)}, issn = {01739565}, journal = {Marine Ecology}, keywords = {Adaptive engagement,Bahia de los Angeles,Bah{\'{i}}a de los Angeles,Baja California [(STT) Mexico],Education,Marine ecology,Mexico [North America],adaptive management,curriculum,ecological approach,higher education,marine ecosystem,marine environment,student}, number = {3}, pages = {268--277}, title = {{Marine ecology as a framework for preparing the next generation of scientific leaders}}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-79961022539{\&}partnerID=40{\&}md5=e0108c9dd8ccb92bbf3c75d621c5ff20}, volume = {32}, year = {2011} } @article{Polis1996a, annote = {Yodzis on perturbation experiments -don't like how most theory simplfies dynamics of food webs into nice linear chains -discuss limits on food chains b/c of energy flows (bbottom up) and the green world hypothesis (top down) - similar to explotation ecosystem hypothesis Omnivory is way to common to have trophic levels Omnivory diffuses effect of consumers, increass web connectence, .. Need to look at more than energy flow to understand food web dynamics (e.g. indirect effects of predation) Argue that you need experimentaion to see how important nodes actually are in a food web Discuss how open food webs actually are- none are actually closed -allochthonous resources can be crucial Detritial pathway is so important Nutriets (e.g. nitrogen) are essential contributors to food web dynamics as well -we see the effect and importance of nutriets when there are food web pulses of nutriets like in marine realms -Prey also have many different types of proetection (via refuges or age class or whatever) from predators Provide "path forward" -combine consumer-resource work with other ecosystem processes (e.g. effect of omnivory or nutrients) -increase or decrease energy in various nodes of a food web -manipulate flow of spatial subsidies}, author = {Polis, Gary A. and Strong, Donald R.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Polis, Strong - 1996 - Food web complexity and community dynamics.pdf:pdf}, journal = {The American Naturalist}, number = {5}, pages = {813--845}, title = {{Food web complexity and community dynamics}}, volume = {147}, year = {1996} } @article{Hastings1999, annote = {-why would density dependence only depend on denisty of juvenile? -compare optimal amount of coastline needed to set aside to optimal fraction of adult population that is allowed to escape}, author = {Hastings, A. and Botsford, Louis W.}, doi = {10.1126/science.284.5419.1537}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Botsford - 1999 - Equivalence in Yield from Marine Reserves and Traditional Fisheries Management.pdf:pdf}, issn = {00368075}, journal = {Science}, number = {5419}, pages = {1537--1538}, title = {{Equivalence in Yield from Marine Reserves and Traditional Fisheries Management}}, url = {http://www.sciencemag.org/cgi/doi/10.1126/science.284.5419.1537}, volume = {284}, year = {1999} } @article{Stapp2003, abstract = {Inputs of energy and nutrients from one ecosystem may subsidize consumers in adjacent ones, with significant consequences for local communities and food webs. We used stable isotope and faecal pellet analysis to quantify use of ocean-derived resources by small mammals on islands in the Gulf of California, Mexico. Rodents were live-trapped on grids originating near shore and extending 125-200 m inland to evaluate the extent to which rodents transport marine nutrients inland, and to determine whether marine foods subsidize island populations, permitting higher densities than would be possible based on terrestrial resources alone. Both faeces and stable carbon and nitrogen isotopes revealed that omnivorous mice (Peromyscus maniculatus) consume ocean-derived prey, including littoral and supralittoral invertebrates, and that their diets differed markedly from those of granivorous rodents (Chaetodipus rudinoris). On a small, seabird roosting island, marine prey were important in the diet of mice regardless of their proximity to shore, underscoring the pervasive influence of the ocean on small islands with relatively large coastline area. On a large island, however, consumption of marine foods declined sharply {\textgreater} or =50 m from shore, which suggests that mice are poor conduits of inland movement of energy and nutrients from the sea. Marine resources seemed to act as subsidies for omnivorous rodents: more P. maniculatus were captured near shore than farther inland and there was an inverse relationship between island area and rodent abundance, suggesting that small islands with large amounts of marine inputs support the highest population densities. Patterns of local and island-wide abundance of P. maniculatus are likely the result of several interacting factors, including frustrated dispersal, competition with C. rudinoris, and the absence of predators. We speculate, however, that the availability of marine resources allows P. maniculatus to reach high densities and to persist on small islands in the Gulf despite low and unpredictable terrestrial productivity. Spatial trophic subsidies thus provide a possible mechanistic explanation for the widely reported inverse relationship between population density and island or habitat area.}, author = {Stapp, Paul and Polis, Gary a}, doi = {10.1007/s00442-002-1146-7}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stapp, Polis - 2003 - Marine resources subsidize insular rodent populations in the Gulf of California, Mexico.pdf:pdf}, isbn = {0029-8549}, issn = {0029-8549}, journal = {Oecologia}, keywords = {chaetodipus rudinoris,island ecology,peromyscus maniculatus,spatial subsidies}, number = {4}, pages = {496--504}, pmid = {12647121}, title = {{Marine resources subsidize insular rodent populations in the Gulf of California, Mexico.}}, volume = {134}, year = {2003} } @article{Gerber2003, abstract = {We synthesize results from existing models of marine reserves to identify key theoretical issues that appear to be well understood, as well as issues in need of further exploration. Models of marine reserves are relatively new in the scientific literature; 32 of the 34 theoretical papers we reviewed were published after 1990. These models have focused primarily on questions concerning fishery management at the expense of other objectives such as conservation, scientific understanding, recreation, education, and tourism. Roughly one-third of the models analyze effects on cohorts while the remaining models have some form of complete population dynamics. Few models explicitly include larval dispersal. In a fisheries context, the primary conclusion drawn by many of the complete population models is that reserves increase yield when populations would otherwise be overfished. A second conclusion, resulting primarily from single-cohort models, is that reserves will provide fewer benefits for species with greater adult rates of movement. Although some models are beginning to yield information on the spatial configurations of reserves required for populations with specific dispersal distances to persist, it remains an aspect of reserve design in need of further analysis. Other outstanding issues include the effects of (1) particular forms of density dependence, (2) multispecies interactions, (3) fisher behavior, and (4) effects of concentrated fishing on habitat. Model results indicate that marine reserves could play a beneficial role in the protection of marine systems against overfishing. Ad- ditional modeling and analysis will greatly improve prospects for a better understanding of the potential of marine reserves for conserving biodiversity.}, annote = {-Could redo this paper now with fresh synthesis - this was basically done by Fulton et al 2015 -reserves provide less benefits for species that have large adult migrations -few models include larval disperal -future work needs to look at density dependence, multispecies interactions, fisher behavior, effects of concentrated fishing on habitat -terrestrial models focus on diversity, marine models are typically of single species -need to determine timeline for measuring success after establishing a protected area -"to be useful, models must include control variable that we actually have potential to inflluence through management or policy actions" -they look at taxonomy of existing models -Hastings and Botsford (2003) - found one large reserve best for conservation, several small reserves best for fisheries -goal could be to increase yield or to decrease variability -}, author = {Gerber, Leah R and Botsford, Louis W and Hastings, Alan and Possingham, Hugh P and Gaines, Steven D and Palumbi, Stephen R and Andelman, Sandy}, doi = {10.1890/1051-0761(2003)013[0047:PMFMRD]2.0.CO;2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gerber et al. - 2003 - Population Models for Marine Reserve Design a Retrospective and Prospective Synthesis.pdf:pdf}, isbn = {10510761}, issn = {1051-0761}, journal = {Ecological Applications}, keywords = {biodiversity,conservation,density dependence,larval pool,marine protected area,migration,population model,spatial harvest,stochasticity,yield per recruit}, number = {1}, pages = {547--564}, title = {{Population Models for Marine Reserve Design : a Retrospective and Prospective Synthesis}}, volume = {13}, year = {2003} } @article{Moore2004, abstract = {Traditional approaches to the study of food webs emphasize the transfer of local primary productivity in the form of living plant organic matter across trophic levels. However, dead organic matter, or detritus, a common feature of most ecosystems plays a frequently overlooked role as a dynamic heterogeneous resource and habitat for many species. We develop an integrative framework for understanding the impact of detritus that emphasizes the ontogeny and heterogeneity of detritus and the various ways that explicit inclusion of detrital dynamics alters generalizations about the structure and functioning of food webs. Through its influences on food web composition and dynamics, detritus often increases system stability and persistence, having substantial effects on trophic structure and biodiversity. Inclusion of detrital heterogeneity in models of food web dynamics is an essential new direction for ecological research.}, annote = {- 1960s ecology split into two camps: species interactions within green-world pathway and flow of energy and matter through ecosystems -most primary productivity is not consumed and is instead returned to detritus -long history of thinking about detritus on some level -however, theories of food webs and trophic dynamics typically ignore detritus -detritus is habitat for many organisms and also acts as a habitat modifier (e.g. may alter water flow) -most ffood webs have a high degree of inter- and intraguild predation and omnivory -detritous is often assumed to be static and homogenous everywhere "Use of stochastic spatial models and individual based models (Durrett {\&} Levin 1994; Dieckmann et al. 1999; Pascual et al. 2002)" -detritous can have dynamics and stablity of food webs, food chain length, distribution of biomass across trophic levels, a trophic cascade, and biodiversity -detritus does not reproduce or affect input of new material directly donor-controlled? weak interactions in food webs (like adding detritous) stablizes food webs detritus changes in amount and ontogeny which is important in models}, author = {Moore, John C. and Berlow, Eric L. and Coleman, David C. and {De Suiter}, Peter C. and Dong, Quan and Hastings, Alan and Johnson, Nancy Collins and McCann, Kevin S. and Melville, Kim and Morin, Peter J. and Nadelhoffer, Knute and Rosemond, Amy D. and Post, David M. and Sabo, John L. and Scow, Kate M. and Vanni, Michael J. and Wall, Diana H.}, doi = {10.1111/j.1461-0248.2004.00606.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moore et al. - 2004 - Detritus, trophic dynamics and biodiversity.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Decomposers,Detritus,Diversity,Ecosystems,Food chain,Food web,Primary productivity,Processing chains,Subsidies,Trophic dynamics}, number = {7}, pages = {584--600}, pmid = {298}, title = {{Detritus, trophic dynamics and biodiversity}}, volume = {7}, year = {2004} } @article{Polis1997, abstract = {We focus on the implications of movement, landscape variables, and spatial heterogeneity for food web dynamics. Movements of nutrients, detritus, prey, and consumers among habitats are ubiquitous in diverse biomes and can strongly influence population, consumer-resource, food web, and community dynamics. Nutrient and detrital subsidies usually increase primary and secondary productivity, both directly and indirectly. Prey subsidies, by movement of either prey or predators, usually enhance predator abundance beyond what local resources can support. Top-down effects occur when spatially subsidized consumers affect local resources by suppressing key resources and occasionally by initiating trophic cascades. Effects on community dynamics vary with the relative amount of input, the trophic roles of the mobile and recipient entities, and the local food web structure. Landscape variables such as the perimeter/area ratio of the focal habitat, permeability of habitat boundaries, and relative productivity of trophically connected habitats affect the degree and importance of spatial subsidization.}, annote = {spatial sybsidy - donor controlled resources from one habitat to a recipient in another habitat -perimeter-to-area ratio is major determinant of resource input possible Allochthounous inputs can increase nutriets (C, N ,P, trace elements) Can organize trophic flows by origin and destiation (water and land) - all combinations may act differently Examples: Water to water: Land to water: Water to land: Land to land Movement can be caused by physical forces or my daily and seasonal movement of animals Movement of prey can move a lot of biomass and energy - examples in many system Movement of consymers - there behavior probably changes over their lifespans Movement of detritus Indirect effect on trophic dynamics: -receipt speceies usually benefit of course -Use ocean island as specific example in last part of paper}, author = {Polis, Gary A. and Anderson, Wendy B. and Holt, Robert D.}, doi = {10.1146/annurev.ecolsys.28.1.289}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Polis, Anderson, Holt - 1997 - Toward an integration of landscape and food web ecology the dynamics of spatially subsidized food webs.pdf:pdf}, isbn = {0066-4162}, issn = {0066-4162}, journal = {Annual Review of Ecology and Systematics}, keywords = {consumer-resource dynamics,food webs,spatial subsidy,trophic dynamics}, number = {1}, pages = {289--316}, pmid = {4606}, title = {{Toward an integration of landscape and food web ecology: the dynamics of spatially subsidized food webs}}, volume = {28}, year = {1997} } @article{Anderson2008b, annote = {- paper tries to think about relationship between subsidies and pulses in ecological communities -{\textgreater} you can't study one in isolation of the other as it will be an incomplete pcture - believe ideas on pulses are well devoloped -Paper is good collection on all work done between 1990 and 2002 on various species on the islands Ostfeld and Keesing (2000) paper Plants can only take advantage of guano derived nutrients in wet years -On islands with subsidies, omnivourous rodents outcompete sead eaters}, author = {Anderson, Wendy B and Wait, D Alexander and Stapp, Paul}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Anderson, Wait, Stapp - 2008 - Resources from another place and time - responses to pulses in a spatially subsidized system.pdf:pdf}, journal = {Ecology}, number = {3}, pages = {660--670}, title = {{Resources from another place and time - responses to pulses in a spatially subsidized system}}, volume = {89}, year = {2008} } @article{Bascompte2009, abstract = {Biodiversity research typically focuses on species richness and has often neglected interactions, either by assuming that such interactions are homogeneously distributed or by addressing only the interactions between a pair of species or a few species at a time. In contrast, a network approach provides a powerful representation of the ecological interactions among species and highlights their global interdependence. Understanding how the responses of pairwise interactions scale to entire assemblages remains one of the great challenges that must be met as society faces global ecosystem change.}, annote = {-diiscusses how small motiffs (e.g. three trophic chains or omnivory) scale up to an entire food web -{\textgreater} sum of parts does not need to scale up -networks generally rely on a few well-coonected species that act as a glue How does population dynamics affect network topology and how does topology afffect dynamics? Need network approach with global challenges as several species are likely to be perturbed}, author = {Bascompte, Jordi}, doi = {10.1126/science.1170749}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bascompte - 2009 - Disentangling the web of life.pdf:pdf}, isbn = {0003-0147}, issn = {1095-9203}, journal = {Science}, number = {July}, pages = {416--419}, pmid = {19628856}, title = {{Disentangling the web of life}}, url = {http://www.sciencemag.org/content/325/5939/416.short}, volume = {325}, year = {2009} } @article{Piovia-Scott2013, abstract = {Flows of energy and materials link ecosystems worldwide and have important consequences for the structure of ecological communities. While these resource subsidies typically enter recipient food webs through multiple channels, most previous studies focussed on a single pathway of resource input. We used path analysis to evaluate multiple pathways connecting chronic marine resource inputs (in the form of seaweed deposits) and herbivory in a shoreline terrestrial ecosystem. We found statistical support for a fertilization effect (seaweed increased foliar nitrogen content, leading to greater herbivory) and a lizard numerical response effect (seaweed increased lizard densities, leading to reduced herbivory), but not for a lizard diet-shift effect (seaweed increased the proportion of marine-derived prey in lizard diets, but lizard diet was not strongly associated with herbivory). Greater seaweed abundance was associated with greater herbivory, and the fertilization effect was larger than the combined lizard effects. Thus, the bottom-up, plant-mediated effect of fertilization on herbivory overshadowed the top-down effects of lizard predators. These results, from unmanipulated shoreline plots with persistent differences in chronic seaweed deposition, differ from those of a previous experimental study of the short-term effects of a pulse of seaweed deposition: while the increase in herbivory in response to chronic seaweed deposition was due to the fertilization effect, the short-term increase in herbivory in response to a pulse of seaweed deposition was due to the lizard diet-shift effect. This contrast highlights the importance of the temporal pattern of resource inputs in determining the mechanism of community response to resource subsidies.}, annote = {-use path analysis to evaluate multiple pathways of marine subsidies -{\textgreater} short term pulses cause shifts in predator diets, whereas long term chronic pulses is dye to a fertilization effect -{\textgreater} temporal sequence and pattern of resource inputs is important -lots of good references}, author = {Piovia-Scott, Jonah and Spiller, David A. and Takimoto, Gaku and Yang, Louie H. and Wright, Amber N. and Schoener, Thomas W.}, doi = {10.1007/s00442-012-2560-0}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Piovia-Scott et al. - 2013 - The effect of chronic seaweed subsidies on herbivory Plant-mediated fertilization pathway overshadows lizar.pdf:pdf}, isbn = {1432-1939 (Electronic)$\backslash$r0029-8549 (Linking)}, issn = {00298549}, journal = {Oecologia}, keywords = {Aboveground-belowground linkage,Detritus,Path analysis,Resource subsidy,Stable isotope analysis}, number = {4}, pages = {1129--1135}, pmid = {23504216}, title = {{The effect of chronic seaweed subsidies on herbivory: Plant-mediated fertilization pathway overshadows lizard-mediated predator pathways}}, volume = {172}, year = {2013} } @article{Marczak2007, author = {Marczak, Laurie B and Thompson, Ross M and Richardson, John S}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Marczak, Thompson, Richardson - 2007 - Meta-analysis - trophic level, habitat, and productivity shape the food web effects of resource s.pdf:pdf}, journal = {Ecology}, keywords = {food webs,functional,resource subsidies,spatial ecology,taxonomic group,trophic level}, number = {1}, pages = {140--148}, title = {{Meta-analysis - trophic level, habitat, and productivity shape the food web effects of resource subsidies}}, volume = {88}, year = {2007} } @article{Callaway2002, abstract = {Energy and nutrient flow between habitats, or allochthonous input, can$\backslash$nhave a significant impact on food web dynamics. Previous theory$\backslash$ndemonstrated that resource abundance decreases in habitats where$\backslash$nconsumers are subsidized. Here we examine the effect of subsidies that$\backslash$nare available in localized parts of a habitat (such as near the shore in$\backslash$na marine-subsidized terrestrial ecosystem) with a two-patch model in$\backslash$nwhich consumers move between patches, resources are stationary, and$\backslash$nconsumers receive the subsidy in only one of the two patches. In$\backslash$ncontrast to previous theory, our results show that subsidized consumers$\backslash$ncan increase resource abundance, though only in the subsidized patch.$\backslash$nFurthermore, the total resource population responds positively to$\backslash$nincreasing consumer movement. These results demonstrate the importance$\backslash$nof spatial heterogeneity in food web dynamics and the need for further$\backslash$nexamination of the role of space in multispecies trophic webs.}, annote = {Not cited a lot -use two patch model to examine spatial characteristics of resource pulse -these spatial processes can mask top down effects when consumers are subsidized -only wants patch gets inputs while consumers can move between patches these inputs can be destablizing if they enter consumer level, consumers grow and eat everthign -examine magnutude of allochthonous input (S) and amount of consumer movement (D) -they find that increasing the amount of subsidies (with enough predator movement) can actually help resources grow in the subsidized patch}, author = {Callaway, Duncan S. and Hastings, Alan}, doi = {10.1046/j.1461-0248.2002.00330.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Callaway, Hastings - 2002 - Consumer movement through differentially subsidized habitats creates a spatial food web with unexpected resu.pdf:pdf}, isbn = {1461-023X}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Allochthonous input,Food web,Metacommunity,Spatial subsidy,Stability}, number = {3}, pages = {329--332}, title = {{Consumer movement through differentially subsidized habitats creates a spatial food web with unexpected results}}, volume = {5}, year = {2002} } @article{Chesson1997, annote = {*Key point - environment harshness or fluctuations cannot by themselves maintain biodiversity but they can interact with other mechanisms to promote coexistence -debate over whether density dependent factors and competion (niche overlap) matter in a world of constant environmental changes -{\textgreater} at some scale niche differences are needed to explain coexistence -They discuss hypotheses of a number of key classic papers (e.g. Hutchinson) -harsh conditions lower pop ggrowth but also lower competition among similar species They argue that harshness is not have a general trend in how it will affect a community, it depends -Discuss how species can have temporal niches -Use general LV model that includes variable environment models and lottery models, but is more general than either Results -Look at an important model ration mu/b, where my is effect of density-independent factors and b is effect of competition -harshness does not prevent competitive exclusion, but it may slow rate of exclusion Discuss more exotic noise processes besides stationary time series (see Halley 1996) Discussion of classic papers: Hutchinson - he thought environmental fluctuatinos should alrter rank order of competition and allow coexistence, this paper predicts competitve exclusion Huston - Grime (1979) - was mostly interested in stress (reduction in biomass production) and disturbance (removal of biomass), beleived competition would be highest in low stress, low disturbance environments Hubbell - thinks coexistence occurs b//c slow species species extinction Alternative models to their general setup: Look at three scenarios that may permit major effects of harshness or fluctuations: 1) flructuations and resource partioning 2) predators as a niche dimension - predators may act differently depending on density of prey species 3) nonadditivity (e.g. the storage effect) - fluctuations matter if their is nonlinear response (basicially discussion of Jensen's inequlaity), go through some math as well 4) spatial variation casued by disturbance}, author = {Chesson, Peter and Huntly, Nancy}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chesson, Huntly - 1997 - The roles of harsh and fluctuating conditions in the dynamics of ecological communities.pdf:pdf}, journal = {American Naturalist}, number = {5}, pages = {519--553}, title = {{The roles of harsh and fluctuating conditions in the dynamics of ecological communities}}, volume = {150}, year = {1997} } @incollection{Melian2014, abstract = {In recent years, there has been a renewed interest in the ecological consequences of individual trait variation within populations. Given that individual variability arises from evolutionary dynamics, to fully understand eco-evolutionary feedback loops, we need to pay special attention to how standing trait variability affects ecological dynamics. There is mounting empirical evidence that intra-specific phenotypic variation can exceed species-level means, but theoretical models of multi-trophic species coexistence typically neglect individual-level trait variability. What is needed are multispecies datasets that are resolved at the individual level that can be used to discriminate among alternative models of resource selection and species coexistence in food webs. Here, using one the largest individual-based datasets of a food web compiled to date, along with an individual trait-based stochastic model that incorporates Approximate Bayesian computation methods, we document intra-population variation in the strength of prey selection by different classes or predator phenotypes which could potentially alter the diversity and coexistence patterns of food webs. In particular, we found that strongly connected individual predators preferentially consumed common prey, whereas weakly connected predators preferentially selected rare prey. Such patterns suggest that food web diversity may be governed by the distribution of predator connectivity and individual trait variation in prey selection. We discuss the consequences of intra-specific variation in prey selection to assess fitness differences among predator classes (or phenotypes) and track longer term food web patterns of coexistence accounting for several phenotypes within each prey and predator species. {\textcopyright} 2014 Elsevier Ltd.}, annote = {-variation in predator behavior in finding prey -not much focus on evolutionary dynamics -found evidence for lots of variation between and within speies for the strength of prey selection -examinie speed of learning and the strength of prey selection -argue that individual variability needs to be taken into account to develop food web and ecological network theory predator fish and prey inverts Predators that were better connected (those with more prey items) eat common food more often Less connected prey consume rare prey (perhaps prey quality is important) Tom: "there's that kinky line"}, author = {Meli{\'{a}}n, Carlos J. and Bald{\'{o}}, Francisco and Matthews, Blake and Vilas, C{\'{e}}sar and Gonz{\'{a}}lez-Orteg{\'{o}}n, Enrique and Drake, Pilar and Williams, Richard J.}, booktitle = {Advances in Ecological Research}, doi = {10.1016/B978-0-12-801374-8.00006-2}, edition = {1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Meli{\'{a}}n et al. - 2014 - Individual trait variation and diversity in food webs.pdf:pdf}, isbn = {0065-2504}, issn = {00652504}, keywords = {Approximate Bayesian computation,Biodiversity theory,Fast and slow prey finders,Food webs,Individual connectivity,Individual trait-based approach,Learning behaviour,Resource abundance,Stochastic modelling,Strength of prey selection}, pages = {207--241}, publisher = {Elsevier Ltd.}, title = {{Individual trait variation and diversity in food webs}}, url = {http://dx.doi.org/10.1016/B978-0-12-801374-8.00006-2}, volume = {50}, year = {2014} } @article{Holling1959, author = {Holling, C.S.}, journal = {The Canadian Entomologist}, number = {5}, pages = {234--261}, title = {{The Components of Predation as Revealed by a Study of Small-Mammal Predation of the European Pine Sawfly1}}, volume = {XCI}, year = {1959} } @article{Polis1997a, abstract = {The tremendous increase in precipitation associated with the 1992-1993 El Nino profoundly affected terrestrial communities on and islands in the Midriff region of the Gulf of California. In 1992, winter precipitation was 5.4 times the historical mean, and winter precipitation over the entire El Nino was the highest two-year amount ever recorded. Increased precipitation led to an explosion of annual plant growth on the previously barren (0-4{\%} cover) islands: plant cover increased 10-160 times over what it had been. With the resumption of arid conditions in 1994, live plant cover returned to the low levels seen before the onset of El Nino. Insect abundance tracked this pulse in plant productivity and approximately doubled in 1992 and 1993 compared to 1991 levels. In 1994, the crash of annual plants caused insect densities to drop to the lowest levels recorded during the 5-yr study. El Nino also affected the composition of the insect assemblage. In the dry years 1990-1991, the assemblage was dominated by insects feeding on products originating in the ocean: detritivores/scavengers on shore drift of marine algae and carcasses, avian parasites, and detritivores of bird products. Herbivores were extremely rare. The heavy plant growth in 1992 stimulated large (40-190 times pre-El Nino levels) increases in herbivores. The great increases in land plant biomass and insect abundance are indicative of an important change in the dynamics of this system. Previously, most material flowing through the food webs of these islands originated directly or indirectly in the ocean. In contrast, during this El Nino, most material originated via productivity by terrestrial plants. Thus, wet El Ninos represent an agent that switches the system from one dependent primarily on allochthonous input to a system driven to a greater extent by in situ productivity. The influence of this pulse of terrestrial productivity extends beyond the El Nino years: the persistence and slow release of plant and detrital biomass reserves may also greatly affect dynamics for years after the El Nino event has passed. We suggest that large-scale climatic events such as El Nino may be long-lasting determinants of community dynamics rather than occasional disturbance events.}, author = {Polis, Gary A. and Hurd, Stephen D. and Jackson, C. Todd and Pin{\~{n}}ero, Francisco Sanchez}, doi = {10.2307/2266109}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Polis et al. - 1997 - El Ni{\~{n}}o effects on the dynamics and control of an island ecosystem in the Gulf of California.pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {arid ecosystems,climatic disturbance,community dynamics,desert arthropods}, number = {6}, pages = {1884--1897}, title = {{El Ni{\~{n}}o effects on the dynamics and control of an island ecosystem in the Gulf of California}}, url = {http://www.jstor.org/stable/2266109?origin=crossref}, volume = {78}, year = {1997} } @article{Bascompte2010, abstract = {Ecologists have a long tradition of studying how species interact. Almost all of this work, however, has focused on networks involved in a single type of interaction. For instance, ecologists have studied either "antagonistic" interactions, such as those in who-eats-who food webs, or, more recently, mutually beneficial interactions, such as those between flowering plants and their insect pollinators. Very few studies have embraced both (13), leaving a key question: To what degree do different kinds of interactions lead to ecological networks with different structures? The answer is crucial to understanding the suite of ecological, evolutionary, and coevolutionary processes that shape these networks and how they may respond to future changes. On page 853 of this issue, Th bault and Fontaine (4) take an important step forward by comparing the structure and dynamics of antagonistic and mutualistic networks.}, annote = {May: the more complex a randomly build food web, the less stable it is -{\textgreater} means complex networks need to have some nonrandom elements (e.g. compartmentalization) in order to be stable}, author = {Bascompte, Jordi}, doi = {10.1126/science.1194255}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bascompte - 2010 - Structure and dynamics of ecological networks.pdf:pdf}, isbn = {0036-8075}, issn = {1095-9203}, journal = {Science}, number = {5993}, pages = {765--766}, pmid = {20705836}, title = {{Structure and dynamics of ecological networks}}, url = {http://www.sciencemag.org/cgi/content/summary/sci;329/5993/765{\%}5Cnhttp://www.ncbi.nlm.nih.gov/pubmed/20705836}, volume = {329}, year = {2010} } @article{Kot1996, abstract = {Models that describe the spread of invading organisms often assume that the dispersal distances of propagules are normally distributed. In contrast, measured dispersal curves are typically leptokurtic, not normal. In this paper, we consider a class of models, integrodifference equations, that directly incorporate detailed dispersal data as well as population growth dynamics. We provide explicit formulas for the speed of invasion for compensatory growth and for different choices of the propagule redistribution kernel and apply these formulas to the spread of D. pseudoobscura. We observe that: (1) the speed of invasion of a spreading population is extremely sensitive to the precise shape of the redistribution kernel and, in particular, to the tail of the distribution; (2) fat-tailed kernels can generate accelerating invasions rather than constant-speed travelling waves; (3) normal redistribution kernels (and by inference, many reaction-diffusion models) may grossly underestimate rates of spread of invading populations in comparison with models that incorporate more realistic leptokurtic distributions; and (4) the relative superiority of different redistribution kernels depends, in general, on the precise magnitude of the net reproductive rate. The addition of an Allee effect to an integrodifference equation may decrease the overall rate of spread. An Allee effect may also introduce a critical range; the population must surpass this spatial threshold in order to invade successfully. Fat-tailed kernels and Allee effects provide alternative explanations for the accelerating rates of spread observed for many invasions}, annote = {-most dispersal data is leptokurtic (most propagules near center and in tails) -one solution is integro-diff equations -apply model to Dobzhansky and Wright (1943) movement data on dropsophila -also looked at models with allee effects Results: -find that speed of invasion is very sensitive to dispersal kernel -danger in extrapolating dispersal data - dispersal curves should have upper bounds art some point}, author = {Kot, Mark and Lewis, Mark A. and {Van Den Driessche}, P.}, doi = {10.2307/2265698}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kot, Lewis, Van Den Driessche - 1996 - Dispersal data and the spread of invading organisms.pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {Allee effect,Biological invasions,Dispersal; integrodifference equations,Seed shadows,Spatial models}, number = {7}, pages = {2027--2042}, pmid = {21574416}, title = {{Dispersal data and the spread of invading organisms}}, volume = {77}, year = {1996} } @article{McDonald-Madden2016, author = {McDonald-Madden, E. and Sabbadin, R. and Game, E. T. and Baxter, P. W. J. and Chad{\`{e}}s, I. and Possingham, H. P.}, doi = {10.1038/ncomms10245}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McDonald-Madden et al. - 2016 - Using food-web theory to conserve ecosystems.pdf:pdf}, issn = {2041-1723}, journal = {Nature Communications}, number = {May 2015}, pages = {10245}, title = {{Using food-web theory to conserve ecosystems}}, url = {http://www.nature.com/doifinder/10.1038/ncomms10245}, volume = {7}, year = {2016} } @article{Scheffer2001, abstract = {All ecosystems are exposed to gradual changes in climate, nutrient loading, habitat fragmentation or biotic exploitation. Nature is usually assumed to respond to gradual change in a smooth way. However, studies on lakes, coral reefs, oceans, forests and arid lands have shown that smooth change can be interrupted by sudden drastic switches to a contrasting state. Although diverse events can trigger such shifts, recent studies show that a loss of resilience usually paves the way for a switch to an alternative state. This suggests that strategies for sustainable management of such ecosystems should focus on maintaining resilience.}, annote = {-begin with introduction to fold bifurcations and alternative stable states -Resilience - basin of attraction or size of valley around each state Examples: lake eutrophication, coral reefs, woodlands and grassy landscapes, vegetation vs deserts, oceans -{\textgreater} all have stabalizing mechanims once system goes to a given state Three results -alternative states are often categorized by loss of some important organism -stochastic events are move system from one state to another -feedbacks stablize different states Small changes in a system may actually reduce size of basin of attraction, reducing resiliance -{\textgreater} want to work on reslience, not stop perturbations from occuring}, author = {Scheffer, M and Carpenter, S and Foley, J a and Folke, C and Walker, B}, doi = {10.1038/35098000}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Scheffer et al. - 2001 - Catastrophic shifts in ecosystems.pdf:pdf}, isbn = {0028-0836}, issn = {0028-0836}, journal = {Nature}, keywords = {Animals,Cnidaria,Conservation of Natural Resources,Desert Climate,Ecosystem,Fresh Water,Models, Biological,Oceans and Seas,Stochastic Processes,Trees}, number = {6856}, pages = {591--6}, pmid = {11595939}, title = {{Catastrophic shifts in ecosystems.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/15448261}, volume = {413}, year = {2001} } @article{Ellner1998, abstract = {We present and evaluate an approach to analyzing population dynamics data using semimechanistic models. These models incorporate reliable information on population structure and underlying dynamic mechanisms but use nonparametric surface-fitting methods to avoid unsupported assumptions about the precise form of rate equations. Using historical data on measles epidemics as a case study, we show how this approach can lead to better forecasts, better characterizations of the dynamics, and a better understanding of the factors causing complex population dynamics relative to either mechanistic models or purely descriptive statistical time-series models. The semimechanistic models are found to have better forecasting accuracy than either of the model types used in previous analyses when tested on data not used to fit the models. The dynamics are characterized as being both nonlinear and noisy, and the global dynamics are clustered very tightly near the border of stability (dominant Lyapunov exponent lambda approximately 0). However, locally in state space the dynamics oscillate between strong short-term stability and strong short-term chaos (i.e., between negative and positive local Lyapunov exponents). There is statistically significant evidence for short-term chaos in all data sets examined. Thus the nonlinearity in these systems is characterized by the variance over state space in local measures of chaos versus stability rather than a single summary measure of the overall dynamics as either chaotic or nonchaotic.}, annote = {-useualy people use simple mechanistic (or phenological models) or descriptive statistical models -try to use semimechanistic models for time series data- believe this is more realistic given what we know about most ecological systems -the model includes structure (SEIR) model of measles but not not specify form of contact rate function, this is instead estimated with data -look at Lyapnov exponents to evaluate the role of chaos in the system}, author = {Ellner, S P and Bailey, B a and Bobashev, G V and Gallant, a R and Grenfell, B T and Nychka, D W}, doi = {10.1086/286130}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ellner et al. - 1998 - Noise and nonlinearity in measles epidemics combining mechanistic and statistical approaches to population modeli.pdf:pdf}, isbn = {0003-0147 (Print)$\backslash$r0003-0147 (Linking)}, issn = {0003-0147}, journal = {The American naturalist}, keywords = {analysis,be addressed,e-mail,edu,ellner,geophysical statistics project,local lyapunov exponents,measles,modeling,national center for atmospheric,ncsu,population dynamics,present address,stat,time-series,to whom correspondence should}, number = {5}, pages = {425--440}, pmid = {18811317}, title = {{Noise and nonlinearity in measles epidemics: combining mechanistic and statistical approaches to population modeling.}}, volume = {151}, year = {1998} } @article{Stapp1999, abstract = {Stable isotope analysis is a powerful tool for unravelling the complex structure of food webs1±3. This technique is particularly well suited for studies at ecosystem boundaries, where physical processes and mobile consumers link the dynamics of seemingly disparate systems4±6. In coastal and insular environments, seabirds play a crucial role in transporting marine-based energy and nutrients to islands7±9. Here we show using stable isotopes that nutrients from the ocean drive the dynamics of terrestrial food webs on small islands. The indirect effects of seabird-derived nutrients on plant productivity are particularly prominent during wet El Nin{\"{A}}o Southern Oscillation years on our Gulf of California study sites. During dry years that characterize the region, many terrestrial consumers are subsidized by carrion and prey from the ocean. Shifts in trophic structure related to El Nin{\"{A}}o Southern Oscillation could only be elucidated because of the distinct nitrogen isotope ratios associated with seabird islands. The contributions of seabirds and other marine sources are re¯ected in the isotope signatures of terrestrial consumers in ways that challenge conventional interpretations of stable isotope results in studies of food webs.}, annote = {-smaller arthropods may be more able to track pulses b/c of fast life histories -use stable isotopes to explore cross ecosystem dynamics -Carbon: Carbon 13 values are enricked in marine phytoplanktin communities compared to plants based on C3 photosynthessis (not true compared to C4 and CAM plants) -Nitrogen: Nitrogen 15 is thought to increase 3-5{\%} with each increase in trophic level -{\textgreater} this is not always sa good rule of thumb -some islands had seabirds and some did not -looked at islands during stron 1997-1998 ENSO event -during dry years, consumers depend a lot on marine resources}, author = {Stapp, P. and Polis, G. a.}, doi = {10.1038/46769}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stapp, Polis - 1999 - Stable isotopes reveal strong marine and El Nino effects on island food webs.pdf:pdf}, isbn = {0028-0836}, issn = {0028-0836}, journal = {Nature}, number = {Table 1}, pages = {467--469}, pmid = {3540}, title = {{Stable isotopes reveal strong marine and El Nino effects on island food webs}}, volume = {401}, year = {1999} } @article{Piovia-Scott2011, abstract = {The effect of environmental change on ecosystems is mediated by species interactions. Environmental change may remove or add species and shift life-history events, altering which species interact at a given time. However, environmental change may also reconfigure multispecies interactions when both species composition and phenology remain intact. Ina Caribbeanisland system, a major manifestation of environmental change is seaweed deposition, which has been linked to eutrophication, overfishing, and hurricanes. Here, we show in a whole-island field experiment that without seaweed two predators—lizards and ants—had a substantially greater-than-additive effect on herbivory. When seaweed was added to mimic deposition by hurricanes, no interactive predator effect occurred. Thus environmental change can substantially restructurefood-web interactions, complicating efforts to predict anthropogenic changes in ecosystem processes.}, annote = {-large seawood deposition (often occuring from hurricanes) changes the effects of *mulitiple* predators on lower trophic levels -ant and lizard predators emerge at different ties of the day -on subsidized islands ants and lizards foraged more on ground to eat detritovores -with no seaweed, higher than expected interaction effects of lizards and ant on suprressing herbivores}, author = {Piovia-Scott, Jonah and Spiller, David A and Schoener, Thomas W}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Piovia-Scott, Spiller, Schoener - 2011 - Predation in an island food web.pdf:pdf}, journal = {Science}, number = {January}, pages = {461--463}, title = {{Predation in an island food web}}, volume = {331}, year = {2011} } @article{Spiller2010, abstract = {The effect of resource subsidies on recipient food webs has received much recent attention. The purpose of this study was to measure the effects of significant seasonal seaweed deposition events, caused by hurricanes and other storms, on species inhabiting subtropical islands. The seaweed represents a pulsed resource subsidy that is consumed by amphipods and flies, which are eaten by lizards and predatory arthropods, which in turn consume terrestrial herbivores. Additionally, seaweed decomposes directly into the soil under plants. We added seaweed to six shoreline plots and removed seaweed from six other plots for three months; all plots were repeatedly monitored for 12 months after the initial manipulation. Lizard density (Anolis sagrei) responded rapidly, and the overall average was 63{\%} higher in subsidized than in removal plots. Stable-isotope analysis revealed a shift in lizard diet composition toward more marine-based prey in subsidized plots. Leaf damage was 70{\%} higher in subsidized than in removal plots after eight months, but subsequent damage was about the same in the two treatments. Foliage growth rate was 70{\%} higher in subsidized plots after 12 months. Results of a complementary study on the relationship between natural variation in marine subsidies and island food web components were consistent with the experimental results. We suggest two causal pathways for the effects of marine subsidies on terrestrial plants: (1) the "fertilization effect" in which seaweed adds nutrients to plants, increasing their growth rate, and (2) the "predator diet shift effect" in which lizards shift from eating local prey (including terrestrial herbivores) to eating mostly marine detritivores.}, annote = {-added or removed seaweed from 3 different islands and monitored for 12 months apparent trohic cascades (Polis et al 1997)- predatotors switch away from herbivores which hurts plants but predators then come back to eating herbivores again later? -time scale of pulses matters -seasonal subisdary pulses (Takimoto et al 2009) Hypothesize that marine subsidies would increase herbivory short term but decrease it in the long run Major increases in subsidized plots possibly for two reasons: seaweed adds nutruets to plants or a predator diet shift -{\textgreater} found evidence for both Also looked at naturally low and high subsizdized islands as a reference and fund similar results}, author = {Spiller, David A. and Piovia-Scott, Jonah and Wright, Amber N. and Yang, Louie H. and Takimoto, Gaku and Schoener, Thomas W. and Iwata, Tomoya}, doi = {10.1890/09-0715.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Spiller et al. - 2010 - Marine subsidies have multiple effects on coastal food webs.pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {Allochthonous inputs,Anolis sagrei,Apparent competition,Apparent mutualism,Central bahamas,Conocarpus erectus,Exumas,Food webs,Herbivory, Lizards,Marine subsidies,Resource pulse,Seaweed}, number = {5}, pages = {1424--1434}, pmid = {20503874}, title = {{Marine subsidies have multiple effects on coastal food webs}}, volume = {91}, year = {2010} } @article{Levin1974b, abstract = {The spatial component of environment, often neglected in modeling of ecological interactions, in general operates to increase species diversity. This arises due to the heterogeneity of the environment, but such heterogeneity can arise in an initially homogeneous environment due to what may be random initial events (e.g., colonization patterns), effects of which are magnified by species interactions. In this way, homogeneous environments may become heterogeneous and heterogeneous environments even more so. In patchy environments, distinct patches are likely to be colonized initially by different species, and thereby a kind of founder effect results whereby individual patches evolve along different paths simply as a consequence of initial colonization patterns. Species which would be unable to invade may nevertheless survive by establishing themselves early and will moreover be found in lower densities in other areas as overflow from their "safe" areas. Spatially continuous environments may evolve toward essentially patchy ones by this kind of process. Overall species richness is expected to be higher in patchy environments but to decrease as the ability of species to migrate becomes large. These results are due to patchiness per se and do not depend on the existence of several kinds of patches, a situation which will tend to reinforce these effects. Diversity is also increased in such environments with spatial extent due to the opportunities for fugitive-type spatio-temporal strategies. In these, local population oscillations provide the salvation for species which are for example competitively inferior or easy victims to predation but which can survive by superior migratory ability and (in patchy environments) talent for recolonization. Again, dependence is on spatial heterogeneity, in addition to temporal heterogeneity; again, this may be externally imposed or the result largely of internal processes. Some gross statistics for these processes, principally patch occupancy fractions, may prove useful for a simplified treatment of colonization-extinction equilibria, as in the approaches of Cohen (1970), Levins and Culver (1971), Horn and MacArthur (1972), and Slatkin (in preparation). For such considerations, however, one cannot assume independence of distributions; and the approach of Cohen (1970) and Slatkin (in preparation), which allows for consideration of covariance, is favored.}, annote = {-discusses lack of work on spatial dynamics and that the little work that does makes space implicit --models where you only look at presence or absecnce -coexistnece is possible in patchy environment but it depends on intitial population distributions and the founder effect -patchty environment essetially increases number of limiting resources -look at two specis, two patch scenario with disperasl b.w the patches -{\textgreater} he species can establish itself on a patch and resist invasion - in spatial landscape with heterogeneity different species will be favored in different locations}, author = {Levin, Simon A.}, doi = {10.1086/282900}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levin - 1974 - Dispersion and population interactions.pdf:pdf}, isbn = {00030147}, issn = {0003-0147}, journal = {The American Naturalist}, number = {960}, pages = {207}, pmid = {1253}, title = {{Dispersion and population interactions}}, volume = {108}, year = {1974} } @article{Rees2014, abstract = {* In order to understand how changes in individual performance (growth, survival or reproduction) influence population dynamics and evolution, ecologists are increasingly using parameterized mathematical models. * For continuously structured populations, where some continuous measure of individual state influences growth, survival or reproduction, integral projection models (IPMs) are commonly used. * We provide a detailed description of the steps involved in constructing an IPM, explaining how to: (i) translate your study system into an IPM; (ii) implement your IPM; and (iii) diagnose potential problems with your IPM. We emphasize how the study organism's life cycle, and the timing of censuses, together determine the structure of the IPM kernel and important aspects of the statistical analysis used to parameterize an IPM using data on marked individuals. * An IPM based on population studies of Soay sheep is used to illustrate the complete process of constructing, implementing and evaluating an IPM fitted to sample data. * We then look at very general approaches to parameterizing an IPM, using a wide range of statistical techniques (e.g. maximum likelihood methods, generalized additive models, nonparametric kernel density estimators). Methods for selecting models for parameterizing IPMs are briefly discussed. * We conclude with key recommendations and a brief overview of applications that extend the basic model. The online Supporting Information provides commented R code for all our analyses.}, annote = {-paper provides detailed account of how to actually implement IPMs in a given study, not just the mathemaical analyses of IPMs IPM for sharks in Bimini???}, author = {Rees, Mark and Childs, Dylan Z. and Ellner, Stephen P.}, doi = {10.1111/1365-2656.12178}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rees, Childs, Ellner - 2014 - Building integral projection models A user's guide.pdf:pdf}, isbn = {1365-2656}, issn = {13652656}, journal = {Journal of Animal Ecology}, keywords = {Integral projection model,Mathematical model,Soay Sheep,Structured population}, number = {3}, pages = {528--545}, pmid = {24219157}, title = {{Building integral projection models: A user's guide}}, volume = {83}, year = {2014} } @incollection{Smallegange2014, abstract = {Ecological and evolutionary population changes are often interlinked, complicating the understanding of how each is affected by environmental change. Using a male dimorphic mite as a model system, we studied concurrent changes in the expression of a conditional strategy and in the population in response to harvesting over 15 generations. We found evolutionary divergence in the expression of alternative male reproductive morphs-fighters and defenceless scramblers (sneakers)-caused by the selective harvesting of each male morph. Regardless of which morph was targeted, the direction of evolution of male morph expression in response to harvesting was always towards scramblers, which, in case of the harvesting of scramblers, we attributed to strong ecological feedback (reduced cannibalism opportunities for fighters) within the closed populations. Current evolutionary theory, however, predicts that the frequency of a morph always decreases when selected against: to understand phenotypic trait evolution fully, evolutionary theory would benefit from including ecological interactions, especially if traits have ecological consequences that in turn feedback to their evolutionary trajectory. {\textcopyright} 2014 Elsevier Ltd.}, annote = {-use environmental threshold model to study evolution of conditional strategies (like reproductive strategy or maybe even dispersal)- nice b.c it includes freq-depend selection and uses quan gen as basis conditional size in last instar to develop into fighter or scrambler mostly plastic, but some genetic control depending on scenario gen of mites is around 11-35 days (saw at least 9 generations in this experiment) -treatments: harvest fighters, harvest scramblers, no harvesting Both treatments decreased prob of fighters - decreased number of scramblers led to decrease number of fighters b/c of lower cannabalism}, author = {Smallegange, Isabel M. and Deere, Jacques A.}, booktitle = {Advances in Ecological Research}, doi = {10.1016/B978-0-12-801374-8.00004-9}, edition = {1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smallegange, Deere - 2014 - Eco-evolutionary interactions as a consequence of selection on a secondary sexual trait.pdf:pdf}, isbn = {9780128013748}, issn = {00652504}, keywords = {Alternative reproductive phenotypes,Alternative reproductive tactics,Environmental threshold model,Life history,Polymorphism,Rhizoglyphus robini}, pages = {145--169}, publisher = {Elsevier Ltd.}, title = {{Eco-evolutionary interactions as a consequence of selection on a secondary sexual trait}}, url = {http://dx.doi.org/10.1016/B978-0-12-801374-8.00004-9}, volume = {50}, year = {2014} } @article{Venner2011, abstract = {BACKGROUND: One major challenge in understanding how biodiversity is organized is finding out whether communities of competing species are shaped exclusively by species-level differences in ecological traits (niche theory), exclusively by random processes (neutral theory of biodiversity), or by both processes simultaneously. Communities of species competing for a pulsed resource are a suitable system for testing these theories: due to marked fluctuations in resource availability, the theories yield very different predictions about the timing of resource use and the synchronization of the population dynamics between the competing species. Accordingly, we explored mechanisms that might promote the local coexistence of phytophagous insects (four sister species of the genus Curculio) competing for oak acorns, a pulsed resource. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed the time partitioning of the exploitation of oak acorns by the four weevil species in two independent communities, and we assessed the level of synchronization in their population dynamics. In accordance with the niche theory, overall these species exhibited marked time partitioning of resource use, both within a given year and between different years owing to different dormancy strategies between species, as well as distinct demographic patterns. Two of the four weevil species, however, consistently exploited the resource during the same period of the year, exhibited a similar dormancy pattern, and did not show any significant difference in their population dynamics. CONCLUSIONS/SIGNIFICANCE: The marked time partitioning of the resource use appears as a keystone of the coexistence of these competing insect species, except for two of them which are demographically nearly equivalent. Communities of consumers of pulsed resources thus seem to offer a promising avenue for developing a unifying theory of biodiversity in fluctuating environments which might predict the co-occurrence, within the same community, of species that are ecologically either very similar, or very different.}, annote = {-believe determining notions between niche or neutral are testable in resource pulse system -{\textgreater} in fluctuating environments, each theory predicts different things niche theory- asynchronous dynaimcs for similar species neutral theory- all species equally affected by changes in resources How would rodents respond to masting event? How do they coexist? study oak masting with four sister species of weevil ***Predict that in order for species to coexist when competing for resources, they must either be very similar or very different -{\textgreater} weird result but has some theory behind it Could you do something similar with island data in the Gulf of California? Do pulses help those species coexist? Do they partition resources in any particular way}, author = {Venner, Samuel and P{\'{e}}lisson, Pierre Fran{\c{c}}ois and Bel-Venner, Marie Claude and D{\'{e}}bias, Fran{\c{c}}ois and Rajon, Etienne and Menu, Fr{\'{e}}d{\'{e}}ric}, doi = {10.1371/journal.pone.0018039}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Venner et al. - 2011 - Coexistence of insect species competing for a pulsed resource Toward a unified theory of biodiversity in fluctuat.pdf:pdf}, isbn = {1932-6203 (Electronic)$\backslash$r1932-6203 (Linking)}, issn = {19326203}, journal = {PLoS ONE}, number = {3}, pmid = {21445318}, title = {{Coexistence of insect species competing for a pulsed resource: Toward a unified theory of biodiversity in fluctuating environments}}, volume = {6}, year = {2011} } @article{Levi2015, abstract = {Many ecological systems are characterized by brief periods of increased resource availability called resource pulses. Empirical studies suggest that some populations of primary consumers grow rapidly in response to resource pulses, but others instead remain at low abundance despite increases in resource availability. Previous theory suggests that the lack of increase in primary consumers might be due to predators, which can respond to increased prey density both numerically, by increasing their own population, and functionally, by killing prey at a faster rate. The complexity of potential population responses to resource pulses can be assessed with simulations, but analytical conditions determining when one observes qualitatively distinct dynamics have yet to be identified. Here we use a graphical method based on a bifurcation diagram to derive the conditions leading to qualitatively distinct steady state and transient prey population dynamics as levels of predation (abundance and diversity) vary. When predation thresholds are crossed, consumer populations respond numerically to increases in their resources and provide a secondary resource pulse to their predators and parasites. These community dynamics have broad implications for the impact of changing predator communities on insect and rodent population outbreaks, which are economically and epidemiologically important.}, annote = {-use model from Ludwig et al (1978) that found alternative stable states in spruce budworm dynamics -not all consumers respond dramatically to a resource pulse. -small mammals only respond to food increase if predators are excluded (interaction effect)}, author = {Levi, Taal and Kilpatrick, A. Marm and Barfield, Michael and Holt, Robert D. and Mangel, Marc and Wilmers, Christopher C.}, doi = {10.1111/oik.01487}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levi et al. - 2015 - Threshold levels of generalist predation determine consumer response to resource pulses.pdf:pdf}, issn = {16000706}, journal = {Oikos}, number = {11}, pages = {1436--1443}, title = {{Threshold levels of generalist predation determine consumer response to resource pulses}}, volume = {124}, year = {2015} } @article{Gurney1980, abstract = {Predicting the binding mode of flexible polypeptides to proteins is an important task that falls outside the domain of applicability of most small molecule and protein−protein docking tools. Here, we test the small molecule flexible ligand docking program Glide on a set of 19 non-$\alpha$-helical peptides and systematically improve pose prediction accuracy by enhancing Glide sampling for flexible polypeptides. In addition, scoring of the poses was improved by post-processing with physics-based implicit solvent MM- GBSA calculations. Using the best RMSD among the top 10 scoring poses as a metric, the success rate (RMSD ≤ 2.0 {\AA} for the interface backbone atoms) increased from 21{\%} with default Glide SP settings to 58{\%} with the enhanced peptide sampling and scoring protocol in the case of redocking to the native protein structure. This approaches the accuracy of the recently developed Rosetta FlexPepDock method (63{\%} success for these 19 peptides) while being over 100 times faster. Cross-docking was performed for a subset of cases where an unbound receptor structure was available, and in that case, 40{\%} of peptides were docked successfully. We analyze the results and find that the optimized polypeptide protocol is most accurate for extended peptides of limited size and number of formal charges, defining a domain of applicability for this approach.}, archivePrefix = {arXiv}, arxivId = {arXiv:1011.1669v3}, author = {Gurney, W.S.C. and Blythe, S.P. and Nisbet, R.M.}, doi = {10.1017/CBO9781107415324.004}, eprint = {arXiv:1011.1669v3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gurney, Blythe, Nisbet - 1980 - Nicholson's blowflies revisted.pdf:pdf}, isbn = {9788578110796}, issn = {1098-6596}, journal = {Nature}, keywords = {icle}, pages = {17--21}, pmid = {25246403}, title = {{Nicholson's blowflies revisted}}, volume = {287}, year = {1980} } @article{Lubchenco1995, annote = {Eight things that need to be conveyed to public and policy-makers on a topic: 1) what is known 2) the certainty with which it is known 3) What is not known 4) What is suspected 5) The limits of science 6) Probable outcomes of diffrent policy options 7) key areas where new information is needed 8) Recommended mechanims for obtainint highh-priority information, for example, via reseach or aaptive management}, author = {Lubchenco, Jane}, journal = {BioScience}, keywords = {policy,science communication}, pages = {S7--S9}, title = {{The role of science in formulating a biodiversity strategy}}, volume = {45}, year = {1995} } @article{Hendry2016, annote = {Chapter 11: Plasticity (related to IIASA thoughts) -using behavior responses of Daphnia to predators to illustrate key ideas of plasticity -either expose genetic clones to different environments to observe plasticity or compare individuals from differ pops (that likely have small variation in genotype within the pop) -fig. 11.2 for different ways plasticity can act -discussions limitations of simply obseving phenotypic changes over time -addresses 7 questions in turn about plasticity -question 4 deals with environmental change and platicty -question 5 explicently asks if plasticity will promote or constrain genetic evolution Chapter 8: Community Structure -lots of ways to study this: pairs of species, see how a focal species affects some community proerty (e.g richness), -evolution can affect pop dyn by changing abundances of organisms, coiuld influence per-capita effects -he then presents a number of models -direct and indirect effects make issues confusing -evolution should affect communities when phenotypic change is greatest, phenotypic trait variation has strong effects on community, focal species is abundant, evolution affects pop dyn, feedbacks present, external drivers predator-prey systems -in two species systems, evo can be stabalizing -in three species (two prey and one predator) evolution can be destabliizng when one prey is allowed to evolve}, author = {Hendry, Andrew P.}, doi = {10.1016/B978-0-12-801374-8.00001-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hendry - 2016 - Eco-Evolutionary Dynamics.pdf:pdf}, isbn = {9780128013748}, issn = {00652504}, journal = {Eco Evolutionary Dynamics}, pages = {1--359}, title = {{Eco-Evolutionary Dynamics}}, year = {2016} } @incollection{Hiltunen2014, annote = {direct and indirect effects are often conflated Hendry generallly cam eto concluciontat evolution should stabalize pred-prey effects Background -have well known antiphase (half cycle) pred-prey cycles b/c of evolution --sibmple predator prey cycles with no evolution produce quarter-period lag -without evo in preu, pop cycles exhibit short period osciallstions -with evolution theory predicts a wide range of possibilities -With two predators, dynamics dpend on if prey can evolve against both predators or only one at a time, predator highest in abundance should be the most selective -there has been past work with the three species system but without evolution- get out of phase pred-prey cycles -cycles should get longer when evolution is allowed On this paper they find that cycle period get longer with evolution, the observed patterns are consistent with prey only being able to evolve defenses to one predator at a time, predator pop rowth rates are more predictable when non evolution occured, and the observed eco-evolutionary dynamics may be a "canard" -marine alga, flagellate, and rotifer -produced three source populations of alga that were exposed to different predators over 6 months -two defenses- clumping against flagellates or passing through rotifer gut unharmed -have a simple model as well, look at a 3d model as a simpler aproximation -have slow evolution periods in full system Canard may explain two results: -you stay near unstable equilbrium for a long time}, author = {Hiltunen, Teppo and Ellner, Stephen P. and Hooker, Giles and Jones, Laura E. and Hairston, Nelson G.}, doi = {10.1016/B978-0-12-801374-8.00002-5}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hiltunen et al. - 2014 - Eco-Evolutionary Dynamics in a Three-Species Food Web with Intraguild Predation.pdf:pdf}, isbn = {9780128013748}, pages = {41--73}, title = {{Eco-Evolutionary Dynamics in a Three-Species Food Web with Intraguild Predation}}, url = {http://linkinghub.elsevier.com/retrieve/pii/B9780128013748000025}, volume = {50}, year = {2014} } @incollection{Lewontin1969a, annote = {neighborhood stability, or Lyapunov stability, is usually most tractable bc we examine nonlinear system as linear system near equilibrium point In physics systems move to minimize energy. Is there an equivalent law in ecology? What do ecological systems try to minimize -explains importance of zero abundance equiblrium can also look at relative stability of different equilbrium poiunts -historical information is destroyed at an equilbrium- can't figure out how system got there}, author = {Lewontin, R. C.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lewontin - 1969 - The meaning of stability.pdf:pdf}, title = {{The meaning of stability}}, year = {1969} } @incollection{Kareiva1989, annote = {-most early work focused on abiotic factors controlling populations -models helped explain importance of biotic factors (explanations for cycles) -most early empirical evidence of models were lab experiments (1930-1960s) -when experiments disagreed with theory, models were changed -with the MacArthur area there seemed to be less discussion between modeling and empirical camps for some time -most focus now on more specific, tactical models More "recent" developments: simple difference equations yield complicated dynamics, spatial dimension can allow coexistence. stochastic environments can allow coexistence, disease is important in pop dyn, age structure can be stabilizing and destabalizing More empirical work needs to be done: -need more microcosm experiments to study chaos -manipulate dispersal -experiments of spatial heterogeneity -test effect of environment variablity on competing species -change landscape geometries -population level consequences of individual variability Empiricists need theorists How do small local experiments scale up over larger spatial structures or time Ecology has little standardization of data collection - Need mechanistic models, and guides to the diversity of models "There is no escaping the fact that ecology is largely a science of births, deaths, numbers, derivatives, and fluxes."}, author = {Kareiva, Peter}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kareiva - 1989 - Renewing the dialogue between theory and experiments in population ecology.pdf:pdf}, pages = {68--88}, title = {{Renewing the dialogue between theory and experiments in population ecology}}, year = {1989} } @article{Ellison2010, author = {Ellison, Aaron M and Dennis, Brian}, doi = {10.1890/080209}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ellison, Dennis - 2010 - Paths to statistical fluency for ecologists.pdf:pdf}, journal = {Front Ecol Environ}, number = {7}, pages = {362--370}, title = {{Paths to statistical fluency for ecologists}}, volume = {8}, year = {2010} } @article{Rose2015, author = {Rose, Naomi A and Parsons, E C M}, doi = {10.1016/j.ocecoaman.2015.04.016}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rose, Parsons - 2015 - Ocean {\&} Coastal Management “Back off, man, I'm a scientist!” When marine conservation science meets policy.pdf:pdf}, issn = {0964-5691}, journal = {Ocean and Coastal Management}, pages = {71--76}, publisher = {Elsevier Ltd}, title = {{Ocean {\&} Coastal Management “Back off, man, I'm a scientist!” When marine conservation science meets policy}}, url = {http://dx.doi.org/10.1016/j.ocecoaman.2015.04.016}, volume = {115}, year = {2015} } @article{Parvinen2013, abstract = {In this article we further develop the theory of adaptive dynamics of function-valued traits. Previous work has concentrated on models for which invasion fitness can be written as an integral in which the integrand for each argument value is a function of the strategy value at that argument value only. For this type of models of direct effect, singular strategies can be found using the calculus of variations, with singular strategies needing to satisfy Euler's equation with environmental feedback. In a broader, more mechanistically oriented class of models, the function-valued strategy affects a process described by differential equations, and fitness can be expressed as an integral in which the integrand for each argument value depends both on the strategy and on process variables at that argument value. In general, the calculus of variations cannot help analyzing this much broader class of models. Here we explain how to find singular strategies in this class of process-mediated models using optimal control theory. In particular, we show that singular strategies need to satisfy Pontryagin's maximum principle with environmental feedback. We demonstrate the utility of this approach by studying the evolution of strategies determining seasonal flowering schedules.}, annote = {Cannot use calculus of variations to find singular strategies in more mechanistic models they call process-mediated models -{\textgreater} need to use optimal control theory then Process-mediated models- function-valued strategy affects a process of ODEs Pontryagin's maximum principle -hvae function s(a) that maximizes equation with integral then.. Two examples: 1) seasonal flowering where plants are limited by where they can allowcate flower production - a cost of plasticity 2) 3) split allocation betweeen leaves and flowers- resource allocation, not flowering intensity, is the trait under natural selection Summary: This paper extends the theory of function-valued AD of Dieckmann et al 2006 and Pavinen et al 2006 by using optimal control theory to find singular strategies. Optimal control theory is needed, instead of calculus of variations, when the function-valued strategy affects a system of ODEs that then feedbacks to the invasion fitness of the mutant. They term these models as process-mediated models, as they are more mechanistic. We now look at equation 10. Singular strategies in these process-mediated models must satisfy Pontryagin's maximum principle. The principle essentially says that if {\$}s(a){\$} is a optimal control funciton that maximizes that invader fitness in eq. 10, then there exists a nonzero vector {\$}\backslashlambda(a){\$} such that {\$}\backslashfrac{\{}d{\}}{\{}da{\}} \backslashlambda{\_}i(a){\$} is equal to a Hamiltonian function. ... Application This paper extends the seasonal flowering models of Diekman et al 2006. There first extension includes a cost of plasticty, in the form of including both {\$}s(a){\$} and {\$}s'(a){\$} in the calculation of invader fitness. This allows for a realistic cost to changing strategy too rapidly. As the cost of plasticity increases, the singular strategy of flowering schedule peaks at the same time as the no cost scenarion, but with a lower and more broad peak. In the next two extensions, they examine a tradeoff between flowering and resource use. In these scenarios optimal control theory is needed to find singular strategies. They specifically examine the evolution of resource allocation which is a function of the flowering schedule. Here an increase in {\$}gamma{\$}, which decreases flower production, tends to evolve a resource-allocation strategy that is more evenly dispersed throughout the season. When flower production is high (low {\$}\backslashgamma{\$}), plants allocate more resources to flowering earlier. Similar to Dieckmann et al 2006, evolutionary branching can occur here as well In the last extension, they look at an explicit tradeoff between leaf growth and flower production. The singular strategies obtained given the particular model setup has plants that prefer to flower later in the season.}, author = {Parvinen, Kalle and Heino, Mikko and Dieckmann, Ulf}, doi = {10.1007/s00285-012-0549-2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Parvinen, Heino, Dieckmann - 2013 - Function-valued adaptive dynamics and optimal control theory.pdf:pdf}, issn = {1432-1416}, journal = {Journal of mathematical biology}, keywords = {Biological Evolution,Ecosystem,Flowers,Flowers: genetics,Flowers: growth {\&} development,Genetic,Models, Genetic,Plants,Plants: genetics,Seasons}, number = {3}, pages = {509--33}, pmid = {22763388}, title = {{Function-valued adaptive dynamics and optimal control theory}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22763388}, volume = {67}, year = {2013} } @article{Witman2015, annote = {quantile regression models look at extremes of things I guess? e.g. upper bounds of spatial extent (not simply spatial extent) have been increasign over time Important paper by Hurlbert 1984 on experimental design}, author = {Witman, Jon D. and Lamb, Robert W. and Byrnes, Jarrett E.K.}, doi = {10.1890/14-2265.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Witman, Lamb, Byrnes - 2015 - Towards an integration of scale and complexity in marine ecology.pdf:pdf}, issn = {0012-9615}, journal = {Ecological Monographs}, keywords = {complexity,coral reef,experimental design,field experiments,human impacts,long-term,mangroves,marine community ecology,monitoring,rocky intertidal,rocky subtidal,scale}, number = {4}, pages = {475--504}, title = {{Towards an integration of scale and complexity in marine ecology}}, volume = {85}, year = {2015} } @article{Smith1983, abstract = {Reproduction in a population of marked pikas (Ochotonaprinceps) was observed over a 3-year period in the Rocky Mountains of Colorado. Pikas were seasonally polyestrous; all adult females initiated two litters each summer. However, most females (24 of 25) weaned only a single litter. The number of successfully weaned litters and offspring was divided evenly between first and second breeding attempts. Previous studies had noted that less than 10{\%} of juveniles emerged from second litters. Apparently females are capable of weaning second litters, but only if first litters are lost. Loss of first litters may result from nest predation or poor maternal condition caused by extreme winters. Reproductive constraints acting on pikas and their evolved reproductive tactics are compared with those of other alpine or boreal long-lived herbivorous small mammals.}, annote = {-latitudal gradient and variability affecting timing of reproduction in various small mammals -could redo the review find here and in Smith 1978}, author = {Smith, Andrew T. and Ivins, Barbara L.}, doi = {10.1139/z83-209}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Ivins - 1983 - Reproductive tactics of pikas why have two litters.pdf:pdf}, issn = {0008-4301}, journal = {Canadian Journal of Zoology}, number = {Severaid 1950}, pages = {1551--1559}, title = {{Reproductive tactics of pikas: why have two litters?}}, volume = {61}, year = {1983} } @article{Gallagher2015, annote = {Article reviews a number of different aspects of shark tourism operations including: behavior and learning by sharks, ecological changes, animal welfare, and human dimensions. At the end of their article they discuss possibility for scientist-operator collaborations and for data to be collected by dive operations. They point to a few examples from the literature. They also briefly provide some suggestions for successful dat acollection (e.g. training of divers). A few key takeaways related to census paper: -tourism operations can create defacto MPAs with people to monitor and protect area -ecotourism is not a good word as practices may not be ecologically sustainable -vailidity of shark tourism programs relies on skills of participants in program Relevent papers: Meyer et al 2009, Torner et al 2013; Fallows et al 2013 O connor et al 2009 on whale watching industry}, author = {Gallagher, Austin J. and Vianna, Gabriel M.S. and Papastamatiou, Yannis P. and Macdonald, Catherine and Guttridge, Tristan L. and Hammerschlag, Neil}, doi = {10.1016/j.biocon.2015.02.007}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gallagher et al. - 2015 - Biological effects, conservation potential, and research priorities of shark diving tourism.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, pages = {365--379}, publisher = {Elsevier Ltd}, title = {{Biological effects, conservation potential, and research priorities of shark diving tourism}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006320715000622}, volume = {184}, year = {2015} } @article{Krebs1972, abstract = {CHAPTER 24 Organization III: Disturbance and Nonequilibrium Communities 485 CHAPTER 25 Ecosystem Metabolism I: Primary 513 CHAPTER 26 Ecosystem Metabolism II: 537 }, annote = {Preface: "Students will find that they can understand ecology without knowing any mathematics, byt that mathematics is neccessary for those who wish to proceed beyond the simplest level of analysis"}, author = {Krebs, C}, isbn = {0321604687, 9780321604682}, journal = {Ecology. New York: Harper and Row}, pages = {1--14}, title = {{The Experimental Analysis of Distribution and Abundance}}, url = {papers2://publication/uuid/6CF270B4-8486-417B-AC07-3E4BB56E8FDF{\%}5Cnhttp://www.ulb.tu-darmstadt.de/tocs/94263906.pdf{\%}5Cnpapers2://publication/uuid/6DD173AA-FBDA-47BB-B9D6-AE476B4CF94A}, year = {1972} } @article{Ernakovich2014, annote = {-temporal variability is expected to increase with climate change -how you define variability does matter (sd, shape of distribution, kurtosis) -for a mechanistic understanding of how these changes might be important you need physiology, ecology, and evolition -past work has shown hown thermal variation can affect population growath rates -discuss jensens inequality -organims can adap to changing environments (like climate change) by genetic differentiaion or phenotypic plasticity e.g. study on red squirrel where they could attribute most of their response to climate change as phenotypic plasticity -variation in vital rates can of course change over time. Hard to predict population repsonse to changing climate}, author = {Ernakovich, Jessica G and Hopping, Kelly A. and Berdanier, Aaron B. and Simpson, Rodney T. and Kachergis, Emily J. and Steltzer, Heidi and Wallenstein, Matthew D.}, doi = {10.1111/gcb.12568}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ernakovich et al. - 2014 - Predicted responses of arctic and alpine ecosystems to altered seasonality under climate change.pdf:pdf}, issn = {13541013}, journal = {Global Change Biology}, keywords = {2014,and accepted 28 january,c cycle,microbial activity,n mineralization,ndvi,phenology,received 17 september 2013,snowpack,trophic interactions,tundra}, number = {10}, pages = {3256--3269}, title = {{Predicted responses of arctic and alpine ecosystems to altered seasonality under climate change}}, url = {http://doi.wiley.com/10.1111/gcb.12568}, volume = {20}, year = {2014} } @article{Anderson2008a, abstract = {It is now clear that fished populations can fluctuate more than unharvested stocks. However, it is not clear why. Here we distinguish among three major competing mechanisms for this phenomenon, by using the 50-year California Cooperative Oceanic Fisheries Investigations (CalCOFI) larval fish record. First, variable fishing pressure directly increases variability in exploited populations. Second, commercial fishing can decrease the average body size and age of a stock, causing the truncated population to track environmental fluctuations directly. Third, age-truncated or juvenescent populations have increasingly unstable population dynamics because of changing demographic parameters such as intrinsic growth rates. We find no evidence for the first hypothesis, limited evidence for the second and strong evidence for the third. Therefore, in California Current fisheries, increased temporal variability in the population does not arise from variable exploitation, nor does it reflect direct environmental tracking. More fundamentally, it arises from increased instability in dynamics. This finding has implications for resource management as an empirical example of how selective harvesting can alter the basic dynamics of exploited populations, and lead to unstable booms and busts that can precede systematic declines in stock levels.}, author = {Anderson, Christian N K and Hsieh, Chih-hao and Sandin, Stuart a and Hewitt, Roger and Hollowed, Anne and Beddington, John and May, Robert M and Sugihara, George}, doi = {10.1038/nature06851}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Anderson et al. - 2008 - Why fishing magnifies fluctuations in fish abundance.pdf:pdf}, isbn = {0028-0836}, issn = {1476-4687}, journal = {Nature}, keywords = {Age Distribution,Age Factors,Animals,Biomass,Body Size,California,Ecosystem,Fisheries,Fishes,Fishes: anatomy {\&} histology,Fishes: growth {\&} development,Fishes: physiology,Larva,Larva: growth {\&} development,Larva: physiology,Models, Biological,Population Dynamics,Survival Analysis}, number = {7189}, pages = {835--9}, pmid = {18421346}, title = {{Why fishing magnifies fluctuations in fish abundance.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18421346}, volume = {452}, year = {2008} } @article{Vazquez2015, annote = {-temporal variability is expected to increase with climate change -how you define variability does matter (sd, shape of distribution, kurtosis) -for a mechanistic understanding of how these changes might be important you need physiology, ecology, and evolition -past work has shown hown thermal variation can affect population growath rates Esat et al 2011 on flutuating temperatures and trii olium -discuss jensens inequality -organims can adap to changing environments (like climate change) by genetic differentiaion or phenotypic plasticity e.g. study on red squirrel where they could attribute most of their response to climate change as phenotypic plasticity -variation in vital rates can of course change over time. Hard to predict population repsonse to changing climate}, author = {V{\'{a}}zquez, Diego P. and Gianoli, Ernesto and Morris, William F. and Bozinovic, Francisco}, doi = {10.1111/brv.12216}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/V{\'{a}}zquez et al. - 2015 - Ecological and evolutionary impacts of changing climatic variability.pdf:pdf}, issn = {14647931}, journal = {Biological Reviews}, number = {October}, pages = {n/a--n/a}, title = {{Ecological and evolutionary impacts of changing climatic variability}}, url = {http://doi.wiley.com/10.1111/brv.12216}, year = {2015} } @article{Heino2015, author = {Heino, Mikko and {D{\'{i}}az Pauli}, Beatriz and Dieckmann, Ulf}, doi = {10.1146/annurev-ecolsys-112414-054339}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Heino, D{\'{i}}az Pauli, Dieckmann - 2015 - Fisheries-Induced Evolution.pdf:pdf}, issn = {1543-592X}, journal = {Annual Review of Ecology, Evolution, and Systematics}, keywords = {applied evolution,behavior,life-history theory,phenotypic change,selection}, number = {1}, pages = {annurev--ecolsys--112414--054339}, title = {{Fisheries-Induced Evolution}}, url = {http://www.annualreviews.org/doi/10.1146/annurev-ecolsys-112414-054339}, volume = {46}, year = {2015} } @article{Keith2015, author = {Keith, David and Ak{\c{c}}akaya, H. Resit and Butchart, Stuart H.M. and Collen, Ben and Dulvy, Nicholas K. and Holmes, Elizabeth E. and Hutchings, Jeffrey A. and Keinath, Doug and Schwartz, Michael K. and Shelton, Andrew O. and Waples, Robin S.}, doi = {10.1016/j.biocon.2015.09.021}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Keith et al. - 2015 - Temporal correlations in population trends Conservation implications from time-series analysis of diverse animal t.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {Endangered species,Population growth rate,Population trend,Time series,Vertebrates,population growth rate}, pages = {247--257}, publisher = {Elsevier B.V.}, title = {{Temporal correlations in population trends: Conservation implications from time-series analysis of diverse animal taxa}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006320715301129}, volume = {192}, year = {2015} } @phdthesis{Koontz2010, author = {Koontz, Michael}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Koontz - 2010 - The eco-evolutionary consequences of multiple introductions for colonizing individuals.pdf:pdf}, title = {{The eco-evolutionary consequences of multiple introductions for colonizing individuals}}, year = {2010} } @article{Zhou2011, abstract = {Many species are responding to global climate change by shifting their ranges poleward in latitude or upward in elevation. We analyze an integrodifference equation that combines growth, dispersal, and a constant-speed, climate-induced range shift and find that a shifting population can die out, even if the width of its range remains constant. We show how to determine the critical range-shift speed (for extinction) and study the effects of the growth rate and of the shape and scale of the dispersal kernel on persistence.}, author = {Zhou, Ying and Kot, Mark}, doi = {10.1007/s12080-010-0071-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Zhou, Kot - 2011 - Discrete-time growth-dispersal models with shifting species ranges.pdf:pdf}, isbn = {1208001000}, issn = {18741738}, journal = {Theoretical Ecology}, keywords = {Climate change,Integrodifference equation,Population persistence,Range shift}, number = {1}, pages = {13--25}, title = {{Discrete-time growth-dispersal models with shifting species ranges}}, volume = {4}, year = {2011} } @book{Costantino1991, address = {New York, NY}, annote = {tunnels- Stanley}, author = {Costantino, R.F. and Desharnais, R.A.}, edition = {1}, pages = {258}, publisher = {Spring-Verlag}, title = {{Population Dynamics and the Tribolium Model: Genetics and Demography}}, year = {1991} } @article{Holt2011, author = {Holt, Robert D and Fryxell, John M}, doi = {10.1093/acprof:oso/9780199568994.003.0003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Holt, Fryxell - 2011 - Theoretical reflections on the evolution of migration.pdf:pdf}, isbn = {9780199569007}, issn = {1575-6343}, journal = {Animal Migration: A Synthesis}, pages = {17--31}, title = {{Theoretical reflections on the evolution of migration}}, year = {2011} } @article{omnicki2006, abstract = {Hypothesis: Dispersal outside a local population maintains population density below the possible maximum, but within a single local population selection acts against dispersal and consequently against such maintenance. Individuals that disperse exhibit lower fitness that is correlated with their smaller body size. Organism: Laboratory populations of Tribolilan confusum beetles. Methods: Four confined populations with no dispersal, four with the progeny of dispersing individuals removed and four with the progeny of non-dispersing individuals removed were maintained and monitored for seven generations. Results: Confined populations were larger than those from which dispersal was allowed. From generation three onwards, dispersal rates were significantly lower in the population in which progeny of dispersing beetles were removed than in the population in which progeny of non-dispersing beetles were removed. The differences in dispersal rates mentioned above affected population density in the native populations but not in the places to which beetles emigrated. The removal of the progeny of dispersing individuals does not eradicate dispersal altogether. Average body weights of dispersing beetles are not lower than of those of nondispersing beetles.}, author = {{\L}omnicki, Adam}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/{\L}omnicki - 2006 - Population regulation by dispersal under selection pressure for and against dispersal An experimental test with beetl.pdf:pdf}, isbn = {1522-0613}, issn = {15220613}, journal = {Evolutionary Ecology Research}, keywords = {Metapopulation,Migration,Population density,Tribolium laboratory populations}, number = {1}, pages = {63--73}, title = {{Population regulation by dispersal under selection pressure for and against dispersal: An experimental test with beetles, Tribolium confusum}}, volume = {8}, year = {2006} } @article{Gerber1999, annote = {-they look at growth rates, not absolute abundance -have threatened criteria used in earlier paper by Gerber -I need to have clear language for contiguious subsets of time series and such -have lambda vs number of years sampled -plot of fraction of subsamples to delist or list as threatened}, author = {Gerber, L R and DeMaster, D P and Kareiva, P M}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gerber, DeMaster, Kareiva - 1999 - Gray whales and the value of monitering data in implementing the U.S. endangered species act.pdf:pdf}, journal = {Conservation Biology}, number = {5}, pages = {1215--1219}, title = {{Gray whales and the value of monitering data in implementing the U.S. endangered species act}}, volume = {13}, year = {1999} } @article{McMeans2015, abstract = {Temporal variation characterizes many of Earth's ecosystems. Despite this, little is known about how food webs respond to regular variation in time, such as occurs broadly with season. We argue that season, and likely any periodicity, structures food webs along a temporal axis in an analogous way to that previously recognized in space; predators shift their diet as different resource compartments and trophic levels become available through time. These characteristics are likely (i) central to ecosystem function and stability based on theory, and (ii) widespread across ecosystem types based on empirical observations. The temporal food web perspective outlined here could provide new insight into the ecosystem-level consequences of altered abiotic and biotic processes that might accompany globally changing environments.}, author = {McMeans, Bailey C. and McCann, Kevin S. and Humphries, Murray and Rooney, Neil and Fisk, Aaron T.}, doi = {10.1016/j.tree.2015.09.001}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McMeans et al. - 2015 - Food web structure in temporally-forced ecosystems.pdf:pdf}, issn = {0169-5347}, journal = {Trends in Ecology {\&} Evolution}, number = {October}, pages = {662--672}, publisher = {Elsevier Ltd}, title = {{Food web structure in temporally-forced ecosystems}}, url = {http://www.cell.com/article/S0169534715002219/fulltext}, volume = {30}, year = {2015} } @article{Dieckmann2006, annote = {Differences between function-valued AD and Lande's model of quan gen: 1) AD describes the expectationof a monomorphic stochastic process and Lande's model describes the mean of a pop's dist. of quantitative traits 2) AD effects of selection when succesfful mutations are rare and small, Lande's model desrbies effect of selection when trait distribution is normal anff var-cov matrix is constant 3) Very similar models but diffeences important when scaling of evo rates with pop size is important, freq depend evo, evo branching is importat, when simplyfing assumptios of models are relaxed Therefore, quan gen models are probabluy better at desribing short-term evo-selection acts on gen var within population (the assumption of constant var-cov funcitons makes sense on short time scales)- {\textgreater} should use these models if I did beetle work on worj on fisheries induced evoulution AD models are probably better for describing long term evolution whee selection depends on rare innovations and fitness funcitons change over time because of density and freq depend. Summary: Function-valued traits arise naturally in a number of ecological scenarios.The evolution of function-valued traits was first developed in a quant gen framework. However, much of this work dealt with frequency-independent selection. An adaptive dynamics framework allows for the study of long-term evolution under more realstictic scenarios of freeqeucy-dependent selection. They point out that two important consideration in these models are evolutionary constraits and the use of infinite-dimensional traits instead of a lower dimensional approximation. They discuss a hierarchy of three models: 1) polymorphic stochastic model, which is a full, individual based model of eco-evolutionary dynamics, 2) monomorphic stochastic model assumes that ecological and evolutiontionary timescales are seperate, and lastly 3) monomorphic deterministic model, which is a deterministic version of the monomorphic stochastic model. They focus on the monomorphic stochastic model and derive a canonical equation of function-valued adaptive dynamics. They apply function valued adaptive dynamics models to two common scenarios. In the first, the examine the evolution of metabolic investment startegies. In addition to deriving the canonical equation for function-valued adaptive dynamics and providing a useful framework, the second example discribed in Dieckmann et al 2006 is of use to our work on pikas. Here they desribe a model of seasonal flowering schedules in a temporlly varying environment. Flowers have to compete for pollinators and avoid herbivores, both of which can vary over the course of the season. They numerically solve for an evolutionary singular strategy of flowering output of the course of a season given a particular set up constraits. They find that flowering schedule tends to a global evolutionary attractor set by the resource availability.}, author = {Dieckmann, Ulf and Heino, Mikko and Parvinen, Kalle}, doi = {10.1016/j.jtbi.2005.12.002}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dieckmann, Heino, Parvinen - 2006 - The adaptive dynamics of function-valued traits.pdf:pdf}, issn = {00225193}, journal = {Journal of Theoretical Biology}, keywords = {adaptive dynamics,canonical equation,evolutionary branching,evolutionary constraints,function-valued traits}, number = {2}, pages = {370--389}, title = {{The adaptive dynamics of function-valued traits}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022519305005266}, volume = {241}, year = {2006} } @article{Segel1972, abstract = {An attempt is made to clarify two frequently used applied mathematical techniques. Section 1 begins with a description of the basic simplification procedure in which a term is neglected under the assumption that it is small, and the consistency of this assumption is later checked. Successful uses of the basic simplification procedure are illustrated. Wretched consistent approximations are presented, showing that the procedure can be misused. The situation is clarified by a discussion of the relation between the size of the residual and the goodness of the approximation in three simple problem classes. Section 2 discusses scaling : how to choose dimensionless variables in such a way that the relative size of the various terms in an equation is explicitly indicated by the magnitudes of the dimensionless parameters which precede them. Scaling is illustrated on a simple physical problem and on several known functions. It is pointed out that more than one scale may be necessary, and the connection with singular perturbation theory is established. Advice is given on circumventing the dilemma of choosing scales for the unknown functions which comprise the solution of the very problem whose investigation one is trying to facilitate by appropriate scaling.}, author = {Segel, Lee a.}, doi = {10.1137/1014099}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Segel - 1972 - Simplification and Scaling.pdf:pdf}, isbn = {0036-1445}, issn = {00361445}, journal = {SIAM Review}, number = {4}, pages = {547--571}, title = {{Simplification and Scaling}}, volume = {14}, year = {1972} } @article{Katz2005, abstract = {The potential advantage of extreme value theory in modeling ecological disturbances is the central theme of this paper. The statistics of extremes have played only a very limited role in ecological modeling, despite the disproportionate influence of unusual disturbances on ecosystems. An overview of this theory is provided, with emphasis on recent developments that both make more efficient use of the available data on extremes and enable applications that are more ecologically realistic. Consistent with the emphasis on scale in ecology, scaling properties of extremes are emphasized. It is argued that the existence of distributions whose extreme upper tail is ‘‘heavy'' (i.e., decreases at a relatively slow rate) implies that ecological disturbances are sometimes regarded as more ‘‘surprising'' than they ought to be. The application focuses on modeling disturbances in paleoecology. Two examples are considered: the first, a sediment yield time series for Nicolay Lake in the high Arctic, reflects only the influence of hydrologic disturbances; the second, a sediment rate time series in the Chesapeake Bay, includes both climatic and anthropogenic influences. Strong evidence supports a heavy-tailed distribution for the Nicolay Lake sediment yield, but not necessarily for the Chesapeake Bay sediment rates. For each example, it is demonstrated how the statistics of extremes can readily incorporate information about covariates, such as large-scale atmospheric–oceanic circulation patterns or land use.}, author = {Katz, Richard W. and Brush, Grace S. and Parlange, Marc B.}, doi = {10.1890/04-0606}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Katz, Brush, Parlange - 2005 - Statistics of extremes Modeling ecological disturbances.pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {Generalized Pareto distribution,Generalized extreme value distribution,Paleoecology,Peaks over threshold,Return level,Return period,Sediment accumulation}, number = {5}, pages = {1124--1134}, pmid = {228960000006}, title = {{Statistics of extremes: Modeling ecological disturbances}}, volume = {86}, year = {2005} } @article{Kirk1997, annote = {integrodifference equations- discrete time, continuous space First meeting: Outline: -intro to scaler DEs -lots of people use Laplace kernel- allows you to itegrate by parts -general idea of space}, author = {Kirk, R.W. Van and Lewis, M.A.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kirk, Lewis - 1997 - Integrodifference models for persistence in fragmented habitats.pdf:pdf}, journal = {Bulletin of Mathematical Biology}, number = {1}, pages = {107--137}, title = {{Integrodifference models for persistence in fragmented habitats}}, volume = {59}, year = {1997} } @article{Ziegler1976, author = {Ziegler, James R.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ziegler - 1976 - Evolution of the migration response emigration by Tribolium and the influence of afe.pdf:pdf}, journal = {Evolution}, number = {3}, pages = {579--592}, title = {{Evolution of the migration response: emigration by Tribolium and the influence of afe}}, volume = {30}, year = {1976} } @article{New2013, author = {New, Emphasizing and To, Ideas and Ecology, I N}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/New, To, Ecology - 2013 - Dynamics of coastal meta-ecosystems the intermttent upwelling hypothesis and a test in rocky intertidal region.pdf:pdf}, keywords = {bottom-up,competition,downwelling regime,ecological subsidies,intermittent upwelling hypothesis,large,marine ecosystems,meta-ecosystems,predation,productivity,recruitment,rocky intertidal,top-down,upwelling}, number = {3}, pages = {283--310}, title = {{Dynamics of coastal meta-ecosystems: the intermttent upwelling hypothesis and a test in rocky intertidal regions}}, volume = {83}, year = {2013} } @article{Yokomizo2010, annote = {What happens if you include mobile predators in model?}, author = {Yokomizo, Hiroyuki and Botsford, Louis W. and Holland, Matthew D. and Lawrence, Cathryn a. and Hastings, Alan}, doi = {10.1007/s12080-009-0053-5}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yokomizo et al. - 2010 - Optimal wind patterns for biological production in shelf ecosystems driven by coastal upwelling.pdf:pdf}, issn = {1874-1738}, journal = {Theoretical Ecology}, keywords = {cross-shelf transport,mixed layer,phytoplankton,upwelling,variable winds,zooplankton}, number = {1}, pages = {53--63}, title = {{Optimal wind patterns for biological production in shelf ecosystems driven by coastal upwelling}}, url = {http://link.springer.com/10.1007/s12080-009-0053-5}, volume = {3}, year = {2010} } @article{Shaw2013, abstract = {Migration, the seasonal movement of individuals among different locations, is a behavior found throughout the animal kingdom. Although migration is widely studied at taxonomically restricted levels, cross-taxonomic syntheses of migration are less common. As a result, we lack answers to broad questions such as what ultimate factors generally drive animal migration. Here we present such a synthesis by using a spatially explicit, individual-based model in which we evolve behavior rules via simulations under a wide range of ecological conditions to answer two questions. First, under what types of ecological conditions can an individual maximize its fitness by migrating (vs. being a resident)? Second, what types of information do individuals use to guide their movement? We show that migration is selected for when resource distributions are dominated more by seasonality than by local patchiness, and residency (nonmigratory behavior) is selected for when the reverse is true. When selected for, migration evolves as both a movement behavior and an information usage strategy. We also find that different types of migration can evolve, depending on the ecological conditions and availability of information. Finally, we present empirical support for our main results, drawn from migration patterns exhibited by a variety of taxonomic groups.}, annote = {highly seasonal environments should select for migratio}, author = {Shaw, Allison K and Couzin, Iain D}, doi = {10.1086/668600}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Shaw, Couzin - 2013 - Migration or residency The evolution of movement behavior and information usage in seasonal environments.pdf:pdf}, isbn = {0003-0147}, issn = {1537-5323}, journal = {The American naturalist}, keywords = {Animal Migration,Animals,Biological Evolution,Environment,Genetic Fitness,Models, Biological,Seasons,Selection, Genetic}, number = {1}, pages = {114--24}, pmid = {23234849}, title = {{Migration or residency? The evolution of movement behavior and information usage in seasonal environments.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23234849}, volume = {181}, year = {2013} } @article{Chapman2015, annote = {compare settling behavior of insects and ocean larvae}, author = {Chapman, Jason W. and Reynolds, Don R. and Wilson, Kenneth}, doi = {10.1111/ele.12407}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chapman, Reynolds, Wilson - 2015 - Long-range seasonal migration in insects mechanisms , evolutionary drivers and ecological consequence.pdf:pdf}, journal = {Ecology Letters}, keywords = {18,2015,287,302,autographa gamma,cens,ecology letters,flight orientation,insect diseases,locusts,monarch butterfly,pantala flaves-,radar entomology,spodoptera exempta,trade-offs,vanessa cardui}, pages = {287--302}, title = {{Long-range seasonal migration in insects: mechanisms , evolutionary drivers and ecological consequences}}, volume = {18}, year = {2015} } @article{Melbourne2009, author = {Melbourne, Brett A and Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Melbourne, Hastings - 2009 - Highly variable spread rates in replicated biological invasions fundamental limits to predictability.pdf:pdf}, journal = {Science}, number = {September}, pages = {1536--1539}, title = {{Highly variable spread rates in replicated biological invasions: fundamental limits to predictability}}, volume = {325}, year = {2009} } @article{Thomas1994, author = {Thomas, Chris D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thomas - 1994 - Metapopulation dynamics and conservation a spatially explicit model applied to butterflies.pdf:pdf}, keywords = {britain,colonization,extinction,finland,metapopulation,spatially explicit model}, pages = {167--180}, title = {{Metapopulation dynamics and conservation: a spatially explicit model applied to butterflies}}, volume = {68}, year = {1994} } @article{Wilson2014a, abstract = {Over the last 15 years, Software Carpentry has evolved from a week-long training course at the US National Laboratories into a worldwide volunteer effort to raise standards in scientific computing. This article explains what we have learned along the way, the challenges we now face, and our plans for the future.}, archivePrefix = {arXiv}, arxivId = {1307.5448}, author = {Wilson, Greg}, doi = {10.12688/f1000research.3-62.v1}, eprint = {1307.5448}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wilson - 2014 - Software Carpentry lessons learned.pdf:pdf}, issn = {2046-1402}, journal = {F1000Research}, pages = {62}, pmid = {24715981}, title = {{Software Carpentry: lessons learned}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3976103{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {3}, year = {2014} } @article{Anderson2013, abstract = {We review literature concerning the impacts of climate change on the migration of marine species, with an emphasis on the adaptation of migration phenology through genetic tracking and phenotypic plasticity. We then develop an individual-based modeling framework characterizing the effects of climate change on phenology and population dynamics. In the framework, an animal's ability to match its environmental preferences, its bioclimate envelope, to the environmental conditions by adjusting its migration timing between foraging and breeding habitats determines its condition, survival, and fecundity. Climate-induced changes in the envelope produce timing mismatches that result in a population adapting its phenology through both genetic and plastic processes. Model results suggest: (1) the temporal size of the bioclimate envelope is an important determinant of a population's sensitivity to climate change and susceptibility to extinction, (2) population extinction can occur if the rate of change in the timing of the envelope exceeds the rate its phenology changes or if the variability in the envelope exceeds the population's inherent capacity for variability, (3) a population with migration timing cued by photoperiod is expected to exhibit weaker phenotypic plasticity than one cued by temperature, and (4) population extinction in response to climate change follows a threshold pattern such that population size may not be a reliable indicator of extinction threat, although variability in average individual condition across years may be an extinction threat indicator. Finally, while the model is intentionally simplistic, we discuss how it can be extended to cover more complex interactions. ?? 2013 Elsevier B.V.}, annote = {use indidivual based modeling to study climate change's effect on phenology and population dynamcis How does selection operate on an individual at each stage of its movement while it migrates Inheritence of phenology}, author = {Anderson, James J. and Gurarie, Eliezer and Bracis, Chloe and Burke, Brian J. and Laidre, Kristin L.}, doi = {10.1016/j.ecolmodel.2013.03.009}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Anderson et al. - 2013 - Modeling climate change impacts on phenology and population dynamics of migratory marine species.pdf:pdf}, isbn = {0304-3800}, issn = {03043800}, journal = {Ecological Modelling}, keywords = {Adaption,Climate change,Migratory marine species,Modeling,Phenology,Phenotypic plasticity}, pages = {83--97}, publisher = {Elsevier B.V.}, title = {{Modeling climate change impacts on phenology and population dynamics of migratory marine species}}, url = {http://dx.doi.org/10.1016/j.ecolmodel.2013.03.009}, volume = {264}, year = {2013} } @article{Gao2005, abstract = {Natural population, whose population numbers are small and generations are non-overlapping, can be modelled by difference equations that describe how the population evolve in discrete time-steps. This paper investigates a recent study on the dynamics complexities in a single-species discrete population model with stage structure and birth pulses. Using the stroboscopic map, we obtain an exact cycle of system, and obtain the threshold conditions for its stability. Above this, there is a characteristic sequence of bifurcations, leading to chaotic dynamics, which implies that this the dynamical behaviors of the single-species discrete model with birth pulses are very complex, including (a) non-unique dynamics, meaning that several attractors and chaos coexist; (b) small-amplitude annual oscillations; (c) large-amplitude multi-annual cycles; (d) chaos. Some interesting results are obtained and they showed that pulsing provides a natural period or cyclicity that allows for a period-doubling route to chaos. ?? 2004 Elsevier Ltd. All rights reserved.}, author = {Gao, Shujing and Chen, Lansun}, doi = {10.1016/j.chaos.2004.05.047}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gao, Chen - 2005 - Dynamic complexities in a single-species discrete population model with stage structure and birth pulses.pdf:pdf}, issn = {09600779}, journal = {Chaos, Solitons and Fractals}, number = {2}, pages = {519--527}, title = {{Dynamic complexities in a single-species discrete population model with stage structure and birth pulses}}, volume = {23}, year = {2005} } @article{Costa2011, abstract = {Highly pelagic large marine vertebrates have evolved the capability of moving across large expanses of the marine environment; some species routinely move across entire ocean basins. Our understanding of these movements has been enhanced by new technologies that now allow us to follow their movements over great distances and long time periods in great detail. This technology provides not only detailed information on the movements of a wide variety of marine species, but also detailed characteristics of the habitats they use and clues to their navigation abilities. Advances in electronic tracking technologies have been coupled with rapid development of statistical and analytical techniques. With these developments, conservation of highly migratory species has been aided by providing new information on where uncommon or endangered species go, what behaviors they perform and why, which habitats are critical, and where they range, as well as, in many cases, better estimates of their population size and the interconnectedness of subpopulations. Together these tools are providing critical insights into the ecology of highly pelagic marine vertebrates that are key for their conservation and management.}, author = {Costa, Daniel P. and Breed, Greg a. and Robinson, Patrick W.}, doi = {10.1146/annurev-ecolsys-102710-145045}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Costa, Breed, Robinson - 2011 - New Insights into Pelagic Migrations Implications for Ecology and Conservation.pdf:pdf}, isbn = {1543-592X 978-0-8243-1443-9}, issn = {1543-592X}, journal = {Annual Review of Ecology, Evolution, and Systematics}, number = {1}, pages = {120830113150004}, title = {{New Insights into Pelagic Migrations: Implications for Ecology and Conservation}}, volume = {43}, year = {2011} } @book{Malthus1798, abstract = {Historic essay on the economical consequences of population growth}, annote = {Chapter 1: "Population, when unchecked increas in a geometrical rati. Subsistence increases onlu in an arithmetical ratio" -b/c of this it would be difficult to "perfect" society Chapter 4: Discusses how customs in developed countries affect the population growth a lot -Talks about Hume and Adam Smith}, author = {Malthus, T.R.}, doi = {10.2307/2064821}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Malthus - 1798 - An essay on the Principle of Population.pdf:pdf}, isbn = {1584777281}, issn = {00943061}, keywords = {Famine,Fertility,Malthusian Catastrophe,Population Growth,Sustainability}, pages = {340}, pmid = {555114740}, title = {{An essay on the Principle of Population}}, year = {1798} } @article{Diekmann2004, author = {Diekmann, Odo}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Diekmann - 2004 - A beginner's guide To adaptive dynamics.pdf:pdf}, journal = {Banach Center Publications}, pages = {47--86}, title = {{A beginner's guide To adaptive dynamics}}, volume = {63}, year = {2004} } @article{Caselle2015, annote = {evaluating the effects of the California Channel Islands MPA network -}, author = {Caselle, Jennifer E and Rassweiler, Andrew and Hamilton, Scott L and Warner, Robert R}, doi = {10.1038/srep14102}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Caselle et al. - 2015 - Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate mari.pdf:pdf}, journal = {Scientific Reports}, number = {14102}, pages = {1--14}, publisher = {Nature Publishing Group}, title = {{Recovery trajectories of kelp forest animals are rapid yet spatially variable across a network of temperate marine protected areas}}, url = {http://dx.doi.org/10.1038/srep14102}, volume = {5}, year = {2015} } @article{Fabina2015, annote = {- find that severity is more important than frequency in determining coral persistence - they determined what to protect based on life history traits - **I think it would be interesting to put this model in a spatial context and see how MPA changes when you include rare events in the model.** Hypothesis: closer MPAs if bleaching in spatially hetergeneous and frequent. Large MPAs if homogeneous bleaching events..? Where do real systems lie on the graph for figure 2?}, author = {Fabina, Nicholas S. and Baskett, Marissa L. and Gross, Kevin}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fabina, Baskett, Gross - 2015 - The differential effects of increasing frequency and magnitude of extreme events on coral populations.pdf:pdf}, journal = {Ecological Applications}, keywords = {alternative stable states,climate change,coral bleaching,ecological projection,global,population dynamics,random forests,sensitivity analysis,species distribution model,symbiodinium}, number = {6}, pages = {1534--1545}, title = {{The differential effects of increasing frequency and magnitude of extreme events on coral populations}}, volume = {25}, year = {2015} } @book{Kessler2012, address = {West Sussex, UK}, annote = {-many different ways to measure syncrony (correlation among pairs of spatially disjunct time series, -useful to look at realtionship betweeen distance and syncrony across popuylations -spatial scale you are considering matters a lot Inverse problem= many processes can lead to the same dynamic outcomes - syncronoy can be driven by dispersal, regional stochasticity, and trophic interactions Many tropical species are multivoltine unlike temperate species Chapter 15: -outbreaks in urban areas common b/c of how we have changed these systems -majority of outbreak cases here were in for mite species -low diversity in urban areas e.g. dutch elm disease -less predation for mites that can invade urban areas -invasive plants may also harbor invasive pests -pulsed stress hypothesis- alternate periods of drought and floods can increase quality of plant material -exmple of spider mites that have quicker development with increases temperature (7 day development) -phenological syncrony -do outbreaks in urban areas occur more or less frequently than natural systems? --could this be related to outbreaks in measles? Density effect? Why are outbreaks associated with agriculture? And not as much in the wild? Chapter 16: -Bt is main example here -{\textgreater} gene that produces Bt has been spliced into various plants -{\textgreater} originally the bacteria that harbored Bt was used as a pesticide -Bt in plants is produced contiuosly during season which allows a lot of time for selection and resistence -if your Bt production is not high enough, insects can survive and resistence can occur much more quickly -want pest management to include refuges of non-Bt plants -Bt doesn't affect mammals, including humans Chapter 18: IPM was implemented to reduce number of outbreaks that may occur due to resistance to insecticies -want to reduce pop numbers not completely relimnate}, booktitle = {Insect Outbreaks Revisited}, doi = {10.1002/9781118295205}, editor = {Kessler, Andr{\'{e}} and Poveda, Katja and Poelman, Erik H.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(2).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(3).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(4).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(5).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(6).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(7).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(8).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(9).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(10).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(11).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(12).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Unknown - 2012 - Insect Outbreaks Revisited(13).pdf:pdf}, isbn = {9781118295205}, keywords = {Direct induced resistance and herbivory,Herbivore performance reduction on plants,Herbivore population dynamics,Multiple faces of plant-induced responses to herbi,Plant tolerance,Plant tolerance on herbivore performance,Plant-induced responses and herbivore population d,Population dynamics and multispecies interactions,Search for mechanisms underlying outbreaks,plant-,predator and parasi,reduced herbivory impact on plant}, publisher = {John Wiley and Sons}, title = {{Insect Outbreaks Revisited}}, url = {http://www.scopus.com/inward/record.url?eid=2-s2.0-84878778867{\&}partnerID=tZOtx3y1}, year = {2012} } @article{Gilbert2012, abstract = {Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains {\textgreater}65{\%} of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.}, annote = {Interesting article that examined 6 years of sequence data in a coastal area. They found strong seasonal trends in abundance and different taxa dominating the community during different times of the year Seasonal patterns were largely correlated with environmental variables like day length}, author = {Gilbert, J a and Steele, J a and Caporaso, J G and Steinbruck, L and Reeder, J and Temperton, B and Huse, S and McHardy, a C and Knight, R and Joint, I and Somerfield, P and Fuhrman, J a and Field, D}, doi = {10.1038/ismej.2011.107}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gilbert et al. - 2012 - Defining seasonal marine microbial community dynamics.pdf:pdf}, isbn = {1751-7370 (Electronic)$\backslash$n1751-7362 (Linking)}, issn = {1751-7370}, journal = {The ISME Journal}, keywords = {Bacteria,Bacteria: classification,Bacteria: genetics,Bacterial Physiological Phenomena,Biodiversity,Environment,Great Britain,Oceans and Seas,Photoperiod,RNA, Ribosomal, 16S,RNA, Ribosomal, 16S: genetics,Seasons}, number = {2}, pages = {298--308}, pmid = {21850055}, title = {{Defining seasonal marine microbial community dynamics}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21850055{\%}5Cnpapers2://publication/doi/10.1038/ismej.2011.107}, volume = {6}, year = {2012} } @article{Møller2008, abstract = {Recent rapid climatic changes are associated with dramatic changes in phenology of plants and animals, with optimal timing of reproduction advancing considerably in the northern hemisphere. However, some species may not have advanced their timing of breeding sufficiently to continue reproducing optimally relative to the occurrence of peak food availability, thus becoming mismatched compared with their food sources. The degree of mismatch may differ among species, and species with greater mismatch may be characterized by declining populations. Here we relate changes in spring migration timing by 100 European bird species since 1960, considered as an index of the phenological response of bird species to recent climate change, to their population trends. Species that declined in the period 1990-2000 did not advance their spring migration, whereas those with stable or increasing populations advanced their migration considerably. On the other hand, population trends during 1970-1990 were predicted by breeding habitat type, northernmost breeding latitude, and winter range (with species of agricultural habitat, breeding at northern latitudes, and wintering in Africa showing an unfavorable conservation status), but not by change in migration timing. The association between population trend in 1990-2000 and change in migration phenology was not confounded by any of the previously identified predictors of population trends in birds, or by similarity in phenotype among taxa due to common descent. Our findings imply that ecological factors affecting population trends can change over time and suggest that ongoing climatic changes will increasingly threaten vulnerable migratory bird species, augmenting their extinction risk.}, author = {M{\o}ller, Anders Pape and Rubolini, Diego and Lehikoinen, Esa}, doi = {10.1073/pnas.0803825105}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/M{\o}ller, Rubolini, Lehikoinen - 2008 - Populations of migratory bird species that did not show a phenological response to climate change.pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {42}, pages = {16195--16200}, pmid = {18849475}, title = {{Populations of migratory bird species that did not show a phenological response to climate change are declining.}}, volume = {105}, year = {2008} } @article{Garcia-Reyes2012, abstract = {The coastal ocean environment off California is largely determined by wind-driven coastal upwelling, with an ecosystem that is tightly coupled to seasonality in this upwelling. Three decades of data measured over the California shelf at NOAA buoys are used to describe the seasonal variability of the winds that force upwelling and the response of the coastal ocean in terms of sea temperature. Moreover, seasonal patterns in surface chlorophyll and alongshore currents are determined from one decade of data. In addition to clear seasonality, all these data exhibit distinct spatial and non-seasonal temporal variability in upwelling. Based on alongshore wind stress characteristics in central and north California, three seasons are defined: Upwelling Season (April-June) with strong upwelling-favorable winds and large standard deviation due to frequent reversals; Relaxation Season (July-September) with weak equatorward winds and low variability; and Storm Season (December-February) characterized by weak mean wind stress but large variability. The remaining months are transitional, falling into one or other season in different years. In addition to large-scale latitudinal differences in wind stress, spatial differences are associated with coastal topography - specifically the acceleration of wind downstream of capes. Latitudinal differences in sea surface temperature depend on wind stress, both local and large-scale, but also on surface heating and offshore influences. Intra-annual and inter-annual anomalies in wind and sea surface temperature are associated with variability in coastal winds, large-scale winds, and offshore basin-scale ocean conditions. Satellite chlorophyll concentration shows an optimal window relation with upwelling forcing, allowing maximum concentrations during moderate winds and minimal during poor or strong winds.}, author = {Garc{\'{i}}a-Reyes, M. and Largier, J. L.}, doi = {10.1029/2011JC007629}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Garc{\'{i}}a-Reyes, Largier - 2012 - Seasonality of coastal upwelling off central and northern California New insights, including temporal an.pdf:pdf}, isbn = {0148-0227}, issn = {0148-0227}, journal = {Journal of Geophysical Research}, keywords = {coastal upwelling,upwelling variability}, number = {C3}, pages = {1--17}, title = {{Seasonality of coastal upwelling off central and northern California: New insights, including temporal and spatial variability}}, volume = {117}, year = {2012} } @article{Haydon1997, abstract = {We present an analysis of the conditions under which migration and global random factors may determine large scale synchrony in the dynamics of spatially structured populations. We derive an analytic approximation which describes how the desynchronizing influence of local environmental stochasticity combines with the synchronizing influences of larger scale environmental stochastic variation and migration to determine population cross correlation coefficients. Despite the simplifications made by this analysis, computer simulations show that the behaviour of more complicated models is well described by our approximation over considerable regions of parameter space. We conclude that population synchrony is largely determined by the coefficients of variation (CVs) of the local and larger scale stochastic processes, and that migration alone is only likely to maintain population synchrony when the CV of the local stochastic process is very small.}, annote = {three causes of synchony: 1) similar environmental conditions for distant populations (Moran effect) 2) density dependent migration between pops 3) roaming predators that can move b/w pops density vague processes (Strong83)- only operate below or above some pop threshold Only need a little stochastic vraiation to disupr feedback process}, author = {Haydon, D. and Steen, H.}, doi = {10.1098/rspb.1997.0191}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Haydon, Steen - 1997 - The effects of large and small-scale random events on the synchrony of metapopulation dynamics a theoretical anal.pdf:pdf}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {Metapopulation Stochastic Variation Migration}, number = {1386}, pages = {1375--1381}, title = {{The effects of large and small-scale random events on the synchrony of metapopulation dynamics: a theoretical analysis}}, volume = {264}, year = {1997} } @phdthesis{Severaid1955, author = {Severaid, Joye Harold}, school = {University of California, Berkeley}, title = {{The Natural History of the Pikas (mammalian Genus Ochotona)}}, type = {PhD dissertation}, year = {1955} } @article{DelMonte-Luna2004, abstract = {We analyse the concept of carrying capacity (CC), from populations to the biosphere, and offer a definition suitable for any level. For communities and ecosystems, the CC evokes density-dependence assumptions analogous to those of population dynamics. At the biosphere level, human CC is uncertain and dynamic, leading to apprehensive rather than practical conclusions. The term CC is widely used among ecological disciplines but remains vague and elusive. We propose the following definition: the CC is 'the limit of growth or development of each and all hierarchical levels of biological integration, beginning with the population, and shaped by processes and interdependent relationships between finite resources and the consumers of those resources'. The restrictions of the concept relate to the hierarchical approach. Emergent properties arise at each level, and environmental heterogeneity restrains the measurement and application of the CC. Because the CC entails a myriad of interrelated, ever-changing biotic and abiotic factors, it must not be assumed constant, if we are to derive more effective and realistic management schemes. At the ecosystem level, stability and resilience are dynamic components of the CC. Historical processes that help shape global biodiversity (e.g. continental drift, glaciations) are likely drivers of large-scale changes in the earth's CC. Finally, world population growth and consumption of resources by humanity will necessitate modifications to the paradigm of sustainable development, and demand a clear and fundamental understanding of how CC operates across all biological levels.}, author = {del Monte-Luna, Pablo and Brook, Barry W. and Zetina-Rej{\'{o}}n, Manuel J. and Cruz-Escalona, Victor H.}, doi = {10.1111/j.1466-822X.2004.00131.x}, isbn = {1466-8238}, issn = {1466822X}, journal = {Global Ecology and Biogeography}, keywords = {Biosphere,Community,Ecosystem,Hierarchy theory,Population,Renewable resource management,Resilience,Stability,Sustainable development}, number = {6}, pages = {485--495}, pmid = {7666}, title = {{The carrying capacity of ecosystems}}, volume = {13}, year = {2004} } @article{Ginzburg1982, annote = {paper that coined term quasiextinction- "population decline to low level"}, author = {Ginzburg, L.R. and Slobodkin, L.B. and Johnson, K. and Bindman, A.G.}, journal = {Risk Analysis}, number = {3}, pages = {171--181}, title = {{Quasiextinction probabilities as a measure of impact on population growth}}, volume = {2}, year = {1982} } @article{Eaton2014, annote = {mostly deals with impefect detection spatial strucutre matters- particuraly who your neighbors are for local extinction ' a number of good citations related to within patch hdynamics and the layout of tpatches and its importance}, author = {Eaton, Mitchell J and Hughes, Phillip T and Hines, James E and Nichols, James D}, doi = {10.1111/oik.01008}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eaton et al. - 2014 - Testing metapopulation concepts effects of patch characteristics and neighborhood occupancy on the dynamics of an.pdf:pdf}, journal = {Oikos}, pages = {662--676}, title = {{Testing metapopulation concepts : effects of patch characteristics and neighborhood occupancy on the dynamics of an endangered lagomorph}}, volume = {123}, year = {2014} } @article{Harrison1991, author = {Harrison, Susan}, journal = {Biological Journal of the Linnean Society}, pages = {73--88}, title = {{Local extinction in a metapopulation context: an empirical evaluation}}, volume = {42}, year = {1991} } @incollection{Levins1970a, abstract = {reference de base pour cell occupancy model avec levins 1969}, author = {Levins, R.A.}, booktitle = {Some Mathematical Questions in Biology, volume 2 of Lectures on Mathematics in the Life Sciences}, pages = {76--107}, title = {{Extinction}}, volume = {2}, year = {1970} } @article{Lafferty2015, author = {Lafferty, Kevin D. and DeLeo, Giulio and Briggs, Cheryl J. and Dobson, Andrew P. and Gross, Thilo and Kuris, Armand M.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lafferty et al. - 2015 - A general consumer-resource population model.pdf:pdf}, journal = {Science}, number = {6250}, pages = {854--857}, title = {{A general consumer-resource population model}}, volume = {349}, year = {2015} } @article{Sutherland2014, annote = {- they include "local dynamics" by}, author = {Sutherland, C S and Elston, Da and Lambin, X}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sutherland, Elston, Lambin - 2014 - A demographic , spatially explicit patch occupancy model of metapopulation dynamics and persistence.pdf:pdf}, journal = {Ecology}, keywords = {abundance,arvicola amphibius,false negative,fragmentation,hierarchical model,migration,occupancy model,site occupancy,spatially realistic metapopulation theory,state-space modeling,stochastic patch,water vole}, number = {11}, pages = {3149--3160}, title = {{A demographic , spatially explicit patch occupancy model of metapopulation dynamics and persistence}}, volume = {95}, year = {2014} } @article{Moilanen2004, abstract = {Classical metapopulations are groups of local populations living in networks of spatially distinct habitat patches in a balance between local extinctions and recolonizations of empty habitat. Models are needed for understanding and predicting metapopulation dynamics in changing landscapes. One particularly important question is what is the effect of habitat loss to the persistence of a metapopulation. A class of metapopulation models that have been successfully used in practical applications are called stochastic patch occupancy models (SPOMs), which model the presence/absence of the species on habitat patches as a Markov chain. The presence-absence assumption makes the model relatively parameter sparse, facilitates empirical data collection, and enables rigorous parameter estimation. This study reviews theory of SPOMs and describes a computational tool, called SPOMSIM, which allows one to simulate SPOMs and estimate parameters for them. SPOMSIM offers a range of choices for submodels; alternatives are provided for the functional forms of local extinction, the dispersal kernel, computation of connectivity, the colonization function, the implementation of the rescue effect and the implementation of regional stochasticity. SPOMSIM includes also, among other things, a utility based on hierarchical clustering for the analysis of the structure of a patch network, a reserve network optimization algorithm, and a patch system editor which makes it possible to investigate the consequences of changes in landscape structure. Potential uses for SPOMSIM include scientific metapopulation studies, teaching and conservation management. ?? 2004 Elsevier B.V. All rights reserved.}, author = {Moilanen, Atte}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moilanen - 2004 - SPOMSIM Software for stochastic patch occupancy models of metapopulation dynamics.pdf:pdf}, isbn = {0304-3800}, issn = {03043800}, journal = {Ecological Modelling}, keywords = {Computer software,Incidence function model,Metapopulation dynamics,Reserve network design,Spatial population dynamics,Stochastic patch occupancy model}, number = {4}, pages = {533--550}, pmid = {2951}, title = {{SPOMSIM: Software for stochastic patch occupancy models of metapopulation dynamics}}, volume = {179}, year = {2004} } @article{Ozgul2009, abstract = {Despite recent advances in biodemography and metapopulation ecology, we still have limited understanding of how local demographic parameters influence short- and long-term metapopulation dynamics. We used long-term data from 17 local populations, along with the recently developed methods of matrix metapopulation modeling and transient sensitivity analysis, to investigate the influence of local demography on long-term (asymptotic) versus short-term (transient) dynamics of a yellow-bellied marmot metapopulation in Colorado. Both long- and short-term dynamics depended primarily on a few colony sites and were highly sensitive to changes in demography at these sites, particularly in survival of reproductive adult females. Interestingly, the relative importance of sites differed between long- and short-term dynamics; the spatial structure and local population sizes, while insignificant for asymptotic dynamics, were influential on transient dynamics. However, considering the spatial structure was uninformative about the relative influence of local demography on metapopulation dynamics. The vital rates that were the most influential on local dynamics were also the most influential on both long- and short-term metapopulation dynamics. Our results show that an explicit consideration of local demography is essential for a complete understanding of the dynamics and persistence of spatially structured populations.}, annote = {Made measurements of growth rate for the meatpopulation and of the same system ignoring spatial strucutre and found that metapop growth rate was lower-{\textgreater} indicating importance of spatial strucuture and dispersal long term and short term dynamics depended on different things Use deterministic, stage and spatially structured matrix model to study metapopulation dynamics}, author = {Ozgul, Arpat and Oli, Madan K and Armitage, Kenneth B and Blumstein, Daniel T and {Van Vuren}, Dirk H}, doi = {10.1086/597225}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ozgul et al. - 2009 - Influence of local demography on asymptotic and transient dynamics of a yellow-bellied marmot metapopulation.pdf:pdf}, isbn = {0003-0147}, issn = {0003-0147}, journal = {The American Naturalist}, keywords = {conservation of fragmented populations,marmota flavi-,matrix metapopulation model,patch value,tivity analysis,transient sensi-,vec-permutation matrix,ventris}, number = {4}, pages = {517--530}, pmid = {19249978}, title = {{Influence of local demography on asymptotic and transient dynamics of a yellow-bellied marmot metapopulation.}}, volume = {173}, year = {2009} } @article{Levins1969, abstract = {Economically important pests usually attack a crop or group of crops over a wide region in which there are geographic, local, and temporal variations in the environment. Effectiveness of any control program will therefore depend on the different responses of the crop, pest, and control organism to this pattern of environment. Usually the environmental heterogeneity is treated as an unavoidable complication in program evaluation, and attempts are made to work with “average” conditions.}, author = {Levins, Richard}, doi = {10.1093/besa/15.3.237}, isbn = {0013-8754}, issn = {00138754}, journal = {Bulletin of the Entomological Society of America}, number = {3}, pages = {237--240}, title = {{Some demographic and genetic consequences of environmental heterogeneity for biological control}}, volume = {15}, year = {1969} } @article{Castorani2015, annote = {Eaton 2014 patch size Hanski 1999}, author = {Castorani, Max C N and Reed, Dan C and Alberto, Filipe and Bell, Tom W and Simons, Rachael D and Cavanaugh, Kyle C and Siegel, David a and Raimondi, Peter T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Castorani et al. - 2015 - Connectivity structures local population dynamics a long-term empirical test in a large metapopulation system.pdf:pdf}, journal = {Ecology}, number = {12}, pages = {3141--3152}, title = {{Connectivity structures local population dynamics: a long-term empirical test in a large metapopulation system}}, volume = {96}, year = {2015} } @misc{Melbourne2015, annote = {Only one math paper, and no empirical work, has examined range expansion when dealing with more than one species 15-20 replicates typically}, author = {Melbourne, Brett A and Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Melbourne, Hastings - 2015 - 2015 Beetle Grant NSF.pdf:pdf}, isbn = {3034926421}, title = {{2015 Beetle Grant NSF}}, year = {2015} } @article{Smith1984, abstract = {Adult spatial relationships and social organization in a marked population of alpine mammals, the pika (Ochotona princeps ), were studied over a 3-year period in the Rocky Mountains of Colorado. Ecological constraints, such as the distribution of food (primarily located in meadows adjacent to the talus) and the short summer reproductive season (placing a premium on early appropriately timed litters) have apparently led to a facultatively monogamous mating system. Males can neither monopolize essential resources sufficiently to attract several females, nor defend groups of females as social repulsion among females further increase their dispersion.}, author = {Smith, A T and Ivins, B L}, journal = {Zeitschrift fur Tierpsychologie}, keywords = {SOCIAL}, number = {4}, pages = {289--308}, title = {{Spatial relationships and social organization in adult pikas: A facultatively monogamous mammal}}, volume = {66}, year = {1984} } @article{Gerber2014, abstract = {1. While most demographic population models used in conservation rely on female vital rates, recent empirical evidence suggests that male dynamics should be included in population models used for assessing extinction risk. 2. Using California sea lions Zalophus californianus as an applied example, we demonstrate that there are situations in which two-sex models are more appropriate than the commonly used female-based model. 3. Two-sex models are relevant in cases where vital rates for sexes differ and for polygamous species such as sea lions. Vital rates targeted for management may therefore respond differently for males and females and for different assumptions about sex ratio. 4. Synthesis and applications. Conservation biologists should carefully consider the social structure and sex ratio of focal species in order to determine whether a two-sex matrix model will yield more accurate estimates of extinction risk than standard one-sex models.}, author = {Gerber, Leah R. and White, Easton R.}, doi = {10.1111/1365-2664.12177}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gerber, White - 2014 - Two-sex matrix models in assessing population viability When do male dynamics matter.pdf:pdf}, isbn = {00218901}, issn = {00218901}, journal = {Journal of Applied Ecology}, keywords = {Extinction risk,Sex ratio,Two-sex models,Zalophus californianus}, number = {1}, pages = {270--278}, title = {{Two-sex matrix models in assessing population viability: When do male dynamics matter?}}, volume = {51}, year = {2014} } @incollection{Smith1987, author = {Smith, Andrew T}, booktitle = {Mammalian Dispersal Patterns: The Effects of Social Structure on Population Genetics}, chapter = {9}, editor = {Chepko-Sade, B. Diane and Halpin, Zuleyma Tang}, pages = {128--142}, publisher = {University of Chicago Press}, title = {{Population structure of pikas: dispersal versus philosophy}}, year = {1987} } @article{Fretwell1972, abstract = {Most organisms live in a seasonal environment. During their life cycles, some species face seasons of cold and heat, aridity and abundant rainfall, migration and stable residence, breeding and nonbreeding. Populations grow and decline as supplies of materials essential to their survival wax and wane. Such qualitative truths as these flow obviously from field observations.In this original monograph, Stephen Fretwell analyzes the highly complex interaction between a population and a regularly varying environment in an attempt to define and measure seasonality as a critical parameter in the general theory of population regulation. Concerned primarily with the size and the habitat distribution of populations, Professor Fretwell develops simple models that, when applied to specific populations, usually of birds, demonstrate the effect of seasonal variations on the regulation of populations. He maintains that seasonality, as a concept, is essential to a full understanding of environmental interaction. During the course of his exposition, the author offers several new hypotheses, including theories affecting the breeding, numbers, distribution, and diversity of wintering birds, and a theory affecting the body size of sparrows.}, annote = {Has interesting intro on how to be an ecologist Lots of citable ideas about seasonality generally pg 20: for shotrt lived species- basic logistic equation with periodic K, piecewise or continuos K(t) -{\textgreater} N can't always keep up with these changes, depends on density dependence Are pops limited by one or multiple seasons? Lots of examples of ideas, especially applied to birds}, author = {Fretwell, S D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fretwell - 1972 - Populations in a seasonal environment.doc:doc}, isbn = {0077-0930}, issn = {0077-0930}, journal = {Monographs in population biology}, pages = {1--217}, pmid = {4680650}, title = {{Populations in a seasonal environment.}}, volume = {5}, year = {1972} } @article{Passuni2015, abstract = {In fluctuating environments, matching breeding timing to periods of high resource availability is crucial for the fitness of many vertebrate species, and may have major consequences on population health. Yet, our understanding of the proximate environmental cues driving seasonal breeding is limited. This is particularly the case in marine ecosystems, where key environmental factors and prey abundance and availability are seldom quantified. The Northern Humboldt Current System (NHCS) is a highly productive, low-latitude ecosystem of moderate seasonality. In this ecosystem, three tropical seabird species (the Guanay Cormorant Phalacrocorax bougainvillii, the Peruvian Booby Sula variegata, and the Peruvian Pelican Pelecanus thagus) live in sympatry and prey almost exclusively on anchovy, Engraulis ringens. From January 2003 to December 2012, we monitored 31 breeding sites along the Peruvian coast to investigate the breeding cycle of these species. We tested for relationships between breeding timing, oceanographic conditions, and prey availability using occupancy models. We found that all three seabird species exhibited seasonal breeding patterns, with marked interspecific differences. Whereas breeding mainly started during the austral winter/early spring and ended in summer/early fall, this pattern was stronger in boobies and pelicans than in cormorants. Breeding onset mainly occurred when upwelling was intense but ecosystem productivity was below its annual maxima, and when anchovy were less available and in poor physiological condition. Conversely, the abundance and availability of anchovy improved during chick rearing and peaked around the time of fledging. These results suggest that breeding timing is adjusted so that fledging may occur under optimal environmental conditions, rather than being constrained by nutritional requirements during egg laying. Adjusting breeding time so that fledglings meet optimal conditions at independence is unique compared with other upwelling ecosystems and could be explained by the relatively high abundances of anchovy occurring throughout the year in the NHCS.}, author = {Passuni, Giannina and Barbraud, Christophe and Chaigneau, Alexis and Demarcq, Herve and Ledesma, Jesus and Bertrand, Arnaud and Castillo, Ramiro and Perea, Angel and Mori, Julia and Viblanc, Vincent A and Torres-Maita, Jose and Bertrand, Sophia}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Passuni et al. - 2016 - Seasonality in marine ecosystems Peruvian seabirds, anchovy and oceanographic conditions.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Passuni et al. - 2016 - Seasonality in marine ecosystems Peruvian seabirds, anchovy and oceanographic conditions(2).pdf:pdf}, journal = {Ecology}, number = {1}, pages = {182--193}, title = {{Seasonality in marine ecosystems: Peruvian seabirds, anchovy and oceanographic conditions}}, volume = {97}, year = {2016} } @article{Rinaldi1993, abstract = {A classical predator-prey model is considered in this paper with reference to the case of periodically varying parameters. Six elementary seasonally mechanisms are identified and analy- sed in detail by means of a continuation technique producing complete bifurcation diagrams. The results show that each elementary mechanism can give rise to multiple attractors and that catastrophic transitions can occur when suitable parameters are slightly changed. Moreover, the two classical routes to chaos, namely, torus destruction and cascade of period doublings, are numerical- ly detected. Since in the case of constant parameters the model cannot have multiple attractors, catastrophes and chaos, the results support the conjecture that seasons can very easily give rise to complex population dynamics}, author = {Rinaldi, Sergio and Muratori, Simona and Kuznetsov, Yuri}, doi = {10.1007/BF02460293}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rinaldi, Muratori, Kuznetsov - 1993 - Multiple attractors, catastrophes and chaos in seasonally perturbed predator-prey communities.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rinaldi, Muratori, Kuznetsov - 1993 - Multiple attractors, catastrophes and chaos in seasonally perturbed predator-prey communities(2).pdf:pdf}, isbn = {0092-8240}, issn = {00928240}, journal = {Bulletin of Mathematical Biology}, number = {1}, pages = {15--35}, title = {{Multiple attractors, catastrophes and chaos in seasonally perturbed predator-prey communities}}, volume = {55}, year = {1993} } @article{Kessel2014, author = {Kessel, S T and Chapman, D d and Franks, B R and Gedamke, T and Gruber, S H and Newman, J M and White, E R and Perkins, R G}, doi = {10.3354/meps10966}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kessel et al. - 2014 - Predictable temperature-regulated residency, movement and migration in a large, highly mobile marine predator (Ne.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kessel et al. - 2014 - Predictable temperature-regulated residency, movement and migration in a large, highly mobile marine predator (2).pdf:pdf}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, keywords = {acoustic telemetry,glmm,lemon shark,of the publisher,permitted without written consent,resale or republication not,seasonal migration,seasonal residency,temperature preference}, pages = {175--190}, title = {{Predictable temperature-regulated residency, movement and migration in a large, highly mobile marine predator (Negaprion brevirostris)}}, url = {http://www.int-res.com/abstracts/meps/v514/p175-190/}, volume = {514}, year = {2014} } @article{Altizer2011, abstract = {Animal migrations are often spectacular, and migratory species harbor zoonotic pathogens of importance to humans. Animal migrations are expected to enhance the global spread of pathogens and facilitate cross-species transmission. This does happen, but new research has also shown that migration allows hosts to escape from infected habitats, reduces disease levels when infected animals do not migrate successfully, and may lead to the evolution of less-virulent pathogens. Migratory demands can also reduce immune function, with consequences for host susceptibility and mortality. Studies of pathogen dynamics in migratory species and how these will respond to global change are urgently needed to predict future disease risks for wildlife and humans alike.}, author = {Altizer, Sonia and Bartel, Rebecca and Han, Barbara a}, doi = {10.1126/science.1194694}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Altizer, Bartel, Han - 2011 - Animal migration and infectious disease risk.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Altizer, Bartel, Han - 2011 - Animal migration and infectious disease risk(2).pdf:pdf}, isbn = {0036-8075 1095-9203}, issn = {0036-8075}, journal = {Science}, number = {6015}, pages = {296--302}, pmid = {21252339}, title = {{Animal migration and infectious disease risk.}}, volume = {331}, year = {2011} } @misc{Hastings1991, author = {Hastings, a and Powell, T}, booktitle = {Ecology}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Powell - 1991 - Chaos in a three species food chain.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Powell - 1991 - Chaos in a three species food chain(2).pdf:pdf}, issn = {0012-9658}, pages = {896--903}, title = {{Chaos in a three species food chain}}, url = {http://www.jstor.org/stable/1940591}, volume = {72}, year = {1991} } @article{Bjørnstad2015, annote = {chaos most likely to be found in tightly coupled, low dimensional, highly nonlinear systems Hastings: transients usually erode footprint of chaos Seasonality drives chaotic behavior}, author = {Bj{\o}rnstad, Ottar N.}, doi = {10.1073/pnas.1507708112}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bj{\o}rnstad - 2015 - Nonlinearity and chaos in ecological dynamics revisited.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bj{\o}rnstad - 2015 - Nonlinearity and chaos in ecological dynamics revisited(2).pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {20}, pages = {201507708}, title = {{Nonlinearity and chaos in ecological dynamics revisited}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1507708112}, volume = {112}, year = {2015} } @article{Klausmeier2010, abstract = {Communities and ecosystems are often far from equilibrium, but our understanding of nonequilibrium dynamics has been hampered by a paucity of analytical tools. Here I describe a novel approach to modeling seasonally forced food webs, called "successional state dynamics" (SSD). It is applicable to communities where species dynamics are fast relative to the external forcing, such as plankton and other microbes, diseases, and some insect communities. The approach treats succession as a series of state transitions driven by both the internal dynamics of species interactions and external forcing. First, I motivate the approach with numerical solutions of a seasonally forced predator-prey model. Second, I describe how to set up and analyze an SSD model. Finally, I apply the techniques to three additional models of two-species interactions: resource competition (r-K selection), facilitation, and flip-flop competition (where the competitive hierarchy alternates over time). This approach allows easy and thorough exploration of how dynamics depend on the environmental forcing regime, and uncovers unexpected phenomena such as multiple stable annual trajectories and year-to-year irregularity in successional trajectories (chaos). ?? 2009 Elsevier Ltd.}, author = {Klausmeier, Christopher A.}, doi = {10.1016/j.jtbi.2009.10.018}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Klausmeier - 2010 - Successional state dynamics A novel approach to modeling nonequilibrium foodweb dynamics.pdf:pdf}, isbn = {1095-8541 (Electronic) 0022-5193 (Linking)}, issn = {00225193}, journal = {Journal of Theoretical Biology}, keywords = {Nonequilibrium dynamics,Seasonality,Succession,Theory}, number = {4}, pages = {584--595}, pmid = {19861131}, publisher = {Elsevier}, title = {{Successional state dynamics: A novel approach to modeling nonequilibrium foodweb dynamics}}, url = {http://dx.doi.org/10.1016/j.jtbi.2009.10.018}, volume = {262}, year = {2010} } @book{Dingle2014, address = {New York}, annote = {daily mass migration of ocean animals}, author = {Dingle, Hugh}, edition = {2}, pages = {326}, publisher = {Oxford University Press}, title = {{Migration: The Biology of Life on the Move}}, year = {2014} } @article{Middleton2013, abstract = {Migration is a striking behavioral strategy by which many animals enhance resource acquisition while reducing predation risk. Historically, the demographic benefits of such movements made migration common, but in many taxa the phenomenon is considered globally threatened. Here we describe a long-term decline in the productivity of elk (Cervus elaphus) that migrate through intact wilderness areas to protected summer ranges inside Yellowstone National Park, USA. We attribute this decline to a long-term reduction in the demographic benefits that ungulates typically gain from migration. Among migratory elk, we observed a 21-year, 70{\%} reduction in recruitment and a 4-year, 19{\%} depression in their pregnancy rate largely caused by infrequent reproduction of females that were young or lactating. In contrast, among resident elk, we have recently observed increasing recruitment and a high rate of pregnancy. Landscape-level changes in habitat quality and predation appear to be responsible for the declining productivity of Yellowstone migrants. From 1989 to 2009, migratory elk experienced an increasing rate and shorter duration of green-up coincident with warmer spring-summer temperatures and reduced spring precipitation, also consistent with observations of an unusually severe drought in the region. Migrants are also now exposed to four times as many grizzly bears (Ursus arctos) and wolves (Canis lupus) as resident elk. Both of these restored predators consume migratory elk calves at high rates in the Yellowstone wilderness but are maintained at low densities via lethal management and human disturbance in the year-round habitats of resident elk. Our findings suggest that large-carnivore recovery and drought, operating simultaneously along an elevation gradient, have disproportionately influenced the demography of migratory elk. Many migratory animals travel large geographic distances between their seasonal ranges. Changes in land use and climate that disparately influence such seasonal ranges may alter the ecological basis of migratory behavior, representing an important challenge for, and a powerful lens into, the ecology and conservation of migratory taxa.}, annote = {migration allows prolonged access to food and reduces predation pressure in seasonal environments predators have to tend to there own young during migratory season -{\textgreater}they found that elk had poor performance if they migrated (low reproductive success) the drought has changed the phenology of vegetation which has decreased the benefits of migration}, author = {Middleton, Arthur D. and Kauffman, Matthew J. and Mcwhirter, Douglas E. and Cook, John G. and Cook, Rachel C. and Nelson, Abigail a. and Jimenez, Michael D. and Klaver, Robert W.}, doi = {10.1890/11-2298.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Middleton et al. - 2013 - Animal migration amid shifting patterns of phenology and predation Lessons from a Yellowstone elk herd.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Middleton et al. - 2013 - Animal migration amid shifting patterns of phenology and predation Lessons from a Yellowstone elk herd(2).pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {Carnivore recovery,Cervus elaphus,Drought,Elk,Grizzly bears,Migration,Trophic mismatch,Vegetation phenology,Wolves,Yellowstone}, number = {6}, pages = {1245--1256}, pmid = {23923485}, title = {{Animal migration amid shifting patterns of phenology and predation: Lessons from a Yellowstone elk herd}}, volume = {94}, year = {2013} } @article{Beninca2015, author = {Beninc{\`{a}}, Elisa and Ballantine, Bill and Ellner, Stephen P. and Huisman, Jef}, doi = {10.1073/pnas.1421968112}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Beninc{\`{a}} et al. - 2015 - Species fluctuations sustained by a cyclic succession at the edge of chaos.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Beninc{\`{a}} et al. - 2015 - Species fluctuations sustained by a cyclic succession at the edge of chaos(2).pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {20}, pages = {201421968}, title = {{Species fluctuations sustained by a cyclic succession at the edge of chaos}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1421968112}, volume = {112}, year = {2015} } @article{Taylor2013a, abstract = {Many natural systems are subject to seasonal environmental change. As a consequence many species exhibit seasonal changes in their life history parameters--such as a peak in the birth rate in spring. It is important to understand how this seasonal forcing affects the population dynamics. The main way in which seasonal models have been studied is through a two dimensional bifurcation approach. We augment this bifurcation approach with extensive simulation in order to understand the potential solution behaviours for a predator-prey system with a seasonally forced prey growth rate. We consider separately how forcing influences the system when the unforced dynamics have either monotonic decay to the coexistence steady state, or oscillatory decay, or stable limit cycles. The range of behaviour the system can exhibit includes multi-year cycles of different periodicities, parameter ranges with coexisting multi-year cycles of the same or different period as well as quasi-periodicity and chaos. We show that the level of oscillation in the unforced system has a large effect on the range of behaviour when the system is seasonally forced. We discuss how the methods could be extended to understand the dynamics of a wide range of ecological and epidemiological systems that are subject to seasonal changes.}, author = {Taylor, Rachel A. and Sherratt, Jonathan A. and White, Andrew}, doi = {10.1007/s00285-012-0612-z}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Taylor, Sherratt, White - 2013 - Seasonal forcing and multi-year cycles in interacting populations Lessons from a predator-prey model.pdf:pdf}, issn = {03036812}, journal = {Journal of Mathematical Biology}, keywords = {Bifurcation diagram,Cyclic populations,Multi-year cycles,Predator-prey,Seasonal forcing,Subharmonics}, number = {6-7}, pages = {1741--1764}, pmid = {23138231}, title = {{Seasonal forcing and multi-year cycles in interacting populations: Lessons from a predator-prey model}}, volume = {67}, year = {2013} } @article{Thomas2011, abstract = {Evidence suggests that Pacific harbor seals Phoca vitulina are likely to alter their for- aging behavior in response to seasonal prey pulses. We hypothesized that spawning herring Clu- pea pallasii aggregations are seasonally important prey for harbor seals, predicting that (1) harbor seal consumption of adult herring would peak during the spawning season, (2) harbor seals would seasonally change their foraging areas to take advantage of spawning herring aggregations, and (3) seal diving behavior would reflect the vertical distribution of herring during the spawning sea- son. The predictions were tested using an analysis of harbor seal prey remains, GPS telemetry, and satellite-linked time/depth recorder data. Contrary to predictions, herring in harbor seal diet was comprised of 74{\%} juveniles and 26{\%} adults in the spawn season, versus 37{\%} juveniles and 63{\%} adults in the post-spawn season. Harbor seal use of documented herring areas was highest during the season when herring did not spawn, and seal diving behavior did not reflect the verti- cal distribution of herring. The lack of response by harbor seals to spawning herring pulses is likely explained by the low energy density of adult herring during the spawn season, and the availability of profitable alternative prey such as juvenile herring. This study highlights the influ- ence of relative prey profitability on the foraging behavior of harbor seals, and may help to explain why predators do not always respond as predicted to resource pulses.}, author = {Thomas, Austen C. and Lance, Monique M. and Jeffries, Steven J. and Miner, Benjamin G. and Acevedo-Guti{\'{e}}rrez, Alejandro}, doi = {10.3354/meps09370}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thomas et al. - 2011 - Harbor seal foraging response to a seasonal resource pulse, spawning Pacific herring.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Thomas et al. - 2011 - Harbor seal foraging response to a seasonal resource pulse, spawning Pacific herring(2).pdf:pdf}, issn = {01718630}, journal = {Marine Ecology Progress Series}, keywords = {Diet,Diving,Marine Predators,Phoca vitulina,Resource pulse,Utilization distribution}, pages = {225--239}, title = {{Harbor seal foraging response to a seasonal resource pulse, spawning Pacific herring}}, volume = {441}, year = {2011} } @article{Henson2000, abstract = {Oscillating discrete autonomous dynamical systems admit multiple oscillatory solutions in the advent of periodic forcing. The multiple cycles are out of phase, and some of their averages may resonate with the forcing amplitude while others attenuate. In application to population biology, populations with stable inherent oscillations in constant habitats are predicted to develop multiple attracting oscillatory final states in the presence of habitat periodicity. The average total population size may resonate or attenuate with the amplitude of the environmental fluctuation depending on the initial population size. The theory has been tested successfully in the laboratory by subjecting cultures of the flour beetle Tribolium to habitat periodicity of various amplitudes. {\textcopyright}2000}, author = {Henson, Shandelle M.}, doi = {10.1016/S0167-2789(99)00231-6}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Henson - 2000 - Multiple attractors and resonance in periodically forced population models.pdf:pdf}, issn = {01672789}, journal = {Physica D: Nonlinear Phenomena}, keywords = {multiple attractors,periodic forcing,periodic habitats,population dynamics}, number = {1-2}, pages = {33--49}, title = {{Multiple attractors and resonance in periodically forced population models}}, volume = {140}, year = {2000} } @article{Mysterud2013, abstract = {Those of us living in a strongly seasonal environment at northern latitudes know how to appreciate longer days and a warming sun after months of winter cold. We can only barely grasp how an ungulate must feel when the spring flush of new green, protein-rich grass emerges after months of starvation and misery. It is no wonder that many ungulates wish to prolong this period of access to fresh spring vegetation by migrating. How will migratory animals cope with changes in plant dynamics due to climate change? What are the consequences of expanding large-carnivore populations in these systems? Why do some individuals remain stationary in nearly all populations of migratory animals? The study by Middleton et al. (2013) shed light on all these issues, without giving a definite answer to the relative role of each process.}, annote = {Cushing 1990 on migration in fish Timing of migration is plastic in ungulates -{\textgreater} how goo dis their cue? Adaptive dynamics of how ungulates should forage? What type of movement is best? How to time things well Why, ib the same population, do you have migratory and non migratory stategies?}, author = {Mysterud, Atle}, doi = {10.1890/12-0505.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mysterud - 2013 - Ungulate migration, plant phenology, and large carnivores The times they are a-changin.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mysterud - 2013 - Ungulate migration, plant phenology, and large carnivores The times they are a-changin(2).pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, number = {6}, pages = {1257--1261}, pmid = {23923486}, title = {{Ungulate migration, plant phenology, and large carnivores: The times they are a-changin}}, volume = {94}, year = {2013} } @article{Remmel2009, abstract = {1. The majority of general life-history models treat the environment as being invariable through time, even though temporal variation in selective agents could dramatically change the outcomes, e.g. in terms of optimal size and time at maturity. For herbivorous insects, seasonal differences in food quality are reasonably well described, but seasonal dynamics of top-down selective forces are poorly documented. 2. The present study attempted to quantify seasonal changes in predation risk of folivorous insect larvae in temperate forest habitats. In a series of field experiments, artificial larvae were exposed to predators, and the resulting bird-inflicted damage was recorded. The trials were repeated regularly throughout the course of two summers. 3. A distinct peak of larval mortality was recorded in mid-June (the nestling period for most insectivorous passerine birds), after which predation risk declined to a plateau of 20-30{\%} below the peak value. 4. The recorded pattern is interpreted as a consequence of seasonal changes in the number and behaviour of insectivorous birds, and the abundance of alternative food resources for these predators. 5. A quantitative analysis based on field data indicated that considering temporal variation in mortality in life-history models is crucial for obtaining realistic predictions concerning central life-history traits, such as final body size in different generations. {\textcopyright} 2008 The Authors.}, author = {Remmel, Triinu and Tammaru, Toomas and M{\"{a}}gi, Marko}, doi = {10.1111/j.1365-2311.2008.01044.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Remmel, Tammaru, M{\"{a}}gi - 2009 - Seasonal mortality trends in tree-feeding insects A field experiment.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Remmel, Tammaru, M{\"{a}}gi - 2009 - Seasonal mortality trends in tree-feeding insects A field experiment(2).pdf:pdf}, isbn = {03076946 (ISSN)}, issn = {03076946}, journal = {Ecological Entomology}, keywords = {Caterpillar phenology,Insectivory,Life-history,Seasonality,Top-down effects}, number = {1}, pages = {98--106}, title = {{Seasonal mortality trends in tree-feeding insects: A field experiment}}, volume = {34}, year = {2009} } @book{Alves2008, address = {Berlin Heidelberg}, author = {Alves, Paulo C{\'{e}}lio and Ferrand, Nuno and Hackl{\"{a}}nder, Klaus}, doi = {10.1007/978-3-540-72446-9}, edition = {1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Alves, Ferrand, Hackl{\"{a}}nder - 2008 - Lagomorph Biology Evolution, Ecology, and Conservation.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Alves, Ferrand, Hackl{\"{a}}nder - 2008 - Lagomorph Biology Evolution, Ecology, and Conservation(2).pdf:pdf}, isbn = {978-3-540-72445-2}, pages = {405}, publisher = {Spring-Verlag}, title = {{Lagomorph Biology: Evolution, Ecology, and Conservation}}, url = {http://link.springer.com/10.1007/978-3-540-72446-9}, year = {2008} } @article{Grenfell1995, abstract = {A body of recent work has used coupled logistic maps to show that these model metapopulations show a decrease in global extinction rate in the chaotic region of model behaviour. In fact, many of the main ecological candidates for low-dimensional chaos are continuous-time host-parasite and predator-prey systems, driven by strong seasonal `forcing' of one or more population parameters. This paper, therefore, explores the relation between seasonal forcing and metapopulation extinction for such systems. We base the analysis on extensive simulations of a stochastic metapopulation model for measles, based on a standard compartmental model, tracking the density of susceptible, exposed, infectious and recovered individuals (the SEIR model). The results show that, by contrast with coupled logistic maps, the increased seasonality which causes chaos maintains or increases levels of global extinction of infection, by increasing the synchrony of sub-population epidemics. The model also illustrates that the population interaction (here between susceptible and infective hosts) has a significant effect on patterns of synchrony and extinction. CR - Copyright {\&}{\#}169; 1995 The Royal Society}, annote = {Will seasonality reduce or enhance extinction risk in metapopulaitons?}, author = {Grenfell, B. T. and Bolker, B. M. and Kleczkowski, a.}, doi = {10.1098/rspb.1995.0015}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Grenfell, Bolker, Kleczkowski - 1995 - Seasonality and Extinction in Chaotic Metapopulations.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Grenfell, Bolker, Kleczkowski - 1995 - Seasonality and Extinction in Chaotic Metapopulations(2).pdf:pdf}, isbn = {09628452}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B: Biological Sciences}, number = {1354}, pages = {97--103}, title = {{Seasonality and Extinction in Chaotic Metapopulations}}, volume = {259}, year = {1995} } @article{Hanski1987, abstract = {1. An outdoor cage experiment was conducted to test the theory that localized interactions facilitate coexistence of species breeding in ephemeral habitats. The same amount of larval resource (50 g of liver) but divided into one, two, four, eight or sixteen pieces was placed into each of fifteen cages once a week from June to September for 4 years. 2. The cage populations were initially mixtures of thirteen species but after 4 years only Lucilia illustris (Meig.), Sarcophaga scoparia Pand. and S.aratrix Pand. remained. Lucilia illustris, by far the most abundant species in the field, predominated in every cage. 3. Sarcophaga went extinct in most cages, but they survived in five cages in which the larval resource was much divided, in agreement with the theoretical prediction. 4. Lucilia silvarum (Meig.) emerged about a week later than L.illustris in early summer; this phenological difference gave rise to a competitive asymmetry between the two species. This difference appears to explain why L.silvarum went extinct in the cages in 3 years, and it may explain why L.silvarum has consistently been lesb abundant than L.illustris in the natural community. 5. Other differences in phenology, voltinism and rate of development in the flies are described, and such differences are suggested to facilitate regional coexistence of many species in seasonal environments.}, annote = {Examines how different species of flies may coexist in seasonal enviornment Emerge and breed at different times when there is less competition...season specialists effectiveluy Here phenology, developmental rates, and blank are important for communityu dynamics}, author = {Hanski, I}, doi = {10.1111/j.1365-2311.1987.tb01004.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hanski - 1987 - Carrion fly community dynamics patchiness, seasonality and coexistence.pdf:pdf}, isbn = {0307-6946}, issn = {1365-2311}, journal = {Ecological Entomology}, keywords = {Finlandia,carrion fly,coexistence,community,competition,diapause,patchiness,seasonality}, pages = {257--266}, title = {{Carrion fly community dynamics: patchiness, seasonality and coexistence}}, url = {http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2311.1987.tb01004.x/abstract}, volume = {12}, year = {1987} } @article{Franken2004a, abstract = {1. The effects of habitat quality, patch size and connectivity between patches on patterns of local extinction and colonization of collared pikas were studied over 7 years in alpine meadows in the south-west Yukon. 2. Although adult population size independently had a significant influence on patch extinction, its influence was minimal when other variables were included in generalized linear models. Instead, an index of habitat quality and the connectivity of a patch were found to be the best predictors of pika extinction. 3. Similarly, patch connectivity only partly explained the recolonization of talus patches by pikas. Other patch characteristics, including aspect, amount of vegetation within the patch and an index of habitat quality based on survival probability of pikas also had a significant influence on recolonization. 4. These results suggest that the influence of patch quality on local extinction and recolonization need to be more fully incorporated into metapopulation models.}, annote = {30-50{\%} of juveniles dispersed on average 332 meters (n=35) -could apply my model to this site}, author = {Franken, Renee J. and Hik, David S.}, doi = {10.1111/j.0021-8790.2004.00865.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Franken, Hik - 2004 - Influence of habitat quality, patch size and connectivity on colonization and extinction dynamics of collared pika.pdf:pdf}, isbn = {00218790}, issn = {00218790}, journal = {Journal of Animal Ecology}, keywords = {Area,Isolation,Metapopulation,Occupancy,Persistence}, number = {5}, pages = {889--896}, title = {{Influence of habitat quality, patch size and connectivity on colonization and extinction dynamics of collared pikas Ochotona collaris}}, volume = {73}, year = {2004} } @article{White2014, author = {White, Easton R and Nagy, John D and Gruber, Samuel H}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White, Nagy, Gruber - 2014 - Modeling the population dynamics of lemon sharks.pdf:pdf}, journal = {Biology Direct}, keywords = {demography,density-dependence,elasmobranch,inverse modeling,population dynamics,stage-based}, number = {23}, pages = {1--18}, title = {{Modeling the population dynamics of lemon sharks}}, volume = {9}, year = {2014} } @misc{Richardson1991, abstract = {Many species of detritivorous invertebrates in small streams depend almost entirely on inputs of leaf litter for their nutritional requirements, however the concentration of this resource varies considerably seasonally. An experiment designed to test the hypothesis that productivity of coarse particle detritus feeders (shredders) is seasonally food limited was performed using replicate streamside channels that received one of three input rates of whole leaf detritus (rates equal to those naturally falling into montane streams, and two levels of increased inputs). Seven of the nine common shredder species attained significantly higher adult mass, higher densities, or both when food was supplemented. Larval densities of Malenka spp. and Brillia retifinis were significantly higher when additional food was added. Brillia retifinis densities were more than 10 x greater in high food additions than in the "natural" treatment; B. retifinis apparently fills a role as a fugitive in this system and is better able to track shifts in resource abundance by virtue of its short generation time. Zapada cinctipes and Z. haysi were more dense in high and intermediate food input treatments during the last half of the summer. Other taxa had nonsignificant trends to higher densities when extra food was provided. Most of the change in benthic densities can be attributed to decreased rates of emigration with increased food supply. Six of the eight taxa for which adult mass at emergence was measured were significantly more massive (4-46{\%}) when food was added. Both sexes exhibited this increase in mass, but females gained proportionally more in most species. There were no detectable changes in the timing of adult emergence due to food manipulations. The biomass of most taxa increased in proportion to the overall increase in biomass of the common coarse-detritus consumers. The main exceptions to that pattern were a disproportionate increase in the percentage of the biomass represented by Brillia retifinis and a decrease in the representation of Zapada cinctipes. The responses of this community to food supplementation demonstrate food limitation of detritivores. The exponential increase in benthic biomass under food addition shows the scope for productivity if food were not limiting. These coexisting species benefitted from enhanced food supply on a spatial scale that is relevant for population level processes. The large seasonal variation in resource abundance under natural conditions creates bottlenecks during periods of low food supply, which constrain subsequent production even during periods when food is abundant}, annote = {Boyce and Daly 1980 Cushing 1986 Manipulated resouces levels in small montane steams in SW BC}, author = {Richardson, J. S.}, booktitle = {Ecology}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Richardson - 1991 - Seasonal food limitation of detritivores in a montane stream an experimental test.pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, number = {3}, pages = {873--887}, pmid = {485}, title = {{Seasonal food limitation of detritivores in a montane stream: an experimental test}}, volume = {72}, year = {1991} } @article{Fukaya2010, abstract = {1. Population growth rate is determined by both density-dependent and density-independent processes. In the temperate zone, the strength and spatial scale of these processes are likely to differ seasonally, but such differences have rarely been quantitatively examined. 2. Coverage, the area occupied by organisms, is a measure of resource use in sessile marine populations. Population models used for density-based studies should be able to characterize effectively fluctuations in coverage, but few have tried to apply such models to sessile populations. 3. We observed coverage of the intertidal barnacle Chthamalus challengeri at 20 plots on four shores along the Pacific coast of Japan over 8 years. We then fitted a population model that incorporated both a density-dependent process (strength of density dependence) and density-independent processes (intrinsic growth rate and stochastic fluctuation at different spatial scales) to these data to analyse the seasonal variation of these processes and answer the following two questions: (i) How do the effects of density-dependent and density-independent processes on population growth vary seasonally? (ii) At what spatial scale, regional (tens of kilometres), shore (hundreds of metres), or rock (tens of centimetres), does density-independent stochastic fluctuation most strongly affect population size changes? 4. Barnacle population size tended to decrease in summer, when population dynamics were characterized by a relatively lower intrinsic growth rate, weaker density dependence and stronger stochastic fluctuation. In contrast, population size tended to increase in winter, reflecting a higher intrinsic growth rate, strong density dependence and weak stochastic fluctuation. 5. In summer, population growth rate was strongly affected by regional-scale stochastic fluctuation, whereas in winter it was affected more by rock-scale stochastic fluctuation, suggesting that populations were strongly affected by regional-scale processes in summer but not in winter. 6. These results indicate that seasonally variable density-dependent and density-independent processes determine the population dynamics of C. challengeri. Therefore, to understand fluctuation patterns of populations of this species, seasonality should be taken into account. Moreover, this study demonstrates that population models commonly used for density-based studies are also applicable to coverage-based population studies.}, author = {Fukaya, Keiichi and Okuda, Takehiro and Nakaoka, Masahiro and Hori, Masakazu and Noda, Takashi}, doi = {10.1111/j.1365-2656.2010.01727.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fukaya et al. - 2010 - Seasonality in the strength and spatial scale of processes determining intertidal barnacle population growth.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fukaya et al. - 2010 - Seasonality in the strength and spatial scale of processes determining intertidal barnacle population growth(2).pdf:pdf}, isbn = {0021-8790}, issn = {00218790}, journal = {Journal of Animal Ecology}, keywords = {Cover,Density dependence,Intertidal rocky shore,Population synchrony,Recruitment,Seasonal variability,State-space model,Thermal stress}, number = {6}, pages = {1270--1279}, pmid = {20636347}, title = {{Seasonality in the strength and spatial scale of processes determining intertidal barnacle population growth}}, volume = {79}, year = {2010} } @article{Sommer1985, abstract = {Chemostat competition experiments with natural phytoplankton communities are compared to experiments in which either one (phosphorus) or two (phosphorus and silicon) key nutrients were added discontinuously at 1-week intervals. In all types of experiments wide ranges of Si:P ratios were tested. Deviation from steady state was found not only to increase the number of coexisting species, but also to shift the regions of dominance of species and of higher taxa along the gradient of Si:P ratios. Pulsed nutrient addition was mainly to the advantage of green algae and to the disadvantage of diatoms.}, author = {Sommer, Ulrich}, doi = {10.4319/lo.1985.30.2.0335}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sommer - 1985 - Comparison between steady state and non-steady state competition Experiments with natural phytoplankton.pdf:pdf}, isbn = {00243590}, issn = {00243590}, journal = {Limnology and Oceanography}, number = {2}, pages = {335--346}, title = {{Comparison between steady state and non-steady state competition: Experiments with natural phytoplankton}}, volume = {30}, year = {1985} } @article{Taylor2013b, abstract = {Seasonality is an important component in many population systems, and factors such as latitude, altitude and proximity to the coastline affect the extent of the seasonal fluctuations. In this paper, we ask how changes in seasonal fluctuations impact on the population cycles. We use the Fennoscandian vole system as a case study, focusing on variations in the length of the breeding season. We use a predator-prey model that includes generalist and specialist predation alongside seasonal forcing. Using a combination of bifurcation analysis and direct simulations, we consider the effects of varying both the level of generalist predation and the length of the breeding season; these are the main changes that occur over a latitudinal gradient in Fennoscandia. We predict that varying the breeding season length leads to changes in the period of the multi-year cycles, with a higher period for shorter breeding season lengths. This concurs with the gradient of periodicity found in Fennoscandia. The Fennoscandian vole system is only one of many populations that are affected by geographical and temporal changes in seasonality; thus our results highlight the importance of considering these changes in other population systems.}, annote = {could we look at voles through AD framework}, author = {Taylor, Rachel A. and White, Andrew and Sherratt, Jonathan A.}, doi = {10.1098/rspb.2012.2714}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Taylor, White, Sherratt - 2013 - How do variations in seasonality affect population cycles.pdf:pdf}, isbn = {1471-2954 (Electronic)$\backslash$n0962-8452 (Linking)}, issn = {1471-2954}, journal = {Proceedings of the Royal Society B: Biological Sciences}, keywords = {Animals,Arvicolinae,Arvicolinae: growth {\&} development,Arvicolinae: physiology,Computer Simulation,Female,Male,Models,Population Dynamics,Predatory Behavior,Predatory Behavior: physiology,Reproduction,Reproduction: physiology,Scandinavia,Seasons,Theoretical}, number = {1754}, pages = {20122714}, pmid = {23325773}, title = {{How do variations in seasonality affect population cycles?}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3574328{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {280}, year = {2013} } @article{Ferrari2012, abstract = {Many Caribbean coral reefs are undergoing a phase shift from coral to macroalgal dominance. Understanding the processes driving changes in algal abundance and community structure requires clarification of the relative effects of top-down (e.g., herbivory) and bottom-up processes (e.g., light, temperature, and nutrients). To date, a number of studies have examined the relative effects of grazing versus nutrification but interactions between herbivory and natural, seasonal fluctuations in temperature and light have not been investigated. This study considered the dynamics of three Caribbean macroalgal species [Lobophora variegata (Lamouroux), Dictyota pulchella (H{\"{o}}rnig and Schnetter), and Halimeda opuntia (Linnaeus)] and algal turf. A field experiment was established to measure species-specific algal dynamics (changes in abundance) over 13 months in the presence and absence of herbivory. Both herbivory and seasonal changes were important processes controlling macroalgal and turf abundance. Water temperature and light had a key role on D. pulchella; this species' abundance significantly increased in the summer, when water temperature and light were the highest, and decreased during winter. Surprisingly, herbivory did not seem to control D. pulchella directly. However, herbivory was the most important process controlling the abundance of L. variegata, H. opuntia, and turf. The abundance of both algal species was correlated with seasonal changes in the environment, but was depleted outside cages throughout the year. The abundance of H. opuntia was positively correlated with temperature and light, but there was no statistical interaction between drivers. The statistical interaction between temperature and light was significant for the abundance of L. variegata and turf, but algal abundance declined as both factors increased. Overall, macroalgal and turf cover were mainly controlled by herbivory, while community structure (which species contributed to the overall cover) was largely influenced by seasonal changes in temperature and light.}, author = {Ferrari, Renata and Gonzalez-Rivero, Manuel and Ortiz, Juan Carlos and Mumby, Peter J.}, doi = {10.1007/s00338-012-0889-9}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ferrari et al. - 2012 - Interaction of herbivory and seasonality on the dynamics of Caribbean macroalgae.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ferrari et al. - 2012 - Interaction of herbivory and seasonality on the dynamics of Caribbean macroalgae(2).pdf:pdf}, isbn = {0722-4028}, issn = {07224028}, journal = {Coral Reefs}, keywords = {Dictyota pulchella,Halimeda opuntia,Herbivory,Lobophora variegata,Macroalgal dynamics,Seasonality}, number = {3}, pages = {683--692}, title = {{Interaction of herbivory and seasonality on the dynamics of Caribbean macroalgae}}, volume = {31}, year = {2012} } @article{Henson1999, abstract = {Mathematical models predict that a population which oscillates in the absence of time-dependent factors can develop multiple attracting final states in the advent of periodic forcing. A periodically-forced, stage-structured mathematical model predicted the transient and asymptotic behaviors of Tribolium (flour beetle) populations cultured in periodic habitats of fluctuating flour volume. Predictions included multiple (2-cycle) attractors, resonance and attenuation phenomena, and saddle influences. Stochasticity, combined with the deterministic effects of an unstable 'saddle cycle' separating the two stable cycles, is used to explain the observed transients and final states of the experimental cultures. In experimental regimes containing multiple attractors, the presence of unstable invariant sets, as well as stochasticity and the nature, location, and size of basins of attraction, are all central to the interpretation of data.}, author = {Henson, S M and Costantino, R F and Cushing, J M and Dennis, B and Desharnais, R a}, doi = {10.1006/bulm.1999.0136}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Henson et al. - 1999 - Multiple attractors, saddles, and population dynamics in periodic habitats.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Henson et al. - 1999 - Multiple attractors, saddles, and population dynamics in periodic habitats(2).pdf:pdf}, issn = {00928240}, journal = {Bulletin of mathematical biology}, number = {6}, pages = {1121--1149}, pmid = {17879873}, title = {{Multiple attractors, saddles, and population dynamics in periodic habitats}}, volume = {61}, year = {1999} } @article{Henson1997, abstract = {Laboratory data show that populations of flour beetles (Tribolium), when grown in a periodically fluctuating volume of flour, can exhibit significant increases in numbers above those attained when grown in a constant volume (of the same average). To analyze and explain this phenomenon a discrete stage- structured model of Tribolium dynamics with periodic environmental forcing is introduced and studied. This model is an appropriately modified version of an experimentally validated model for flour beetle populations growing in a constant volume of flour, in which cannibalism rates are assumed inversely proportional to flour volume. This modeling assumption has been confirmed by laboratory experiments. Theorems implying the existence and stability of periodic solutions of the periodically forced model are proved, The time averages of periodic solutions of the forced model are compared with the equilibrium levels of the unforced model (with the same average flour volume). Parameter constraints are determined for which the average population numbers in the periodic environment are greater than (or less than) the equilibrium population numbers in the associated constant environment, Sample parameter estimates taken from the literature show that these constraints are fulfilled. These theoretical results provide an explanation for the experimentally observed increase in flour beetle numbers as a result of periodically fluctuating flour volumes. More generally, these integrated theoretical and experimental results provide the first convincing example illustrating the possibility of increased population numbers in a periodically fluctuating environment}, author = {Henson, Shandelle M. and Cushing, J. M.}, doi = {10.1007/s002850050098}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Henson, Cushing - 1997 - The effect of periodic habitat fluctuations on a nonlinear insect population model.pdf:pdf}, issn = {0303-6812}, journal = {Journal of Mathematical Biology}, number = {2}, pages = {201--226}, title = {{The effect of periodic habitat fluctuations on a nonlinear insect population model}}, volume = {36}, year = {1997} } @article{Jillson1980, annote = {-Switch between a lot of medium and only a little at reugular intervals -More interested in length of fluctuating period May's model on periodic systems}, author = {Jillson, David A.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Jillson - 1980 - Insect populations respond to fluctuating environments.pdf:pdf}, journal = {Nature}, number = {December}, pages = {699--700}, title = {{Insect populations respond to fluctuating environments}}, volume = {288}, year = {1980} } @article{Banobi2011, abstract = {In theory, rebuttals play a vital role in the progression of science, pointing out flaws in published articles, and ensuring that science self-corrects. However, the effect of rebuttals has not been tested in practice. We examined seven high-profile original articles and their rebuttals, finding that original articles were cited 17 times more than rebuttals, and that annual citation numbers were unaffected by rebuttals. When citations did not mention rebuttals, 95{\%} accepted the thesis of the original article uncritically, and support remained high over time. On the rare occasions when rebuttals were cited, the citing papers on average had neutral views of the original article, and 8{\%} actually believed that the rebuttal agreed with the original article. Overall, only 5{\%} of all citations were critical of the original paper. Our results point to an urgent need to change current publishing models to ensure that rebuttals are prominently linked to original articles.}, author = {Banobi, Jeannette a. and Branch, Trevor a. and Hilborn, Ray}, doi = {10.1890/ES10-00142.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Banobi, Branch, Hilborn - 2011 - Do rebuttals affect future science.pdf:pdf}, isbn = {9221142213}, issn = {2150-8925}, journal = {Ecosphere}, keywords = {10,2011,3,a,accepted 26 january 2011,and r,art37,banobi,branch,c,citation,citation analysis,corresponding editor,d,do rebuttals affect future,doi,ecosphere 2,final version received 9,fisheries,hilborn,j,march 2011,p,peters,published 30 march 2011,rebuttals,received 29 october 2010,revised 25 january 2011,science,scientific publishing,t}, number = {March}, pages = {art37}, title = {{Do rebuttals affect future science?}}, volume = {2}, year = {2011} } @article{Courchamp2015, author = {Courchamp, Franck and Dunne, Jennifer a and Maho, Yvon Le and May, Robert M and Hochberg, Michael E}, doi = {10.1016/j.tree.2014.11.005}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Courchamp et al. - 2015 - Fundamental ecology is fundamental.pdf:pdf}, journal = {Trends in Ecology {\&} Evolution}, keywords = {applied ecology,basic ecology,blue-skies research,fundamental research,research priorities}, number = {1}, pages = {9--16}, title = {{Fundamental ecology is fundamental}}, volume = {30}, year = {2015} } @article{Bjørnstad2001, author = {Bj{\o}rnstad, Ottar N and Grenfell, Bryan T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bj{\o}rnstad, Grenfell - 2001 - Noisy Clockwork Time Series Analysis of Population Fluctuations in Animals.pdf:pdf}, journal = {Science}, number = {July}, pages = {638--643}, title = {{Noisy Clockwork : Time Series Analysis of Population Fluctuations in Animals}}, volume = {293}, year = {2001} } @article{Krebs2015, author = {Krebs, Charles J.}, doi = {10.1111/1749-4877.12130}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Krebs - 2015 - One hundred years of population ecology Successes, failures and the road ahead.pdf:pdf}, issn = {17494877}, journal = {Integrative Zoology}, keywords = {abundance,geographic distributions,history of ecology,population models}, pages = {233--240}, title = {{One hundred years of population ecology: Successes, failures and the road ahead}}, url = {http://doi.wiley.com/10.1111/1749-4877.12130}, volume = {10}, year = {2015} } @article{Head2015, author = {Head, Megan L. and Holman, Luke and Lanfear, Rob and Kahn, Andrew T. and Jennions, Michael D.}, doi = {10.1371/journal.pbio.1002106}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Head et al. - 2015 - The Extent and Consequences of P-Hacking in Science.pdf:pdf}, issn = {1545-7885}, journal = {PLOS Biology}, pages = {e1002106}, title = {{The Extent and Consequences of P-Hacking in Science}}, url = {http://dx.plos.org/10.1371/journal.pbio.1002106}, volume = {13}, year = {2015} } @article{Fahrig2003, abstract = {The literature on effects of habitat fragmentation on biodiversity is huge. It is also very diverse, with different authors measuring fragmentation in different ways and, as a consequence, drawing different conclusions regarding both the magnitude and direction of its effects. Habitat fragmentation is usually defined as a landscape-scale process involving both habitat loss and the breaking apart of habitat. Results of empirical studies of habitat fragmentation are often difficult to interpret because (a) many researchers measure fragmentation at the patch scale, not the landscape scale and (b) most researchers measure fragmentation in ways that do not distinguish between habitat loss and habitat fragmentation per se, i.e., the breaking apart of habitat after controlling for habitat loss. Empirical studies to date suggest that habitat loss has large, consistently negative effects on biodiversity. Habitat fragmentation per se has much weaker effects on biodiversity that are at least as likely to be positive as negative. Therefore, to correctly interpret the influence of habitat fragmentation on biodiversity, the effects of these two components of fragmentation must be measured independently. More studies of the independent effects of habitat loss and fragmentation per se are needed to determine the factors that lead to positive versus negative effects of fragmentation per se. I suggest that the term "fragmentation" should be reserved for the breaking apart of habitat, independent of habitat loss.}, author = {Fahrig, Lenore}, doi = {10.1146/annurev.ecolsys.34.011802.132419}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fahrig - 2003 - Effects of habitat framentation on biodiversity.pdf:pdf}, isbn = {00664162 (ISSN)}, issn = {1543-592X}, journal = {Annual Review of Ecology, Evolution, and Systematics}, keywords = {extinction threshold,habitat configuration,habitat loss,landscape complementation,landscape scale,patch isolation,patch size}, pages = {487--515}, pmid = {220102000018}, title = {{Effects of habitat framentation on biodiversity}}, url = {http://www.jstor.org/stable/30033784{\%}5Cnhttp://www.annualreviews.org/doi/abs/10.1146/annurev.ecolsys.34.011802.132419}, volume = {34}, year = {2003} } @article{Erb2014, abstract = {Species distributions are responding rapidly to global change. While correlative studies of local extinction have been vital to understanding the ecological impacts of global change, more mechanistic lines of inquiry are needed for enhanced forecasting. The current study assesses whether the predictors of local extinction also explain population density for a species apparently impacted by climate change. We tested a suite of climatic and habitat metrics as predictors of American pika (Ochotona princeps) relative population density in the Southern Rocky Mountains, USA. Population density was indexed as the density of pika latrine sites. Negative binomial regression and AICc showed that the best predictors of pika latrine density were patch area followed by two measures of vegetation quality: the diversity and relative cover of forbs. In contrast with previous studies of habitat occupancy in the Southern Rockies, climatic factors were not among the top predictors of latrine density. Populations may be buffered from decline and ultimately from extirpation at sites with high- quality vegetation. Conversely, populations at highest risk for declining density and extirpation are likely to be those in sites with poor-quality vegetation.}, annote = {try to get at mechanistic causes of local extinctions- but still use correlative analyses}, author = {Erb, Liesl P. and Ray, Chris and Guralnick, Robert}, doi = {10.1890/13-1072.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Erb, Ray, Guralnick - 2014 - Determinants of pika population density vs. occupancy in the Southern Rocky Mountains.pdf:pdf}, issn = {10510761}, journal = {Ecological Applications}, keywords = {American pika,Climate change,Forbs,Graminoids,Habitat quality,Latrines,Occupancy,Ochotona princeps,Population density,Southern Rocky Mountains, USA,Vegetation quality}, number = {3}, pages = {429--435}, title = {{Determinants of pika population density vs. occupancy in the Southern Rocky Mountains}}, volume = {24}, year = {2014} } @incollection{Levins1970, abstract = {reference de base pour cell occupancy model avec levins 1969}, author = {Levins, Richard}, booktitle = {Some Mathematical Questions in Biology, volume 2 of Lectures on Mathematics in the Life Sciences}, pages = {76--107}, title = {{Extinction}}, volume = {2}, year = {1970} } @article{Smith2015, abstract = {Metapopulation dynamics of American pikas (Ochotona princeps) at Bodie, California, were investigated with a series of annual-biennial occupancy surveys from 1989-2010 and compared with earlier censuses in 1972 and 1977. The pika population at Bodie represents one of the best examples of a classic metapopulation system: the pikas live in spatially distinct habitat patches scattered across an open landscape, all local populations are small and have a significant risk of extinction (patch extinction), dispersal among patches appears to be distance-dependent, and the dynamics of local populations appear to be asynchronous. Observed occurrences of patch extinctions (114) and re-colonizations (109) varied greatly among the 18 census intervals. Multiple non-trivial patch extinctions and re-colonizations refute an earlier finding claiming the occupancy pattern of pikas at Bodie could be explained by an extinction-disk model. By 1991 the southern constellation of patches underwent a metapopulation collapse, apparently the result of stochasticity of metapopulation dynamics in a small network that amplified the tendency toward regional extinction. Because of recent concern that American pikas may be increasingly vulnerable to warm temperatures due to climate change, and because the Bodie pika population represents the longest study of the species in a low-elevation (warm) environment, the potential impact of temperature on metapopulation dynamics was examined. There were no meaningful relationships between number of patch extinctions or re-colonizations with mean monthly maximum temperature in June, July and August, or number of days greater than or equal to 25o C and greater than or equal to 28o C, in the same or prior year. Further, there has been no decline in percent patch occupancy in the northern constellation of patches since 1989. Thus, there is no evidence that warm temperatures have negatively affected pika persistence directly. Warm temperatures, however, could have impeded the dispersal of colonists moving from north to south, thus contributing to the failure of this region to become repopulated.}, annote = {Paper examines the Bodie pika population from 1972-present. The study focuses on the south going extinct, and recolonization/extinction events. They found that temperature had no significant effect on these events. They point out that warm weather could have impeded pikas from dispersing from North to South -discuss problems associated with gaps in census intervals -6.3 extinctions/year, 6.1 recolonizations/year between 1989 and 2010 -no sig. decline in patch occupancy during this time -temp. has increased by 1 degree C since 1895 **argue that 15 patches should no longer be used in future modeling of the metapopulation- patches becoming unsuitable over a given time period (have not has pikas since 1972) Discuss how many factors should affect the south and north the same b/c of the proximity, instead talus or climate may be the cuplprite}, author = {Smith, Andrew T and Nagy, John D}, doi = {10.1093/jmammal/gyv040}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Nagy - 2015 - Population resilience in an American pika (emph{\{}Ochotona princeps{\}}).pdf:pdf}, issn = {1545-1542}, journal = {Journal of Mammalogy}, keywords = {pika}, number = {2}, pages = {393--404}, title = {{Population resilience in an American pika ($\backslash$emph{\{}Ochotona princeps{\}})}}, volume = {96}, year = {2015} } @article{Fahrig1998, abstract = {The goal of this study was to delineate the circumstances in which fragmentation of breeding habitat affects population survival. Fragmentation is defined (literally) as the breaking apart of habitat; note fragmentation does not imply loss of habitat. I developed a spatially explicit simulation model in which I varied the spatial pattern of breeding habitat in the landscape from contagious to fragmented, while also varying a disturbance regime, breeding habitat permanence, and the life history and movement attributes of organisms living in the landscape. The simulation results suggest that fragmentation of breeding habitat affects population survival only under the following relatively narrow set of conditions: (1) the average between-generation movement distance of the organism is about 1-3 times the expected nearest distance between breeding sites; (2) the breeding habitat of the organism covers less than 20{\%} of the landscape: (3) the habitat is not ephemeral; (4) the organism has high breeding site fidelity; and (5) the mortality rate in the non-breeding habitat areas is much higher than the mortality rate in breeding habitat areas. Note that all of these conditions must hold for there to be an effect of breeding habitat fragmentation on population survival. These results suggest that spatially explicit simulation modelling of population dynamics is only necessary under a relatively narrow range of conditions.}, author = {Fahrig, Lenore}, doi = {10.1016/S0304-3800(97)00163-4}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fahrig - 1998 - When does fragmentation of breeding habitat affect population survival.pdf:pdf}, isbn = {0304-3800}, issn = {03043800}, journal = {Ecological Modelling}, keywords = {Habitat fragmentation,Habitat loss,Spatially explicit modelling}, pages = {273--292}, pmid = {2062}, title = {{When does fragmentation of breeding habitat affect population survival?}}, volume = {105}, year = {1998} } @article{Vermeij2013, abstract = {Organisms have been important agents of selection throughout the history of life. The processes and outcomes of this selection are the subject of this review. Among these, escalation is the most widespread. The primary selective agents are powerful competitors and consumers, which together push many populations toward higher performance in acquiring and defending resources while relegating less competitive species to physiologically marginal settings, where escalation also ensues. The extent to which performance standards rise depends on enabling factors, which control availability of and access to resources. By establishing positive feedbacks between species and enabling factors, effective competitors regulate and enhance resource supply. The pace of escalation toward greater power and reach is dictated by geological factors as well as by growing interdependencies between species and their resources. Evolutionary events on land related to the production of oxygen may have been instrumental in triggering the major episodes of escalation.}, author = {Vermeij, Geerat J}, doi = {doi:10.1146/annurev-earth-050212-124123}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vermeij - 2013 - On Escalation.pdf:pdf}, issn = {0084-6597}, journal = {Annual Review of Earth and Planetary Sciences}, keywords = {coevolution,enabling factors,phanerozoic,predation,red queen}, pages = {1--19}, title = {{On Escalation}}, url = {http://www.annualreviews.org/doi/abs/10.1146/annurev-earth-050212-124123}, volume = {41}, year = {2013} } @incollection{Vermeij2005, annote = {-over the longterm, invasions can have beneficial effects for ecosystems}, author = {Vermeij, Geerat J}, booktitle = {Species invasions insights into ecology, evolution, and biogeography}, chapter = {12}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vermeij - 2005 - Invasion as expectation a historical fact of life.pdf:pdf}, pages = {315--339}, title = {{Invasion as expectation: a historical fact of life}}, url = {http://www.cabdirect.org/abstracts/20073059162.html}, year = {2005} } @article{Wooley2010, author = {Wooley, John C and Godzik, Adam and Friedberg, Iddo}, doi = {10.1371/journal.pcbi.1000667}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wooley, Godzik, Friedberg - 2010 - A Primer on Metagenomics.pdf:pdf}, journal = {PLoS Computational Biology}, keywords = {genetics,genomics,review}, number = {2}, title = {{A Primer on Metagenomics}}, volume = {6}, year = {2010} } @article{Higham2015, annote = {Investigated pattern of loss of an innovation, or a simplification- adhesive system in geckos Typically losses in innovation are thought about with limbless snakes, vision loss (cave fish) Packy-dacky-lus can't place digits all the way down if you have an adhesive pad-incline makes this even worse A{\_}simp geckos have evolved longer or shortter limb segments compared to fully functional adhesive systems PC1- femur depression at footfall, knee angle, and a bunch of other things PC2- contains a number of similar variables as PC1 Identical rates of evolution for knematic variables on the level surface, on the incline surface A{\_}simp is evolving 2.7 times faster}, author = {Higham, Timothy E. and Birn-Jeffery, Aleksandra V. and Collins, Clint E. and Hulsey, C. Darrin and Russell, Anthony P.}, doi = {10.1073/pnas.1418979112}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Higham et al. - 2015 - Adaptive simplification and the evolution of gecko locomotion Morphological and biomechanical consequences of los.pdf:pdf}, isbn = {1418979112}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {18}, pages = {809--814}, title = {{Adaptive simplification and the evolution of gecko locomotion: Morphological and biomechanical consequences of losing adhesion}}, url = {http://www.pnas.org/lookup/doi/10.1073/pnas.1418979112}, volume = {112}, year = {2015} } @article{Price2012, annote = {could trickle down in Haemulon affect inference about reef fish in general}, author = {Price, Samantha a and Tavera, Jose J and Near, Thomas J and Wainwright, Peter C}, doi = {10.5061/dryad.s049s}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Price et al. - 2012 - Elevated Rates of Morphological and Functional Diversification in Reef-Dwelling Haemulid Fishes.pdf:pdf}, journal = {Evolution}, keywords = {as habitat complexity increases,complexity and species richness,e,g,is well established,live in the habitat,macarthur,number of species that,so does the,the area,the relationship between habitat}, number = {2}, pages = {417--428}, title = {{Elevated Rates of Morphological and Functional Diversification in Reef-Dwelling Haemulid Fishes}}, volume = {67}, year = {2012} } @article{Gavrilets2009, abstract = {Biologists have long been fascinated by the exceptionally high diversity displayed by some evolutionary groups. Adaptive radiation in such clades is not only spectacular, but is also an extremely complex process influenced by a variety of ecological, genetic, and developmental factors and strongly dependent on historical contingencies. Using modeling approaches, we identify 10 general patterns concerning the temporal, spatial, and genetic/morphological properties of adaptive radiation. Some of these are strongly supported by empirical work, whereas for others, empirical support is more tentative. In almost all cases, more data are needed. Future progress in our understanding of adaptive radiation will be most successful if theoretical and empirical approaches are integrated, as has happened in other areas of evolutionary biology.}, author = {Gavrilets, Sergey and Losos, Jonathan B}, doi = {10.1126/science.1157966}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gavrilets, Losos - 2009 - Adaptive radiation contrasting theory with data.pdf:pdf}, isbn = {0036-8075}, issn = {0036-8075}, journal = {Science (New York, N.Y.)}, pages = {732--737}, pmid = {19197052}, title = {{Adaptive radiation: contrasting theory with data.}}, volume = {323}, year = {2009} } @article{Steltzer2009, annote = {-we don't always see the ecological response in plants to GCC that we would expect because of evolutionary constraits --earlier flowering also leads to earlier senescence}, author = {Steltzer, Heidi and Post, Eric}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Steltzer, Post - 2009 - Seasons and Life Cycles.pdf:pdf}, journal = {Science}, number = {May}, pages = {2--4}, title = {{Seasons and Life Cycles}}, volume = {324}, year = {2009} } @article{Takemoto2014, annote = {-found that seasonality in rainfall affected freshwater systems -temperature seasonality influences mutualistic network structure}, author = {Takemoto, Kazuhiro and Kanamaru, Saori and Feng, Wenfeng}, doi = {10.1016/j.biosystems.2014.06.002}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Takemoto, Kanamaru, Feng - 2014 - Climatic seasonality may affect ecological network structure Food webs and mutualistic networks.pdf:pdf}, issn = {0303-2647}, journal = {BioSystems}, keywords = {Climate,Modularity,Network analysis,Network complexity,Seasonal variation}, pages = {29--37}, publisher = {Elsevier Ireland Ltd}, title = {{Climatic seasonality may affect ecological network structure: Food webs and mutualistic networks}}, url = {http://dx.doi.org/10.1016/j.biosystems.2014.06.002}, volume = {121}, year = {2014} } @article{Price2014, abstract = {Speciation generally involves a three-step process--range expansion, range fragmentation and the development of reproductive isolation between spatially separated populations. Speciation relies on cycling through these three steps and each may limit the rate at which new species form. We estimate phylogenetic relationships among all Himalayan songbirds to ask whether the development of reproductive isolation and ecological competition, both factors that limit range expansions, set an ultimate limit on speciation. Based on a phylogeny for all 358 species distributed along the eastern elevational gradient, here we show that body size and shape differences evolved early in the radiation, with the elevational band occupied by a species evolving later. These results are consistent with competition for niche space limiting species accumulation. Even the elevation dimension seems to be approaching ecological saturation, because the closest relatives both inside the assemblage and elsewhere in the Himalayas are on average separated by more than five million years, which is longer than it generally takes for reproductive isolation to be completed; also, elevational distributions are well explained by resource availability, notably the abundance of arthropods, and not by differences in diversification rates in different elevational zones. Our results imply that speciation rate is ultimately set by niche filling (that is, ecological competition for resources), rather than by the rate of acquisition of reproductive isolation.}, annote = {rfind that repdouctive isolation and competition limit speciation -{\textgreater} find that body size and general morphologies evolved early in randiation of songbirds and isolation evolving secondarily -argue that speciation is result of niche filling (ie competition for resources) and not through reproductive isolation -niche filling hypothesis: -alternative hypothesis: speciation rate would be constant if drift was the only process driving diversification how general are these results given birds can expand their ranges so quickly based on range expansion if you don't sample randomly to build you phlogeny you may lose information on how many species you would expect over time -you will less estimate a slowdone in diversification rate if you don't sample enough of the species -as you saturate niches, speciation rate will also decline}, author = {Price, Trevor D and Hooper, Daniel M and Buchanan, Caitlyn D and Johansson, Ulf S and Tietze, D Thomas and Alstr{\"{o}}m, Per and Olsson, Urban and Ghosh-Harihar, Mousumi and Ishtiaq, Farah and Gupta, Sandeep K and Martens, Jochen and Harr, Bettina and Singh, Pratap and Mohan, Dhananjai}, doi = {10.1038/nature13272}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Price et al. - 2014 - Niche filling slows the diversification of Himalayan songbirds.pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {Altitude,Animals,Body Size,China,Ecosystem,Genetic Speciation,India,Phylogeny,Reproduction,Songbirds,Songbirds: anatomy {\&} histology,Songbirds: classification,Songbirds: physiology,Tibet}, pages = {222--5}, pmid = {24776798}, title = {{Niche filling slows the diversification of Himalayan songbirds.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24776798}, volume = {509}, year = {2014} } @article{Seehausen2004, abstract = {Whether interspecific hybridization is important as a mechanism that generates biological diversity is a matter of controversy. Whereas some authors focus on the potential of hybridization as a source of genetic variation, functional novelty and new species, others argue against any important role, because reduced fitness would typically render hybrids an evolutionary dead end. By drawing on recent developments in the genetics and ecology of hybridization and on principles of ecological speciation theory, I develop a concept that reconciles these views and adds a new twist to this debate. Because hybridization is common when populations invade new environments and potentially elevates rates of response to selection, it predisposes colonizing populations to rapid adaptive diversification under disruptive or divergent selection. I discuss predictions and suggest tests of this hybrid swarm theory of adaptive radiation and review published molecular phylogenies of adaptive radiations in light of the theory.}, annote = {proposes idea that hybridization occures both before and during adaptations radiations argues to reconcile tradeoff between fitness costs of hybrids and the role of hybridization as sounce of genetic variation hybridization is common when species invade new evironments which elevates rates of reponse to selection-{\textgreater} causes these populations to have rapid adaptive diversification through diruptive or divergent selection =essentially similar conditions are appropriate for both hybridization and adaptive radiation hybridization allows for new adaptive trait combinations that would allow diversification Why is hybridization interesting? -it definitely happens, plant biologists have recongnized this b/c of alloploidy. Zoologists typically think of hybrids as simply being slected against -hybridization creates lots of variation that can help during an adaptive radiation If a species is near a adaptive peak, how will they ever get to another adaptive peak -{\textgreater} he argues that hybridzation allows F1 progeny to be close to other adaptive peaks}, author = {Seehausen, Ole}, doi = {10.1016/j.tree.2004.01.003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Seehausen - 2004 - Hybridization and adaptive radiation.pdf:pdf}, isbn = {0169-5347}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {4}, pages = {198--207}, pmid = {16701254}, title = {{Hybridization and adaptive radiation}}, volume = {19}, year = {2004} } @article{Lande1983, abstract = {Natural selection acts on phenotypes, regardless of their genetic basis, and produces immediate phenotypic effects within a generation that can be measured without recourse to principles of heredity or evolution. In contrast, evolutionary response to selection, the genetic change that occurs from one generation to the next, does depend on genetic variation. Animal and plant breeders routinely distinguish phenotypic selection from evolutionary response to selection (Mayo, 1980; Falconer, 1981). Upon making this critical distinction, emphasized by Haldane (1954), precise methods can be formulated for the measurement of phenotypic natural selection.}, author = {Lande, R. and Arnold, S.J. J}, doi = {10.2307/2408842}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lande, Arnold - 1983 - The measurement of selection on correlated characters.pdf:pdf}, isbn = {00143820}, issn = {0014-3820}, journal = {Evolution}, number = {6}, pages = {1210--1226}, pmid = {279}, title = {{The measurement of selection on correlated characters}}, url = {http://www.jstor.org/stable/2408842}, volume = {37}, year = {1983} } @article{Holder2003, abstract = {The construction of evolutionary trees is now a standard part of exploratory sequence analysis. Bayesian methods for estimating trees have recently been proposed as a faster method of incorporating the power of complex statistical models into the process. Researchers who rely on comparative analyses need to understand the theoretical and practical motivations that underlie these new techniques, and how they differ from previous methods. The ability of the new approaches to address previously intractable questions is making phylogenetic analysis an essential tool in an increasing number of areas of genetic research.}, author = {Holder, Mark and Lewis, Paul O}, doi = {10.1038/nrg1044}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Holder, Lewis - 2003 - Phylogeny estimation traditional and Bayesian approaches.pdf:pdf}, isbn = {1471-0056}, issn = {14710056}, journal = {Nature reviews. Genetics}, number = {April}, pages = {275--284}, pmid = {12671658}, title = {{Phylogeny estimation: traditional and Bayesian approaches.}}, volume = {4}, year = {2003} } @article{White1998, author = {White, Frances J}, doi = {10.1023/A:1020314001349}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White - 1998 - The Importance of Seasonality in Primatology.pdf:pdf}, isbn = {0164-0291}, issn = {0164-0291}, journal = {International Journal of Primatology}, number = {6}, pages = {1981--1984}, title = {{The Importance of Seasonality in Primatology}}, volume = {19}, year = {1998} } @article{Gomulkiewicz2013, abstract = {Laboratory model systems and mathematical models have shed considerable light on the fundamental properties and processes of evolutionary rescue. But it remains to determine the extent to which these model-based findings can help biologists predict when evolution will fail or succeed in rescuing natural populations that are facing novel conditions that threaten their persistence. In this article, we present a prospectus for transferring our basic understanding of evolutionary rescue to wild and other non-laboratory populations. Current experimental and theoretical results emphasize how the interplay between inheritance processes and absolute fitness in changed environments drive population dynamics and determine prospects of extinction. We discuss the challenge of inferring these elements of the evolutionary rescue process in field and natural settings. Addressing this challenge will contribute to a more comprehensive understanding of population persistence that combines processes of evolutionary rescue with developmental and ecological mechanisms.}, annote = {A few key properties determine if evolutionary rescue will happen and work: -form of environ change -size of the population -rate of pop growth -amount of gen var Challenges to detecting evo rescue}, author = {Gomulkiewicz, Richard and Shaw, Ruth G}, doi = {10.1098/rstb.2012.0093}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gomulkiewicz, Shaw - 2013 - Evolutionary rescue beyond the models.pdf:pdf}, isbn = {0962-8436}, issn = {1471-2970}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {Adaptation, Physiological,Angiosperms,Angiosperms: genetics,Angiosperms: physiology,Biological Evolution,Climate,Ecosystem,Empirical Research,Extinction, Biological,Genetic Variation,Models, Biological,Phenotype,Seeds,Seeds: physiology,Selection, Genetic,Stress, Physiological}, number = {December 2012}, pages = {20120093}, pmid = {23209173}, title = {{Evolutionary rescue beyond the models.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3538458{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {368}, year = {2013} } @article{Drake2013, author = {Drake, Patrick T. and Edwards, Christopher a. and Morgan, Steven G. and Dever, Edward P.}, doi = {10.1357/002224013808877099}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Drake et al. - 2013 - Influence of larval behavior on transport and population connectivity in a realistic simulation of the California.pdf:pdf}, issn = {00222402}, journal = {Journal of Marine Research}, pages = {317--350}, title = {{Influence of larval behavior on transport and population connectivity in a realistic simulation of the California Current System}}, url = {http://openurl.ingenta.com/content/xref?genre=article{\&}issn=0022-2402{\&}volume=71{\&}issue=4{\&}spage=317}, volume = {71}, year = {2013} } @article{Carlson2014, abstract = {Evolutionary rescue occurs when adaptive evolutionary change restores positive growth to declining populations and prevents extinction. Here we outline the diagnostic features of evolutionary rescue and distinguish this phenomenon from demographic and genetic rescue. We then synthesize the rapidly accumulating theoretical and experimental studies of evolutionary rescue, highlighting the demographic, genetic, and extrinsic factors that affect the probability of rescue. By doing so, we clarify the factors to target through management and conservation. Additionally, we identify several putative cases of evolutionary rescue in nature, but conclude that compelling evidence remains elusive. We conclude with a horizon scan of where the field might develop, highlighting areas of potential application, and suggest areas where experimental evaluation will help to evaluate theoretical predictions. {\textcopyright} 2014 The Authors.}, annote = {If dispersal is limited or plasticity is not enough, adaptation might be neccesary evolutionary rescues show a u-shaped pattern- but other phenomena will also cause this pattern migration load- when maladapted individuals are arriving via immmirgation Different meanings of rescue effect (demographic rescue), genetic, and evolutionary rescue Does short term rescue hinder or help populations in the long term? In a metapopulation, could you overshoot your optimal dispersal value (adaptively) b/c of time delays between patches?}, author = {Carlson, Stephanie M. and Cunningham, Curry J. and Westley, Peter a H}, doi = {10.1016/j.tree.2014.06.005}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Carlson, Cunningham, Westley - 2014 - Evolutionary rescue in a changing world.pdf:pdf}, isbn = {0169-5347}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {9}, pages = {521--530}, pmid = {25038023}, publisher = {Elsevier Ltd}, title = {{Evolutionary rescue in a changing world}}, url = {http://dx.doi.org/10.1016/j.tree.2014.06.005}, volume = {29}, year = {2014} } @article{Kremer2012, abstract = {Ecology Letters (2012) ABSTRACT: Forest trees are the dominant species in many parts of the world and predicting how they might respond to climate change is a vital global concern. Trees are capable of long-distance gene flow, which can promote adaptive evolution in novel environments by increasing genetic variation for fitness. It is unclear, however, if this can compensate for maladaptive effects of gene flow and for the long-generation times of trees. We critically review data on the extent of long-distance gene flow and summarise theory that allows us to predict evolutionary responses of trees to climate change. Estimates of long-distance gene flow based both on direct observations and on genetic methods provide evidence that genes can move over spatial scales larger than habitat shifts predicted under climate change within one generation. Both theoretical and empirical data suggest that the positive effects of gene flow on adaptation may dominate in many instances. The balance of positive to negative consequences of gene flow may, however, differ for leading edge, core and rear sections of forest distributions. We propose future experimental and theoretical research that would better integrate dispersal biology with evolutionary quantitative genetics and improve predictions of tree responses to climate change.}, author = {Kremer, Antoine and Ronce, Oph{\'{e}}lie and Robledo-Arnuncio, Juan J. and Guillaume, Fr{\'{e}}d{\'{e}}ric and Bohrer, Gil and Nathan, Ran and Bridle, Jon R. and Gomulkiewicz, Richard and Klein, Etienne K. and Ritland, Kermit and Kuparinen, Anna and Gerber, Sophie and Schueler, Silvio}, doi = {10.1111/j.1461-0248.2012.01746.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kremer et al. - 2012 - Long-distance gene flow and adaptation of forest trees to rapid climate change.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Adaptation,Climate change,Forest trees,Gene flow,Selection}, number = {May}, pages = {378--392}, pmid = {22372546}, title = {{Long-distance gene flow and adaptation of forest trees to rapid climate change}}, volume = {15}, year = {2012} } @article{VanderWal2013, abstract = {The current rapid rate of human-driven environmental change presents wild populations with novel conditions and stresses. Theory and experimental evidence for evolutionary rescue present a promising case for species facing environmental change persisting via adaptation. Here, we assess the potential for evolutionary rescue in wild vertebrates. Available information on evolutionary rescue was rare and restricted to abundant and highly fecund species that faced severe intentional anthropogenic selective pressures. However, examples from adaptive tracking in common species and genetic rescues in species of conservation concern provide convincing evidence in favour of the mechanisms of evolutionary rescue. We conclude that low population size, long generation times and limited genetic variability will result in evolutionary rescue occurring rarely for endangered species without intervention. Owing to the risks presented by current environmental change and the possibility of evolutionary rescue in nature, we suggest means to study evolutionary rescue by mapping genotype → phenotype → demography → fitness relationships, and priorities for applying evolutionary rescue to wild populations.}, author = {{Vander Wal}, E and Garant, D and Festa-Bianchet, M and Pelletier, F}, doi = {10.1098/rstb.2012.0090}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vander Wal et al. - 2013 - Evolutionary rescue in vertebrates evidence, applications and uncertainty.pdf:pdf}, isbn = {0962-8436}, issn = {1471-2970}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, keywords = {Adaptation, Biological,Alleles,Animals,Biological Evolution,Conservation of Natural Resources,Conservation of Natural Resources: methods,Environment,Genetic Association Studies,Genetic Fitness,Genetic Variation,Genetics, Population,Genetics, Population: methods,Population Density,Rabbits,Rats,Selection, Genetic,Stress, Physiological,Time Factors}, pages = {20120090}, pmid = {23209171}, title = {{Evolutionary rescue in vertebrates: evidence, applications and uncertainty.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3538456{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {368}, year = {2013} } @article{Hoffmann2015, annote = {is gene expression use being oversold? is genetic variation important? Or is load the more important measure? -if you can survive you may be able to actually purge deleterious alleles}, author = {Hoffmann, Ary and Griffin, Philippa and Dillon, Shannon and Catullo, Renee and Rahulraneunimelbeduau, Rahul Rane and Margaretbyrnedpawwagovau, Margaret Byrne and Jordan, Rebecca and Oakeshott, John and Weeks, Andrew and Lockhart, Peter}, doi = {10.1186/s40665-014-0009-x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hoffmann et al. - 2015 - A framework for incorporating evolutionary genomics into biodiversity conservation and management.pdf:pdf}, isbn = {4066501400}, journal = {Climate Change Responses}, keywords = {1,Decision framework,Evolutionary adaptation,Genomics,Management,Plasticity,about current and accelerating,biodiversity,climate change,climate change threats to,decision framework,even if,evolutionary adaptation,genomics,management,picture,plasticity,provides a very clear,the latest ipcc report}, number = {1}, pages = {23}, title = {{A framework for incorporating evolutionary genomics into biodiversity conservation and management}}, volume = {2}, year = {2015} } @article{Wolda1988, author = {Wolda, H}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wolda - 1988 - Insect seasonality Why.pdf:pdf}, journal = {Annual}, pages = {1--18}, title = {{Insect seasonality: Why?}}, volume = {19}, year = {1988} } @article{Kopp2014, abstract = {An increasing number of studies demonstrate phenotypic and genetic changes in natural populations that are subject to climate change, and there is hope that some of these changes will contribute to avoiding species extinctions ('evolutionary rescue'). Here, we review theoretical models of rapid evolution in quantitative traits that can shed light on the potential for adaptation to a changing climate. Our focus is on quantitative-genetic models with selection for a moving phenotypic optimum. We point out that there is no one-to-one relationship between the rate of adaptation and population survival, because the former depends on relative fitness and the latter on absolute fitness. Nevertheless, previous estimates that sustainable rates of genetically based change usually do not exceed 0.1 haldanes (i.e., phenotypic standard deviations per generation) are probably correct. Survival can be greatly facilitated by phenotypic plasticity, and heritable variation in plasticity can further speed up genetic evolution. Multivariate selection and genetic correlations are frequently assumed to constrain adaptation, but this is not necessarily the case and depends on the geometric relationship between the fitness landscape and the structure of genetic variation. Similar conclusions hold for adaptation to shifting spatial gradients. Recent models of adaptation in multispecies communities indicate that the potential for rapid evolution is strongly influenced by interspecific competition.}, annote = {-review of models used to study selection for a moving phenotypic optimum---mostly focused on quantative genetics models -most models are based on models of stabalizing selection with an optimum that moves --look at abrupt change, constant change, or fluctuating change -strong selection only works i there is high mean fitness -under climate change there should be iincreases in variation of fluctuating selection -important point that pop dyn depend on absolute fitness and evolution depends on relative fitnes -these models assume linear change in environment. Why not make it more specific to climate change or something else?}, author = {Kopp, Michael and Matuszewski, Sebastian}, doi = {10.1111/eva.12127}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kopp, Matuszewski - 2014 - Rapid evolution of quantitative traits Theoretical perspectives.pdf:pdf}, isbn = {1752-4571}, issn = {17524563}, journal = {Evolutionary Applications}, keywords = {Adaptation,Climate change,Habitat degradation,Natural selection and contemporary evolution,Phenotypic plasticity,Population dynamics,Population genetics,Quantitative genetics}, pages = {169--191}, pmid = {24454555}, title = {{Rapid evolution of quantitative traits: Theoretical perspectives}}, volume = {7}, year = {2014} } @article{Fiedler2002, abstract = {Interannual variability of the physical environment in the eastern tropical Pacific Ocean (ETP) and biological effects of this variability are reviewed and compared to variability in the north- eastern Pacific. El Ni{\~{n}}o Southern Oscillation (ENSO) scale variability of 2 to 7 yr periods is dominant in the eastern equatorial Pacific and decadal scale variability of 10 to 30 yr periods is dominant in the northeastern Pacific. In the eastern Pacific warm pool at the center of the ETP, temporal variability at any scale is relatively low. ENSO warm (El Ni{\~{n}}o) and cold (La Ni{\~{n}}a) events have had a variety of effects on marine populations and ecosystems, but these effects are generally followed by recovery within a few years. El Ni{\~{n}}o effects such as mortality or reproductive failure are most severe on pop- ulations dependent on local feeding or breeding grounds in coastal waters or around islands. Decadal variability has also caused change in populations and ecosystems. Most of these effects have been observed in the California Current, Gulf of Alaska, and other well studied regions of the Pacific. The 1976–1977 phase change or ‘regime shift' is the most well known case of decadal variability. It affected the physical environment throughout the Pacific Ocean and had major effects on North Pacific ecosystems. No regime shift has been detected in the ETP since 1977. However, ENSO vari- ability continues, an unusually persistent warming prevailed in the early 1990s and the thermocline has shoaled in the ETP warm pool area since 1980. Potential population effects on dolphin stocks are discussed. Interaction of environmental changes with other factors, such as fishery stress or mortality, may also induce population effects.}, author = {Fiedler, Pc}, doi = {10.3354/meps244265}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fiedler - 2002 - Environmental change in the eastern tropical Pacific Ocean review of ENSO and decadal variability.pdf:pdf}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, pages = {265--283}, title = {{Environmental change in the eastern tropical Pacific Ocean: review of ENSO and decadal variability}}, volume = {244}, year = {2002} } @article{Rosenblat1980, author = {Rosenblat, S.}, doi = {10.1007/s00285-006-0020-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rosenblat - 1980 - Population models in a periodically fluctuating environment.pdf:pdf}, isbn = {0028500302622}, journal = {Journal of Mathematical Biology}, keywords = {competing species,fluctuating environment - -}, pages = {23--36}, title = {{Population models in a periodically fluctuating environment}}, volume = {9}, year = {1980} } @article{Betini2015, author = {Betini, Gustavo S. and Fitzpatrick, Mark J. and Norris, D. Ryan}, doi = {10.1111/ele.12432}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Betini, Fitzpatrick, Norris - 2015 - Experimental evidence for the effect of habitat loss on the dynamics of migratory networks.pdf:pdf}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {1,2015,betini,climate change,drosophila melanogaster,ecology letters,graph theory,gustavo s,mark j,migratory connectivity}, pages = {1--9}, title = {{Experimental evidence for the effect of habitat loss on the dynamics of migratory networks}}, url = {http://doi.wiley.com/10.1111/ele.12432}, year = {2015} } @article{Felsenstein2001, abstract = {none}, author = {Felsenstein, J}, doi = {10.1080/10635150119297}, isbn = {1063-5157}, issn = {1063-5157}, journal = {Systematic biology}, number = {4}, pages = {465--467}, pmid = {12116645}, title = {{The troubled growth of statistical phylogenetics.}}, volume = {50}, year = {2001} } @article{Sheth2014, annote = {Is it obvious that range size is correlated with temperature breadth? Take five species pairs on phylogeny that have different levels of widespread vs not widespread ranges Did restricted species simply branch off from widespread species?- maybe restricted species will expand out over time}, author = {Sheth, Seema N. and Angert, Amy L.}, doi = {10.1111/evo.12494}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sheth, Angert - 2014 - The Evolution of Environmental Tolerance and Range Size a Comparison of Geographically Restricted and Widespread.pdf:pdf}, issn = {00143820}, journal = {Evolution}, keywords = {climatic variability hypothesis,generalist trade-,genetic variation,geographic range size,geographic range size can,magnitude among,niche breadth,offs,specialist,thermal performance curve,vary by orders of}, pages = {2917--2931}, title = {{The Evolution of Environmental Tolerance and Range Size: a Comparison of Geographically Restricted and Widespread Mimulus}}, url = {http://doi.wiley.com/10.1111/evo.12494}, volume = {68}, year = {2014} } @article{Boyce1979, author = {Boyce, Mark S.}, doi = {10.2307/2678832}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Boyce - 1979 - Seasonality and patterns of natural selection for life histories.pdf:pdf}, isbn = {1630130044}, issn = {10773711}, journal = {The American Naturalist}, number = {4}, pages = {569--583}, title = {{Seasonality and patterns of natural selection for life histories}}, volume = {114}, year = {1979} } @article{Stenseth2003, abstract = {Voles and lemmings show extensive variation in population dynamics regulated across and within species. In an attempt to develop and test generic hypotheses explaining these differences, we studied 84 populations of the gray-sided vole (Clethrionomys rufocanus) in Hokkaido, Japan. We show that these populations are limited by a combination of density-independent factors (such as climate) and density-dependent processes (such as specialist predators). We show that density-dependent regulation primarily occurs in winter months, so that populations experiencing longer winters tend to have a stronger delayed density-dependence and, as a result, exhibit regular density cycles. Altogether, we demonstrate that seasonality plays a key role in determining whether a vole population is cyclic or not.}, author = {Stenseth, Nils Chr and Viljugrein, Hildegunn and Saitoh, Takashi and Hansen, Thomas F and Kittilsen, Marte O and B{\o}lviken, Erik and Gl{\"{o}}ckner, Fredrik}, doi = {10.1073/pnas.1935306100}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stenseth et al. - 2003 - Seasonality, density dependence, and population cycles in Hokkaido voles.pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {TStenseth, N. C., H. Viljugrein, T. Saitoh, T. F. Hansen, M. O. Kittilsen, E. B{\o}lviken, and F. Gl{\"{o}}ckner. 2003. Seasonality, density dependence, and population cycles in Hokkaido voles. Proceedings of the National Academy of Sciences of the United States o}, pages = {11478--11483}, pmid = {14504382}, title = {{Seasonality, density dependence, and population cycles in Hokkaido voles.}}, volume = {100}, year = {2003} } @article{Kaltz1998, author = {Kaltz, Oliver and Shykoff, Jacqui a}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kaltz, Shykoff - 1998 - Local adaptation in host – parasite systems.pdf:pdf}, journal = {Heredity}, keywords = {coevolution,conventional wisdom,frequency-dependent selection,it is conventional wisdom,metapopulation,parasites are locally adapted,short,sympatry,that parasites with relatively,time-lagged cycles}, number = {May}, pages = {361--370}, title = {{Local adaptation in host – parasite systems}}, volume = {81}, year = {1998} } @article{Morehouse2013, abstract = {Seasonal polyphenisms are widespread in nature, yet the selective pressures responsible for their evolution remain poorly understood. Previous work has largely focussed either on the developmental regulation of seasonal polyphenisms or putative 'top-down' selective pressures such as predation that may have acted to drive phenotypic divergence. Much less is known about the influence of seasonal variation in resource availability or seasonal selection on optimal resource allocation. We studied seasonal variation in resource availability, uptake and allocation in Araschnia levana L., a butterfly species that exhibits a striking seasonal colour polyphenism consisting of predominantly orange 'spring form' adults and black-and-white 'summer form' adults. 'Spring form' individuals develop as larvae in the late summer, enter a pupal diapause in the fall and emerge in the spring, whereas 'summer form' individuals develop directly during the summer months. We find evidence for seasonal declines in host plant quality, and we identify similar reductions in resource uptake in late summer, 'spring form' larvae. Further, we report shifts in the body composition of diapausing 'spring form' pupae consistent with a physiological cost to overwintering. However, these differences do not translate into detectable differences in adult body composition. Instead, we find minor seasonal differences in adult body composition consistent with augmented flight capacity in 'summer form' adults. In comparison, we find much stronger signatures of sex-specific selection on patterns of resource uptake and allocation. Our results indicate that resource dynamics in A. levana are shaped by seasonal fluctuations in host plant nutrition, climatic conditions and intraspecific interactions.}, author = {Morehouse, N. I. and Mandon, N. and Christides, J. P. and Body, M. and Bimbard, G. and Casas, J.}, doi = {10.1111/jeb.12051}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Morehouse et al. - 2013 - Seasonal selection and resource dynamics in a seasonally polyphenic butterfly.pdf:pdf}, isbn = {1420-9101 (Electronic)$\backslash$r1010-061X (Linking)}, issn = {1010061X}, journal = {Journal of Evolutionary Biology}, keywords = {Araschnia levana,Diapause,Nutritional ecology,Polyphenism,Seasonal selection,Sexual dimorphism}, pages = {175--185}, pmid = {23194094}, title = {{Seasonal selection and resource dynamics in a seasonally polyphenic butterfly}}, volume = {26}, year = {2013} } @article{Hastings1984, author = {Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 1984 - Evolution in a seasonal environment simplicity lost.pdf:pdf}, journal = {Evolution}, number = {2}, pages = {350--358}, title = {{Evolution in a seasonal environment: simplicity lost?}}, volume = {38}, year = {1984} } @article{Betini2014, abstract = {In seasonal populations, vital rates are not only determined by the direct effects of density at the beginning of each season, but also by density at the beginning of past seasons. Such delayed density dependence can arise via non-lethal effects on individuals that carry over to influence per capita rates. In this study, we examine (i) whether parental breeding density influences offspring size, (ii) how this could carry over to affect offspring survival during the subsequent non-breeding period and (iii) the population consequences of this relationship. Using Drosophila melanogaster, the common fruit fly, submitted to distinct breeding and non-breeding seasons, we first used a controlled laboratory experiment to show that high parental breeding density leads to small offspring size, which then affects offspring survival during the non-breeding period but only at high non-breeding densities. We then show that a model with the interaction between parental breeding density and offspring density at the beginning of the non-breeding season best explained offspring survival over 36 replicated generations. Finally, we developed a biseasonal model to show that the positive relationship between parental density and offspring survival can dampen fluctuations in population size between breeding and non-breeding seasons. These results highlight how variation in parental density can lead to differences in offspring quality which result in important non-lethal effects that carry over to influence per capita rates the following season, and demonstrate how this phenomenon can have important implications for the long-term dynamics of seasonal populations.}, author = {Betini, Gustavo S and Griswold, Cortland K and Prodan, Livia and Norris, D Ryan}, doi = {10.1111/1365-2656.12225}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Betini et al. - 2014 - Body size, carry-over effects and survival in a seasonal environment consequences for population dynamics.pdf:pdf}, issn = {1365-2656}, journal = {The Journal of Animal Ecology}, keywords = {Drosophila melanogaster,delayed density dependence,seasonal density dependence,seasonality}, pages = {1313--1321}, pmid = {24708450}, title = {{Body size, carry-over effects and survival in a seasonal environment: consequences for population dynamics}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24708450}, volume = {83}, year = {2014} } @phdthesis{Betini2014a, author = {Betini, Gustavo Sigrist}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Betini - 2014 - Dynamics of Populations in Seasonal Environments.pdf:pdf}, title = {{Dynamics of Populations in Seasonal Environments}}, year = {2014} } @article{Sexton2009, abstract = {Species range limits involve many aspects of evolution and ecology, from species distribution and abundance to the evolution of niches. Theory sug- gests myriad processes by which range limits arise, including competitive exclusion, Allee effects, and gene swamping; however, most models remain empirically untested. Range limits are correlated with a number of abiotic and biotic factors, but further experimentation is needed to understand un- derlying mechanisms. Range edges are characterized by increased genetic isolation, genetic differentiation, and variability in individual and population performance, but evidence for decreased abundance and fitness is lacking. Evolution of range limits is understudied in natural systems; in particular, the role of gene flow in shaping range limits is unknown. Biological invasions and rapid distribution shifts caused by climate change represent large-scale experiments on the underlying dynamics of range limits. A better fusion of experimentation and theory will advance our understanding of the causes of range limits.}, annote = {abundance and fitness do not generally decline as you get closer to range limits Role of LA: -edge pops may adapt with enough gen var to respond to select. -fitness may be lower at edge of range- empirical data do not support this claim -data does not support idea that abundance is lower at range margin Role of dispersal/gene flow: -from central to edge can be bad Empirical example to test theory move species beyond range}, author = {Sexton, Jason P. and McIntyre, Patrick J. and Angert, Amy L. and Rice, Kevin J.}, doi = {10.1146/annurev.ecolsys.110308.120317}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sexton et al. - 2009 - Evolution and Ecology of Species Range Limits.pdf:pdf}, isbn = {1543-592X}, issn = {1543-592X}, journal = {Annual Review of Ecology, Evolution, and Systematics}, keywords = {abiotic factors,adaptation,biogeography,biotic factors,climate change,gene flow,geographic,geographic boundary,geographic distribution,invasive species,mechanistic models,natural selection,niche,range}, pages = {415--436}, title = {{Evolution and Ecology of Species Range Limits}}, volume = {40}, year = {2009} } @article{Elton1924, abstract = {I. Four main points are dealt with :--(a) The widespread existence of fluctuations in the numbers of animals.(b) The existence, in many birds and mammals, of periodic fluctuations (p.f.).(c) The cause of the latter, which must be some periodic climatic change acting over wide areas.(d) The effects of fluctuations in general, and in particular of the p.f., on the method of evolution and other biological phenomena.2. A short sketch is given of what is known about short- period climatic cycles (2 to 20 years), and their causes.3. P.f. of lemmings have an average period of about 3[1/2] years. The maxima in numbers occur synchronously in North America and Europe, and probably all round the arctic regions.The varying hare in Canada has a period of 10 to 11 years.5. The only regular periods shown by the animals dealt with are the short one of 3[1/2] years and the longer one of 10 to 11 years. The former is probably more marked in the arctic and the other further south.6. The sandgrouse p.f. point to the existence of an 11-year climatic cycle in the deserts of Central Asia.7. The effects of these p.f. on evolution must be very great, although at present problematical; but the following suggestions are made :--(a) Natural selection of some characters must be periodic.(b) There will be different types of natural selection at the maxima and minima of numbers.(c) The struggle for existence, and therefore natural selection, tend to cease temporarily during the rapid expansion in numbers from a minimum, and new mutations have then a chance to get established and spread, i.e. without the aid of natural selection. This might happen only rarely.(d) This would explain the origin and survival of non adaptive characters in a species.(e) On the other hand periodic reduction in numbers will act as an important factor causing uniformity in the species.(f) The opposing factors (c) and (e) will vary much in different species, and the problem will require the combined attentions of mathematicians, and of ecologists working on the methods of regulation of the numbers of animals.(g) This mechanical uniformity factor, since it acts independently of natural selection, explains how a particular structure or habit may evolve, when it only has a general adaptive significance.}, annote = {-begins with fluctuations in climate caused by sunspots, the moon, volcanos, etc -He then goes into periodic fluctuations in animal numbers Mostly discusses interannual fluctuations that result in cycles Talks about winter and summer seasons}, author = {Elton, C S}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Elton - 1924 - Periodic fluctuations in the numbers of animals their causes and effects.pdf:pdf}, isbn = {0022-0949}, issn = {0022-0949}, journal = {British Journal of Experimental Biology}, pages = {119--163}, pmid = {2059}, title = {{Periodic fluctuations in the numbers of animals: their causes and effects}}, volume = {2}, year = {1924} } @article{Lowry2010, abstract = {The role of chromosomal inversions in adaptation and speciation is controversial. Historically, inversions were thought to contribute to these processes either by directly causing hybrid sterility or by facilitating the maintenance of co-adapted gene complexes. Because inversions suppress recombination when heterozygous, a recently proposed local adaptation mechanism predicts that they will spread if they capture alleles at multiple loci involved in divergent adaptation to contrasting environments. Many empirical studies have found inversion polymorphisms linked to putatively adaptive phenotypes or distributed along environmental clines. However, direct involvement of an inversion in local adaptation and consequent ecological reproductive isolation has not to our knowledge been demonstrated in nature. In this study, we discovered that a chromosomal inversion polymorphism is geographically widespread, and we test the extent to which it contributes to adaptation and reproductive isolation under natural field conditions. Replicated crosses between the prezygotically reproductively isolated annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus, revealed that alternative chromosomal inversion arrangements are associated with life-history divergence over thousands of kilometers across North America. The inversion polymorphism affected adaptive flowering time divergence and other morphological traits in all replicated crosses between four pairs of annual and perennial populations. To determine if the inversion contributes to adaptation and reproductive isolation in natural populations, we conducted a novel reciprocal transplant experiment involving outbred lines, where alternative arrangements of the inversion were reciprocally introgressed into the genetic backgrounds of each ecotype. Our results demonstrate for the first time in nature the contribution of an inversion to adaptation, an annual/perennial life-history shift, and multiple reproductive isolating barriers. These results are consistent with the local adaptation mechanism being responsible for the distribution of the two inversion arrangements across the geographic range of M. guttatus and that locally adaptive inversion effects contribute directly to reproductive isolation. Such a mechanism may be partially responsible for the observation that closely related species often differ by multiple chromosomal rearrangements.}, annote = {examine the role of inversions driving local adaptation an inversion suppresses recombination- contributing to local adaptation}, author = {Lowry, David B. and Willis, John H.}, doi = {10.1371/journal.pbio.1000500}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lowry, Willis - 2010 - A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation,.pdf:pdf}, isbn = {15449173}, issn = {15449173}, journal = {PLoS Biology}, number = {9}, pmid = {20927411}, title = {{A widespread chromosomal inversion polymorphism contributes to a major life-history transition, local adaptation, and reproductive isolation}}, volume = {8}, year = {2010} } @article{Arnegard2014, abstract = {Ecological differences often evolve early in speciation as divergent natural selection drives adaptation to distinct ecological niches, leading ultimately to reproductive isolation. Although this process is a major generator of biodiversity, its genetic basis is still poorly understood. Here we investigate the genetic architecture of niche differentiation in a sympatric species pair of threespine stickleback fish by mapping the environment-dependent effects of phenotypic traits on hybrid feeding and performance under semi-natural conditions. We show that multiple, unlinked loci act largely additively to determine position along the major niche axis separating these recently diverged species. We also find that functional mismatch between phenotypic traits reduces the growth of some stickleback hybrids beyond that expected from an intermediate phenotype, suggesting a role for epistasis between the underlying genes. This functional mismatch might lead to hybrid incompatibilities that are analogous to those underlying intrinsic reproductive isolation but depend on the ecological context.}, author = {Arnegard, Matthew E and McGee, Matthew D and Matthews, Blake and Marchinko, Kerry B and Conte, Gina L and Kabir, Sahriar and Bedford, Nicole and Bergek, Sara and Chan, Yingguang Frank and Jones, Felicity C and Kingsley, David M and Peichel, Catherine L and Schluter, Dolph}, doi = {10.1038/nature13301}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Arnegard et al. - 2014 - Genetics of ecological divergence during speciation.pdf:pdf}, isbn = {1476-4687 (Electronic)$\backslash$r0028-0836 (Linking)}, issn = {1476-4687}, journal = {Nature}, keywords = {10,1038,doi,during,genetics of ecological divergence,icle,nature13301}, number = {7509}, pages = {307--311}, pmid = {24909991}, publisher = {Nature Publishing Group}, title = {{Genetics of ecological divergence during speciation.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24909991}, volume = {511}, year = {2014} } @article{Altizer2006, abstract = {Seasonal variations in temperature, rainfall and resource availability are ubiquitous and can exert strong pressures on population dynamics. Infectious diseases provide some of the best-studied examples of the role of seasonality in shaping population fluctuations. In this paper, we review examples from human and wildlife disease systems to illustrate the challenges inherent in understanding the mechanisms and impacts of seasonal environmental drivers. Empirical evidence points to several biologically distinct mechanisms by which seasonality can impact host-pathogen interactions, including seasonal changes in host social behaviour and contact rates, variation in encounters with infective stages in the environment, annual pulses of host births and deaths and changes in host immune defences. Mathematical models and field observations show that the strength and mechanisms of seasonality can alter the spread and persistence of infectious diseases, and that population-level responses can range from simple annual cycles to more complex multiyear fluctuations. From an applied perspective, understanding the timing and causes of seasonality offers important insights into how parasite-host systems operate, how and when parasite control measures should be applied, and how disease risks will respond to anthropogenic climate change and altered patterns of seasonality. Finally, by focusing on well-studied examples of infectious diseases, we hope to highlight general insights that are relevant to other ecological interactions.}, annote = {COuld cite this paper in our work as how seasonal dynamics affect host-parasite systems}, author = {Altizer, Sonia and Dobson, Andrew and Hosseini, Parviez and Hudson, Peter and Pascual, Mercedes and Rohani, Pejman}, doi = {10.1111/j.1461-0248.2005.00879.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Altizer et al. - 2006 - Seasonality and the dynamics of infectious diseases.pdf:pdf}, isbn = {1461-023X}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Annual cycle,Climate variation,Host-parasite interaction,Population dynamics,Transmission}, pages = {467--484}, pmid = {16623732}, title = {{Seasonality and the dynamics of infectious diseases}}, volume = {9}, year = {2006} } @article{Skellam1967, abstract = {Pielou's 1977 book, p. 53: Skellam (1967) has explored the use of projection matrices in modelling the periodic seasonal changes in populations that do not live in temporally uniform, unchanging conditions.}, annote = {As Skellum 1967 pointed out "the assumption that the vital coefiicients are independent of time has receivd little attention from mathematical ecologits" discusses how birth rates that are constant over seasons or years is probably only applicable for humans discusses work by Lotka and Leslie on matrices}, author = {Skellam, J G}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Skellam - 1967 - Seasonal periodicity in theoretical population ecology.pdf:pdf}, journal = {Proceedings of the 5th Berkeley Symposium on Mathematics, Statistics, and Probability}, keywords = {Frasera,variability}, pages = {179--205}, title = {{Seasonal periodicity in theoretical population ecology}}, volume = {4}, year = {1967} } @article{Ghalambor2007, abstract = {1. The role of phenotypic plasticity in evolution has historically been a contentious issue because of debate over whether plasticity shields genotypes from selection or generates novel opportunities for selection to act. Because plasticity encompasses diverse adaptive and non-adaptive responses to environmental variation, no single conceptual framework adequately predicts the diverse roles of plasticity in evolutionary change. 2. Different types of phenotypic plasticity can uniquely contribute to adaptive evolution when populations are faced with new or altered environments. Adaptive plasticity should promote establishment and persistence in a new environment, but depending on how close the plastic response is to the new favoured phenotypic optimum dictates whether directional selection will cause adaptive divergence between populations. Further, non-adaptive plasticity in response to stressful environments can result in a mean phenotypic response being further away from the favoured optimum or alternatively increase the variance around the mean due to the expression of cryptic genetic variation. The expression of cryptic genetic variation can facilitate adaptive evolution if by chance it results in a fitter phenotype. 3. We conclude that adaptive plasticity that places populations close enough to a new phenotypic optimum for directional selection to act is the only plasticity that predictably enhances fitness and is most likely to facilitate adaptive evolution on ecological time-scales in new environments. However, this type of plasticity is likely to be the product of past selection on variation that may have been initially non-adaptive. 4. We end with suggestions on how future empirical studies can be designed to better test the importance of different kinds of plasticity to adaptive evolution.}, annote = {"adaptive plasticity that places pops close to new optimumn for directional selection to act is the only type of plastiicty that will enhance fitness predictably" Phenotypic plasticty- a genotype produces different phenotypes in response to environmental conditions "process by which non-heritable environmentally induced variation leads to adaptive heritable variation is often referred to as the Baldwin Effect or more commonly as genetic assimilation"}, author = {Ghalambor, C. K. and McKay, J. K. and Carroll, S. P. and Reznick, D. N.}, doi = {10.1111/j.1365-2435.2007.01283.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ghalambor et al. - 2007 - Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new enviro.pdf:pdf}, isbn = {0269846313652435}, issn = {02698463}, journal = {Functional Ecology}, keywords = {Adaptive divergence,Contemporary adaptation,Genetic assimilation,Genotype x environment interaction,Phenotypic plasticity}, pages = {394--407}, pmid = {21866984}, title = {{Adaptive versus non-adaptive phenotypic plasticity and the potential for contemporary adaptation in new environments}}, volume = {21}, year = {2007} } @article{Kot1984, annote = {Me: should seasonality reduce growth rates via Jensen's inequality -examining role of seasonality in multivoltine (reproduce several times in a given year) species -Some species, like cabbage-whites, reproduce at the same time to start the season but there is great variability between them after that Is seasonality stablizing? -chaos occures when environements are not very productive -in more productive environments, seasonalitu may be stabalizing}, author = {Kot, M. and Schaffer, W.M.}, doi = {10.1016/0040-5809(84)90038-8}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kot, Schaffer - 1984 - The effects of seasonality on discrete models of population growth.pdf:pdf}, issn = {00405809}, journal = {Theoretical Population Biology}, pages = {340--360}, title = {{The effects of seasonality on discrete models of population growth}}, volume = {26}, year = {1984} } @article{Coop2015, author = {Coop, Graham}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Coop - 2015 - Notes on Population Genetics.pdf:pdf}, pages = {1--66}, title = {{Notes on Population Genetics}}, year = {2015} } @article{Klausmeier2008, abstract = {Many ecological systems experience periodic $\backslash$nvariability. Theoretical investigation of population and $\backslash$ncommunity dynamics in periodic environments has $\backslash$nbeen hampered by the lack of mathematical tools rela- $\backslash$ntive to equilibrium systems. Here, I describe one such $\backslash$nmathematical tool that has been rarely used in the $\backslash$necological literature but has widespread use: Floquet $\backslash$ntheory. Floquet theory is the study of the stability of $\backslash$nlinear periodic systems in continuous time. Floquet ex- $\backslash$nponents/multipliers are analogous to the eigenvalues of $\backslash$nJacobian matrices of equilibrium points. In this paper, $\backslash$nI describe the general theory, then give examples to $\backslash$nillustrate some of its uses: it defines fitness of struc- $\backslash$ntured populations, it can be used for invasion criteria $\backslash$nin models of competition, and it can test the stability of $\backslash$nlimit cycle solutions. I also provide computer code to $\backslash$ncalculate Floquet exponents and multipliers.}, author = {Klausmeier, Christopher A.}, doi = {10.1007/s12080-008-0016-2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Klausmeier - 2008 - Floquet theory A useful tool for understanding nonequilibrium dynamics.pdf:pdf}, isbn = {1874-1738}, issn = {18741738}, journal = {Theoretical Ecology}, keywords = {Floquet theory,Nonequilibrium dynamics}, pages = {153--161}, title = {{Floquet theory: A useful tool for understanding nonequilibrium dynamics}}, volume = {1}, year = {2008} } @article{Gould2014, author = {Gould, Billie a. and McCouch, Susan and Geber, Monica a.}, doi = {10.1111/mec.12893}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gould, McCouch, Geber - 2014 - Variation in soil aluminum tolerance genes is associated with rapid evolution at the Park Grass Experimen.pdf:pdf}, issn = {1365294X}, journal = {Molecular Ecology}, keywords = {2014,accepted 8 august 2014,aluminium tolerance,anthoxanthum odoratum,local adaptation,ment,park grass experi-,rapid evolution,received 3 march 2014,revision received 6 august,soil acidification,standing variation}, pages = {6058--6072}, pmid = {25145641}, title = {{Variation in soil aluminum tolerance genes is associated with rapid evolution at the Park Grass Experiment}}, year = {2014} } @article{Blanquart2013, abstract = {Patterns of local adaptation are expected to emerge when selection is spatially heterogeneous and sufficiently strong relative to the action of other evolutionary forces. The observation of local adaptation thus provides important insight into evolutionary processes and the adaptive divergence of populations. The detection of local adaptation, however, suffers from several conceptual, statistical and methodological issues. Here, we provide practical recommendations regarding (1) the definition of local adaptation, (2) the analysis of transplant experiments and (3) the optimisation of the experimental design of local adaptation studies. Together, these recommendations provide a unified approach for measuring local adaptation and understanding the adaptive divergence of populations in a wide range of biological systems.}, author = {Blanquart, Fran{\c{c}}ois and Kaltz, Oliver and Nuismer, Scott L. and Gandon, Sylvain}, doi = {10.1111/ele.12150}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Blanquart et al. - 2013 - A practical guide to measuring local adaptation.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Experimental evolution,Host-parasite coevolution,Linear model,Spatial heterogeneity,Specialisation,Statistics,Transplant experiments}, pages = {1195--1205}, pmid = {23848550}, title = {{A practical guide to measuring local adaptation}}, volume = {16}, year = {2013} } @article{Hine2014, abstract = {Abstract Genetic variation for individual traits is typically abundant, but for some multivariate combinations it is very low, suggesting that evolutionary limits might be generated by the geometric distribution of genetic variance. To test this prediction, we artificially selected along all eight genetic eigenvectors of a set of eight quantitative traits in Drosophila serrata. After six generations of 50{\%} truncation selection, at least one replicate population of all treatments responded to selection, allowing us to reject a null genetic subspace as a cause of evolutionary constraint in this system. However, while all three replicate populations of the first five selection treatments displayed a significant response, the remaining three, characterized by low genetic variance in their selection indexes in the base population, displayed inconsistent responses to selection. The observation that only four of the nine replicate populations evolved in response to the direct selection applied to them in these low genetic variance treatments, led us to conclude that a nearly null subspace did limit evolution. Dimensions associated with low genetic variance are often found in multivariate analyses of standing genetic variance in morphological traits, suggesting that the nearly null genetic subspace may be a common mechanism of evolutionary constraint in nature.}, author = {Hine, Emma and McGuigan, Katrina and Blows, Mark W}, doi = {10.1086/676504}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hine, McGuigan, Blows - 2014 - Evolutionary constraints in high-dimensional trait sets.pdf:pdf}, issn = {1537-5323}, journal = {The American naturalist}, keywords = {adapta-,artificial selection,constraints,genetic variance}, number = {1}, pages = {119--31}, pmid = {24921605}, title = {{Evolutionary constraints in high-dimensional trait sets.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24921605}, volume = {184}, year = {2014} } @article{Kawecki2004, abstract = {Studies of local adaptation provide important insights into the power of natural selection relative to gene flow and other evolutionary forces. They are a paradigm for testing evolutionary hypotheses about traits favoured by particular environmental factors. This paper is an attempt to summarize the conceptual framework for local adaptation studies. We first review theoretical work relevant for local adaptation. Then we discuss reciprocal transplant and common garden experiments designed to detect local adaptation in the pattern of deme x habitat interaction for fitness. Finally, we review research questions and approaches to studying the processes of local adaptation - divergent natural selection, dispersal and gene flow, and other processes affecting adaptive differentiation of local demes. We advocate multifaceted approaches to the study of local adaptation, and stress the need for experiments explicitly addressing hypotheses about the role of particular ecological and genetic factors that promote or hinder local adaptation. Experimental evolution of replicated populations in controlled spatially heterogeneous environments allow direct tests of such hypotheses, and thus would be a valuable way to complement research on natural populations.}, annote = {Genotype-environment is needed for local adaptation to occur, this can happen for several reasons: anatagonistic pleiotophy, Also need resticted gene flow for local adaptation *Several ecological factors promote local adaptation: low gene flow, strong selection againist against genotypes optimally adapted to the wrond habitat, low temporal variation in selection, small difference in habitat size and quality, and costs of adaptive plasticity Try to detect local adaptation in a recipricol transport or common garden setting When are phenotypic differences b/w pops really adaptive?}, author = {Kawecki, Tadeusz J. and Ebert, Dieter}, doi = {10.1111/j.1461-0248.2004.00684.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kawecki, Ebert - 2004 - Conceptual issues in local adaptation.pdf:pdf}, isbn = {1461-023X}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Adaptive deme formation,Adaptive evolution,Coevolution,Gene flow,Heterogeneous environments,Metapopulations,Natural selection,Population differentiation,Reciprocal transplant,Review}, pages = {1225--1241}, pmid = {1418097585842656351}, title = {{Conceptual issues in local adaptation}}, volume = {7}, year = {2004} } @article{Betini2013, abstract = {Most animal populations have distinct breeding and non-breeding periods, yet the implications of seasonality on population dynamics are not well understood. Here, we introduce an experimental model system to study the population dynamics of two important consequences of seasonality: sequential density dependence and carry-over effects (COEs). Using a replicated seasonal population of Drosophila, we placed individuals at four densities in the non-breeding season and then, among those that survived, placed them to breed at three different densities. We show that COEs arising from variation in non-breeding density negatively impacts individual performance by reducing per capita breeding output by 29-77{\%}, implying that non-lethal COEs can have a strong influence on population abundance. We then parametrized a bi-seasonal population model from the experimental results, and show that both sequential density dependence and COEs can stabilize long-term population dynamics and that COEs can reduce population size at low intrinsic rates of growth. Our results have important implications for predicting the successful colonization of new habitats, and for understanding the long-term persistence of seasonal populations in a wide range of taxa, including migratory organisms.}, annote = {During the non-breeding system they placed individuals in low, medium, and high densities and for those that survived they did the same in the breeding system with a fully crossed design (i.e. individuals originally placed in low densities were then split into three groups to be placed in low, medium, or high densitities). -parameterized a Ricker model for each season and included carry over effects-{\textgreater}used to assess long-term dynamics}, author = {Betini, Gustavo S and Griswold, Cortland K and Norris, D Ryan}, doi = {10.1098/rspb.2013.0110}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Betini, Griswold, Norris - 2013 - Carry-over effects, sequential density dependence and the dynamics of populations in a seasonal enviro.pdf:pdf}, isbn = {1471-2954 (Electronic)$\backslash$r0962-8452 (Linking)}, issn = {1471-2954}, journal = {Proceedings of the Royal Society B}, keywords = {behaviour,ecology,evolution}, pages = {20130110}, pmid = {23516241}, title = {{Carry-over effects, sequential density dependence and the dynamics of populations in a seasonal environment.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23516241}, volume = {280}, year = {2013} } @article{Colautti2013, abstract = {Adaptation to climate, evolving over contemporary time scales, could facilitate rapid range expansion across environmental gradients. Here, we examine local adaptation along a climatic gradient in the North American invasive plant Lythrum salicaria. We show that the evolution of earlier flowering is adaptive at the northern invasion front where it increases fitness as much as, or more than, the effects of enemy release and the evolution of increased competitive ability. However, early flowering decreases investment in vegetative growth, which reduces fitness by a factor of 3 in southern environments where the North American invasion commenced. Our results demonstrate that local adaptation can evolve quickly during range expansion, overcoming environmental constraints on propagule production.}, annote = {-have historical records of where the invasive species moved -look at flowering time In the north, you have to flower early enough or else you don't flower at all (short season)}, author = {Colautti, Robert I and Barrett, Spencer C H}, doi = {10.1126/science.1242121}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Colautti, Barrett - 2013 - Rapid adaptation to climate facilitates range expansion of an invasive plant.pdf:pdf}, isbn = {1095-9203 (Electronic)$\backslash$n0036-8075 (Linking)}, issn = {1095-9203}, journal = {Science (New York, N.Y.)}, keywords = {Acclimatization,Acclimatization: genetics,Acclimatization: physiology,Climate Change,Evolution, Molecular,Genetic Fitness,Lythrum,Lythrum: genetics,Lythrum: physiology,Plant Weeds,Plant Weeds: genetics,Plant Weeds: physiology}, pages = {364--6}, pmid = {24136968}, title = {{Rapid adaptation to climate facilitates range expansion of an invasive plant.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24136968}, volume = {342}, year = {2013} } @article{Capone2013, abstract = {Coastal upwelling regimes associated with eastern boundary currents are the most biologically productive ecosystems in the ocean. As a result, they play a disproportionately important role in the microbially mediated cycling of marine nutrients. These systems are characterized by strong natural variations in carbon dioxide concentrations, pH, nutrient levels and sea surface temperatures on both seasonal and interannual timescales. Despite this natural variability, changes resulting from human activities are starting to emerge. Carbon dioxide derived from fossil fuel combustion is adding to the acidity of upwelled low-pH waters. Low-oxygen waters associated with coastal upwelling systems are growing in their extent and intensity as a result of a rise in upper ocean temperatures and productivity. And nutrient inputs to the coastal ocean continue to grow. Coastal upwelling systems may prove more resilient to changes resulting from human activities than other ocean ecosystems because of their ability to function under extremely variable conditions. Nevertheless, shifts in primary production, fish yields, nitrogen gain and loss, and the flux of climate-relevant gases could result from the perturbation of these highly productive and dynamic ecosystems.}, author = {Capone, Douglas G. and Hutchins, David a.}, doi = {10.1038/ngeo1916}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Capone, Hutchins - 2013 - Microbial biogeochemistry of coastal upwelling regimes in a changing ocean.pdf:pdf}, isbn = {1752-0894}, issn = {1752-0894}, journal = {Nature Geoscience}, number = {9}, pages = {711--717}, publisher = {Nature Publishing Group}, title = {{Microbial biogeochemistry of coastal upwelling regimes in a changing ocean}}, url = {http://www.nature.com/doifinder/10.1038/ngeo1916}, volume = {6}, year = {2013} } @article{Savolainen2013, abstract = {It is increasingly important to improve our understanding of the genetic basis of local adaptation because of its relevance to climate change, crop and animal production, and conservation of genetic resources. Phenotypic patterns that are generated by spatially varying selection have long been observed, and both genetic mapping and field experiments provided initial insights into the genetic architecture of adaptive traits. Genomic tools are now allowing genome-wide studies, and recent theoretical advances can help to design research strategies that combine genomics and field experiments to examine the genetics of local adaptation. These advances are also allowing research in non-model species, the adaptation patterns of which may differ from those of traditional model species.}, annote = {good definitations throughout the paper}, author = {Savolainen, Outi and Lascoux, Martin and Meril{\"{a}}, Juha}, doi = {10.1038/nrg3522}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Savolainen, Lascoux, Meril{\"{a}} - 2013 - Ecological genomics of local adaptation.pdf:pdf}, isbn = {1471-0064 (Electronic)$\backslash$r1471-0056 (Linking)}, issn = {1471-0064}, journal = {Nature reviews. Genetics}, keywords = {Adaptation, Physiological,Adaptation, Physiological: genetics,Animals,Biological Evolution,Climate Change,Conservation of Natural Resources,Ecosystem,Fishes,Fishes: genetics,Genetic Variation,Genetics, Population,Genome,Genomics,Phenotype,Plants,Plants: genetics,Species Specificity}, number = {11}, pages = {807--20}, pmid = {24136507}, publisher = {Nature Publishing Group}, title = {{Ecological genomics of local adaptation.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24136507}, volume = {14}, year = {2013} } @article{Harley2006, abstract = {Anthropogenically induced global climate change has profound implications for marine ecosystems and the economic and social systems that depend upon them. The relationship between temperature and individual performance is reasonably well understood, and much climate-related research has focused on potential shifts in distribution and abundance driven directly by temperature. However, recent work has revealed that both abiotic changes and biological responses in the ocean will be substantially more complex. For example, changes in ocean chemistry may be more important than changes in temperature for the performance and survival of many organisms. Ocean circulation, which drives larval transport, will also change, with important consequences for population dynamics. Furthermore, climatic impacts on one or a few 'leverage species' may result in sweeping community-level changes. Finally, synergistic effects between climate and other anthropogenic variables, particularly fishing pressure, will likely exacerbate climate-induced changes. Efforts to manage and conserve living marine systems in the face of climate change will require improvements to the existing predictive framework. Key directions for future research include identifying key demographic transitions that influence population dynamics, predicting changes in the community-level impacts of ecologically dominant species, incorporating populations' ability to evolve (adapt), and understanding the scales over which climate will change and living systems will respond.}, author = {Harley, Christopher D G and Hughes, a. Randall and Hultgren, Kristin M. and Miner, Benjamin G. and Sorte, Cascade J B and Thornber, Carol S. and Rodriguez, Laura F. and Tomanek, Lars and Williams, Susan L.}, doi = {10.1111/j.1461-0248.2005.00871.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Harley et al. - 2006 - The impacts of climate change in coastal marine systems.pdf:pdf}, isbn = {1461-0248}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {Anthropogenic climate change,Carbon dioxide (CO2),Coastal oceanography,Community structure,Distributional shifts,Marine ecosystems,Ocean pH,Population dynamics,Synergistic effects,Temperature}, pages = {228--241}, pmid = {16958887}, title = {{The impacts of climate change in coastal marine systems}}, volume = {9}, year = {2006} } @article{Fakheran2010, abstract = {Competition and disturbance are potent ecological forces that shape evolutionary trajectories. These forces typically work in opposition: when disturbance is infrequent, densities are high and competition is intense. In contrast, frequent disturbance creates a low-density environment in which competition is weak and good dispersal essential. We exploited recent advances in genomic research to quantify the response to selection by these powerful ecological forces at the phenotypic and molecular genetic level in experimental landscapes. We grew the annual plant Arabidopsis thaliana in discrete patches embedded in a hostile matrix and varied the number and size of patches and the intensity of disturbance, by creating both static and dynamic landscapes. In static landscapes all patches were undisturbed, whereas in dynamic landscapes all patches were destroyed in each generation, forcing seeds to disperse to new locations. We measured the resulting changes in phenotypic, genetic, and genotypic diversity after five generations of selection. Simulations revealed that the observed loss of genetic diversity dwarfed that expected under drift, with dramatic diversity loss, particularly from dynamic landscapes. In line with ecological theory, static landscapes favored good competitors; however, competitive ability was linked to growth rate and not, as expected, to seed mass. In dynamic landscapes, there was strong selection for increased dispersal ability in the form of increased inflorescence height and reduced seed mass. The most competitive genotypes were almost eliminated from highly disturbed landscapes, raising concern over the impact of increased levels of human-induced disturbance in natural landscapes.}, annote = {compare static environment to dynamics disturbance environment Found that after only a couple of generations, there was both phenotypic and genetic differences between plants exposed to static versus disturbance environments}, author = {Fakheran, Sima and Paul-Victor, Clo{\'{e}} and Heichinger, Christian and Schmid, Bernhard and Grossniklaus, Ueli and Turnbull, Lindsay a}, doi = {10.1073/pnas.1010846107}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fakheran et al. - 2010 - Adaptation and extinction in experimentally fragmented landscapes.pdf:pdf}, isbn = {8415683111}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, pages = {19120--19125}, pmid = {20956303}, title = {{Adaptation and extinction in experimentally fragmented landscapes.}}, volume = {107}, year = {2010} } @article{Schmidt2008, abstract = {Some of the clearest examples of the ramifying effects of resource pulses exist in deciduous forests dominated by mast-producing trees, such as oaks, beech, and hornbeam. Seed production in these forests represents only the first of several pulsed events. Secondary pulses emerge as mast-consuming small rodents numerically respond to seed production and tertiary pulses emerge as generalist predators numerically respond to rodents. Raptors may also respond behaviorally (i.e., diet shifts) to subsequent crashes in small rodents following the crash phase in seed production. In oak-dominated forest in the Hudson Valley, New York, these various pulse and crash phases act synergistically, although not simultaneously, to influence thrush population dynamics through predation on nests, juveniles, and adults. As a consequence, factors limiting population growth rate and their age-specific action vary as a function of past acorn production. We highlight these interactions based on our eight-year study of thrush demography, acorn production, and small mammal abundance coupled with information on regional adult thrush population trends from the Breeding Bird Survey. We use these data sets to demonstrate the sequence of primary to tertiary pulses and how they influence breeding thrush populations. To extend our discussion beyond masting phenomena in the eastern United States, we briefly review the literature of alternative avian prey within pulsed systems to show (1) numerical and behavioral responses by generalist predators are ubiquitous in pulsed systems, and this contributes to (2) variability in reproduction and survivorship of avian prey linked to the underlying dynamics of the pulse. We conclude by exploring the broad consequences of cascading resource pulses for alternative prey based upon the indirect interaction of apparent competition among shared prey and the nature of temporal variability on populations.}, author = {Schmidt, Kenneth a. and Ostfeld, Richard S.}, doi = {10.1890/07-0199.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Schmidt, Ostfeld - 2008 - Numerical and behavioral effects within a pulse-driven system Consequences for shared prey.pdf:pdf}, isbn = {0012-9658}, issn = {00129658}, journal = {Ecology}, keywords = {Apparent competition,Predation,Resource pulse,Temporal variability,Trophic cascade}, number = {3}, pages = {635--646}, pmid = {18459328}, title = {{Numerical and behavioral effects within a pulse-driven system: Consequences for shared prey}}, volume = {89}, year = {2008} } @article{Otto2007a, author = {Otto, Sarah P. and Day, Troy}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Otto, Day - 2007 - Chapter 1 Mathematical Modeling in Biology.pdf:pdf}, journal = {A biologist's guide to mathematical modeling in ecology and evolution}, pages = {1--16}, title = {{Chapter 1: Mathematical Modeling in Biology}}, url = {http://books.google.com/books?hl=en{\&}lr={\&}id=Z{\_}bFNHJi{\_}VQC{\&}oi=fnd{\&}pg=PR1{\&}dq=A+Biologist's+Guide+to+Mathematical+Modeling+in+Ecology+and+Evolution{\&}ots=5SCMFUKpSp{\&}sig=VpXb7OWKoIYEHwi-3s{\_}KJoijqfM}, volume = {13}, year = {2007} } @article{Weis2014, annote = {What does the model predict about the shape of the fitness function? Why? How will the function change with season length? How will changes in the pop dist affect selectiion? How can you test these predictions?}, author = {Weis, Arthur E. and Wadgymar, Susana M. and Sekor, Michael and Franks, Steven J.}, doi = {10.1007/s10682-014-9719-6}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Weis et al. - 2014 - The shape of selection Using alternative fitness functions to test predictions for selection on flowering time.pdf:pdf}, isbn = {1068201497196}, issn = {02697653}, journal = {Evolutionary Ecology}, keywords = {Brassica rapa,Directional selection,Fitness function,Fitness surface,Flowering time,Non-linear selection,Stabilizing selection}, pages = {885--904}, title = {{The shape of selection: Using alternative fitness functions to test predictions for selection on flowering time}}, volume = {28}, year = {2014} } @article{Reichstein2015, author = {Reichstein, Birte and Persson, Lennart and {De Roos}, Andr{\'{e}} M.}, doi = {10.1038/ncomms7441}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reichstein, Persson, De Roos - 2015 - Ontogenetic asymmetry modulates population biomass production and response to harvest.pdf:pdf}, issn = {2041-1723}, journal = {Nature Communications}, pages = {6441}, title = {{Ontogenetic asymmetry modulates population biomass production and response to harvest}}, url = {http://www.nature.com/doifinder/10.1038/ncomms7441}, volume = {6}, year = {2015} } @article{Stocker2013, abstract = {IPCC (2007) Climate change: The physical science basis. Contribution of Working Group I to the Fourth Assessment Report of the IPCC. Cambridge: Cambridge University Press. 4.}, author = {Stocker, T.F. and {D. Qin}, G.-K. and Plattner, L.V. and Alexander, S.K. and Allen, N.L. and Bindoff, F.-M. and Br{\'{e}}on, J.a. and Church, U. and Cubasch, S. and Emori, P. and Forster, P. and Friedlingstein, N. and Gillett, J.M. and Gregory, D.L. and Hartmann, E. and Jansen, B. and Kirtman, R. and Knutti, K. and {Krishna Kumar}, P. and Lemke, J. and Marotzke, V. and Masson-Delmotte, G.a. and Meehl, I.I. and Mokhov, S. and Piao, V. and Ramaswamy, D. and Randall, M. and Rhein, M. and Rojas, C. and Sabine, D. and Shindell, L.D. and Talley, D.G. and Xie, Vaughan and S.-P.}, doi = {10.1017/ CBO9781107415324.005}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stocker et al. - 2013 - Technical Summary.pdf:pdf}, isbn = {9781107661820}, journal = {Climate Change 2013: The Physical Science Basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change}, pages = {33--115}, title = {{Technical Summary}}, year = {2013} } @article{Kingsolver2012, abstract = {There are now thousands of estimates of phenotypic selection in natural populations, resulting in multiple synthetic reviews of these data. Here we consider several major lessons and limitations emerging from these syntheses, and how they may guide future studies of selection in the wild. First, we review past analyses of the patterns of directional selection. We present new meta-analyses that confirm differences in the direction and magnitude of selection for different types of traits and fitness components. Second, we describe patterns of temporal and spatial variation in directional selection, and their implications for cumulative selection and directional evolution. Meta-analyses suggest that sampling error contributes importantly to observed temporal variation in selection, and indicate that evidence for frequent temporal changes in the direction of selection in natural populations is limited. Third, we review the apparent lack of evidence for widespread stabilizing selection, and discuss biological and methodological explanations for this pattern. Finally, we describe how sampling error, statistical biases, choice of traits, fitness measures and selection metrics, environmental covariance and other factors may limit the inferences we can draw from analyses of selection coefficients. Current standardized selection metrics based on simple parametric statistical models may be inadequate for understanding patterns of non-linear selection and complex fitness surfaces. We highlight three promising areas for expanding our understanding of selection in the wild: (1) field studies of stabilizing selection, selection on physiological and behavioral traits, and the ecological causes of selection; (2) new statistical models and methods that connect phenotypic variation to population demography and selection; and (3) availability of the underlying individual-level data sets from past and future selection studies, which will allow comprehensive modeling of selection and fitness variation within and across systems, rather than meta-analyses of standardized selection metrics. {\textcopyright} 2012 Springer Science+Business Media B.V.}, author = {Kingsolver, Joel G. and Diamond, Sarah E. and Siepielski, Adam M. and Carlson, Stephanie M.}, doi = {10.1007/s10682-012-9563-5}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kingsolver et al. - 2012 - Synthetic analyses of phenotypic selection in natural populations Lessons, limitations and future directions.pdf:pdf}, isbn = {0269-7653}, issn = {02697653}, journal = {Evolutionary Ecology}, keywords = {Fitness,Meta-analysis,Natural selection,Phenotypic selection}, pages = {1101--1118}, title = {{Synthetic analyses of phenotypic selection in natural populations: Lessons, limitations and future directions}}, volume = {26}, year = {2012} } @article{White2015, abstract = {Fishing pressure has increased the extinction risk of many elasmobranch (shark and ray) species. Although many countries have established no-take marine reserves, a paucity of monitoring data means it is still unclear if reserves are effectively protecting these species. We examined data collected by a small group of divers over the past 21 years at one of the world's oldest marine protected areas (MPAs), Cocos Island National Park, Costa Rica. We used mixed effects models to determine trends in relative abundance, or probability of occurrence, of 12 monitored elasmobranch species while accounting for variation among observers and from abiotic factors. Eight of 12 species declined significantly over the past 2 decades. We documented decreases in relative abundance for 6 species, including the iconic scalloped hammerhead shark (Sphyrna lewini) (-45{\%}), whitetip reef shark (Triaenodon obesus) (-77{\%}), mobula ray (Mobula spp.) (-78{\%}), and manta ray (Manta birostris) (-89{\%}) rays, and decreases in the probability of occurrence for 2 other species. Several of these species have small home ranges and should be better protected by an MPA, which underscores the notion that declines of marine megafauna will continue unabated in MPAs unless there is adequate enforcement effort to control fishing. In addition, probability of occurrence at Cocos Island of tiger (Galeocerdo cuvier), Galapagos (Carcharhinus galapagensis), blacktip (Carcharhinus limbatus), and whale (Rhincodon typus) sharks increased significantly. The effectiveness of MPAs cannot be evaluated by examining single species because population responses can vary depending on life history traits and vulnerability to fishing pressure.}, author = {White, Easton R. and Myers, Mark C. and Flemming, Joanna Mills and Baum, Julia K.}, doi = {10.1111/cobi.12478}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2015 - Shifting elasmobranch community assemblage at Cocos Island-an isolated marine protected area.pdf:pdf}, issn = {08888892}, journal = {Conservation Biology}, keywords = {MPA,citizen science,cocos,eastern tropical Pacific,endagered,fisheries,generalized linear mixed models,marine reserve,population,sharks,zero-inflated}, mendeley-tags = {cocos,endagered,population,sharks}, month = {mar}, pages = {1--12}, pmid = {25807991}, title = {{Shifting elasmobranch community assemblage at Cocos Island-an isolated marine protected area}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25807991}, year = {2015} } @article{Pigliucci2005, abstract = {The study of phenotypic plasticity has progressed significantly over the past few decades. We have moved from variation for plasticity being considered as a nuisance in evolutionary studies to it being the primary target of investigations that use an array of methods, including quantitative and molecular genetics, as well as of several approaches that model the evolution of plastic responses. Here, I consider some of the major aspects of research on phenotypic plasticity, assessing where progress has been made and where additional effort is required. I suggest that some areas of research, such the study of the quantitative genetic underpinning of plasticity, have been either settled in broad outline or superseded by new approaches and questions. Other issues, such as the costs of plasticity are currently at the forefront of research in this field, and are likely to be areas of major future development. ?? 2005 Elsevier Ltd. All rights reserved.}, author = {Pigliucci, Massimo}, doi = {10.1016/j.tree.2005.06.001}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pigliucci - 2005 - Evolution of phenotypic plasticity Where are we going now.pdf:pdf}, issn = {01695347}, journal = {Trends in Ecology and Evolution}, number = {9}, pages = {481--486}, pmid = {16701424}, title = {{Evolution of phenotypic plasticity: Where are we going now?}}, volume = {20}, year = {2005} } @article{Mcelreath2015a, archivePrefix = {arXiv}, arxivId = {arXiv:1503.02780v1}, author = {Mcelreath, Richard and Smaldino, Paul E}, eprint = {arXiv:1503.02780v1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mcelreath, Smaldino - 2015 - Replication, communication, and the population dynamics of scientific discovery.pdf:pdf}, journal = {arXiv}, keywords = {a nthropology,a venue,d avis ca,epistemology,o ne s hields,publication bias,replication,scientific method,uc d avis}, pages = {1--22}, title = {{Replication, communication, and the population dynamics of scientific discovery}}, year = {2015} } @article{Sih2010, author = {Sih, Andrew and Bell, Alison M. and Johnson, J. Chadwick}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sih, Bell, Johnson - 2010 - Behavioral syndromes.pdf:pdf}, journal = {Evolutionary Behavioral Ecology}, pages = {516--530}, title = {{Behavioral syndromes}}, year = {2010} } @book{Sih2008, abstract = {After placing the study of behavioral syndromes into historical perspective and clarifying some misconceptions about the term, the aim of this chapter is to illustrate some of the important questions that come into focus when viewing animal behavior through "behavioral syndromes lenses." In general, we see two particularly exciting research directions. One of these focuses on trying to understand variation in behavioral syndromes. The other applies the behavioral syndromes approach to topics of interest to behavioral ecologists that have not historically focused on individual variation: For any given behavior, do individuals behave consistently differently from each other? If so, are those differences correlated across contexts? The next major task in studies of behavioral syndromes themselves is to quantify and explain the patterns of variation in behavioral syndromes. As a first step, for example, we would like to know which behaviors tend to occur in clusters and which tend to be independent? When do correlations break down over ontogenetic and evolutionary time? Then, the challenge is to explain those patterns from both a proximate and ultimate perspective- how does selection act on differences in the lability of proximate mechanisms to produce variable correlations? At the same time, we expect that the next major wave of studies on behavioral syndromes will apply these ideas to understand topics of interest to behavioral ecologists, things like mate choice, cooperation, and group living. We described several relatively understudied axes of behavioral variation, for example environmental and social sensitivity, learning, choosiness, cooperativeness, etc, all of which could offer new insights into long-standing questions. Along the way, we highlighted other priorities for research such as consideration of nonbehavioral traits such as physiology and morphology as part of an integrated phenotype and the inclusion of conceptual (e.g., dynamic programming, network theory, and path analysis) and empirical (e.g., genomics) tools. ?? 2008 Elsevier Inc. All rights reserved.}, author = {Sih, Andrew and Bell, Alison M.}, booktitle = {Advances in the Study of Behavior}, doi = {10.1016/S0065-3454(08)00005-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sih, Bell - 2008 - Chapter 5 Insights for Behavioral Ecology from Behavioral Syndromes.pdf:pdf}, isbn = {9780120045389}, issn = {00653454}, pages = {227--281}, pmid = {24991063}, title = {{Chapter 5 Insights for Behavioral Ecology from Behavioral Syndromes}}, volume = {38}, year = {2008} } @article{Brannstrom2013, author = {Br{\"{a}}nnstr{\"{o}}m, {\AA}ke and Johansson, Jacob and von Festenberg, Niels}, doi = {10.3390/g4030304}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Br{\"{a}}nnstr{\"{o}}m, Johansson, von Festenberg - 2013 - The hitchhiker's guide to Adaptive Dynamics.pdf:pdf}, issn = {2073-4336}, journal = {Games}, pages = {304--328}, title = {{The hitchhiker's guide to Adaptive Dynamics}}, volume = {4}, year = {2013} } @article{Ling2015, annote = {-more regime shift work has been possible on benthic systems that are easier to sample and experiment on -Using size-structured community dynamics, Gardmark was able to identify alternative stable states in pelagic food webs -arguments over importance of top-down vs bottom-up --may not make since in marine setting as many trophic levels are affected by environment and many species have a larvae stage -need to look at many drivers simustanesly -stressers can move system closer to unstable equilibrium and/or change the shape of the basin of attraction -time-delayed interactions (causing some version of extinction debt) are important and may not be recongnized until it is too late}, author = {Ling, Scott and Conversi, Alessandra and Dakos, Vasilis and Gardmark, Anna and Ling, Scott and Folke, Carl and Mumby, Peter J and Greene, Charles and Edwards, Martin and Blenckner, Thorsten and Casini, Michele and Pershing, Andrew and Mollmann, Christian}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ling et al. - 2015 - A holistic view of marine regime shifts.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, keywords = {ecology,environmental science}, pages = {20130279}, title = {{A holistic view of marine regime shifts}}, volume = {370}, year = {2015} } @article{Noble2015, annote = {Irsing model is good at desrbiing phenomena like magnets where a bunch of small magnets aline to create a larger magnet Moran effect says regional affects or dispersal can cause synchrony on local scale Iring model says synchrony can occur on distances greater than the dispersal kernel Syncronoy in MPAs? In metapopulations?}, author = {Noble, Andrew E. and Machta, Jonathan and Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Noble, Machta, Hastings - Unknown - Emergence of long-range synchronization from local dispersal.pdf:pdf}, journal = {Nature Communications}, title = {{Emergence of long-range synchronization from local dispersal}}, year = {2015} } @article{Nowak2006, abstract = {Cooperation is needed for evolution to construct new levels of organization. Genomes, cells, multicellular organisms, social insects, and human society are all based on cooperation. Cooperation means that selfish replicators forgo some of their reproductive potential to help one another. But natural selection implies competition and therefore opposes cooperation unless a specific mechanism is at work. Here I discuss five mechanisms for the evolution of cooperation: kin selection, direct reciprocity, indirect reciprocity, network reciprocity, and group selection. For each mechanism, a simple rule is derived that specifies whether natural selection can lead to cooperation.}, annote = {could have cooperation from: -kin selection (being related enough by hamilton's rule) -direct reciprocity (Trivers), related to repeated Prisoner''s dilemna- Tourney by Axelrod -indirect reciprocity- established through your reputation, others will work with you (mostly seen in humans) -network reciprocity- structure in network so it is not well-mixed -group selection- group of cooperates could out compete group of defectors For all of these you look at the ratio of benefit to cost for an individual compared to some critical value}, author = {Nowak, Martin a}, doi = {10.1126/science.1133755}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nowak - 2006 - Five rules for the evolution of cooperation.pdf:pdf}, isbn = {doi:10.1126/science.1133755}, issn = {0036-8075}, journal = {Science (New York, N.Y.)}, number = {2006}, pages = {1560--1563}, pmid = {17158317}, title = {{Five rules for the evolution of cooperation.}}, volume = {314}, year = {2006} } @article{Anderson2008, author = {Anderson, Wendy B. and Wait, D. Alexander and Stapp, Paul}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Anderson, Wait, Stapp - 2008 - Resources from another place and time- responses to pulses in a spatially subsidized system.pdf:pdf}, journal = {Ecology}, keywords = {community dynamics,deserts,gulf of california,islands,lizards,nutrient subsidies,physiology,plant,population dynamics,primary productivity,rodents,spiders}, number = {3}, pages = {660--670}, title = {{Resources from another place and time- responses to pulses in a spatially subsidized system}}, volume = {89}, year = {2008} } @incollection{Jennions, author = {Jennions, Michael D. and Kokko, Hanna}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Jennions, Kokko - Unknown - Chapter 20 Sexual Selection.pdf:pdf}, title = {{Chapter 20 Sexual Selection}} } @article{McCann2000a, author = {McCann, Kevin Shear}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McCann - 2000 - The diversity–stability debate.pdf:pdf}, journal = {Nature}, number = {May}, pages = {228--233}, title = {{The diversity–stability debate}}, volume = {405}, year = {2000} } @article{Jennions2012, author = {Jennions, Michael D. and Kahn, Andrew T. and Kelly, Clint D. and Kokko, Hanna}, doi = {10.1007/s10682-012-9567-1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Jennions et al. - 2012 - Meta-analysis and sexual selection past studies and future possibilities.pdf:pdf}, journal = {Evolutionary Ecology}, pages = {1119--1151}, title = {{Meta-analysis and sexual selection: past studies and future possibilities}}, volume = {26}, year = {2012} } @article{Ives2007, author = {Ives, Anthony R and Carpenter, Stephen R}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ives, Carpenter - 2007 - Stability and Diversity of Ecosystems.pdf:pdf}, journal = {Science}, number = {July}, pages = {58--63}, title = {{Stability and Diversity of Ecosystems}}, volume = {317}, year = {2007} } @article{King2015, author = {King, Jacquelynne R. and McFarlane, Gordon A. and Punt, Andre E.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/King, McFarlane, Punt - 2015 - Shifts in fisheries management adapting to regime shifts.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, keywords = {environmental science}, number = {1996}, pages = {1--8}, title = {{Shifts in fisheries management: adapting to regime shifts}}, volume = {370}, year = {2015} } @article{Westerling2011, abstract = {Climate change is likely to alter wildfire regimes, but the magnitude and timing of potential climate-driven changes in regional fire regimes are not well understood. We considered how the occurrence, size, and spatial location of large fires might respond to climate projections in the Greater Yellowstone ecosystem (GYE) (Wyoming), a large wildland ecosystem dominated by conifer forests and characterized by infrequent, high-severity fire. We developed a suite of statistical models that related monthly climate data (1972-1999) to the occurrence and size of fires {\textgreater}200 ha in the northern Rocky Mountains; these models were cross-validated and then used with downscaled (∼12 km × 12 km) climate projections from three global climate models to predict fire occurrence and area burned in the GYE through 2099. All models predicted substantial increases in fire by midcentury, with fire rotation (the time to burn an area equal to the landscape area) reduced to {\textless}30 y from the historical 100-300 y for most of the GYE. Years without large fires were common historically but are expected to become rare as annual area burned and the frequency of regionally synchronous fires increase. Our findings suggest a shift to novel fire-climate-vegetation relationships in Greater Yellowstone by midcentury because fire frequency and extent would be inconsistent with persistence of the current suite of conifer species. The predicted new fire regime would transform the flora, fauna, and ecosystem processes in this landscape and may indicate similar changes for other subalpine forests.}, author = {Westerling, Anthony L and Turner, Monica G and Smithwick, Erica a H and Romme, William H and Ryan, Michael G}, doi = {10.1073/pnas.1110199108}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Westerling et al. - 2011 - Continued warming could transform Greater Yellowstone fire regimes by mid-21st century.pdf:pdf}, isbn = {0027-8424}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {31}, pages = {13165--13170}, pmid = {21788495}, title = {{Continued warming could transform Greater Yellowstone fire regimes by mid-21st century.}}, volume = {108}, year = {2011} } @article{Hastings1994, author = {Hastings, Alan and Harrison, Susan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Harrison - 1994 - Metapopulation dynamics and genetics.pdf:pdf}, journal = {Annu. Rev. Ecol. Syst.}, pages = {167--188}, title = {{Metapopulation dynamics and genetics}}, volume = {25}, year = {1994} } @incollection{Brooks, author = {Brooks, Robert C. and Griffith, Simon C.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brooks, Griffith - Unknown - Chapter 24 Mate Choice.pdf:pdf}, title = {{Chapter 24 Mate Choice}} } @article{Hastings1993, abstract = {We review the role of chaos and the study of chaos in ecology. We$\backslash$nuse sensitive dependence on initial conditions as the best heuristic$\backslash$ndefinition of chaos. This definition forms the common theme for our$\backslash$nreview of approaches for demonstrating the importance of chaos in$\backslash$necology. We emphasize that this definition of chaos can include the$\backslash$neffects of noise, and that there is no dichotomy between stochasticity$\backslash$nand chaos. We review three classes of approaches for studying chaos$\backslash$nin ecology: models, analysis of time series, and experiments. Current$\backslash$nideas from modelling approaches demonstrate the plausibility of chaos.$\backslash$nNew approaches for analyzing time series are based on using the presence$\backslash$nof a positive Lyapunov exponent to indicate sensitive dependence$\backslash$non initial conditions. The methods can deal with relatively short$\backslash$ntime series that include the effects of noise, with chaotic dynamics$\backslash$nappearing in at least some cases. Experimental work is just beginning,$\backslash$nspurred by modelling results and the new methods for analyzing times$\backslash$nseries. We suggest directions for further work in each of these approaches.}, annote = {- make arfguemnt that focusing on equilbrium approaches is not a good one -need analyses that can evaluate chaos in stochastic systems specifically -have whole section on "seaonality or periodicity" Schaffer and Kot, Witteman et al al, and other reviews where 70+ time series were assessed for chaotic dynamics probably need around 50 data points to determine chaotic dynamics Use of permance as ecological notion of stability (Hutson and Schmittt 1992) math biosciences}, author = {Hastings, A and Hom, Carole L and Ellner, Stephen and Turchin, Peter and Godfray, H Charles J}, doi = {10.1146/annurev.es.24.110193.000245}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings et al. - 1993 - Chaos in Ecology Is Mother Nature a Strange Attractor.pdf:pdf}, isbn = {00664162}, issn = {0066-4162}, journal = {Annual Review of Ecology and Systematics}, keywords = {stability}, number = {1993}, pages = {1--33}, pmid = {340}, title = {{Chaos in Ecology: Is Mother Nature a Strange Attractor?}}, volume = {24}, year = {1993} } @article{Nowak2010, abstract = {Eusociality, in which some individuals reduce their own lifetime reproductive potential to raise the offspring of others, underlies the most advanced forms of social organization and the ecologically dominant role of social insects and humans. For the past four decades kin selection theory, based on the concept of inclusive fitness, has been the major theoretical attempt to explain the evolution of eusociality. Here we show the limitations of this approach. We argue that standard natural selection theory in the context of precise models of population structure represents a simpler and superior approach, allows the evaluation of multiple competing hypotheses, and provides an exact framework for interpreting empirical observations.}, author = {Nowak, Martin a and Tarnita, Corina E and Wilson, Edward O}, doi = {10.1146/annurev.es.15.110184.001121}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nowak, Tarnita, Wilson - 2010 - The evolution of eusociality.pdf:pdf}, isbn = {1476-4687 (Electronic)$\backslash$n0028-0836 (Linking)}, issn = {0066-4162}, journal = {Nature}, number = {7310}, pages = {1057--1062}, pmid = {20740005}, publisher = {Nature Publishing Group}, title = {{The evolution of eusociality.}}, url = {http://dx.doi.org/10.1038/nature09205}, volume = {466}, year = {2010} } @article{Sih2001, author = {Sih, Andrew and Christensen, Bent}, doi = {10.1006/anbe.2000.1592}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sih, Christensen - 2001 - Optimal diet theory when does it work , and when and why does it fail.pdf:pdf}, journal = {Animal Behavior}, pages = {379--390}, title = {{Optimal diet theory: when does it work , and when and why does it fail?}}, volume = {61}, year = {2001} } @article{Hooper2012a, abstract = {Evidence is mounting that extinctions are altering key processes important to the productivity and sustainability of Earth's ecosystems. Further species loss will accelerate change in ecosystem processes, but it is unclear how these effects compare to the direct effects of other forms of environmental change that are both driving diversity loss and altering ecosystem function. Here we use a suite of meta-analyses of published data to show that the effects of species loss on productivity and decomposition--two processes important in all ecosystems--are of comparable magnitude to the effects of many other global environmental changes. In experiments, intermediate levels of species loss (21-40{\%}) reduced plant production by 5-10{\%}, comparable to previously documented effects of ultraviolet radiation and climate warming. Higher levels of extinction (41-60{\%}) had effects rivalling those of ozone, acidification, elevated CO(2) and nutrient pollution. At intermediate levels, species loss generally had equal or greater effects on decomposition than did elevated CO(2) and nitrogen addition. The identity of species lost also had a large effect on changes in productivity and decomposition, generating a wide range of plausible outcomes for extinction. Despite the need for more studies on interactive effects of diversity loss and environmental changes, our analyses clearly show that the ecosystem consequences of local species loss are as quantitatively significant as the direct effects of several global change stressors that have mobilized major international concern and remediation efforts.}, author = {Hooper, David U and Adair, E Carol and Cardinale, Bradley J and Byrnes, Jarrett E K and Hungate, Bruce a and Matulich, Kristin L and Gonzalez, Andrew and Duffy, J Emmett and Gamfeldt, Lars and O'Connor, Mary I}, doi = {10.1038/nature11118}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hooper et al. - 2012 - A global synthesis reveals biodiversity loss as a major driver of ecosystem change(2).pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {Animals,Biodiversity,Ecology,Ecosystem,Extinction, Biological,Models, Biological}, month = {jun}, number = {7401}, pages = {105--8}, pmid = {22678289}, publisher = {Nature Publishing Group}, title = {{A global synthesis reveals biodiversity loss as a major driver of ecosystem change.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22678289}, volume = {486}, year = {2012} } @article{Hardin1968, annote = {-like nuclear proliferation, Hardin believes that the population boom is no longer a technical problem, rather it is a social issue -in finite world, exponentially growing pop should decrease the goods of the world -what should we optimize? Population? Amount of goods? Happiness? --Max good per person depends on the person -Adam Smith would argue that individual decisions will help promote the public interest. Is this really true? Consider reproduciton -discusses trategy of commons and ocean resources -a welfare state system does not select out those who overbreed -argues agiansst the usefulness of guilt -you don't need to forbid things, just make it expensive to take things to extremens, change the incentives}, author = {Hardin, Garrett}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hardin - 1968 - The Tragedy of the Commons.pdf:pdf}, journal = {Science}, pages = {1243--1248}, title = {{The Tragedy of the Commons}}, volume = {162}, year = {1968} } @article{Clark2009, abstract = {Biodiversity science is unusual in that an emerging paradigm is not based on a specific process, but rather depends largely on stochastic elements, perceived as neutral forces. Here I suggest that these forces, which have been justified, in part, by the concepts of symmetry and equalizing mechanisms, have application to the understanding of stochastic models but do not constitute forces that operate in nature. Another process now regularly classified as a neutral force, limited dispersal, represents a fundamental demographic process that is not neutral with respect to species differences, but rather differs among species in important ways. Finally, I suggest that the dramatic shift in ecological research to focus on neutrality could have a cost in terms of scientific understanding and relevance to real biodiversity threats.}, author = {Clark, James S}, doi = {10.1016/j.tree.2008.09.004}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Clark - 2009 - Beyond neutral science.pdf:pdf}, issn = {0169-5347}, journal = {Trends in Ecology {\&} Evolution}, keywords = {Animals,Biodiversity,Competitive Behavior,Competitive Behavior: physiology,Ecology,Ecology: trends,Ecosystem}, month = {jan}, number = {1}, pages = {8--15}, pmid = {19026462}, title = {{Beyond neutral science}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19026462}, volume = {24}, year = {2009} } @article{Hastings2004, author = {Hastings, Alan}, doi = {10.1016/j.tree.2003.09.007}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 2004 - Transients the key to long-term ecological understanding.pdf:pdf}, journal = {Trends in Ecology {\&} Evolution}, number = {1}, pages = {39--45}, title = {{Transients: the key to long-term ecological understanding?}}, volume = {19}, year = {2004} } @article{Hastings2014, annote = {-f age does not matter, the pop growth rate would be the same for rapid or slow environmental variation -which resource regime is better depends on if juvs or adults have higher reproduction -"Thus the influence of the remporal scale of variability depends on the age dependence of the life history parameters" Cohen 1970s on long term growth - in response to Boyce paper Will White first author paper Moore et al review in Eco Letters on detrital pathways alloc tis Strathman paper after Lewontin and Cohen - dispersal gets you arithematic mean Feller volume 1 Cunnington Hastings Oikos new paper}, author = {Hastings, Alan}, doi = {10.1016/j.ecocom.2013.08.003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 2014 - Temporal scales of resource variability Effects on population dynamics of structured populations.pdf:pdf}, issn = {1476-945X}, journal = {Ecological Complexity}, pages = {6--9}, publisher = {Elsevier B.V.}, title = {{Temporal scales of resource variability: Effects on population dynamics of structured populations}}, url = {http://dx.doi.org/10.1016/j.ecocom.2013.08.003}, volume = {18}, year = {2014} } @article{Hastings2012, annote = {importance of geometric mean of resources rather than simple mean of inputs}, author = {Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 2012 - Temporally varying resources amplify the importance of resource input in ecological populations.pdf:pdf}, journal = {Biology Letters}, keywords = {allochthonous inputs,life histories,persistence,resource pulses}, number = {August}, pages = {1067--1069}, title = {{Temporally varying resources amplify the importance of resource input in ecological populations}}, volume = {8}, year = {2012} } @article{Pershing2015, annote = {Use three data sets from the Black Sea, Baltic, Eastern Scotian Shelf Examine correlation structures between variables Black sea- zooplankton had strongest effects on interannual variability b/c when they were removed from the analysis, significant correlations are reduced Baltic- removing salinity reduces correlations between physical and lower trophic level variables. but correlations between NAO and nutrues, harring, and zooplankton emerhe -removing the cod signal also elimnated most correlations Eastern Scotian shelf- removing the stratification signal impacts correlation more than groudfish-{\textgreater} bottom up forcing has more of an effect Black Sea- data from paper on trophic cascades triggered by overfishing Baltic- previous paper found mult. causes of trophic cascade Eastern Scotian shelf-previous work identified cod as cause of trophic cascade Only look at one variable in top versus down debate- interaction effects? Why are trophic cascades rare in pelagic systems: they argue it is because of spatial aspect of pelegic system}, author = {Pershing, Andrew J and Mills, Katherine E and Record, Nicholas R and Stamieszkin, Karen and Wurtzell, Katharine V and Byron, Carrie J and Fitzpatrick, Dominic and Golet, Walter J and Koob, Elise}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pershing et al. - 2015 - Evaluating trophic cascades as drivers of regime shifts in different ocean ecosystems.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, keywords = {ecology,environmental science}, title = {{Evaluating trophic cascades as drivers of regime shifts in different ocean ecosystems}}, year = {2015} } @article{Ling2014, author = {Ling, S.D. and Scheibling, R.E. and Rassweiler, A. and Johnson, C.R. and Shears, N. and Connell, S.D. and Salomon, A.K. and Norderhaug, K.M. and Perez-Matus, A. and Hernandez, J.C. and Clemente, S. and Blamey, L.K. and Hereu, B. and Ballesteros, E. and Sala, E. and Garrabou, J. and Cebrian, E. and Zabala, M. and Fujita, D. and Johnson, L.E.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ling et al. - 2014 - Global regime shift dynamics of catastrophic sea urchin overgrazing.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, pages = {20130269}, title = {{Global regime shift dynamics of catastrophic sea urchin overgrazing}}, volume = {370}, year = {2014} } @article{Sumaila2015, author = {Sumaila, U Rashid and Lam, Vicky W Y and Miller, Dana D and Teh, Louise and Watson, Reg A and Zeller, Dirk and Cheung, William W.L. and Cote, Isabelle M. and Rogers, Alex D and Roberts, Callum and Sala, Enric and Pauly, Daniel}, doi = {10.1038/srep08481}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sumaila et al. - 2015 - Winners and losers in a world where the high seas is closed to fishing.pdf:pdf}, journal = {Scientific Reports}, number = {8481}, pages = {1--6}, title = {{Winners and losers in a world where the high seas is closed to fishing}}, volume = {5}, year = {2015} } @article{Adler2007, abstract = {Ecologists now recognize that controversy over the relative importance of niches and neutrality cannot be resolved by analyzing species abundance patterns. Here, we use classical coexistence theory to reframe the debate in terms of stabilizing mechanisms (niches) and fitness equivalence (neutrality). The neutral model is a special case where stabilizing mechanisms are absent and species have equivalent fitness. Instead of asking whether niches or neutral processes structure communities, we advocate determining the degree to which observed diversity reflects strong stabilizing mechanisms overcoming large fitness differences or weak stabilization operating on species of similar fitness. To answer this question, we propose combining data on per capita growth rates with models to: (i) quantify the strength of stabilizing processes; (ii) quantify fitness inequality and compare it with stabilization; and (iii) manipulate frequency dependence in growth to test the consequences of stabilization and fitness equivalence for coexistence.}, author = {Adler, Peter B and HilleRislambers, Janneke and Levine, Jonathan M}, doi = {10.1111/j.1461-0248.2006.00996.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Adler, HilleRislambers, Levine - 2007 - A niche for neutrality.pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {Adaptation,Biological,Ecosystem,Models,Physiological,Plants,Plants: genetics,Plants: metabolism,Population Growth}, month = {feb}, number = {2}, pages = {95--104}, pmid = {17257097}, title = {{A niche for neutrality}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17257097}, volume = {10}, year = {2007} } @article{Vellend2013a, author = {Vellend, Mark and Baeten, Lander and Myers-Smith, Isla H and Elmendorf, Sarah C and Beaus{\'{e}}jour, Robin and Brown, Carissa D}, doi = {10.1073/pnas.1312779110/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1312779110}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vellend et al. - 2013 - Global meta-analysis reveals no net change in local-scale plant biodiversity over time(2).pdf:pdf}, journal = {Proceedings of the National Academy of Sciences}, number = {48}, pages = {19456--19459}, title = {{Global meta-analysis reveals no net change in local-scale plant biodiversity over time}}, volume = {110}, year = {2013} } @article{Lyles2009, author = {Lyles, Danielle and Rosenstock, Todd S and Hastings, Alan and Brown, Patrick H}, doi = {10.1016/j.jtbi.2009.04.015}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lyles et al. - 2009 - The role of large environmental noise in masting General model and example from pistachio trees.pdf:pdf}, journal = {Journal of Theoretical Biology}, pages = {701--713}, title = {{The role of large environmental noise in masting: General model and example from pistachio trees}}, volume = {259}, year = {2009} } @article{Hastings2013, author = {Hastings, Alan}, doi = {10.1007/s10144-013-0416-z}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 2013 - Persistence and management of spatially distributed populations.pdf:pdf}, journal = {Population Ecology}, keywords = {connectivity {\'{a}} dispersal {\'{a}},extinction {\'{a}}}, pages = {1--6}, title = {{Persistence and management of spatially distributed populations}}, year = {2013} } @article{Beaugrand2015, annote = {METAL theory- linking individuals to climate and such In North Sea, they realized "regime shift" was actually just driven by climate Hard to tell if there is causal versus correlative trends Do you need long time series before you actually test for anything?}, author = {Beaugrand, Gregory}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Beaugrand - 2015 - Theoretical basis for predicting climate-induced abrupt shifts in the oceans.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, keywords = {environmental science,regime shifts}, pages = {20130264}, title = {{Theoretical basis for predicting climate-induced abrupt shifts in the oceans}}, volume = {370}, year = {2015} } @article{Norstro2015, annote = {unimodel distribution does not say the alternative stable states do not exist -{\textgreater} maybe most are moving slowly between states -go back to original Mumby and Hastings model paper of coral reefs (with Julie?) no way to identify hysteresis with single time point}, author = {Norstro, Albert V and Jouffray, Jean-baptiste and Nystro, Magnus and Williams, Ivor D and Wedding, Lisa M and Kittinger, John N and Williams, Gareth J}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Norstro et al. - 2015 - Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, keywords = {ecology,environmental,systems biology}, title = {{Identifying multiple coral reef regimes and their drivers across the Hawaiian archipelago}}, year = {2015} } @book{Gelman, author = {Gelman, Andrew and Carlin, John B. and Stern, Hal S. and Rubin, Donald B.}, title = {{Bayesian Data Analysis}} } @article{Zelnik2015, author = {Zelnik, Yuval R and Solomon, Sorin and Yaari, Gur}, doi = {10.1038/srep07877}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Zelnik, Solomon, Yaari - 2015 - Species survival emerge from rare events of individual migration.pdf:pdf}, journal = {Scientific Reports}, pages = {1--10}, title = {{Species survival emerge from rare events of individual migration}}, year = {2015} } @article{Rabosky, author = {Rabosky, Daniel and Hurlbert, Allen H.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rabosky, Hurlbert - Unknown - Species richness at continental scales is dominated by ecological limits.pdf:pdf}, title = {{Species richness at continental scales is dominated by ecological limits}} } @article{Stewart2015, author = {Stewart, Joseph A E and Perrine, John D and Nichols, Lyle B and Thorne, James H. and Millar, Constance I and Goehring, Kenneth E and Massing, Cody P and Wright, David H}, doi = {10.1111/jbi.12466}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stewart et al. - 2015 - Revisiting the past to foretell the future summer temperature and habitat area predict pika extirpations in Cali.pdf:pdf}, journal = {Journal of Biogeography}, keywords = {climate change,correspondence,e,earth,global warming,historical resurvey,joseph a,metapopulation,ochotona,pika,princeps,range shift,species distribution modelling,stewart,talus}, pages = {1--11}, title = {{Revisiting the past to foretell the future: summer temperature and habitat area predict pika extirpations in California}}, year = {2015} } @article{Mittelbach2007a, abstract = {A latitudinal gradient in biodiversity has existed since before the time of the dinosaurs, yet how and why this gradient arose remains unresolved. Here we review two major hypotheses for the origin of the latitudinal diversity gradient. The time and area hypothesis holds that tropical climates are older and historically larger, allowing more opportunity for diversification. This hypothesis is supported by observations that temperate taxa are often younger than, and nested within, tropical taxa, and that diversity is positively correlated with the age and area of geographical regions. The diversification rate hypothesis holds that tropical regions diversify faster due to higher rates of speciation (caused by increased opportunities for the evolution of reproductive isolation, or faster molecular evolution, or the increased importance of biotic interactions), or due to lower extinction rates. There is phylogenetic evidence for higher rates of diversification in tropical clades, and palaeontological data demonstrate higher rates of origination for tropical taxa, but mixed evidence for latitudinal differences in extinction rates. Studies of latitudinal variation in incipient speciation also suggest faster speciation in the tropics. Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research.}, author = {Mittelbach, Gary G and Schemske, Douglas W and Cornell, Howard V and Allen, Andrew P and Brown, Jonathan M and Bush, Mark B and Harrison, Susan P and Hurlbert, Allen H and Knowlton, Nancy and Lessios, Harilaos a and McCain, Christy M and McCune, Amy R and McDade, Lucinda a and McPeek, Mark a and Near, Thomas J and Price, Trevor D and Ricklefs, Robert E and Roy, Kaustuv and Sax, Dov F and Schluter, Dolph and Sobel, James M and Turelli, Michael}, doi = {10.1111/j.1461-0248.2007.01020.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mittelbach et al. - 2007 - Evolution and the latitudinal diversity gradient speciation, extinction and biogeography(2).pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {Animals,Biodiversity,Biological Evolution,Extinction, Biological,Geography,Paleontology,Phylogeny,Plants}, month = {apr}, number = {4}, pages = {315--31}, pmid = {17355570}, title = {{Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17355570}, volume = {10}, year = {2007} } @article{Bozec2015, annote = {do you already have to be degraded in order to have alternative stable states? How would this actually be used for management? - just gives you rule of thumb of what chronic versus acute stress$\backslash$ -Should always use multiple climate change projection scenarios}, author = {Bozec, Yves-Marie and Mumby, Peter J}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bozec, Mumby - 2015 - Synergistic impacts of global warming on the resilience of coral reefs.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, title = {{Synergistic impacts of global warming on the resilience of coral reefs}}, year = {2015} } @article{Fronhofer2012, annote = {look at patch turnover, occupancy, and F{\_}st to identify which combinations of parameters lead to classic metapopulation dynamics}, author = {Fronhofer, Emanuel A and Kubisch, Alexander and Hilker, Frank M and Hovestadt, Thomas and Poethke, Hans Joachim}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Fronhofer et al. - 2012 - Why are metapopulations so rare.pdf:pdf}, journal = {Ecology}, keywords = {dispersal evolution,fixation index,habitat fragmentation,life-history,metapopulation,occupancy,spatially structured population,turnover}, number = {8}, pages = {1967--1978}, title = {{Why are metapopulations so rare?}}, volume = {93}, year = {2012} } @article{Ricklefs2015, author = {Ricklefs, Robert E}, doi = {10.1111/ele.12398}, keywords = {18,200,2015,217,community assembly,diversification,ecology letters,ecosystem functioning,genomics,island biogeography,islands as model systems,speciation}, pages = {200--217}, title = {{REVIEW AND Islands as model systems in ecology and evolution : prospects fifty years after MacArthur-Wilson}}, year = {2015} } @article{Yang2010, annote = {Cannibalism pulses? Would be interesting to look a variation of pulses in a single type of system}, author = {Yang, Louie H and Edwards, Kyle F and Byrnes, Jarrett E and Bastow, Justin L and Wright, Amber N and Spence, Kenneth O}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yang et al. - 2010 - A meta-analysis of resource pulse — consumer interactions.pdf:pdf}, journal = {Ecological Monographs}, number = {1}, pages = {125--151}, title = {{A meta-analysis of resource pulse — consumer interactions}}, volume = {80}, year = {2010} } @article{Powell2013, author = {Powell, Kristin I and Chase, Jonathan M and Knight, Tiffany M}, doi = {10.1126/science.1226817}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Powell, Chase, Knight - 2013 - Invasive Plants Have Scale-Dependent Species-Area Relationships.pdf:pdf}, journal = {Science}, pages = {316--318}, title = {{Invasive Plants Have Scale-Dependent Species-Area Relationships}}, volume = {339}, year = {2013} } @article{Harmon, author = {Harmon, Luke J. and Harrison, Susan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Harmon, Harrison - Unknown - Species diversity is dynamic and unbounded at local and continental scale.pdf:pdf}, pages = {1--34}, title = {{Species diversity is dynamic and unbounded at local and continental scale}} } @article{Yang2008, annote = {resource pulses in form of upwelling, animal carcasses, huricanes, small mammal populations,mastings, heavy rainfall -how does distribution of resource availabilty affect system (what happens if we increase just fatness of tails) preditable vs unpredicatble pulses Caused by: climate or enviornmatal, temporal accumulatino and release, outbreak pop dynamics, 1927 Elton: "The personnel of every community of animals is constantly chaging with the ebb and flow of the seasons, with changing weather, and a number of other periodic ryhthms is the out envinorment. [At the same time,] the food relations of anmals are extemeley complicated and form avery closely and intricatley woven fabric--so elaborate that is is uaully quite imposttble to predict the precise effects of twitchinf one thread in the fabric"}, author = {Yang, Louie H and Bastow, Justin L and Spence, Kenneth O and Wright, Amber N}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yang et al. - 2008 - What Can We Learn from Resource Pulses.pdf:pdf}, journal = {Ecology}, number = {3}, pages = {621--634}, title = {{What Can We Learn from Resource Pulses ?}}, volume = {89}, year = {2008} } @article{Power2008, author = {Power, Mary E and Parker, Michael S and Dietrich, William E}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Power, Parker, Dietrich - 2008 - Seasonal reassembly of a river food web floods, droughts, and impacts of fish.pdf:pdf}, journal = {Ecological Monographs}, keywords = {chain length,interaction strength,lavinia,long-term studies,mediterranean,symmetricus}, number = {2}, pages = {263--282}, title = {{Seasonal reassembly of a river food web: floods, droughts, and impacts of fish}}, volume = {78}, year = {2008} } @article{Polis1996, author = {Polis, Gary A and Hurd, Stephen D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Polis, Hurd - 1996 - Linking Marine and Terrestrial Food Webs Allochthonous Input from the Ocean Supports High Secondary Productivity o.pdf:pdf}, journal = {The American Naturalist}, number = {3}, pages = {396--423}, title = {{Linking Marine and Terrestrial Food Webs : Allochthonous Input from the Ocean Supports High Secondary Productivity on Small Islands and Coastal Land Communities}}, volume = {147}, year = {1996} } @article{Doak2008, author = {Doak, Daniel F and Estes, James A and Halpern, Benjamin S and Jacob, Ute and Lindberg, David R and Lovvorn, James and Monson, Daniel H and Tinker, M Timothy and Williams, Terrie M and Timothy, J and Carroll, Ian and Emmerson, Mark and Micheli, Fiorenza and Novak, Mark and Doak, F and Monson, H and Timothy, M and Halpern, S and Lindberg, R and Williams, M and Wootton, J Timothy}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Doak et al. - 2008 - Understanding and Predicting Ecological Dynamics Are Major surprises Inevitable.pdf:pdf}, journal = {Ecology}, number = {4}, pages = {952--961}, title = {{Understanding and Predicting Ecological Dynamics: Are Major surprises Inevitable?}}, volume = {89}, year = {2008} } @article{Dixon2005, annote = {-includes good references on Bayesian inference in ecology Four ways to improve precision: using additional information to inform priors, stratifying the data apriori, using covariates, aggregating data for larger spatial or temporal scales and using some type of model -A bayesian model with an informative prior does well here for decreases the CV}, author = {Dixon, Philip M and Ellison, Aaron M and Gotelli, Nicholas J}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dixon, Ellison, Gotelli - 2005 - Improving the Precision of Estimates of the Frequency of Rare Events.pdf:pdf}, journal = {Ecology}, number = {5}, pages = {1114--1123}, title = {{Improving the Precision of Estimates of the Frequency of Rare Events}}, volume = {86}, year = {2005} } @article{Polis1995, annote = {Interesting line here relevent to pika work}, author = {Polis, Gary A and Hurd, Stephen D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Polis, Hurd - 1995 - Extraordinarily high spider densities on islands Flow of energy from the marine to terrestrial food webs and the ab.pdf:pdf}, journal = {Proceedings of the National Academy of Sciences}, number = {May}, pages = {4382--4386}, title = {{Extraordinarily high spider densities on islands: Flow of energy from the marine to terrestrial food webs and the absence of predation}}, volume = {92}, year = {1995} } @article{Rose1998, author = {Rose, Michael D and Polis, Gary A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rose, Polis - 1998 - The Distribution and Abundance of Coyotes The Effects of Allochthonous Food Subsidies from the Sea.pdf:pdf}, journal = {Ecology}, keywords = {allochthonous flow,canis latrans,coastal ecosystems,community structure,coyotes,food habits,marine input,population density,trophic subsidies}, number = {3}, pages = {998--1007}, title = {{The Distribution and Abundance of Coyotes: The Effects of Allochthonous Food Subsidies from the Sea}}, volume = {79}, year = {1998} } @book{Botsforda, author = {Botsford, Louis W. and Hastings, Alan and White, William T.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botsford, Hastings, White - Unknown - Chapter Two Simple population models.pdf:pdf}, pages = {1--46}, title = {{Chapter Two: Simple population models}} } @article{Strogatz2001, author = {Strogatz, Steven H}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Strogatz - 2001 - Exploring complex networks.pdf:pdf}, journal = {Nature}, number = {March}, pages = {268--276}, title = {{Exploring complex networks}}, volume = {410}, year = {2001} } @book{Botsfordb, annote = {-}, author = {Botsford, Louis W. and Hastings, Alan and White, William T.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botsford, Hastings, White - Unknown - Chapter One Philosophical Approach to Population Modeling.pdf:pdf}, title = {{Chapter One: Philosophical Approach to Population Modeling}} } @article{Barnosky2011, author = {Barnosky, Anthony D and Matzke, Nicholas and Tomiya, Susumu and Wogan, Guinevere O U and Swartz, Brian and Quental, Tiago B and Marshall, Charles and Mcguire, Jenny L and Lindsey, Emily L and Maguire, Kaitlin C and Mersey, Ben and Ferrer, Elizabeth A}, doi = {10.1038/nature09678}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barnosky et al. - 2011 - Has the Earth's sixth mass extinction already arrived.pdf:pdf}, issn = {0028-0836}, journal = {Nature}, number = {7336}, pages = {51--57}, publisher = {Nature Publishing Group}, title = {{Has the Earth's sixth mass extinction already arrived?}}, url = {http://dx.doi.org/10.1038/nature09678}, volume = {470}, year = {2011} } @article{Brusatte2014, author = {Brusatte, Stephen L and Butler, Richard J and Barrett, Paul M and Carrano, Matthew T and Evans, David C and Lloyd, Graeme T and Mannion, Philip D and Norell, Mark A and Peppe, Daniel J and Upchurch, Paul and Williamson, Thomas E}, doi = {10.1111/brv.12128}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brusatte et al. - 2014 - The extinction of the dinosaurs.pdf:pdf}, journal = {Biological Reviews}, keywords = {chicxulub impact,cretaceous,deccan traps,dinosaurs,end-cretaceous,extinctions,global change,macroevolution,mass extinction,palaeontology,paleogene}, title = {{The extinction of the dinosaurs}}, year = {2014} } @article{Brockhurst2014, author = {Brockhurst, Michael A and Chapman, Tracey and King, Kayla C and Mank, Judith E and Paterson, Steve and Hurst, Gregory D D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brockhurst et al. - 2014 - Running with the Red Queen the role of biotic conflicts in evolution Darwin review.pdf:pdf}, journal = {Proceedings of the Royal Society B}, number = {20141382}, title = {{Running with the Red Queen : the role of biotic conflicts in evolution Darwin review}}, volume = {281}, year = {2014} } @article{Gardmark2015, annote = {Cultivation-depensation: prey affect early life stages of predators Overcompensation: predation-induced competitive release in prey -in stage structued models a number of important processes are proportional to body size Size structure can cause a bottleneck or resources in one size class versus another **To show model works- see if all mechanims are actually present and see how well model predictions match up with time series}, author = {Gardmark, Anna and Casini, Michele and Huss, Magnus and van Leeuwen, Anieke and Hjelm, Joakim and Persson, Lennart and de Roos, Andre M.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gardmark et al. - 2015 - Regime shifts in exploited marine food webs detecting mechanisms underlying alternative stable states using si.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, keywords = {ecology,theoretical biology}, pages = {1--10}, title = {{Regime shifts in exploited marine food webs : detecting mechanisms underlying alternative stable states using size- structured community dynamics theory}}, volume = {370}, year = {2015} } @article{Vermeij2013a, author = {Vermeij, Geerat J. and Roopnarine, Peter D.}, doi = {10.1666/13009}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vermeij, Roopnarine - 2013 - Reining in the Red Queen the dynamics of adaptation and extinction reexamined.pdf:pdf}, issn = {0094-8373}, journal = {Paleobiology}, month = {jun}, number = {4}, pages = {560--575}, title = {{Reining in the Red Queen: the dynamics of adaptation and extinction reexamined}}, url = {http://www.bioone.org/doi/abs/10.1666/13009}, volume = {39}, year = {2013} } @article{Dakos2014, annote = {saddle node bifurcation gives you alternative stables states but other things can also gave you alternative stable states are eigenvalues real things in nature? these ideas were originally supposed to allow you to use some metric of impending doom in systems in which you do not know the mechanism, turns out you probably do need to know the mechanism, so you might as well not use CSD decoupling- When is this going to be useful to a manager? - you need to have management system with the ability of a rapid response}, author = {Dakos, Vasilis and Carpenter, Stephen R and Nes, Egbert H Van and Scheffer, Marten}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dakos et al. - 2014 - Resilience indicators prospects and limitations for early warnings of regime shifts.pdf:pdf}, journal = {Phil. Trans. R. Soc. B}, keywords = {ecology,environmental science}, pages = {1--10}, title = {{Resilience indicators: prospects and limitations for early warnings of regime shifts}}, volume = {370}, year = {2014} } @article{Barnosky2012, author = {Barnosky, Anthony D and Hadly, Elizabeth A and Bascompte, Jordi and Berlow, Eric L and Brown, James H and Fortelius, Mikael and Getz, Wayne M and Harte, John and Hastings, Alan and Marquet, Pablo A and Martinez, Neo D and Mooers, Arne and Roopnarine, Peter}, doi = {10.1038/nature11018}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barnosky et al. - 2012 - Approaching a state shift in Earth's biosphere.pdf:pdf}, issn = {0028-0836}, journal = {Nature}, number = {7401}, pages = {52--58}, publisher = {Nature Publishing Group}, title = {{Approaching a state shift in Earth's biosphere}}, url = {http://dx.doi.org/10.1038/nature11018}, volume = {486}, year = {2012} } @book{Botsford, author = {Botsford, Louis W. and Hastings, Alan and White, William T.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botsford, Hastings, White - Unknown - Chapter Three Linear, Age-Structured Models.pdf:pdf}, pages = {1--31}, title = {{Chapter Three: Linear, Age-Structured Models}} } @article{Botsford2003, author = {Botsford, Louis W. and Micheli, Fiorenza and Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botsford, Micheli, Hastings - 2003 - Principles for the design of marine reserves.pdf:pdf}, journal = {Ecological Applications}, keywords = {conservation,dispersal,fisheries,marine reserves,models}, number = {1}, pages = {S25--S31}, title = {{Principles for the design of marine reserves}}, volume = {13}, year = {2003} } @book{Mcelreath2015, author = {Mcelreath, Richard}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mcelreath - 2015 - Statistical Rethinking.pdf:pdf}, title = {{Statistical Rethinking}}, year = {2015} } @article{Clinchy2002, annote = {argue that extinction disks can cause same patch occupancy patterns as dispersal processes in metapopulation dynamics also found that changes in patch occupancy can also be ascribed to extinction disks instead of the rescue effect argue that extinction events at Bodie have tended to occur in clusters argue experimental manipulations and not simply census data are needed}, author = {Clinchy, Michael and Haydon, Daniel T and Smith, Andrew T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Clinchy, Haydon, Smith - 2002 - Pattern does not equal process what does patch occupancy really tell us about metapopulation dynamics.pdf:pdf}, journal = {The American Naturalist}, keywords = {colonization,dispersal,extinction,metapopulation,pikas}, mendeley-tags = {extinction,metapopulation,pikas}, number = {4}, pages = {351--362}, title = {{Pattern does not equal process: what does patch occupancy really tell us about metapopulation dynamics?}}, volume = {159}, year = {2002} } @article{Servedio2014, author = {Servedio, Maria R and Brandvain, Yaniv and Dhole, Sumit and Fitzpatrick, Courtney L and Goldberg, Emma E and Stern, Caitlin A and Cleve, Jeremy Van and Yeh, D Justin}, doi = {10.1371/journal.pbio.1002017}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Servedio et al. - 2014 - Not Just a Theory — The Utility of Mathematical Models in Evolutionary Biology.pdf:pdf}, journal = {PLoS Biology}, keywords = {evolution,mathematics,model}, mendeley-tags = {evolution,mathematics,model}, number = {12}, pages = {1--5}, title = {{Not Just a Theory — The Utility of Mathematical Models in Evolutionary Biology}}, volume = {12}, year = {2014} } @article{Vermeij2011, annote = {Why are monopolies in nature so rare? In economies, how do we get rid of monoplies? -Inovate the monopoly out of existence -change criteria of what it means to be successful (e.g. grasslands emerge b/c herbivory on trees Efficiancy is an overused concept in biology -instead you simply need to take up resources, efficiancy doesn't matter that much You care about efficiancy when you are losing A lot of models in biology are based on optimality theory. But evoution doesn't care about optimality. Evolution cares about what works, regardless of how wasteful you might be. Suffiancy should matter more}, author = {Vermeij, Geerat J. and Leigh, Egbert G.}, doi = {10.1890/ES11-00004.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vermeij, Leigh - 2011 - Natural and human economies compared.pdf:pdf}, issn = {2150-8925}, journal = {Ecosphere}, keywords = {2011,4,accepted 23 february 2011,and e,art39,c,citation,compared,corresponding editor,d,doi,economy,ecosphere 2,ecosystems,final version received 15,g,j,jr,leigh,march 2011,monopoly,natural and human economies,p,peters,published 1 april 2011,received 5 january 2011,revised 22 february 2011,tragedy of the commons,trends,vermeij}, month = {apr}, number = {4}, pages = {39}, title = {{Natural and human economies compared}}, url = {http://www.esajournals.org/doi/abs/10.1890/ES11-00004.1}, volume = {2}, year = {2011} } @article{Carroll2014, author = {Carroll, Scott P and J{\o}rgensen, Peter S{\o}gaard and Michael, T and Bergstrom, Carl T and Denison, R Ford and Gluckman, Peter and Smith, Thomas B and Strauss, Sharon Y and Tabashnik, Bruce E}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Carroll et al. - 2014 - Applying evolutionary biology to address global challenges.pdf:pdf}, journal = {Sciencexpress}, keywords = {evolution,global}, mendeley-tags = {evolution,global}, pages = {1--16}, title = {{Applying evolutionary biology to address global challenges}}, year = {2014} } @article{Millar2013, author = {Millar, Constance I and Westfall, Robert D and Delany, Diane L}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Millar, Westfall, Delany - 2013 - New records of marginal locations for American pika (emph{\{}Ochotona princeps{\}}) in the western Great Bas.pdf:pdf}, journal = {Western North American Naturalist}, keywords = {natural history,pika}, mendeley-tags = {natural history,pika}, number = {4}, pages = {457--476}, title = {{New records of marginal locations for American pika ($\backslash$emph{\{}Ochotona princeps{\}}) in the western Great Basin}}, volume = {73}, year = {2013} } @article{Gravel2011, annote = {This is a review of on how stochasticity affects species coexistence. -Do species coexist because of niche differetiation despite high variance that would seemingly have many species overlap? Or does this variance allow species to interact. Talk about demographic stochasticty and it's effects}, author = {Gravel, Dominique and Guichard, Frederic and Hochberg, Michael E.}, doi = {10.1111/j.1461-0248.2011.01643.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gravel, Guichard, Hochberg - 2011 - Species coexistence in a variable world.pdf:pdf}, journal = {Ecology Letters}, keywords = {coexistence,ecological drift,ecology letters,extinction risk,neutral theory,niche,nonlinear averaging,stability,stochasticity}, mendeley-tags = {coexistence,ecological drift,ecology letters,extinction risk,neutral theory,niche,nonlinear averaging,stability,stochasticity}, pages = {828--839}, title = {{Species coexistence in a variable world}}, volume = {14}, year = {2011} } @article{Yi2010, abstract = {Residents of the Tibetan Plateau show heritable adaptations to extreme altitude. We sequenced 50 exomes of ethnic Tibetans, encompassing coding sequences of 92{\%} of human genes, with an average coverage of 18x per individual. Genes showing population-specific allele frequency changes, which represent strong candidates for altitude adaptation, were identified. The strongest signal of natural selection came from endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1), a transcription factor involved in response to hypoxia. One single-nucleotide polymorphism (SNP) at EPAS1 shows a 78{\%} frequency difference between Tibetan and Han samples, representing the fastest allele frequency change observed at any human gene to date. This SNP's association with erythrocyte abundance supports the role of EPAS1 in adaptation to hypoxia. Thus, a population genomic survey has revealed a functionally important locus in genetic adaptation to high altitude.}, annote = {Class discussion:}, author = {Yi, Xin and Liang, Yu and Huerta-Sanchez, Emilia and Jin, Xin and Cuo, Zha Xi Ping and Pool, John E and Xu, Xun and Jiang, Hui and Vinckenbosch, Nicolas and Korneliussen, Thorfinn Sand and Zheng, Hancheng and Liu, Tao and He, Weiming and Li, Kui and Luo, Ruibang and Nie, Xifang and Wu, Honglong and Zhao, Meiru and Cao, Hongzhi and Zou, Jing and Shan, Ying and Li, Shuzheng and Yang, Qi and Asan and Ni, Peixiang and Tian, Geng and Xu, Junming and Liu, Xiao and Jiang, Tao and Wu, Renhua and Zhou, Guangyu and Tang, Meifang and Qin, Junjie and Wang, Tong and Feng, Shuijian and Li, Guohong and Huasang and Luosang, Jiangbai and Wang, Wei and Chen, Fang and Wang, Yading and Zheng, Xiaoguang and Li, Zhuo and Bianba, Zhuoma and Yang, Ge and Wang, Xinping and Tang, Shuhui and Gao, Guoyi and Chen, Yong and Luo, Zhen and Gusang, Lamu and Cao, Zheng and Zhang, Qinghui and Ouyang, Weihan and Ren, Xiaoli and Liang, Huiqing and Zheng, Huisong and Huang, Yebo and Li, Jingxiang and Bolund, Lars and Kristiansen, Karsten and Li, Yingrui and Zhang, Yong and Zhang, Xiuqing and Li, Ruiqiang and Li, Songgang and Yang, Huanming and Nielsen, Rasmus and Wang, Jun and Wang, Jian}, doi = {10.1126/science.1190371}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Yi et al. - 2010 - Sequencing of 50 human exomes reveals adaptation to high altitude.pdf:pdf}, issn = {1095-9203}, journal = {Science}, keywords = {Acclimatization,Acclimatization: genetics,Altitude,Asian Continental Ancestry Group,Asian Continental Ancestry Group: genetics,Basic Helix-Loop-Helix Transcription Factors,Basic Helix-Loop-Helix Transcription Factors: gene,Basic Helix-Loop-Helix Transcription Factors: phys,Bayes Theorem,China,DNA,Erythrocyte Count,Ethnic Groups,Ethnic Groups: genetics,Exons,Female,Gene Frequency,Genetic,Genetic Association Studies,Genome,Hemoglobins,Hemoglobins: analysis,Human,Humans,Male,Oxygen,Oxygen: blood,Polymorphism,Selection,Sequence Analysis,Single Nucleotide,Tibet,adaptation,evolution,genomics}, mendeley-tags = {adaptation,evolution,genomics}, month = {jul}, number = {5987}, pages = {75--8}, pmid = {20595611}, title = {{Sequencing of 50 human exomes reveals adaptation to high altitude.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3711608{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {329}, year = {2010} } @incollection{Leo2012, address = {Berkeley and Los Angeles}, author = {de Leo, Giulio and Wood, Chelsea L}, booktitle = {Encyclopedia of Theoretical Ecology}, editor = {Hastings, Alan and Gross, Louis J.}, pages = {179--187}, publisher = {University of California Press}, title = {{Disease Dynamics}}, year = {2012} } @article{Holt2008, annote = {Scattered theoretical work related to resource pulses -transient dynamics (Hastings, Neubert, Caswell) Makes a few points with simple models -Ricker map -it matters a lot of pulses are recurrent (could then be predictable and have evo effects) -a lot of work on coexistence in temporally variable environments}, author = {Holt, Robert D.}, doi = {10.1890/07-0348.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Holt - 2008 - Theoretical Perspectives on Resource Pulses.pdf:pdf}, issn = {0012-9658}, journal = {Ecology}, keywords = {reactivity,resource pulse,resource pulses,spatiotemporal variation,stochasticity,transient,transient dynamics}, mendeley-tags = {resource pulse,stochasticity,transient}, month = {mar}, number = {3}, pages = {671--681}, title = {{Theoretical Perspectives on Resource Pulses}}, url = {http://www.esajournals.org/doi/abs/10.1890/07-0348.1}, volume = {89}, year = {2008} } @article{Lloyd-Smith2013, author = {Lloyd-Smith, James O}, journal = {Phil. Trans. R. Soc. B}, keywords = {ecology,epidemiology,health and disease and}, number = {20120150}, title = {{Vacated niches, competitive release and the community ecology of pathogen eradication}}, volume = {368}, year = {2013} } @article{Melbourne2008, abstract = {Extinction risk in natural populations depends on stochastic factors that affect individuals, and is estimated by incorporating such factors into stochastic models. Stochasticity can be divided into four categories, which include the probabilistic nature of birth and death at the level of individuals (demographic stochasticity), variation in population-level birth and death rates among times or locations (environmental stochasticity), the sex of individuals and variation in vital rates among individuals within a population (demographic heterogeneity). Mechanistic stochastic models that include all of these factors have not previously been developed to examine their combined effects on extinction risk. Here we derive a family of stochastic Ricker models using different combinations of all these stochastic factors, and show that extinction risk depends strongly on the combination of factors that contribute to stochasticity. Furthermore, we show that only with the full stochastic model can the relative importance of environmental and demographic variability, and therefore extinction risk, be correctly determined. Using the full model, we find that demographic sources of stochasticity are the prominent cause of variability in a laboratory population of Tribolium castaneum (red flour beetle), whereas using only the standard simpler models would lead to the erroneous conclusion that environmental variability dominates. Our results demonstrate that current estimates of extinction risk for natural populations could be greatly underestimated because variability has been mistakenly attributed to the environment rather than the demographic factors described here that entail much higher extinction risk for the same variability level.}, annote = {Many different types of stochasticity can affect population dynamics and extinction risk. Often the distinctions between environmental and demographic stochasticity are not properly made, which may underestimate extinction risk. Melbourne and Hastings (2008) delineate four different tyes of stochasticity: birth and death rates at level of individuals (demographic stochasticty), variation in birth and death rates over time or space (environmental stochasticity), sex of individuals, and the variation of vital rates among individuals in population (demographic heterogeneity). Melbourne and Hastings (2008) investigate the role of these different types of stochastities by constructing models with different combinations of said types in Ricker models. They then compare these models to population data of tribolium and found that the model that includes all four types of stochasticity performed best.}, author = {Melbourne, Brett A and Hastings, Alan}, doi = {10.1038/nature06922}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Melbourne, Hastings - 2008 - Extinction risk depends strongly on factors contributing to stochasticity.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Melbourne, Hastings - 2008 - Extinction risk depends strongly on factors contributing to stochasticity(2).pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {Animals,Biological,Environment,Extinction,Female,Fishes,Life Cycle Stages,Male,Models,Risk Factors,Statistical,Stochastic Processes,Tribolium,Tribolium: physiology,extinction risk,stochasticity,tribolium}, mendeley-tags = {extinction risk,stochasticity,tribolium}, month = {jul}, number = {7200}, pages = {100--3}, pmid = {18596809}, title = {{Extinction risk depends strongly on factors contributing to stochasticity}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18596809}, volume = {454}, year = {2008} } @article{Keeling2001, author = {Keeling, Matt J and Woolhouse, Mark E J and Shaw, Darren J and Matthews, Louise and Chase-Topping, Margo and Haydon, Dan T and Cornell, Stephen J and Kappey, Jens and Wilesmith, John and Grenfell, Bryan T}, doi = {10.1126/science.1065973}, journal = {Science}, pages = {813--817}, title = {{Dynamics of the 2001 UK foot and mouth epidemic: stochastic dispersal in a heterogeneous landscape}}, volume = {294}, year = {2001} } @article{Johnston2013, abstract = {Sexual selection, through intra-male competition or female choice, is assumed to be a source of strong and sustained directional selection in the wild. In the presence of such strong directional selection, alleles enhancing a particular trait are predicted to become fixed within a population, leading to a decrease in the underlying genetic variation. However, there is often considerable genetic variation underlying sexually selected traits in wild populations, and consequently, this phenomenon has become a long-discussed issue in the field of evolutionary biology. In wild Soay sheep, large horns confer an advantage in strong intra-sexual competition, yet males show an inherited polymorphism for horn type and have substantial genetic variation in their horn size. Here we show that most genetic variation in this trait is maintained by a trade-off between natural and sexual selection at a single gene, relaxin-like receptor 2 (RXFP2). We found that an allele conferring larger horns, Ho(+), is associated with higher reproductive success, whereas a smaller horn allele, Ho(P), confers increased survival, resulting in a net effect of overdominance (that is, heterozygote advantage) for fitness at RXFP2. The nature of this trade-off is simple relative to commonly proposed explanations for the maintenance of sexually selected traits, such as genic capture ('good genes') and sexually antagonistic selection. Our results demonstrate that by identifying the genetic architecture of trait variation, we can determine the principal mechanisms maintaining genetic variation in traits under strong selection and explain apparently counter-evolutionary observations.}, annote = {Although the idea of maintained genetic variation makes a lot of intuitive sense, under sexual selection (which should be directional), it is unclear how this variation would persist. The trait that is being selected for should become fixed in the population. In Soay sheep, large horns offer an advantage when males compete for mates. Yet, a polymorphism still exists at a locus determining horn type and size. This locus explained almost all of the genetic variation for both horn type and size. One version of the allele is correlated with greater reproductive success (big horn allele) and the other allele increases survival rate. The combination of these two processes leads to overdominance (the heterozygote being favored). Instead of proposing some crazy mechanism for how this polymorphism could exist, it just took getting to the actual mechanisms to explain what is happening. I wonder if this mechanism could have been started because a small population was intially isolated on the island. How replicable is this study for other populations? They have an enourmous data set Talk about the females more.}, author = {Johnston, Susan E and Gratten, Jacob and Berenos, Camillo and Pilkington, Jill G and Clutton-Brock, Tim H and Pemberton, Josephine M and Slate, Jon}, doi = {10.1038/nature12489}, issn = {1476-4687}, journal = {Nature}, keywords = {Animal,Animal: physiology,Animals,Female,G-Protein-Coupled,G-Protein-Coupled: genetics,Genetic,Genetic Variation,Genotype,Horns,Male,Mating Preference,Phenotype,Polymorphism,Receptors,Reproduction,Reproduction: genetics,Selection,Survival Analysis,genetics,sexual selection,sheep}, mendeley-tags = {genetics,sexual selection,sheep}, month = {oct}, number = {7469}, pages = {93--5}, pmid = {23965625}, publisher = {Nature Publishing Group}, title = {{Life history trade-offs at a single locus maintain sexually selected genetic variation.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23965625}, volume = {502}, year = {2013} } @article{Questad2008, abstract = {The effect of spatial heterogeneity on species coexistence relies on the degree of niche heterogeneity in the habitat and the ability of species to exploit the available niche opportunities. We studied species coexistence in a perennial grassland, and tested whether small-scale disturbances create environmental heterogeneity that affects coexistence and whether the functional diversity of species in the species pool affects the ability of community composition to reflect heterogeneity through species sorting. We manipulated the spatio-temporal heterogeneity of disturbance and the functional diversity of species added as seed and measured their impact on the spatial turnover of species composition. Disturbance increased environmental heterogeneity and spatial turnover, and the effect of heterogeneity on turnover was greatest in the presence of a functionally diverse species pool, showing the importance of trait variation among species for exploiting environmental heterogeneity, and suggesting that coexistence occurred due to species sorting among heterogeneous niches.}, annote = {-found that the species pool itself mattered, as opposed to neutral theory which would predict that turnover should be independentic of life history traits of species involved. -heterogeenity increases diversity but has largest effect when the is more functional diversity to begin with}, author = {Questad, Erin J and Foster, Bryan L}, doi = {10.1111/j.1461-0248.2008.01186.x}, issn = {1461-0248}, journal = {Ecology Letters}, keywords = {Biodiversity,Ecosystem,Poaceae,biodiversity,heterogeneity,plant,stochasticity}, mendeley-tags = {biodiversity,heterogeneity,plant,stochasticity}, month = {jul}, number = {7}, pages = {717--26}, pmid = {18445035}, title = {{Coexistence through spatio-temporal heterogeneity and species sorting in grassland plant communities}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18445035}, volume = {11}, year = {2008} } @incollection{LeahEdelstein-Keshet1987, author = {{Leah Edelstein-Keshet}}, booktitle = {Mathematical models in biology}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Leah Edelstein-Keshet - 1987 - Partial Differential Equation Models in Biology.pdf:pdf}, publisher = {SIAM}, title = {{Partial Differential Equation Models in Biology}}, year = {1987} } @incollection{Stone2012, address = {Berkeley and Los Angeles}, author = {Stone, Lewi and Katriel, Guy and Hilker, Frank M}, booktitle = {Encyclopedia of Theoretical Ecology}, editor = {Hastings, Alan and Gross, Louis J.}, pages = {648--659}, publisher = {University of California Press}, title = {{SIR models}}, year = {2012} } @article{Tilman1994a, annote = {This paper builds upon Nee and May (1992). Here a multispecies model in a metapopulation context is developed. They find that with even mild levels of patch destruction, the dominant competitor (and most abundant species) will go extinct, after some time delay. As the amount of habitat destruction increases, more and more of the top competitors also go extinct. The inherit time delays to extinction also generate a type of extinction debt- a population is doomed to extinction, but the effects may not be seen for generations. These results have important implicaitons in management. They point to the idea that habitat degragation might have particurly bad effects on the most abundant species- as opposed to the rare ones. question: if the best competitor may go extinct because of habitat fragmentation, could invasive species be rid of by fragmenting their landscapes, therby increasing abundance of all other species}, author = {Tilman, David and May, Robert M. and Lehman, Clarence L. and Nowak, Martin A.}, journal = {Nature}, keywords = {disturbance,extinction,habitat}, mendeley-tags = {disturbance,extinction,habitat}, pages = {65--66}, title = {{Habitat destruction and the extinction debt}}, volume = {371}, year = {1994} } @article{Ryall2006, annote = {A number of papers have looked at the interplay between predation and loss of habitat, from both an empirical and theoretical perspective. The empirical literature has produced a number of simingly contradiciting results and no general trends. However, this may be due to more mechanistic factors. Many of these factors have been flushed out in the theoretical literature. The life history characterisitcs of the predator under question are of particular importance. Specifically, the feeding stragegy and the habitat occupied by the predator . In addition, the dispersal rates of the prey population is important. Empirical work needs to be better associated with theoretical knowledge to really understand the role of habitat loss in predator-prey systems. In general, omnivores (or generalists) should be less vulnerable to prey habitat loss compared to specialist predators. Prey respond to habitat loss in many different ways depending on the predator in the system. Dispersal abilities of both prey and predator is also important in examining the effect of habitat fragmentation. A number of issues should be addressed by experimental setups when assessing effect of habitat fragmentation: predator feeding strategy, habitat used by the predator, habitat loss or fragmentation, spatial scale, comparing systems with predators to those without, and dispersal ability of prey and predators. }, author = {Ryall, Krista L. and Fahrig, Lenore}, journal = {Ecology}, keywords = {conservation,fragmentation,habitat loss,predation,predator,prey interaction,spatial scale,theoretical models}, mendeley-tags = {conservation,fragmentation,predation}, number = {5}, pages = {1086--1093}, title = {{Response of predators to loss and fragmentation of prey habitat- a review of theory}}, volume = {87}, year = {2006} } @article{Nee1992, annote = {Nee and May (1992) explore the consequences of habitat destruction on a two species system living in a patchy environment. They assume a tradeoff between colonization-competition. Essentially, the better ccompetitor is a worse colonizer. They found that habitat destruction, via patch removal, can actually increase the number of patches occupied by the inferior competitor. This is surprising as empty patches are needed for an inferior species to colonize. Instead of two species, you could use the same model to examine two phenotypes. This could provide insight of how a disperser phenotype may start to dominate if there is habitat loss. It is unclear to me if a species like a lionfish would increase or decrease in face of habitat degragation. Are they the better competitor or colonizer? Or is it more difficult because they are actually predators.}, author = {Nee, Sean and May, Robert M}, journal = {Journal of Animal Ecology}, keywords = {conservation,disturbance,metapopulation}, mendeley-tags = {conservation,disturbance,metapopulation}, number = {1}, pages = {37--40}, title = {{Dynamics of metapopulations: habitat destruction and competitive coexistence}}, volume = {61}, year = {1992} } @article{Baskett2007, annote = {Most work on marine reserves has focused on single species models. However, incorporating the interactions amongst species may be important for reserve design and fisheries management. Baskett et al (2007) review theoretical and empirical work to explain the effects of including different types of species interactions in thinking about marine reserves. They find a number of general conclusions. Larger and less fragmented reserves tend to do better when accounting for species interactions (competition, predation, mutualisms). After a marine reserve is implemented there may be inherit time delays and trophic cascades are possible if a previously harvested predator is now better protected. Generally, the most vulnerable species will be top predators, long-distance dispersers, and poor colonizers. Interaction types, dispersal, harvest regimes outside the reserve, and ontogenetic shifts are all important considerations when implementing marine reserves. In addition, they found that the dynamics outside the marine reserve may be very important.}, author = {Baskett, Marissa L. and Micheli, Fiorenza and Levin, Simon A.}, doi = {10.1016/j.biocon.2007.02.013}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Baskett, Micheli, Levin - 2007 - Designing marine reserves for interacting species Insights from theory.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {marine protected areas}, month = {jun}, number = {2}, pages = {163--179}, title = {{Designing marine reserves for interacting species: Insights from theory}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006320707000833}, volume = {137}, year = {2007} } @article{Poelstra2014, abstract = {The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region ({\textless}2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.}, annote = {Although species can seperate and gene flow can be stopped to generate speciation events, it is unclear how much gene flow is required. The black and gray crows of Europe are different in color and assortively mate according to color, but they still hybridize on occasion. By sequencing crows (for both their genomes and RNA to capture expression information) across Europe, researchers found evidence of substantial gene flow between black and gray crows. However, a small number (about 82 sites) has been fixed and appears to be unaffected even with high levels of gene flow. This just happens to be the region that encodes for pigmentation and visual acuity. The authors conclude that even with little differences (less than one percent) of genome between black and gray crows, this is enough to allow phenotypic differences. Assortitive mating and sexual selection, alone, can cause differentiation. Class discussion: -loci that are linked or close together may be important for evolution -these subspecies were seperatly and have been able to reconnect since the last glaciation -inversion ties two alleles together -Shuting down recombination}, author = {Poelstra, J W and Vijay, N and Bossu, C M and Lantz, H and Ryll, B and M{\"{u}}ller, I and Baglione, V and Unneberg, P and Wikelski, M and Grabherr, M G and Wolf, J B W}, doi = {10.1126/science.1253226}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Poelstra et al. - 2014 - The genomic landscape underlying phenotypic integrity in the face of gene flow in crows.pdf:pdf}, issn = {1095-9203}, journal = {Science}, keywords = {Animals,Crows,Crows: genetics,Evolution,Feathers,Feathers: cytology,Feathers: enzymology,Gene Flow,Genetic,Genetic Variation,Genomics,Hybridization,Melanocytes,Melanocytes: enzymology,Molecular,Phenotype,Pigmentation,Pigmentation: genetics,Polymorphism,Selection,Single Nucleotide}, month = {jun}, number = {6190}, pages = {1410--4}, pmid = {24948738}, title = {{The genomic landscape underlying phenotypic integrity in the face of gene flow in crows}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24948738}, volume = {344}, year = {2014} } @article{Reznick1997, abstract = {Natural populations of guppies were subjected to an episode of directional selection that mimicked natural processes. The resulting rate of evolution of age and size at maturity histories had thus evolved to be similar to was similar to rates typically obtained for traits subjected to artificial selection in labo- those of guppies naturally occurring in ratory settings and up to seven orders of magnitude greater than rates inferred from the low-predation communities. paleontological record. Male traits evolved more rapidly than female traits largely be- We evaluated the response to selection cause males had more genetic variation upon which natural selection could act. These by fish in the El Cedro River 4 (7) and 7.5 results are considered in light of the ongoing debate about the importance of natural years after the introduction. Males from the selection versus other processes in the paleontological record of evolution.}, annote = {Large discrepency in evolution rates between lab setting and paleological record. Why did males evolve more quickly? I thought this was an interesting study that used experiments in a natural setting and in the lab. I just had a few questions: Are darwins the standard measure for this type of analysis? They propose the hypothesis that males may have evolved more quickly because of higher variation in their population. I am not sure where they show this though. They don{\&}{\#}039;t really address this later in the discussion, but do talked about the higher herittability of traits for males. I don{\&}{\#}039;t think it is appropriate to run tests twice at year 4 and then at year 7 and report p-values. You would have to use a more Bayesian approach if you want to retest your data or account for this in the calculation of your p-values. }, author = {Reznick, David N and Shaw, Frank H and Rodd, F Helen and Shaw, Ruth G}, doi = {10.1126/science.275.5308.1934}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reznick et al. - 1997 - Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata).pdf:pdf}, journal = {Science}, keywords = {Adaptation,evolution,fish,predation}, mendeley-tags = {Adaptation,evolution,fish,predation}, pages = {1934--1937}, title = {{Evaluation of the rate of evolution in natural populations of guppies (Poecilia reticulata)}}, volume = {275}, year = {1997} } @article{Hastings1977, annote = {In the early 1970s, there was a number of investigations into the role of predation in determining equilibrium and stability of both predators and prey. Hastings (1977) developed a simple predator-prey model in a metapopulation of identical patches. He then looked at which combinations of parameters produced which dynamics. He found that when predator dispersal is too low, the predator will go extinct. If predator dispersal is high, but prey dispersal is low, there is no stable equilbrium. If both predator and prey dispersal is high there is stability. Thus, depending on the life history traits of the predator and prey, predatation can be stabalizing. I'm not sure where the spatial heterogeneity comes in; is it simply the fact that you have patches? Key assumptions: -*global dispersal among patches -all patches identical -can have empty, prey only, or predator and prey patches -ignore within patch dynamics (Caswell 1977) THe location of the nontrivial equilbrium is important (if stochastic fluctuations are present) -prey pop levels can be regulated by predators even when predators are at low density and prey are good dispersers}, author = {Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 1977 - Spatial Heterogeneity and the stability of predator-prey systems.pdf:pdf}, journal = {Theoretical Population Biology}, keywords = {heterogeneity,predation,spatial,stability}, mendeley-tags = {heterogeneity,predation,spatial,stability}, pages = {37--48}, title = {{Spatial Heterogeneity and the stability of predator-prey systems}}, volume = {12}, year = {1977} } @incollection{LeahEdelstein-Keshet1987a, author = {{Leah Edelstein-Keshet}}, booktitle = {Mathematical models in biology}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Leah Edelstein-Keshet - 1987 - An Introduction to Partial Differential Equations and Diffusion in Biological Settings.pdf:pdf}, publisher = {SIAM}, title = {{An Introduction to Partial Differential Equations and Diffusion in Biological Settings}}, year = {1987} } @article{Leffler2012, abstract = {Understanding why some species have more genetic diversity than others is central to the study of ecology and evolution, and carries potentially important implications for conservation biology. Yet not only does this question remain unresolved, it has largely fallen into disregard. With the rapid decrease in sequencing costs, we argue that it is time to revive it.}, annote = {Beginning in the 1960{\&}{\#}039;s, researchers have been interested in the genetic diversity differences among species. These original studies looked at allozumes to estimate genetic diversity of hundreds of species. These data are limited because allozymes don{\&}{\#}039;t show all genetic changes. These limitations led to a lack of interest in the question of genetic diversity in different species. With new sequencing technologies, it should be much easier to address this question. The authors compiled a small dataset (167 species) of diversity levels in euakrayotes. Generally, they found that species with larger populaiton sizes, do have more neutral genetic diversity. They also correlate diversity with a number of ecological and life-history traits. They found that the most diverse phyla were aquatic organisms. Species with large ranges, are usually most diverse. Although diversity levels increased for species that had larger population sizes, they did not increase near as much as theory would predict. In order to really address this question, mutation rates for various species are also needed. It is possible that mutation rates are inversly related to effective population size. Information on genetic diversity is important in an applied context. The small range of genetic diversity in nature may hint at some lower bound neccesary for species to persist (population may be too inbred at some point). Further too much diversity, may lead to reproductive incompatibilies. It is unclear how this latter idea would affect conservation science. Questions: 1. Would more recently evolved species have less diversity? 2. Genetic diversity allows for evolution to act, but how much does ecology then affect the amount of genetic diversity? }, author = {Leffler, Ellen M and Bullaughey, Kevin and Matute, Daniel R and Meyer, Wynn K and S{\'{e}}gurel, Laure and Venkat, Aarti and Andolfatto, Peter and Przeworski, Molly}, doi = {10.1371/journal.pbio.1001388}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Leffler et al. - 2012 - Revisiting an old riddle what determines genetic diversity levels within species.pdf:pdf}, issn = {1545-7885}, journal = {PLoS Biology}, keywords = {Animals,Biological,Chromosomes,Drosophila,Drosophila: genetics,Ecosystem,Genetic,Genetic Variation,Geography,Insect,Insect: genetics,Models,Nucleotides,Nucleotides: genetics,Phylogeny,Selection,Sex Chromosomes,Sex Chromosomes: genetics,Species Specificity}, month = {jan}, number = {9}, pages = {e1001388}, pmid = {22984349}, title = {{Revisiting an old riddle: what determines genetic diversity levels within species?}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3439417{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {10}, year = {2012} } @article{Wang2011, annote = {Wang et al (2011) Science Conflicting evidence has emerged for the identity of avian wing digits between paleotological and embryological studies. This paper tried to address this question by using transcriptomic data from 40 chicken forelimb and hindlimb digits. This seems like a lot of RNA was needed. Would this be useful for other, potentially rare, species? They found that the first wing digit and the first foot digit have transcriptomes that are highly correlated. This is interesting because the first wing digit is known to develop from embryological position 2. In addition, they found that hindlimb an forelimb digits were very differentiated. This is the first study to use transcriptomic data to examine digit homologies. Technology 40 inviduals embyonic chicken digits were used to perform mRNA sequencing on an Illumina machine. Over 14000 genes were available for analysis. mRNA-seq data was then analyzing to look for correlation between different digits and to examine differential gene expression. Is correlation all you can really obtain from this type of analysis? Reads obtained from mRNA-seq were assembled to a known chicken genome. Software was used to examine the different gene expression levels in the different digits. They were able to identify the specific genes that were more highly expressed in different digits, providing clues to their origin. There methods really seem like more of a way to an end, with so much focus on the science rather than the technique itself. I find this much more interesting than the alternative.}, author = {Wang, Zhe and Young, Rebecca L and Xue, Huiling and Wagner, Guther P.}, doi = {10.1038/nature10391}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wang et al. - 2011 - Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds.pdf:pdf}, journal = {Nature}, pages = {1--5}, title = {{Transcriptomic analysis of avian digits reveals conserved and derived digit identities in birds}}, year = {2011} } @article{Marquet2014, annote = {At first glance, it may appear that ecology is theory-rich. But how many of these theories are useful or efficient? Marquet et al (2014) define an efficient theory as one grounded in first principles, usually expressed through mathematics, few assumptions, large number of predictions per free parameter, approximate, and generates predictions that can be compared to emphircal data. Although theory is important there is a continuous feedback loop between data and theory. A lot of people seem to confuse model or hypothesis and theory. -focus on developing *efficient* theories The review provides a examples of efficient theories: Fisher's sec ratio theory, optimal foraging theory, metabolic thoery of ecology, maximum entropy theory of ecology, and the neutral theory of biodiversity. Is their definition of theory accurate? "A well-substantiated explanation of some aspect of the natural world that can incorporatefacts, [natural] laws, inferences and "tested hypotheses." -NAS Discussion:}, author = {Marquet, P. a. and Allen, a. P. and Brown, J. H. and Dunne, J. a. and Enquist, B. J. and Gillooly, J. F. and Gowaty, P. a. and Green, J. L. and Harte, J. and Hubbell, S. P. and O'Dwyer, J. and Okie, J. G. and Ostling, a. and Ritchie, M. and Storch, D. and West, G. B.}, doi = {10.1093/biosci/biu098}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Marquet et al. - 2014 - On Theory in Ecology.pdf:pdf}, issn = {0006-3568}, journal = {BioScience}, keywords = {big data,ecology,maximum entropy theory of,metabolic theory,neutral theory of biodiversity,theory unification}, month = {jul}, number = {8}, pages = {701--710}, title = {{On Theory in Ecology}}, url = {http://bioscience.oxfordjournals.org/cgi/doi/10.1093/biosci/biu098}, volume = {64}, year = {2014} } @article{Levin1974, annote = {-build model of disturbance that allows the renewal of some limiting resource (e.g space) -{\textgreater} this leads to spatial heterogenity -applicaitons to marine rocky intertidal --sampled along a disturbance gradident Set up pde (Forestor eq) and reduce it to ode using method of characteristics}, author = {Levin, S. A. and Paine, R. T.}, doi = {10.1073/pnas.71.7.2744}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levin, Paine - 1974 - Disturbance, Patch Formation, and Community Structure.pdf:pdf}, issn = {0027-8424}, journal = {PNAS}, keywords = {biodiversity,disturbance}, mendeley-tags = {biodiversity,disturbance}, month = {jul}, number = {7}, pages = {2744--2747}, title = {{Disturbance, Patch Formation, and Community Structure}}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.71.7.2744}, volume = {71}, year = {1974} } @article{McManus2010, annote = {McManus et al (2010) Science All sequencing of genomes can provide some information on the diversity of species, more detailed studies on gene expression are also needed. Diversity of gene expression is probably an important component of phenotypic diversity and evolution. This study looked at total and allele-specific expression in two Drosophila species and their hybrids. They showed an impressive 78{\%} of expressed genes had differing levels of expression between species. They also found evidence that seems to reject the idea that increases or decreases in gene expression are equally likely (a neutral model). Cis- and trans-regulatory divergence did differ between species, 51{\%} and 66{\%} respectively. This is important as cis-regulatory sequences deal with allele-specific effects and trans-regulatory factors affect both alleles. Different levels of cis- and trans- changes may be a reflection upon the evolutionary history of D. sechellia. This is an island species with low genetic variation and a smaller population than the other species. Thus natural selection in this species should be less effective. They specifically found that regulatory diveragence may have led to the evolution of different feeding behaviors in the two Drosophila species. I'm interested in how gene expression may change depending on environmental conditions or a setup in a lab. Depending on the trait I imagine a gene could be up- or down-regulated. Technology Gene expression of two species of Drosophila, and their hybrid offspring, were examined by paired-end sequencing (mRNA-seq). About 4.5 micrograms of RNA was needed from each species. Between 26 million and 42 million reads were obtained for the three groups. Any ambgigious reads were not used when mapping the sequencing to a reference genome. They do point out that for their analyses a reference genome isn't actually needed, though it does make the analysis much simpler. An error rate of only 0.8{\%} was find for all species combined. Gene expression levels were determined by comparing mRNA-seq data to that using pyrosequencing. They conducted pyrosequencing for 15 genes and determined the relative expression between the two species.}, author = {McManus, C Joel and Coolon, Joseph D and Duff, Michael O and Eipper-Mains, Jodi and Graveley, Brenton R and Wittkopp, Patricia J}, doi = {10.1101/gr.102491.109.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McManus et al. - 2010 - Regulatory divergence in Drosophila revealed by mRNA-seq.pdf:pdf}, journal = {Genome Research}, pages = {816--825}, title = {{Regulatory divergence in Drosophila revealed by mRNA-seq}}, year = {2010} } @book{May2001, address = {Princeton, NJ}, author = {May, Robert M.}, edition = {8}, keywords = {biodiversity,complexity,conservation,mathematics,stage-based}, mendeley-tags = {biodiversity,complexity,conservation,mathematics,stage-based}, pages = {265}, publisher = {Princeton University Press}, title = {{Stability and Complexity in Model Ecosystems}}, year = {2001} } @article{Smillie2011, abstract = {Horizontal gene transfer (HGT), the acquisition of genetic material from non-parental lineages, is known to be important in bacterial evolution. In particular, HGT provides rapid access to genetic innovations, allowing traits such as virulence, antibiotic resistance and xenobiotic metabolism to spread through the human microbiome. Recent anecdotal studies providing snapshots of active gene flow on the human body have highlighted the need to determine the frequency of such recent transfers and the forces that govern these events. Here we report the discovery and characterization of a vast, human-associated network of gene exchange, large enough to directly compare the principal forces shaping HGT. We show that this network of 10,770 unique, recently transferred (more than 99{\%} nucleotide identity) genes found in 2,235 full bacterial genomes, is shaped principally by ecology rather than geography or phylogeny, with most gene exchange occurring between isolates from ecologically similar, but geographically separated, environments. For example, we observe 25-fold more HGT between human-associated bacteria than among ecologically diverse non-human isolates (P = 3.0 × 10(-270)). We show that within the human microbiome this ecological architecture continues across multiple spatial scales, functional classes and ecological niches with transfer further enriched among bacteria that inhabit the same body site, have the same oxygen tolerance or have the same ability to cause disease. This structure offers a window into the molecular traits that define ecological niches, insight that we use to uncover sources of antibiotic resistance and identify genes associated with the pathology of meningitis and other diseases.}, annote = {Science: It has been unclear at how important horizontal gene transfer is for bacterial evolution, specifically in the human microbiome. This has important implications for work on virulence and antibiotic resistence. This paper found that ecology, as opposed to geography or phylogeny, is more important for horizontal gene transfer in the human microbiome. By ecology, the authors mean the actual ecological similarity in bacteria determine the complex networks of gene exchange. The study looked at one particular example of gene transfer involing meningitis isolates. Though there are a number of genes ({\~{}}24,000) associated with meningitis. This would be untractable to study, but the author's approach would allow researchers to look at the most recently transferred genes (in this case only 13). These types of approaches could also have clinical implications for cases of antibiotic resistence. Technology: In this study, gene information was pulled from a established database. After filtering out some genomes, a total of 2,235 different genomes were used to study horizontal gene transfer. Protein-coding regions were identified by comparing to another database. In their more applied analysis, data on specific antibiotic resistance genes was also used. This paper really used a lot of previous methods and databases instead of creating "new methods".}, author = {Smillie, Chris S and Smith, Mark B and Friedman, Jonathan and Cordero, Otto X and David, Lawrence a and Alm, Eric J}, doi = {10.1038/nature10571}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smillie et al. - 2011 - Ecology drives a global network of gene exchange connecting the human microbiome.pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {Bacteria,Bacteria: genetics,Bacteria: isolation {\&} purification,Bacteria: metabolism,Bacteria: pathogenicity,Biological Evolution,Drug Resistance, Microbial,Drug Resistance, Microbial: genetics,Ecosystem,Gene Transfer, Horizontal,Gene Transfer, Horizontal: genetics,Genes, Bacterial,Genes, Bacterial: genetics,Genome, Bacterial,Genome, Bacterial: genetics,Humans,Metagenome,Metagenome: genetics,Organ Specificity,Phylogeny,Phylogeography,RNA, Ribosomal, 16S,RNA, Ribosomal, 16S: genetics}, month = {dec}, number = {7376}, pages = {241--4}, pmid = {22037308}, publisher = {Nature Publishing Group}, title = {{Ecology drives a global network of gene exchange connecting the human microbiome.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22037308}, volume = {480}, year = {2011} } @article{Mackelprang2011, abstract = {Permafrost contains an estimated 1672 Pg carbon (C), an amount roughly equivalent to the total currently contained within land plants and the atmosphere. This reservoir of C is vulnerable to decomposition as rising global temperatures cause the permafrost to thaw. During thaw, trapped organic matter may become more accessible for microbial degradation and result in greenhouse gas emissions. Despite recent advances in the use of molecular tools to study permafrost microbial communities, their response to thaw remains unclear. Here we use deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes, and relate these data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses reveal that during transition from a frozen to a thawed state there are rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5 °C, permafrost metagenomes converge to be more similar to each other than while they are frozen. We find that multiple genes involved in cycling of C and nitrogen shift rapidly during thaw. We also construct the first draft genome from a complex soil metagenome, which corresponds to a novel methanogen. Methane previously accumulated in permafrost is released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.}, author = {Mackelprang, Rachel and Waldrop, Mark P and DeAngelis, Kristen M and David, Maude M and Chavarria, Krystle L and Blazewicz, Steven J and Rubin, Edward M and Jansson, Janet K}, doi = {10.1038/nature10576}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mackelprang et al. - 2011 - Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {16S,16S: genetics,Alaska,Arctic Regions,Bacteria,Bacteria: genetics,Bacteria: isolation {\&} purification,Bacteria: metabolism,Carbon,Carbon Cycle,Carbon Cycle: genetics,Carbon: metabolism,DNA,DNA: analysis,DNA: genetics,Freezing,Genes,Metagenome,Metagenome: genetics,Metagenomics,Methane,Methane: metabolism,Nitrogen,Nitrogen Cycle,Nitrogen Cycle: genetics,Nitrogen: metabolism,Oxidation-Reduction,Phylogeny,RNA,Ribosomal,Soil,Soil Microbiology,Soil: chemistry,Temperature,Time Factors,rRNA,rRNA: genetics}, month = {dec}, number = {7377}, pages = {368--71}, pmid = {22056985}, publisher = {Nature Publishing Group}, title = {{Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22056985}, volume = {480}, year = {2011} } @article{Angert2009, abstract = {How biological diversity is generated and maintained is a fundamental question in ecology. Ecologists have delineated many mechanisms that can, in principle, favor species coexistence and hence maintain biodiversity. Most such coexistence mechanisms require or imply tradeoffs between different aspects of species performance. However, it remains unknown whether simple functional tradeoffs underlie coexistence mechanisms in diverse natural systems. We show that functional tradeoffs explain species differences in long-term population dynamics that are associated with recovery from low density (and hence coexistence) for a community of winter annual plants in the Sonoran Desert. We develop a new general framework for quantifying the magnitude of coexistence via the storage effect and use this framework to assess the strength of the storage effect in the winter annual community. We then combine a 25-year record of vital rates with morphological and physiological measurements to identify functional differences between species in the growth and reproductive phase of the life cycle that promote storage-effect coexistence. Separation of species along a tradeoff between growth capacity and low-resource tolerance corresponds to differences in demographic responses to environmental variation across years. Growing season precipitation is one critical environmental variable underlying the demographic decoupling of species. These results demonstrate how partially decoupled population dynamics that promote local biodiversity are associated with physiological differences in resource uptake and allocation between species. These results for a relatively simple system demonstrate how long-term community dynamics relate to functional biology, a linkage scientists have long sought for more complex systems.}, annote = {Angert et al (2009) examine a guild of desert annuals to study the role of the storage effect in determining coexistence of several similar species. They take this one step further by examining the relationship between growth and reproduction and vital rates that are related to environmental effects.}, author = {Angert, Amy L and Huxman, Travis E and Chesson, Peter and Venable, D Lawrence}, doi = {10.1073/pnas.0904512106}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Angert et al. - 2009 - Functional tradeoffs determine species coexistence via the storage effect.pdf:pdf}, issn = {1091-6490}, journal = {PNAS}, keywords = {Analysis of Variance,Arizona,Biological,Desert Climate,Ecosystem,Models,Plant Development,Population Dynamics,Reproduction,Reproduction: physiology,Species Specificity}, month = {jul}, number = {28}, pages = {11641--5}, pmid = {19571002}, title = {{Functional tradeoffs determine species coexistence via the storage effect}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2710622{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {106}, year = {2009} } @article{Nygaard2011, abstract = {We present a high-quality ({\textgreater}100× depth) Illumina genome sequence of the leaf-cutting ant Acromyrmex echinatior, a model species for symbiosis and reproductive conflict studies. We compare this genome with three previously sequenced genomes of ants from different subfamilies and focus our analyses on aspects of the genome likely to be associated with known evolutionary changes. The first is the specialized fungal diet of A. echinatior, where we find gene loss in the ant's arginine synthesis pathway, loss of detoxification genes, and expansion of a group of peptidase proteins. One of these is a unique ant-derived contribution to the fecal fluid, which otherwise consists of "garden manuring" fungal enzymes that are unaffected by ant digestion. The second is multiple mating of queens and ejaculate competition, which may be associated with a greatly expanded nardilysin-like peptidase gene family. The third is sex determination, where we could identify only a single homolog of the feminizer gene. As other ants and the honeybee have duplications of this gene, we hypothesize that this may partly explain the frequent production of diploid male larvae in A. echinatior. The fourth is the evolution of eusociality, where we find a highly conserved ant-specific profile of neuropeptide genes that may be related to caste determination. These first analyses of the A. echinatior genome indicate that considerable genetic changes are likely to have accompanied the transition from hunter-gathering to agricultural food production 50 million years ago, and the transition from single to multiple queen mating 10 million years ago.}, annote = {This paper tries to answer evolutionary questions about a cooperative ant species. They sequenced a specific leaf cutter species and compared it to published genomes of of three other ant species, a bee, and a fly species. They found that their leaf cutter ant has less detoxification genes and expressed peptidase proteins more. This is advantageous for the ant{\&}{\#}039;s specialized fungal diet. They also found that the evolution of eusociality where a highly conserved set of neuropeptide genes may play a role. With the genomic data the authors are also able to put a timeline of these evolutionary changes. I thought this paper was interesting, because of the evolutionary questions it was trying to address, but I did find it difficult to follow in parts.  The authors use Illimina HiSeq platform to get 60.7Gb of raw reads and de nova assembly generatred a 300 Mb genome sequence for the leaf cutter ant species. They sequenced both DNA and RNA to answer their various questions. Simply because of amount of expression that RNA information tells you? Compared to the other study, these authors use read lengths that are several 100 or thousand base pairs long. I am guessing this is because this is whole genome DNA instead of that from transcriptomes. Specifically, this genome DNA may be more complicated with lots of similar sequences of base pairs, so longer read lengths are needed. I am not sure how I would change this study if I was working on it today. Maybe I'll know in the next two weeks! }, author = {Nygaard, Sanne and Zhang, Guojie and Schi{\o}tt, Morten and Li, Cai and Wurm, Yannick and Hu, Haofu and Zhou, Jiajian and Ji, Lu and Qiu, Feng and Rasmussen, Morten and Pan, Hailin and Hauser, Frank and Krogh, Anders and Grimmelikhuijzen, Cornelis J P and Wang, Jun and Boomsma, Jacobus J}, doi = {10.1101/gr.121392.111}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nygaard et al. - 2011 - The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fu.pdf:pdf}, issn = {1549-5469}, journal = {Genome research}, keywords = {Adaptation, Physiological,Animals,Ants,Ants: genetics,Fungi,Fungi: genetics,Genes, Fungal,Genome,Insect Proteins,Insect Proteins: genetics,Insect Proteins: metabolism,Male,Molecular Sequence Data,Phylogeny,Sexual Behavior, Animal,Symbiosis}, month = {aug}, number = {8}, pages = {1339--48}, pmid = {21719571}, title = {{The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3149500{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {21}, year = {2011} } @article{Levin1974a, author = {Levin, Simon A}, journal = {The American Naturalist}, number = {960}, pages = {207--228}, title = {{Dispersion and Population Interactions}}, volume = {108}, year = {1974} } @article{Andolfatto2011, abstract = {We present a new approach to genotyping based on multiplexed shotgun sequencing that can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. We first describe a simple library construction protocol that uses just 10 ng of genomic DNA per individual and makes the approach accessible to any laboratory with standard molecular biology equipment. Sequencing this library results in a large number of sequence reads widely distributed across the genomes of multiplexed bar-coded individuals. We develop a Hidden Markov Model to estimate ancestry at all genomic locations in all individuals using these data. We demonstrate the utility of the approach by mapping a dominant marker allele in D. simulans to within 105 kb of its true position using 96 F1-backcross individuals genotyped in a single lane on an Illumina Genome Analyzer. We further demonstrate the utility of our method by genetically mapping more than 400 previously unassembled D. simulans contigs to linkage groups and by evaluating the quality of targeted introgression lines. At this level of multiplexing and divergence between strains, our method allows estimation of recombination breakpoints to a median of 38-kb intervals. Our analysis suggests that higher levels of multiplexing and/or use of strains with lower levels of divergence are practicable.}, annote = {Science: This study was more of a methods paper than one that addressed specific scientific questions. With increasing technological capabilities genotyping has become easier and cheaper, but methods for the intermediate scales (100s-1000s of markers and individuals) have lacked behind. RAD tag approach and whole genome resequencing (WGR) are useful approaches, but require shearing DNA and therefore require a lot of DNA. This paper proposed a new method called "multiplexed shotgun genotyping" to overcome the limitations of RAD and WGR. This method uses a more frequent cutter enzyme that creates a large number of small reads. The paper multiplexes 96 individuals and show how accurate the method performs (less than 1{\%} error rate.. The method used a lot less DNA (only 10ng) and was a lot cheaper than typical methods. Technology: Multiplexed shotgun sequencing is similar to RAD and WGR, but uses a more frequent cutter enzyme--producing many short fragments. These fragments are randomly scattered across the whole genome. Hidden Markov Models can then be used to stich these small reads back together with high accuracy. Sequencing of 96 indiviudals led to about 22 million 101-bp reads. This technology can do all of this with only 2 days of lab work. A lot less DNA is also needed which is important for many non-model organism studies. The authors also tested there method with more individuals, by resampling, and found the method to still be robust. In addition, they found that that multiplexing will also work for larger genomes, as they had only worked with Drosophila. There method does need an assembled genome for one individual to be effective. But this may be a small price to pay for all the results, for low cost, that are returned by multiplexed shotgun sequencing.}, author = {Andolfatto, Peter and Davison, Dan and Erezyilmaz, Deniz and Hu, Tina T and Mast, Joshua and Sunayama-Morita, Tomoko and Stern, David L}, doi = {10.1101/gr.115402.110}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Andolfatto et al. - 2011 - Multiplexed shotgun genotyping for rapid and efficient genetic mapping.pdf:pdf}, issn = {1549-5469}, journal = {Genome research}, keywords = {Animals,Chromosome Breakpoints,Chromosome Mapping,Chromosome Mapping: methods,Computational Biology,Drosophila,Drosophila: genetics,Female,Genes, Dominant,Genes, Dominant: genetics,Genetic Markers,Genotype,Male,Molecular Typing,Molecular Typing: methods,Phenotype,Quantitative Trait Loci,Quantitative Trait Loci: genetics,Recombination, Genetic,Recombination, Genetic: genetics,Research Design,Sequence Analysis, DNA,Sequence Analysis, DNA: methods}, month = {apr}, number = {4}, pages = {610--7}, pmid = {21233398}, title = {{Multiplexed shotgun genotyping for rapid and efficient genetic mapping.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3065708{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {21}, year = {2011} } @article{Amores2011, abstract = {Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes that sometimes obfuscate connectivity. Genomic information representing a fish lineage that diverged before the teleost genome duplication (TGD) would provide an outgroup for exploring the mechanisms of evolution after whole-genome duplication. We exploited massively parallel DNA sequencing to develop meiotic maps with thrift and speed by genotyping F(1) offspring of a single female and a single male spotted gar (Lepisosteus oculatus) collected directly from nature utilizing only polymorphisms existing in these two wild individuals. Using Stacks, software that automates the calling of genotypes from polymorphisms assayed by Illumina sequencing, we constructed a map containing 8406 markers. RNA-seq on two map-cross larvae provided a reference transcriptome that identified nearly 1000 mapped protein-coding markers and allowed genome-wide analysis of conserved synteny. Results showed that the gar lineage diverged from teleosts before the TGD and its genome is organized more similarly to that of humans than teleosts. Thus, spotted gar provides a critical link between medical models in teleost fish, to which gar is biologically similar, and humans, to which gar is genomically similar. Application of our F(1) dense mapping strategy to species with no prior genome information promises to facilitate comparative genomics and provide a scaffold for ordering the numerous contigs arising from next generation genome sequencing.}, annote = {Science: This study attempts to study Spotted Gar and it's role as an outgrpup for telosts, which are important for medical research. Ancient duplicated genomes in teleost fish make it difficult to interpret trends in its genome. Gar diverged before this whole-genome duplication in telost so they provide a suitable outgroup. The authors genotyped first generation offspring of a single mated pair of gar. They use DNA sequencing to create meiotic maps. This sequencing revealed that gar did in fact diverage prior to that genome duplication. This makes Gar more closely related to humans than telost and provide a useful genetic link. They also tested the idea of whole-genome duplicationis important in syntenic rearrangements. They were not able to rule out this hypothesis because there was a coservation of synteny between the human and gar genomes. Technology: About 100 first generation fish were selected for genotyping (a lot of genetic material was needed)- each provided about a million sequences. Rad-tag libraries were sequenced using Illumina technology. A bioinformatics program differentiated between true SNPs or sequencing errors. In ambigious cases, reads were simply thrown out. This may cause issues if the ambigous reads were not randomly assorted in the genome and there was some important reason they appeared ambigious. There method was a lot cheaper than other approaches, but whole genome sequencing may be better in the future if the price continues to decline.}, author = {Amores, Angel and Catchen, Julian and Ferrara, Allyse and Fontenot, Quenton and Postlethwait, John H}, doi = {10.1534/genetics.111.127324}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Amores et al. - 2011 - Genome evolution and meiotic maps by massively parallel DNA sequencing spotted gar, an outgroup for the teleost g.pdf:pdf}, issn = {1943-2631}, journal = {Genetics}, keywords = {Animals,Base Sequence,Comparative Genomic Hybridization,DNA,Evolution,Female,Fishes,Fishes: classification,Fishes: genetics,Gene Duplication,Gene Duplication: genetics,Gene Expression Regulation,Gene Rearrangement,Gene Rearrangement: genetics,Genetic Linkage,Genome,Genome: genetics,Genomics,High-Throughput Nucleotide Sequencing,Humans,Male,Meiosis,Meiosis: genetics,Molecular,Molecular Sequence Data,Phylogeny,Sequence Alignment,Sequence Analysis,Transcriptome}, month = {aug}, number = {4}, pages = {799--808}, pmid = {21828280}, title = {{Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3176089{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {188}, year = {2011} } @article{Hastings1980, annote = {Hastings built a simple model to examine how competition for space can lead to support for the intermediate disturbance hypothesis. He assumes a large number of discrete, identical patches where only a single species can occupy any given patch. All patches are connected via dispersal, but only dispersers landing on empty patches, or those with a weak competitor, can succeed. Competitiion is modeled with a competitive hierarchy. An obvious question is how species affect each other in the heirarchy. A system where one the presence of one species won't elimate another is a noninteractive system. Alternativly, an interactive system means a species could elinate another (one equation's dynamics affects another). For the non-interactive case, Hastings found that an intermediate level of disturbance produced the highest diversity (with a downward facing parabola desribing this relationship). The same is true in the interactive case, but multiple peaks may be present. Hastings also compares his model to coral reef data. He found that a poorer competitor must be a better colonizer in order to persist.}, author = {Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 1980 - Disturbance, coexistence, history, and competition for space.pdf:pdf}, journal = {Theoretical Population Biology}, number = {1980}, pages = {363--373}, title = {{Disturbance, coexistence, history, and competition for space}}, volume = {18}, year = {1980} } @article{Yu2001, author = {Yu, Douglas W and Wilson, Howard B}, journal = {The American Naturalist}, keywords = {alternative stable states,can coexist in a,colonizer,competitor and the other,habitat destruction,is a superior,metapopulation,metapopulation if one species,species,species is a superior,tilman 1994,tings 1980,who showed that two}, number = {1}, pages = {49--63}, title = {{The Competition-Colonization Trade-off Is Dead; Long Live the Competition-Colonization Trade-off}}, volume = {158}, year = {2001} } @article{Robinson2008, abstract = {source-sink; spatial; population; predator}, annote = {Culling often employed as a population regulation strategy for large carnivores. However, it is unclear if this strategy works on a local scale when immigration from nearby sites occur. Robinson et al (2008) examine cougar populations in a small, heavily-managed area of Washington State. They found that hunting of cougars only led to the habitat being more suitable (less density) and nearby cougars dispersed into the area. Using Leslie matrix models, the authors determined the population should be declining with the amount of reported hunting. However, the population had an observed growth rate close to one, implying that animals had to be dispersing into the site. This turned the site into a “sink” population that has to be supported by immigration in order to persist. I thought this was a pretty creative use of matrix models. I also liked how they used both deterministic and stochastic growth rates.  Why figure 4 doesn't include error bars I'm not sure It is a little unclear what their matrix model actually is (it is not described anywhere)- this makes their study hard to replicate}, author = {Robinson, Hugh S. and Wielgus, Robert B. and Cooley, Hilary S. and Cooley, Skype W.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Robinson et al. - 2008 - Sink populations in carnivore management cougar demography and immigration in a hunted population.pdf:pdf}, journal = {Ecological Applications}, keywords = {attractive sink,carnivore,cougar,hunting,immigration,mortality,population,population dynamics,predator,puma concolor,sink,source,source-sink,spatial,survival}, mendeley-tags = {population,predator,source-sink,spatial}, number = {4}, pages = {1028--1037}, title = {{Sink populations in carnivore management: cougar demography and immigration in a hunted population}}, volume = {18}, year = {2008} } @article{Hittinger2010, abstract = {Assembling the tree of life is a major goal of biology, but progress has been hindered by the difficulty and expense of obtaining the orthologous DNA required for accurate and fully resolved phylogenies. Next-generation DNA sequencing technologies promise to accelerate progress, but sequencing the genomes of hundreds of thousands of eukaryotic species remains impractical. Eukaryotic transcriptomes, which are smaller than genomes and biased toward highly expressed genes that tend to be conserved, could potentially provide a rich set of phylogenetic characters. We sampled the transcriptomes of 10 mosquito species by assembling 36-bp sequence reads into phylogenomic data matrices containing hundreds of thousands of orthologous nucleotides from hundreds of genes. Analysis of these data matrices yielded robust phylogenetic inferences, even with data matrices constructed from surprisingly few sequence reads. This approach is more efficient, data-rich, and economical than traditional PCR-based and EST-based methods and provides a scalable strategy for generating phylogenomic data matrices to infer the branches and twigs of the tree of life.}, annote = {Science: It is difficult to acquire DNA and fully assemble phylogies for complicated genomes. Eukaroyotic transcriptomes are smaller and are bias towards highly expressed genes. Therefore you could use these transciptomes to resolve phylogenies for much cheaper. Technology: Use Illumina Solexa next-gen DNA sequecncing platform, assembled de novo, and then construted a phylogeny -millionsof 36-bp sequencing reads for 10 different species }, author = {Hittinger, Chris Todd and Johnston, Mark and Tossberg, John T and Rokas, Antonis}, doi = {10.1073/pnas.0910449107}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hittinger et al. - 2010 - Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life.pdf:pdf}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, keywords = {Animals,Culicidae,Culicidae: genetics,Gene Expression,Gene Expression Profiling,Gene Expression Profiling: economics,Gene Expression Profiling: methods,Genome, Insect,Phylogeny,Sequence Analysis, RNA,Sequence Analysis, RNA: economics,Sequence Analysis, RNA: methods,Transcription, Genetic}, month = {jan}, number = {4}, pages = {1476--81}, pmid = {20080632}, title = {{Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2824393{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {107}, year = {2010} } @article{Tilman1994, annote = {Spatial structure has a large effect on dynamics and composition of communities. Adding just a spatial aspect to a model can allow many species to coexist even if they are all limited by the same single resource (as opposed to the competitive exclusion hypothesis). This is due to a tradeoff in competition and dispersal ability. After working through the models of Levins (1969), Hastings (1980), and Nee and May (1992), Tilman modifies there models to examine how stable coexistence can emerge. As we see with other models, a portion of sites will always be unoccupied if the species (or multiple species) are at an equilbria. This means that there is always space for a new competitor with appropriate life history traits. In order to have high levels of biodiversity, high levels of disturbance are not even needed, some sort of spatial structure is all that is needed. "Neighborhood interactions and local dispersal increase intraspecifc competition relative to interspecific, and this encourage stable coexistence"}, author = {Tilman, David}, journal = {Ecology}, keywords = {biodiversity,lations,spatial competition hypothesis,spatial subdivision}, number = {1}, pages = {2--16}, title = {{Competition and biodiversity in spatially structured habitats}}, volume = {75}, year = {1994} } @article{Hanski1998, annote = {Although I have read Hanski's review paper before, in conjuction with my own work, it was interesting to read it again in the light of what we have discussed so far in the Core. I really like Hanski's progression from the simple Levin's model to more complicated models like the incidence function model. I was surprised he didn't explictly make the point that the Levin's model is essentially the logisitic model analague for populations. I also appreciated how Hanski explained why the study of metapopulations applies more generally in ecology and conservation biology. A lot has been developed since 1998, but the importance of local dynamics has become increasingly reconginized. I would hope that a recent review of the subject would highlight this point. One of the important points I had forgotten about was the idea of time lags in metapopulations. The idea here being that a metapopulation may be doomed to go extinct, but it may take a significant amount of time for that extinction to occur. With this delay, it is hard to know how long "transient dynamics" may actually last. Maybe no metapopulations will actually persist in nature, but they may persist long enough for us to think they are in fact at some equilibrium. I was thinking about how a metapopulation might be able to accomondate more species simply because heterogeneity exists with different numbers of each species occupying each patch. In other words, the metapopulation strucuture itself playing the role of spatial heterogeneity that would allow species to coexist. However, most metapopulations I know of are of single species. I'm not sure if this is a bias in how we study metapopulations or if only single species actually persist in metapopulations.}, author = {Hanski, Ilkka}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hanski - 1998 - Metapopulation dynamics.pdf:pdf}, journal = {Nature}, number = {November}, pages = {41--50}, title = {{Metapopulation dynamics}}, volume = {396}, year = {1998} } @article{Emerson2010, annote = {Science This paper was primarily a "methods" type paper that tried to use DNA tags (RAD tags) to examine fine scale relationships. Usually it would be very expensive to simply sequence a whole bunch of closely related species or populations to examine differences between them. Rad tag technique is relatively inexpensive and allows for the discovery of single nucleotide polymorphisms. I thought it was interesting that RAD tags can be used even without any prior genomic information. This aspect, combined with its cost, make it very attractive. The paper examined a single pitcher plant mosquito species across a number of populations in North America. Using the Rad tag sequences, the authors were able to constuct a phylogeny for the various populations and were able to group them into specific clades. Such a detailed phylogeny from RAD tag data gave me some interesting ideas of how to study a system of small mammals I{\&}{\#}039;ve been working on. Technology Six individuals for each of the 21 distinct populations were sampled. SNPs were then identified using RAD tag techniques. This SNP dataset was then analyzed using a number of statisitcal methods to construct a phylogeny. I think it would be interesting to test this technique, and I{\&}{\#}039;m sure people have now, with sequencing of whole genomes from a number of populations to see how well RAD tag techniques perfor. }, author = {Emerson, Kevin J and Merz, Clayton R and Catchen, Julian M and Hohenlohe, Paul A and Cresko, William A and Bradshaw, William E and Holzapfel, Christina M}, doi = {10.1073/pnas.1006538107/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1006538107}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Emerson et al. - 2010 - Resolving postglacial phylogeography using high-throughput sequencing.pdf:pdf}, journal = {PNAS}, number = {37}, pages = {16196--16200}, title = {{Resolving postglacial phylogeography using high-throughput sequencing}}, volume = {107}, year = {2010} } @article{Domingues2012, abstract = {To understand how organisms adapt to novel habitats, which involves both demographic and selective events, we require knowledge of the evolutionary history of populations and also selected alleles. There are still few cases in which the precise mutations (and hence, defined alleles) that contribute to adaptive change have been identified in nature; one exception is the genetic basis of camouflaging pigmentation of oldfield mice (Peromyscus polionotus) that have colonized the sandy dunes of Florida's Gulf Coast. To quantify the genomic impact of colonization as well as the signature of selection, we resequenced 5000 1.5-kb noncoding loci as well as a 160-kb genomic region surrounding the melanocortin-1 receptor (Mc1r), a gene that contributes to pigmentation differences, in beach and mainland populations. Using a genome-wide phylogenetic approach, we recovered a single monophyletic group comprised of beach mice, consistent with a single colonization event of the Gulf Coast. We also found evidence of a severe founder event, estimated to have occurred less than 3000 years ago. In this demographic context, we show that all beach subspecies share a single derived light Mc1r allele, which was likely selected from standing genetic variation that originated in the mainland. Surprisingly, we were unable to identify a clear signature of selection in the Mc1r region, despite independent evidence that this locus contributes to adaptive coloration. Nonetheless, these data allow us to reconstruct and compare the evolutionary history of populations and alleles to better understand how adaptive evolution, following the colonization of a novel habitat, proceeds in nature.}, annote = {Examine adaptive change that took place when a population of mice recently colonized an island. After a adaptive event, selection (becuase of drift?) and demography play a large role -need to seperate the two Science When organisms colonize new habitats both demographic and selection events will take place. However, it can be very difficult to seperate the two processes. Here, the authors reconstruct both the evolutionary history of populations of mice and alleles that have been selected in the population. They specifically investigated camoflauge pigmenetation as the genetic basis for this phenotype is known. They sequenced mice from both mainland (presumbly ancestral) and a recently conlinized island population. They found that mice colonized the island less than 3000 years ago and that a single recolonization event took place. I felt it was a great use of the technology to address meaningful evolutionary questions. Technology The authors collected mice tissue samples at 13 locations including both mainland and island populations. Using a Autogen kit, they collected genomic data from each tissue sample. This data was processed with Illumina technology and collected 1.5kb reads at random locations in the genome. This generated 601 million paired-end reads with a high level that could be correctly assigned. This data was then used to estimate genetic diversity, differentiaion, and the demography of the colonized beach sites.}, author = {Domingues, Vera S and Poh, Yu-Ping and Peterson, Brant K and Pennings, Pleuni S and Jensen, Jeffrey D and Hoekstra, Hopi E}, doi = {10.1111/j.1558-5646.2012.01669.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Domingues et al. - 2012 - Evidence of adaptation from ancestral variation in young populations of beach mice.pdf:pdf}, issn = {1558-5646}, journal = {Evolution}, keywords = {Adaptation,Alleles,Animals,Biological,Biological Evolution,Founder Effect,Genetic,Genetic Variation,Genome,Melanocortin,Peromyscus,Peromyscus: genetics,Pigmentation,Pigmentation: genetics,Receptor,Selection,Southeastern United States,Type 1,Type 1: genetics}, month = {oct}, number = {10}, pages = {3209--23}, pmid = {23025610}, title = {{Evidence of adaptation from ancestral variation in young populations of beach mice}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23025610}, volume = {66}, year = {2012} } @article{Lloyd-Smith2005, annote = {In epidemiological models it is common to use a basic reproductive value that is simply an average number across a population.}, author = {Lloyd-Smith, J.O. and Schreiber, S.J. and Kopp, P. E. and Getz, W. M.}, doi = {10.1038/nature04153}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lloyd-Smith et al. - 2005 - Superspreading and the effect of individual variation on disease emergence.pdf:pdf}, journal = {Nature}, keywords = {disease,individual heterogeneity,stochasticity}, mendeley-tags = {disease,individual heterogeneity,stochasticity}, number = {November}, pages = {355--359}, title = {{Superspreading and the effect of individual variation on disease emergence}}, volume = {438}, year = {2005} } @article{Warner1985, annote = {Models that demostrate storage effect: Lottery Model- simply get established by chance of a space opening up. Competive exclusion occurs unless you add envionmental variability want benefits gained during favorable periods to be greater than costs during unfavorable periods (i.e. the storage effect) Coexistence is fosted by: within-species (low mortality, high and age-structured fecundity, sensitivity in environment in young) and between-species (similar reproductive rates but different response to environement) characteristics Storage effect versus other mechanisms of coexistence:}, author = {Warner, Robert R. and Chesson, Peter L.}, journal = {The American Naturalist}, keywords = {biodiversity,coexistence,stochasticity,storage effect}, mendeley-tags = {biodiversity,coexistence,stochasticity,storage effect}, number = {6}, pages = {769--787}, title = {{Coexistence mediated by recruitment fluctuations: a field guide to the storage effect}}, volume = {125}, year = {1985} } @article{Adler2006, abstract = {How expected increases in climate variability will affect species diversity depends on the role of such variability in regulating the coexistence of competing species. Despite theory linking temporal environmental fluctuations with the maintenance of diversity, the importance of climate variability for stabilizing coexistence remains unknown because of a lack of appropriate long-term observations. Here, we analyze three decades of demographic data from a Kansas prairie to demonstrate that interannual climate variability promotes the coexistence of three common grass species. Specifically, we show that (i) the dynamics of the three species satisfy all requirements of "storage effect" theory based on recruitment variability with overlapping generations, (ii) climate variables are correlated with interannual variation in species performance, and (iii) temporal variability increases low-density growth rates, buffering these species against competitive exclusion. Given that environmental fluctuations are ubiquitous in natural systems, our results suggest that coexistence based on the storage effect may be underappreciated and could provide an important alternative to recent neutral theories of diversity. Field evidence for positive effects of variability on coexistence also emphasizes the need to consider changes in both climate means and variances when forecasting the effects of global change on species diversity.}, author = {Adler, Peter B and HilleRisLambers, Janneke and Kyriakidis, Phaedon C and Guan, Qingfeng and Levine, Jonathan M}, doi = {10.1073/pnas.0600599103}, issn = {0027-8424}, journal = {PNAS}, keywords = {Climate,Ecosystem,Poaceae,Poaceae: growth {\&} development,Time Factors}, month = {aug}, number = {34}, pages = {12793--8}, pmid = {16908862}, title = {{Climate variability has a stabilizing effect on the coexistence of prairie grasses}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1550767{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {103}, year = {2006} } @article{Chase2005, annote = {Neutral theory may do a good job on small spatial scales}, author = {Chase, Jonathan M.}, doi = {10.1111/j.0269-8463.2005.00937.x}, issn = {0269-8463}, journal = {Functional Ecology}, month = {feb}, number = {1}, pages = {182--186}, title = {{Towards a really unified theory for metacommunities}}, url = {http://doi.wiley.com/10.1111/j.0269-8463.2005.00937.x}, volume = {19}, year = {2005} } @incollection{Hubbell2012, address = {Berkeley and Los Angeles}, author = {Hubbell, Stephen P}, booktitle = {Encyclopedia of Theoretical Ecology}, editor = {Hastings, Alan and Gross, Louis J.}, pages = {478--485}, publisher = {University of California Press}, title = {{Neutral Community}}, year = {2012} } @incollection{Snyder2012, annote = {Jensen's inequality}, author = {Snyder, Robin}, booktitle = {Encyclopedia of Theoretical Ecology}, edition = {1}, editor = {Hastings, Alan and Gross, Louis}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Snyder - 2012 - Storage effect.pdf:pdf}, pages = {722--728}, title = {{Storage effect}}, year = {2012} } @article{Hubbell1997, abstract = {Theories of island biogeography and of relative species abundance are of central importance in biogeogra- phy and community ecology, yet these two bodies of theory heretofore have been largely unconnected. Incor- porating speciation into the theory of island biogeography unexpectedly results in unification of these two theories. The unified theory predicts the existence of a fundamental biodiversity number ? that controls not only species rich- ness, but also relative species abundance in the source area metacommunity at equilibrium between speciation and extinction. With additional parameters for island size and migration rate, the theory also predicts relative species abundance on islands or local regions of continuous land- scapes. Application of the theory to the biogeography and biodiversity of communities of tropical trees and reef- building corals are discussed. One important result is that only relatively modest migration rates are sufficient to dynamically couple the regional metacommunity and sta- bilize community structure on large spatiotemporal scales. Thus, regional, long-term compositional stasis in tropical rain forests and coral reefs can arise just as easily from the stabilizing effect of large numbers as from niche- assembly rules that limit species membership in communi- ties. Because of the higher intrinsic vagility of corals, the theory predicts greater regional similarity in coral reef communities than in tropical tree communities}, author = {Hubbell, S P}, journal = {Coral Reefs}, keywords = {biodiversity,coral reef}, mendeley-tags = {biodiversity,coral reef}, pages = {9--21}, title = {{A unified theory of biogeography and relative species abundance and its application to tropical rain forests and coral reefs}}, volume = {16}, year = {1997} } @incollection{Holyoak2012, address = {Berkeley and Los Angeles}, author = {Holyoak, Marcel and Kneitel, Jamie M}, booktitle = {Encyclopedia of Theoretical Ecology}, doi = {10.1126/science.1162302.Peters}, editor = {Hastings, Alan and Gross, Louis J.}, pages = {434--438}, publisher = {University of California Press}, title = {{Metacommunities}}, year = {2012} } @article{Morris2008, annote = {Climate models predict increasing variability in temperature and precipation. This variablity may affect vital rates of animals and plants which then could affect their population dynamics. The effect of variability will almost cetaintly depend on the specific life history traits of a given population or species. Morris et al (2008) found that species with longer lifespans are more resiliant to variablity in the climate. This makes sense as they are able to endure good and bad years, where short-lived species depend on every year being good. Essentially, longetivity can be thought of as a evolutionary strategy to endure temporal variation in general. The authors found that life history traits are far more important in predicting species' response to changing climate than taxonomic relationshops. In addition, in local areas where climate variablity is expected to decrease, short-lived pests and bugs may actually have increased stochastic growth rates. Perhaps surprising, the elasticity of all the different vital rates was about the same. Also surprising, was that envionmental autocorrelation did not affect the elasticity of vital rates. Although vital rate variability is important, mean vital rates still hvae a stronger influence on population growth.}, author = {Morris, William F. and Pfister, Catherine A. and Tuljapurkar, Shripad and Haridas, Chirrakal V. and Boggs, Carol L. and Boyce, Mark S. and Bruna, Emilio M. and Church, Don R. and Coulson, Tim and Doak, Daniel F. and Forsyth, Stacey and Gaillard, Jean-Michel and Horvitz, Carol C. and Kalisz, Susan and Kendall, Bruce E. and Knight, Tiffany M. and Lee, Charlotte T. and Menges, Eric S.}, doi = {10.1890/07-0774.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Morris et al. - 2008 - Longevity Can Buffer Plant and Animal Populations Against Changing Climatic Variability.pdf:pdf}, issn = {0012-9658}, journal = {Ecology}, keywords = {climate change,climate variability,conservation,elasticity,longevity,stochastic demography,stochasticity}, mendeley-tags = {climate change,conservation,elasticity,stochasticity}, month = {jan}, number = {1}, pages = {19--25}, title = {{Longevity Can Buffer Plant and Animal Populations Against Changing Climatic Variability}}, url = {http://www.esajournals.org/doi/abs/10.1890/07-0774.1}, volume = {89}, year = {2008} } @incollection{Cornell2012, address = {Berkeley and Los Angeles}, author = {Cornell, Howard V}, booktitle = {Encyclopedia of Theoretical Ecology}, editor = {Hastings, Alan and Gross, Louis J.}, pages = {489--498}, publisher = {University of California Press}, title = {{Niche overlap}}, year = {2012} } @article{Haugen2006, abstract = {The ideal free distribution (IFD) theory is one of the most influential theories in evolutionary ecology. It predicts how animals ought to distribute themselves within a heterogeneous habitat in order to maximize lifetime fitness. We test the population level consequence of the IFD theory using 40-year worth data on pike (Esox lucius) living in a natural lake divided into two basins. We do so by employing empirically derived density-dependent survival, dispersal and fecundity functions in the estimation of basin-specific density-dependent fitness surfaces. The intersection of the fitness surfaces for the two basins is used for deriving expected spatial distributions of pike. Comparing the derived expected spatial distributions with 50 years data of the actual spatial distribution demonstrated that pike is ideal free distributed within the lake. In general, there was a net migration from the less productive north basin to the more productive south basin. However, a pike density-manipulation experiment imposing shifting pike density gradients between the two basins managed to switch the net migration direction and hence clearly demonstrated that the Windermere pike choose their habitat in an ideal free manner. Demonstration of ideal free habitat selection on an operational field scale like this has never been undertaken before.}, annote = {The ideal free distribution hypothesis was proposed over 40 years ago, but empirical evidence has been lacking. Haugen et al (2006) used an amazing data set (over four decades) of pike populations in two basins of the same lake. The ideal free distribution says that pike should disperse between the two basins in order to maximize their individual fitness. They found that a fitness gradient did exist between the two basins and pika would increase/decrease their dispersal accordingly. Typically, the southern basin was more productive, but a density-reduction in the north lowered the population enough to change the fitness gradient and pike dispersed accordingly. This density-reduction experiment provided the clearest evidence for me the pike did in fact follow an ideal free distribution.  I was surprised their population estimates did not include estimates of error, as the population size was estimated from fishery data.  How do pike assess their environments?  I'm not sure what “profound” annual fluctuations actually means}, author = {Haugen, Thrond O and Winfield, Ian J and V{\o}llestad, L Asbj{\o}rn and Fletcher, Janice M and James, J Ben and Stenseth, Nils Chr}, doi = {10.1098/rspb.2006.3659}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Haugen et al. - 2006 - The ideal free pike 50 years of fitness-maximizing dispersal in Windermere.pdf:pdf}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B}, keywords = {Animals,Biological,Biological Evolution,Ecosystem,Esocidae,Esocidae: growth {\&} development,Female,Fertility,Fertility: physiology,Food Chain,Fresh Water,Male,Models,Population Density,Population Dynamics,Survival,Survival: physiology,evolution,ideal free distribution,spatial}, mendeley-tags = {evolution,ideal free distribution,spatial}, month = {dec}, number = {1604}, pages = {2917--24}, pmid = {17015363}, title = {{The ideal free pike: 50 years of fitness-maximizing dispersal in Windermere.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1639511{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {273}, year = {2006} } @article{Boyce2006, abstract = {Recent advances in stochastic demography provide unique insights into the probable effects of increasing environmental variability on population dynamics, and these insights can be substantially different compared with those from deterministic models. Stochastic variation in structured population models influences estimates of population growth rate, persistence and resilience, which ultimately can alter community composition, species interactions, distributions and harvesting. Here, we discuss how understanding these demographic consequences of environmental variation will have applications for anticipating changes in populations resulting from anthropogenic activities that affect the variance in vital rates. We also highlight new tools for anticipating the consequences of the magnitude and temporal patterning of environmental variability.}, annote = {Ecological systems are inheritantly full of demographic and enironmental stochastiticty. However, models often only look at constant values for demographic parameters that do not change over time. These parameters can be allowed to change with time as the enironment changes. Allowing these parameters to vary with time can have a strong influence on population growth rates and persistence. The authors define stochastic demography as the study of stage-structured models where the environment is determined by some random process. I don't find it all that surprising that population dynamics in a temporally varying environment may be different than in a constant environment. However, I disagree that deterministic models cannot tell us anything. If models are too complicated (e.g. lots of stochastic elements), we cannot learn very much about the theory as well. In addition, stochastic models require the estimation of a lot more parameters. I do agree that the role of variability is important when discussing how global climate change will affect populations. How populations will respond to global change depends on our understandings of a long link of important concepts: have to know what the climate will do, how vital rates of populations are affected by changes in the environment, and changing vital rates then affects population persisistence and growth rates. It will take a lot of effort to get at each piece in this puzzle.}, author = {Boyce, Mark S and Haridas, Chirakkal V and Lee, Charlotte T and {The NCEAS Stochastic Demography Working Group}}, doi = {10.1016/j.tree.2005.11.018}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Boyce et al. - 2006 - Demography in an increasingly variable world.pdf:pdf}, issn = {0169-5347}, journal = {Trends in Ecology {\&} Evolution}, keywords = {Animals,Demography,Population Growth,Stochastic Processes,demography,stochasticity,variablity}, mendeley-tags = {demography,stochasticity,variablity}, month = {mar}, number = {3}, pages = {141--8}, pmid = {16701490}, title = {{Demography in an increasingly variable world.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16701490}, volume = {21}, year = {2006} } @article{Chesson1981, author = {Chesson, Peter L and Warner, Robert R}, journal = {The American Naturalist}, keywords = {biodiversity,stochasticity,storage effect}, mendeley-tags = {biodiversity,stochasticity,storage effect}, number = {6}, pages = {923--943}, title = {{Environmental variability promotes coexistence in lottery competitive systems}}, volume = {117}, year = {1981} } @article{Morris2006, abstract = {The ideal free distribution (IFD) theory is one of the most influential theories in evolutionary ecology. It predicts how animals ought to distribute themselves within a heterogeneous habitat in order to maximize lifetime fitness. We test the population level consequence of the IFD theory using 40-year worth data on pike (Esox lucius) living in a natural lake divided into two basins. We do so by employing empirically derived density-dependent survival, dispersal and fecundity functions in the estimation of basin-specific density-dependent fitness surfaces. The intersection of the fitness surfaces for the two basins is used for deriving expected spatial distributions of pike. Comparing the derived expected spatial distributions with 50 years data of the actual spatial distribution demonstrated that pike is ideal free distributed within the lake. In general, there was a net migration from the less productive north basin to the more productive south basin. However, a pike density-manipulation experiment imposing shifting pike density gradients between the two basins managed to switch the net migration direction and hence clearly demonstrated that the Windermere pike choose their habitat in an ideal free manner. Demonstration of ideal free habitat selection on an operational field scale like this has never been undertaken before.}, annote = {ideal free distribution- assumes that individuals can assess surrondings and move to wherever maximizes fitness}, author = {Morris, Douglas W.}, doi = {10.1098/rspb.2006.3659}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Morris - 2006 - Moving to the ideal free home.pdf:pdf}, issn = {0962-8452}, journal = {Nature}, keywords = {Animals,Biological,Biological Evolution,Ecosystem,Esocidae,Esocidae: growth {\&} development,Female,Fertility,Fertility: physiology,Food Chain,Fresh Water,Male,Models,Population Density,Population Dynamics,Survival,Survival: physiology,evolution,ideal free distribution,spatial}, mendeley-tags = {evolution,ideal free distribution,spatial}, month = {dec}, pages = {645--646}, pmid = {17015363}, title = {{Moving to the ideal free home}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1639511{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {443}, year = {2006} } @article{Pimm1988, author = {Pimm, Stuart L. and Redfearn, Andrew}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Pimm, Redfearn - 1988 - The variability of population densities.pdf:pdf}, journal = {Nature}, keywords = {stochasticity,time series}, mendeley-tags = {stochasticity,time series}, pages = {613--614}, title = {{The variability of population densities}}, volume = {334}, year = {1988} } @article{Kreitman1983, author = {Kreitman, Martin}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kreitman - 1983 - Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster.pdf:pdf}, journal = {Nature}, keywords = {evolution}, mendeley-tags = {evolution}, pages = {412--417}, title = {{Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster}}, volume = {304}, year = {1983} } @article{Crouse1987a, annote = {Crouse et al (1987) uses a stage-based model to examine conservation options for loggerhead sea turtles. The paper does a really good job at laying out both the biology and mathematics background needed. With a simple stage-based model, the authors are able to make population projections, determine the sensitivity of model parameters, and make recommendations for conservation based on elasticity analysis. They are able to show that conservation of sea turtle eggs (the usual strategy employed at the time) isn't as effective as increasing survival rates for large juveniles. I think this is a classic example of how mathematics can be helpful in conservation. It would be almost impossible to figure out the effect of conserving certain life stages in such long-lived species. This paper (and one's that built on it) dramatically changed the way biologist's manage and conserve sea turtle populations. Bioligists now put a lot more resources to protecting older sea turtles from fishing pressures.}, author = {Crouse, Deborah T and Crowder, Larry B and Caswell, Hal}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Crouse, Crowder, Caswell - 1987 - A Stage-Based Population Model for Loggerhead Sea Turtles and Implications for Conservation.pdf:pdf}, journal = {Ecology}, keywords = {marine,matrix,model,stage-based}, mendeley-tags = {marine,matrix,model,stage-based}, number = {5}, pages = {1412--1423}, title = {{A Stage-Based Population Model for Loggerhead Sea Turtles and Implications for Conservation}}, volume = {68}, year = {1987} } @article{Hutchinson1961, annote = {How many similar species can coexist is a core issue in ecology and evolution. The term "plankton" includes a number of species that are very similar in regards to their habitat use and resource demands. However, many plankton species can be seen to coexist. In a constant environent, we would expect that one species would eventually be able to take over and outcompete all the other species (i.e. competive exclusion). To avoid competion, species may distribute themselves in time or space differently. Competition may also be reduced through anumber of mechanims: symbiosis, commensalism, predation, or if the environement was not in constant.}, author = {Hutchinson, G. E.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hutchinson - 1961 - The Paradox of the Plankton.pdf:pdf}, journal = {The American Naturalist}, keywords = {biodiversity,diversity,evolution,plankton}, mendeley-tags = {biodiversity,diversity,evolution,plankton}, number = {882}, pages = {137--145}, title = {{The Paradox of the Plankton}}, volume = {95}, year = {1961} } @article{McLaughlin2002, abstract = {Climate change is expected to alter the distribution and abundance of many species. Predictions of climate-induced population extinctions are supported by geographic range shifts that correspond to climatic warming, but few extinctions have been linked mechanistically to climate change. Here we show that extinctions of two populations of a checkerspot butterfly were hastened by increasing variability in precipitation, a phenomenon predicted by global climate models. We model checkerspot populations to show that changes in precipitation amplified population fluctuations, leading to rapid extinctions. As populations of checkerspots and other species become further isolated by habitat loss, climate change is likely to cause more extinctions, threatening both species diversity and critical ecosystem services.}, annote = {Few studies have been able to link specific mechanisms to climate-induced population extinctions. McLaughlin et al (2002) model butterfly populations to show that increased temporal variation in precipitation can lead to extinction behavior. Because of a fragmented landscape it is unlikely that these populations will be recolonized as they would have in extinction events in the past. Differences in topography probably affect the effect on the individual pops by the environement}, author = {McLaughlin, John F and Hellmann, Jessica J and Boggs, Carol L and Ehrlich, Paul R}, doi = {10.1073/pnas.052131199}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McLaughlin et al. - 2002 - Climate change hastens population extinctions.pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, keywords = {Animals,Butterflies,Butterflies: physiology,Climate,Ecosystem,Extinction,Psychological,Time Factors,climate change,extinction,stochasticity}, mendeley-tags = {climate change,extinction,stochasticity}, month = {apr}, number = {9}, pages = {6070--6074}, pmid = {11972020}, title = {{Climate change hastens population extinctions}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=122903{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {99}, year = {2002} } @article{Hutchinson1959a, author = {Hutchinson, G. E.}, journal = {The American Naturalist}, keywords = {biodiversity,evolution}, mendeley-tags = {biodiversity,evolution}, number = {870}, pages = {145--159}, title = {{Homage to Santa Rosalia or Why Are There So Many Kinds of Animals}}, volume = {93}, year = {1959} } @article{Childs2010, abstract = {Understanding the adaptations that allow species to live in temporally variable environments is essential for predicting how they may respond to future environmental change. Variation at the intergenerational scale can allow the evolution of bet-hedging strategies: a novel genotype may be favoured over an alternative with higher arithmetic mean fitness if the new genotype experiences a sufficiently large reduction in temporal fitness variation; the successful genotype is said to have traded off its mean and variance in fitness in order to 'hedge its evolutionary bets'. We review the evidence for bet-hedging in a range of simple plant systems that have proved particularly tractable for studying bet-hedging under natural conditions. We begin by outlining the essential theory, reiterating the important distinction between conservative and diversified bet-hedging strategies. We then examine the theory and empirical evidence for the canonical example of bet-hedging: diversification via dormant seeds in annual plants. We discuss the complications that arise when moving beyond this simple case to consider more complex life-history traits, such as flowering size in semelparous perennial plants. Finally, we outline a framework for accommodating these complications, emphasizing the central role that model-based approaches can play.}, annote = {Childs et al (2010) review the theory and emphircal evidence for bet hedging. Bet heding is the idea that a strategy that could imporove it's mean fitness if it reduces it's temporal fitness variation (e.g. flowing at different times by a single plant throughout a year). Conservative bet-hedging is risk avoidance at an indivdual level. Diversified bet-hedging is when risk is spread amonst many indidviuals of the same genotype (e.g. see dromancy in annual plants). There are a number of difficulties when examining taxa with complicated life histories (i.e. not annual plants with seed banks).}, author = {Childs, Dylan Z and Metcalf, C J E and Rees, Mark}, doi = {10.1098/rspb.2010.0707}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Childs, Metcalf, Rees - 2010 - Evolutionary bet-hedging in the real world empirical evidence and challenges revealed by plants.pdf:pdf}, issn = {1471-2954}, journal = {Proceedings of the Royal Society B}, keywords = {Adaptation,Biological Evolution,Genetic,Germination,Physiological,Plant Development,Plant Dormancy,Selection,Stochastic Processes,evolution,stochasticity}, mendeley-tags = {evolution,stochasticity}, month = {oct}, number = {1697}, pages = {3055--64}, pmid = {20573624}, title = {{Evolutionary bet-hedging in the real world: empirical evidence and challenges revealed by plants}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2982066{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {277}, year = {2010} } @article{Venable2007, annote = {Although bet hedging is predicted theoretically and their are a few weak examples of it, there hasn't been direct empirical evidence to examine possible mechanisms. Using 10 desert annual plants, Venable (2007) found that species with greater variation in reproduction succes also had lower average germination fractions. -if there is high variance in reprduction success (presumably due to environment) there is incentive to germinate less seeds in any given year How does this test mechanism? What are assumptions?}, author = {Venable, D. Lawrence}, doi = {10.1890/06-1495}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Venable - 2007 - Bet hedging in a guild of desert annuals.pdf:pdf}, issn = {0012-9658}, journal = {Ecology}, keywords = {bet hedging,delayed germination,desert annuals,evolution,long-term demographic variation,seed,stochasticity}, mendeley-tags = {evolution,stochasticity}, month = {may}, number = {5}, pages = {1086--1090}, title = {{Bet hedging in a guild of desert annuals}}, url = {http://www.esajournals.org/doi/abs/10.1890/06-1495}, volume = {88}, year = {2007} } @article{Lewontin1969, annote = {Lewontin and Cohen (1969) use an extremely simple discrete time exponential growth model where the growth term is a random variable. They wanted to investigate what happens if the growth rate is related to something in the environement and has nothing to do with the population. Instead of simply looking at mean population size they also want to examine variance in population size. Thet find that the expected value of population size may go to infinite as t is large, but they also find that every population is almost guarented to go extinct. If the geometric mean of the growth rate is less than one, the population will go extinct even if the arimetic mean is greater than one. However, in continuous time the geometric and arithemetic means are the same.}, author = {Lewontin, R. C. and Cohen, D.}, doi = {10.1073/pnas.62.4.1056}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lewontin, Cohen - 1969 - On Population Growth in a Randomly Varying Environment.pdf:pdf}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, keywords = {environment,extinction,stochasticity}, mendeley-tags = {environment,extinction,stochasticity}, month = {apr}, number = {4}, pages = {1056--1060}, title = {{On Population Growth in a Randomly Varying Environment}}, url = {http://www.pnas.org/cgi/doi/10.1073/pnas.62.4.1056}, volume = {62}, year = {1969} } @article{Connell1978, annote = {It was once believed that extremely diverse ecosystems (e.g. rain forests and coral reefs) must also be near equilibrium and relatively stable. However, the frequency of disturbances (in particular at medium levels of disturbace, more notably the intermediate distrubtance hypothesis) and the time it takes to return to the pre-disturbed state suggest most systems are probably not at equilbrium. This has been shown in a variety of settings, most notetibly in studies of forest succession. Diversity from a dsisturbanes can relate to the frequency, intensity, or the amount of area affected. The equal chance hypothesis would assume that all species have an equal chance of colonizing a empty space. The gradual change hypothesis (as proposed by Hutchinson to explain plankton diversity) is that idea that the environment changes enough to where no species can really gain an edge on all other species. In support of equilibrium, a number of hypotheses have been proposed. The niche diversification hypothesis states that species are able to coexist because they are able to specialize to certain parts of a n-dimensional space. There is enough space for a lot of different species. A circular network could also maintain diversity if species acted as in a game of rock paper scissors. A compensatory mortality hypothesis would lead to a diverse system if the most competive species were also most strongly affected by some type of mortality. Those species couldn't really ever dominat than.}, author = {Connell, Joseph H.}, journal = {Science}, keywords = {biodiversity,coral reef,evolution}, mendeley-tags = {biodiversity,coral reef,evolution}, number = {4335}, pages = {1302--1310}, title = {{Diversity in Tropical Rain Forests and Coral Reefs Author}}, volume = {199}, year = {1978} } @article{Felsenstein1981, author = {Felsenstein, Joseph}, journal = {Evolution}, keywords = {biodiversity,evolution}, mendeley-tags = {biodiversity,evolution}, number = {1}, pages = {124--138}, title = {{Skepticism Towards Santa Rosalia, or Why are There so Few Kinds of Animals?}}, volume = {35}, year = {1981} } @article{Lawton1988, author = {Lawton, John H.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lawton - 1988 - More time means more variation.pdf:pdf}, journal = {Nature}, keywords = {stochasticity,time series}, mendeley-tags = {stochasticity,time series}, pages = {563}, title = {{More time means more variation}}, volume = {334}, year = {1988} } @article{Courchamp1999, abstract = {The Allee effect describes a scenario in which populations at low numbers are affected by a positive relationship between population growth rate and density, which increases their likelihood of extinction. The importance of this dynamic process in ecology has been under-appreciated and recent evidence now suggests that it might have an impact on the population dynamics of many plant and animal species. Studies of the causal mechanisms generating Allee effects in small populations could provide a key to understanding their dynamics}, annote = {Allee effects were originally proposed by Warder Allee in the 1930s. Half a century later, Courchamp et al reviewed the subject. An Allee effect strictly refers to the inverse density dependence at low density. There are three broad categories of Allee effects: 1) genetic inbreeding, 2) demographic stochaticity, and 3) lack of facilitation. There are several examples of Allee effects from theoretical, experimental, and field efforts.}, author = {Courchamp, Franck and Clutton-Brock, Tim and Grenfell, Bryan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Courchamp, Clutton-Brock, Grenfell - 1999 - Inverse density dependence and the Allee effect.pdf:pdf}, journal = {Trends in Ecology and Evolution}, keywords = {allee,density,extinction}, mendeley-tags = {allee,density,extinction}, number = {10}, pages = {405--410}, title = {{Inverse density dependence and the Allee effect}}, volume = {14}, year = {1999} } @article{Knape2012, abstract = {Density dependence in population growth rates is of immense importance to ecological theory and application, but is difficult to estimate. The Global Population Dynamics Database (GPDD), one of the largest collections of population time series available, has been extensively used to study cross-taxa patterns in density dependence. A major difficulty with assessing density dependence from time series is that uncertainty in population abundance estimates can cause strong bias in both tests and estimates of strength. We analyse 627 data sets in the GPDD using Gompertz population models and account for uncertainty via the Kalman filter. Results suggest that at least 45{\%} of the time series display density dependence, but that it is weak and difficult to detect for a large fraction. When uncertainty is ignored, magnitude of and evidence for density dependence is strong, illustrating that uncertainty in abundance estimates qualitatively changes conclusions about density dependence drawn from the GPDD.}, annote = {-Does long time series mean that density dependence may not be important on short time scale -lagged density dependence may be very important -always hard to seperate true density dependence from autocorrelated environmental factors -models like Gompertz are log-linear in their dynamics and probably do a bad job at evaluating any non-linear dynamics Knape and de Valpine examine the role that uncertainty might play in detected density dependence. They use the Global Population Dynamics Database to examine 627 unique data sets. They found that when they ignored uncertainty in population estimates, there is stronger evidence for density dependence.}, author = {Knape, Jonas and de Valpine, Perry}, doi = {10.1111/j.1461-0248.2011.01702.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Knape, de Valpine - 2012 - Are patterns of density dependence in the Global Population Dynamics Database driven by uncertainty about pop.pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {Biological,Databases,Ecosystem,Factual,Models,Population Density,Population Dynamics,Uncertainty,density,model,population dynamics}, mendeley-tags = {density,model,population dynamics}, month = {jan}, number = {1}, pages = {17--23}, pmid = {22017744}, title = {{Are patterns of density dependence in the Global Population Dynamics Database driven by uncertainty about population abundance?}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22017744}, volume = {15}, year = {2012} } @article{Hastings2003, annote = {-how do we better collaborate between biology and mathematics -example of Threshold theorem being applied to number of people who need vaccine for population to be safe-{\textgreater} led to development of SIR model -some of the key areas in math biology: --spatial dynamics --stochastic (nonlinear) dynamics --how models best fit data specific areas include natural resource management, GCC, animal movement, marine reserve size}, author = {Hastings, Alan and Palmer, Margaret A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings, Palmer - 2003 - A Bright Future for Biologists and Mathematicians.pdf:pdf}, journal = {Science}, keywords = {complexity,mathematics,model,quantitative}, mendeley-tags = {complexity,mathematics,model,quantitative}, number = {March}, pages = {2003--2004}, title = {{A Bright Future for Biologists and Mathematicians?}}, volume = {299}, year = {2003} } @article{Green2005, author = {Green, Jessica L and Hastings, Alan and Arzberger, Peter and Ayala, Francisco J and Cottingham, Kathryn L and Cuddington, K I M and Davis, Frank and Dunne, Jennifer A and Fortin, Marie-jos{\'{e}}e and Gerber, Leah}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Green et al. - 2005 - Complexity in Ecology and Conservation Mathematical , Statistical , and Computational Challenges.pdf:pdf}, journal = {BioScience}, keywords = {complexity,cyberinfrastructure,ecological complexity,ecology,metadata,model,quantitative,quantitative conservation biology,semantic web}, mendeley-tags = {complexity,ecology,model,quantitative}, number = {6}, pages = {501--510}, title = {{Complexity in Ecology and Conservation: Mathematical , Statistical , and Computational Challenges}}, volume = {55}, year = {2005} } @article{Levin1997, author = {Levin, Simon A and Grenfell, Bryan and Hastings, Alan and Perelson, Alan S}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levin et al. - 1997 - Mathematical and Computational Challenges in Population Biology and Ecosystems Science.pdf:pdf}, journal = {Science}, keywords = {complexity,conservation,model,population}, mendeley-tags = {complexity,conservation,model,population}, number = {January}, pages = {334--343}, title = {{Mathematical and Computational Challenges in Population Biology and Ecosystems Science}}, volume = {275}, year = {1997} } @article{Boettiger2013, abstract = {The realization that complex systems such as ecological communities can collapse or shift regimes suddenly and without rapid external forcing poses a serious challenge to our understanding and management of the natural world. The potential to identify early warning signals that would allow researchers and managers to predict such events before they happen has therefore been an invaluable discovery that offers a way forward in spite of such seemingly unpredictable behavior. Research into early warning signals has demonstrated that it is possible to define and detect such early warning signals in advance of a transition in certain contexts. Here we describe the pattern emerging as research continues to explore just how far we can generalize these results. A core of examples emerges that shares three properties: the phenomenon of rapid regime shifts, a pattern of 'critical slowing down' that can be used to detect the approaching shift, and a mechanism of bifurcation driving the sudden change. As research has expanded beyond these core examples, it is becoming clear that not all systems that show regime shifts exhibit critical slowing down, or vice versa. Even when systems exhibit critical slowing down, statistical detection is a challenge. We review the literature that explores these edge cases and highlight the need for (a) new early warning behaviors that can be used in cases where rapid shifts do not exhibit critical slowing down, (b) the development of methods to identify which behavior might be an appropriate signal when encountering a novel system; bearing in mind that a positive indication for some systems is a negative indication in others, and (c) statistical methods that can distinguish between signatures of early warning behaviors and noise.}, annote = {-need early warning signals of impending regime shifts -one tool is phenomenon of "critical slowing down" ---{\textgreater} increasing variaincaec or autocorrelation in a system Not all systems show CSD, nor do all CSD systems exhibit regime shifts CSD occurs as domnant eigenvalue approaches 0-{\textgreater} response to perturbations slows Three distinct phenomena: rapid regime shifts, bifurcations, critical slowing down Crises - sudden changes in dynamics of chaotic attractors due to respone to small change in parameters In subcritical hopf and transcritical bifurcations, system slows down near bifurcation but catastophe does not ensue Behavior may or may not be present in a system, but it may also just be difficult to detect -e.g. could use receiver-operator cuves to examine how system perofrms for both false nevgatives and positives}, archivePrefix = {arXiv}, arxivId = {1305.6700}, author = {Boettiger, Carl and Ross, Noam and Hastings, Alan}, doi = {10.1007/s12080-013-0192-6}, eprint = {1305.6700}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Boettiger, Ross, Hastings - 2013 - Early warning signals The charted and uncharted territories.pdf:pdf}, journal = {Theoretical Ecology}, keywords = {bifurcation,critical slowing down,early warning signals,regime shifts}, month = {may}, number = {3}, pages = {255--264}, title = {{Early warning signals: The charted and uncharted territories}}, url = {http://arxiv.org/abs/1305.6700}, volume = {6}, year = {2013} } @article{Beninca2008, abstract = {Mathematical models predict that species interactions such as competition and predation can generate chaos. However, experimental demonstrations of chaos in ecology are scarce, and have been limited to simple laboratory systems with a short duration and artificial species combinations. Here, we present the first experimental demonstration of chaos in a long-term experiment with a complex food web. Our food web was isolated from the Baltic Sea, and consisted of bacteria, several phytoplankton species, herbivorous and predatory zooplankton species, and detritivores. The food web was cultured in a laboratory mesocosm, and sampled twice a week for more than 2,300 days. Despite constant external conditions, the species abundances showed striking fluctuations over several orders of magnitude. These fluctuations displayed a variety of different periodicities, which could be attributed to different species interactions in the food web. The population dynamics were characterized by positive Lyapunov exponents of similar magnitude for each species. Predictability was limited to a time horizon of 15-30 days, only slightly longer than the local weather forecast. Hence, our results demonstrate that species interactions in food webs can generate chaos. This implies that stability is not required for the persistence of complex food webs, and that the long-term prediction of species abundances can be fundamentally impossible.}, annote = {Beninca et al examine a mesocosm of plankton and detected chaotic populations amongst the different functional groups. The feel that the food web itself, although stable, is comprised of chaotic populations. Because of this chaotic behavior, any long term forecasts of population density were impossible. The study used several tests to detect chaos in there system: examined periodicities, predictability, and the Lyapunov exponent.}, author = {Beninc{\`{a}}, Elisa and Huisman, Jef and Heerkloss, Reinhard and J{\"{o}}hnk, Klaus D and Branco, Pedro and {Van Nes}, Egbert H and Scheffer, Marten and Ellner, Stephen P}, doi = {10.1038/nature06512}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Beninc{\`{a}} et al. - 2008 - Chaos in a long-term experiment with a plankton community.pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {Animals,Bacteria,Bacteria: metabolism,Biological,Food Chain,Models,Nonlinear Dynamics,Oceans and Seas,Plankton,Plankton: metabolism,Population Dynamics,Species Specificity,Time Factors,chaos,density,plankton,population}, mendeley-tags = {chaos,density,plankton,population}, month = {feb}, number = {7180}, pages = {822--5}, pmid = {18273017}, title = {{Chaos in a long-term experiment with a plankton community.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18273017}, volume = {451}, year = {2008} } @article{Tillman1991, author = {Tillman, David and Wedin, David}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Tillman, Wedin - 1991 - Oscillations and chaos in the dynamics of perennial grass.pdf:pdf}, journal = {Nature}, keywords = {chaos,model,population dynamics}, mendeley-tags = {chaos,model,population dynamics}, pages = {653--655}, title = {{Oscillations and chaos in the dynamics of perennial grass}}, volume = {353}, year = {1991} } @incollection{Turchin1995, annote = {For the past half-century ecologists have argued about how density-dependence may affect population regulation. Although it is generally well-known that density-dependence must play some role, detecting it's presence in natural popualtion has proved difficult. When examining natural populations, nonlinearity and time lags can obsurcre possible density-dependence. -"population regulation is the presence of a long-term staionary probability distribution of pop densitities" -attractor is a more general version of a table point equilibria (e.g. periodic, or limit, cycles) -in a stochastic system, a deterministic atttractor becomes a stationary probability distribution of the population size or density -density dependence = the dependence of per capita growth rate on present or past population densitities --direct is negative effects --inverse is positive effects In order for density dependence to force regulation: 1) density dependence must be of the right sign 2) return tendency needs to be strong to counteract density-independent forces 3) lag time for return tendency to occur must not be too long. With more data, it has become clear that many population experience density-dependence. The length of the time series investigated is of critical importance, as longer time series detect more density effects. Complex systems can be examined by looking at the relative strength of endoedous versus exogenous forces. The degree of periodicity and stability are both important aspects of any complex system. The degree of stability is measured by the Lyapunov exponent (long-term average divergence rate). Discussion post: -density depence when combined with nonlinearities and lags It is interesting to read this paper with the ecological training we now receive. I take for granted that there was ever a debate whether density-dependence factors were present. It is encouraging that most people eventually went the way the data was pointing–that population regulation required density-dependence. Certainly, the question as to whether density-dependent versus independent factors has more of an effect on a given population is still of great interest. It was not too surprising to read that the longer the time series (i.e. more adequate data) led to actually identifying density-dependence in natural systems. However, this did make me rethink papers I've read in the past that claimed they found density-dependence, but used data on short time scales. The potential confounding variables of observation errors, nonlinear processes, and time or spatial lags are also of great concern. These issues make experiments difficult enough that I feel theory will have to lead the way. I enjoyed the explanation and clarification of all the different terms for equilbria and which apply in which contexts. Phrasing these types of questions in the terms of dynamical systems gives you a lot of useful tools and theory. The paper does such a good job at discussing the importance of stochasticity, but only in the context of describing the "ensemble mean" of a population density. I think identifying the role of density-dependence in driving the variance we observe in population density would be interesting.   The definitions for direct versus inverse density-dependence were a bit confusing. In the past, I have typically associated density-dependent factors being solely related to intrinsic processes. It makes sense that such factors could also be driven by external or environmental factors, as the paper makes clear.}, author = {Turchin, Peter}, booktitle = {Population Dynamics}, chapter = {2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Turchin - 1995 - Chapter 2 Population Regulation Old Arguments and a New Synthesis.pdf:pdf}, keywords = {density,population}, mendeley-tags = {density,population}, number = {1}, pages = {19--39}, title = {{Chapter 2: Population Regulation: Old Arguments and a New Synthesis}}, year = {1995} } @article{Hastings2005, abstract = {Using a carefully chosen set of examples, we illustrate the importance and ubiquity of quantitative reasoning in the biological sciences. The examples range across many different levels of biological organization, from diseases through ecosystems, and the problems addressed range from basic to applied. In addition to the overall theme that mathematical and statistical approaches are essential for understanding biological systems, three particular and interacting mathematical themes emerge. First, nonlinearity is pervasive; second, inclusion of stochasticity is essential; and third, issues of scale are common to all applications of quantitative approaches. Future progress in understanding many biological systems will depend on continued applications and developments in these three areas, and on understanding how nonlinearity, stochasticity, and scale interact.}, address = {San Diego, CA}, annote = {There are three themes that emerge when considering biological questions throught the lens of mathematics: nonlinearity, stochasticity, and the issue of scale. Issues of stochasity and nonlinearity occur at many scales within ecology and environmental science from disease outbreaks to macroecology. Often simple approaches, like maximumn sustainable yield, are far to simple and ignore critical aspects such as economics and social theory. In addition, fruitful opportunities between physics and biology exist in fisheries where life cycle and physical dynamics play an important role.}, author = {Hastings, Alan and Arzberger, Peter and Bolker, Ben and Collins, Scott and Ives, Anthony R. and Johnson, Norman and Palmer, Margaret A}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings et al. - 2005 - Quantitative Biology for the 21st Century.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings et al. - 2005 - Quantitative Biology for the 21st Century(2).pdf:pdf}, institution = {University of California}, journal = {BioScience}, keywords = {complexity,mathematics,model,quantitative}, mendeley-tags = {complexity,mathematics,model,quantitative}, number = {6}, pages = {511--517}, title = {{Quantitative Biology for the 21st Century}}, volume = {55}, year = {2005} } @article{Brook2006, abstract = {Population limitation is a fundamental tenet of ecology, but the relative roles of exogenous and endogenous mechanisms remain unquantified for most species. Here we used multi-model inference (MMI), a form of model averaging, based on information theory (Akaike's Information Criterion) to evaluate the relative strength of evidence for density-dependent and density-independent population dynamical models in long-term abundance time series of 1198 species. We also compared the MMI results to more classic methods for detecting density dependence: Neyman-Pearson hypothesis-testing and best-model selection using the Bayesian Information Criterion or cross-validation. Using MMI on our large database, we show that density dependence is a pervasive feature of population dynamics (median MMI support for density dependence = 74.7-92.2{\%}), and that this holds across widely different taxa. The weight of evidence for density dependence varied among species but increased consistently, with the number of generations monitored. Best-model selection methods yielded similar results to MMI (a density-dependent model was favored in 66.2-93.9{\%} of species time series), while the hypothesis-testing methods detected density dependence less frequently (32.6-49.8{\%}). There were no obvious differences in the prevalence of density dependence across major taxonomic groups under any of the statistical methods used. These results underscore the value of using multiple modes of analysis to quantify the relative empirical support for a set of working hypotheses that encompass a range of realistic population dynamical behaviors.}, annote = {Brook and Bradshaw used aspects of AIC to determine the weight given towards density dependent versus density independent models. They used this approach and found that between 75-90{\%} of 1200 time series were better fit using density dependent models. Length of time series was an important factor in deteacing density dependence. Issues: -AIC gives you best model but it does not say if any of the models are useful-{\textgreater} when examing R2 they could only account for 2.5{\%} of the variance}, author = {Brook, Barry W and Bradshaw, Corey J a}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brook, Bradshaw - 2006 - Strength of evidence for density dependence in abundance time series of 1198 species.pdf:pdf}, issn = {0012-9658}, journal = {Ecology}, keywords = {Biological,Ecosystem,Genetic,Models,Plant Development,Selection,Stochastic Processes,density,model,time series}, mendeley-tags = {density,model,time series}, month = {jun}, number = {6}, pages = {1445--51}, pmid = {16869419}, title = {{Strength of evidence for density dependence in abundance time series of 1198 species}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16869419}, volume = {87}, year = {2006} } @article{Cohen2004, abstract = {complexity; model; physics}, annote = {-challenges in biology will require advances in mathematics (how to handle different scales) "Charles Darwin was right when he wrote that people with an understanding “of the great leading principles of mathematics{\ldots} seem to have an extra sense” (F. Darwin 1905)" -William Harvey in the 1600's used mathematics to examine blood circulation-{\textgreater} predicted blood flow and capillaries -classic work of Fisher, Haldane, and Wright "Those who understand the calculus, ordinary and partial differential equations, and probability theory have a way of seeing and understanding the world, including the biological world, that is unavailable to those who do not" -with better and faster computers-{\textgreater} we need an even deeper understanding of what is actually happening beneath the hood}, author = {Cohen, Joel E}, doi = {10.1371/journal.pbio.0020439}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cohen - 2004 - Mathematics Is Biology's Next Microscope, Only Better Biology Is Mathematics' Next Physics, Only Better.pdf:pdf}, journal = {PLoS Biology}, keywords = {complexity,model,physics}, mendeley-tags = {complexity,model,physics}, number = {12}, pages = {2017--2023}, title = {{Mathematics Is Biology's Next Microscope, Only Better; Biology Is Mathematics' Next Physics, Only Better}}, volume = {2}, year = {2004} } @article{Scheffer2003, annote = {Dramatic regime shifts have now been documented in a number of systems. At first, it makes sense that such changes would be caused by an equally dramatic change in the environment. However, the shift from one regime, or attractor, to another may simply reflect even a tiny change in system that then crossed some type of threshold point. Although it is not easy to identify regime shifts in field data, there are a few ways to provide evidence: 1) jumps in time series, 2) multimodality of the frequency dist of states, and 3) dual relationship to control factors. hysteresis- the difference between forward and backward switches -different initial conditions may be a reflection of a chaotic system -how would a regime shift then change the environement around it? Making it a different landscape that would need to be navigated to leave that stable state -the philosopical discussion at the end is a bit weird -how does evolution play into stable states}, author = {Scheffer, Marten and Carpenter, Stephen R.}, doi = {10.1016/j.tree.2003.09.002}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Scheffer, Carpenter - 2003 - Catastrophic regime shifts in ecosystems linking theory to observation.pdf:pdf}, issn = {01695347}, journal = {Trends in Ecology {\&} Evolution}, keywords = {ecosystem,regime}, mendeley-tags = {ecosystem,regime}, month = {dec}, number = {12}, pages = {648--656}, title = {{Catastrophic regime shifts in ecosystems: linking theory to observation}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0169534703002787}, volume = {18}, year = {2003} } @article{Williams2011, abstract = {Counterintuitive dynamics of various biological phenomena occur when composite system dynamics differ qualitatively from that of their component systems. Such composite systems typically arise when modelling situations with time-varying biotic or abiotic conditions, and examples range from metapopulation dynamics to population genetic models. These biological, and related physical, phenomena can often be modelled as simple financial games, wherein capital is gained and lost through gambling. Such games have been developed and used as heuristic devices to elucidate the processes at work in generating seemingly paradoxical outcomes across a spectrum of disciplines, albeit in a field-specific, ad hoc fashion. Here, we propose that studying these simple games can provide a much deeper understanding of the fundamental principles governing paradoxical behaviours in models from a diversity of topics in evolution and ecology in which fluctuating environmental effects, whether deterministic or stochastic, are an essential aspect of the phenomenon of interest. Of particular note, we find that, for a broad class of models, the ecological concept of equilibrium reactivity provides an intuitive necessary condition that must be satisfied in order for environmental variability to promote population persistence. We contend that further investigations along these lines promise to unify aspects of the study of a range of topics, bringing questions from genetics, species persistence and coexistence and the evolution of bet-hedging strategies, under a common theoretical purview.}, annote = {reversal behavior- when the transient behavior observed conflicts with the long-term behavior Evolutionary game playing (i.e. phenotype switching)}, author = {Williams, Paul David and Hastings, Alan}, doi = {10.1098/rspb.2010.2074}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Williams, Hastings - 2011 - Paradoxical persistence through mixed-system dynamics towards a unified perspective of reversal behaviours i.pdf:pdf}, issn = {1471-2954}, journal = {Proceedings of the Royal Society B}, keywords = {Biological,Biological Evolution,Biota,Ecological and Environmental Processes,Game Theory,Models,Population Dynamics,Stochastic Processes,eco-evolutionary,population,stochastics}, mendeley-tags = {eco-evolutionary,population,stochastics}, month = {may}, number = {1710}, pages = {1281--90}, pmid = {21270032}, title = {{Paradoxical persistence through mixed-system dynamics: towards a unified perspective of reversal behaviours in evolutionary ecology.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3061147{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {278}, year = {2011} } @phdthesis{Seppanen2014, author = {Sepp{\"{a}}nen, Anne}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sepp{\"{a}}nen - 2014 - Mathematics Inspired by Darwin- Adaptive dynamics of dispersal and cooperation.pdf:pdf}, isbn = {9789512956418}, pages = {61}, school = {University of Turku}, title = {{Mathematics Inspired by Darwin- Adaptive dynamics of dispersal and cooperation}}, type = {PhD}, year = {2014} } @article{Parvinen2012, abstract = {The question of how dispersal behavior is adaptive and how it responds to changes in selection pressure is more relevant than ever, as anthropogenic habitat alteration and climate change accelerate around the world. Inmetapopulationmodels where local populations are large, and thus local population size is measured in den- sities, density-dependent dispersal is expected to evolve to a single-threshold strat- egy, in which individuals stay in patches with local population density smaller than a threshold value and move immediately away from patches with local population den- sity larger than the threshold. Fragmentation tends to convert continuous populations into metapopulations and also to decrease local population sizes. Therefore we ana- lyze a metapopulation model, where each patch can support only a relatively small local population and thus experience demographic stochasticity.We investigated the evolution of density-dependent dispersal, emigration and immigration, in two scenar- ios: adult and natal dispersal. We show that density-dependent emigration can also evolve to a nonmonotone, “triple-threshold” strategy. This interesting phenomenon results from an interplay between the direct and indirect benefits of dispersal and the costs of dispersal.We also found that, compared to juveniles, dispersing adults may benefit more from density-dependent vs. density-independent dispersal strategies.}, author = {Parvinen, Kalle and Sepp{\"{a}}nen, Anne and Nagy, John D}, doi = {10.1007/s11538-012-9770-9}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Parvinen, Sepp{\"{a}}nen, Nagy - 2012 - Evolution of Complex Density-Dependent Dispersal Strategies.pdf:pdf}, journal = {Bull Math Biol}, keywords = {dispersal,evolution,life history,pika}, mendeley-tags = {dispersal,evolution,life history,pika}, number = {11}, pages = {2622--49}, title = {{Evolution of Complex Density-Dependent Dispersal Strategies}}, volume = {74}, year = {2012} } @book{Levin1999, annote = {Fragile Dominion is Simon Levin's attempt to summarize and explain the environment and ecosystems as complex adaptive systems. He uses literature from economics, applied mathematics, physics, evolution, and ecology to illustrate his thesis. He begins by laying out some challenges in environemental science and ecology and summarizes these into six fundamental questions in ecology. Through the rest of the book, Levin attempts to provide answers and to identify holes in the literature in regards to each questions. He ends the book with suggestions of how humans can be environmental stewards and what the next steps should be. Levin uses a lot of interesting examples from physics and evolution in particular. His focus is really on how you can undestand complex systems. In particular, understanding adaptive complex sytems. This certainly ignited my interests in complexity and dynamical systems. I book marked a few references and particurarily interesting passages: page 98: the idea of physics envy and simple versus complex models page 107: statistical mechanics and ecology page 112: complexity and evolution, self-organized criticality page 181: self-organized criticality}, author = {Levin, SImon}, edition = {3}, keywords = {complexity,conservation,sustainability}, mendeley-tags = {complexity,conservation,sustainability}, pages = {250}, publisher = {Perseus Publishing}, title = {{Fragile Dominion: Complexity and the Commons}}, year = {1999} } @article{Robinson2014, author = {Robinson, James P.W. and White, Easton R. and Wiwchar, Logan D. and Claar, Danielle C. and Suraci, Justin P. and Baum, Julia K.}, doi = {10.1016/j.marpol.2014.03.012}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Robinson et al. - 2014 - The limitations of diversity metrics in directing global marine conservation.pdf:pdf}, issn = {0308597X}, journal = {Marine Policy}, keywords = {Evenness,Functional diversity,Macroecology,Marine fish,Reef ecosystems,Underwater visual census}, month = {sep}, pages = {123--125}, publisher = {Elsevier}, title = {{The limitations of diversity metrics in directing global marine conservation}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0308597X14000840}, volume = {48}, year = {2014} } @article{Cole1954, author = {Cole, Lamont C.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cole - 1954 - The population consequences of life history phenomena.pdf:pdf}, journal = {The Quarterly Review of Biology}, keywords = {life history,population}, mendeley-tags = {life history,population}, number = {2}, pages = {103--137}, title = {{The population consequences of life history phenomena}}, volume = {29}, year = {1954} } @book{Gould1980, author = {Gould, Stephen Jay}, booktitle = {The Panda's Thumb: More Reflections in Natural History}, title = {{The Panda's Thumb: More Reflections in Natural History}}, year = {1980} } @article{Hastings2010, annote = {What are the individual pops at Bodie doing over time? Any patterns on individual populations that could result in behavior at the whole metapop scale Sometimes equilibrium or asymptoic behavior is not only uninteresting, it can be misleading depending on the questions being asked -Temporal or spatial scales are nearly always important but are often not explicently considered -transient dynamics are often ignored but may be the most important thing to study depending on the question -Internal and external forces are important in looking at time scales -upwelling events are good examples of resource impulses that have two processes acting on different time scales (the ecology of phytoplankton that need upwellings and the upwellings themselves) -different time scales within and between patches that are part of a metapopulation -interesting note about Lotka's model that recongnized time scales}, author = {Hastings, Alan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastings - 2010 - Timescales, dynamics, and ecological understanding.pdf:pdf}, journal = {Ecology}, keywords = {coexistence,dynamics,persistence,stochasticity,time,time series,timescales,transients}, mendeley-tags = {dynamics,stochasticity,time}, number = {12}, pages = {3471--3480}, title = {{Timescales, dynamics, and ecological understanding}}, volume = {91}, year = {2010} } @techreport{Foundation2011, author = {{MarViva Foundation}}, keywords = {cocos,elasmobranch,mpa}, mendeley-tags = {cocos,elasmobranch,mpa}, pages = {4}, title = {{Costa Rica Seamounts Marine Management Area}}, year = {2011} } @article{Stevenson2007, abstract = {On coral reefs in Palmyra—a central Pacific atoll with limited fishing pressure—total fish biomass was 428 and 299{\%} greater than on reefs in nearby Christmas and Fanning Islands. Large apex predators, groupers, sharks, snappers, and jacks larger than 50 cm in length, accounted for 56{\%} of total fish biomass in Palmyra on average, but only 7 and 3{\%} on Christmas and Fanning. These biomass proportions are remarkably similar to those previously reported for the remote and uninhabited Northwest Hawaiian Islands (NWHI) and densely populated Main Hawaiian Islands (MHI), although Palmyra's reefs are dominated in biomass by sharks (44{\%} of the total), whereas the NWHI by jacks (39{\%}). Herbivorous fish biomass was also greater on Palmyra than on Christmas and Fanning (343 and 207{\%}, respectively). These results and previous findings indicate that remote, uninhabited islands support high levels of consumers, and highlight the importance of healthy coral reef ecosystems as reference points for assessment of human impacts and establishment of restoration goals.}, author = {Stevenson, Charlotte and Katz, Laure S. and Micheli, Fiorenza and Block, Barbara and Heiman, Kimberly W. and Perle, Chris and Weng, Kevin and Dunbar, Robert and Witting, Jan}, doi = {10.1007/s00338-006-0158-x}, isbn = {0722-4028}, issn = {07224028}, journal = {Coral Reefs}, keywords = {Coral reefs,Fishing impacts,Food webs,Line Islands,Palmyra,Top predators}, pages = {47--51}, title = {{High apex predator biomass on remote Pacific islands}}, volume = {26}, year = {2007} } @book{Bivand2008, address = {New York, NY}, annote = {Analysing Spatial Data: simple introduction Chapter 7: Spatial Point Pattern Analysis - want to examine distribution of points in space and the possible interactions between the points - test for complete spatial randomness, clustered, or regular patterns --G, F --G function- measues the dist. of the distance from an event to its nearest event --F funciton- measures the dist of all distance from an arbitrary point to its nearest event (measure of average space left between events) First order props- measure distribution of events (e.g. intensity and spatial density) 2nd order props- measures interaction between points (clustering) HPP and IPP Poisson point processes -events are distributed independetly according to given intensity -the intensity in an IPP varies spatially HPP is stationary (intensity is constant and second-order intensity depends only on the relative positions of two points) and isotrophic (second-order intensity is invariant to rotation) -{\textgreater} HPP is the formal defin. of a point process which is CSR -can estimate intensity non-parametrically by kernal smoothing or parametrically by proposing a specific function for the intensity whose parameters are estimated by maxmizing the liklihood of the point process (min the MSE) --the bandwidth is much more important than the kernal choice Second order props (e.g. use K function) -strength and type of interactions between pts -prob of any pair of events occuring nearby pts x and y -K function- measures number of events found up to a given dist from any particular event) -Could use GAM to examine role of co variates in producing pattern CHAPTER 8: GEOSTATISTICS -pattern of locations is not of interest, want to examine the measurements of variables at each given point -random fields, Z(s), Z is random, s is not -try to estimate Z at unkown locations (s0) Non-geostats. Interpolation methods -inverse distance weighted interpolation (distance based weighted average at each point)- produces similar results to variogram with small nugget -linear regression -trend surface analysis (linear regression but with polynomial terms) Variogram (usually semivariogram) examines spatial correlation -need to assume stationarity in order the estimate spatial correlation (says variance of Z is constant and spatial correlation does not depend on location), isotrophy is also helpful -to ensure only non-negative prediction variance, the matrix of semivariance values needs to be non-negative definite -the nuggest represents measurement error and/or microvariability Mutivariable variogram modeling- use cross variogram to estimate semivariances Can find the best linear unbiased predictor (BLUP) of Z(s0) if we know the predictor values for s0, the covariance of Z(s) and the covariance vector of Z(s) and Z(s0) --Kriging (simple, orginary, and universal)- R would choose which type would be appropraiate based on the info provided --Can also do block and stratisfied kriging Cross validation splits data into modelling (training) and validation sets Geostatistical simulation- refers to simulation of possible outcomes of a random field Can estimate error of variogram coefficients using model-based geostatistical predictions Chapter 9: Areal Data and Spatial Autocorr -examining data collected in plane that is divided up into neighborhoods (areal units) that is a tessellation of the whole area -measure spatial autocorrelation between neighbors, then assign spatial weights to neighbors the way the area is divided up can affect the results- modifiable areal unit problem -Neighbors can be chosen via a number of different weights: queen contiguity, rook contiguity, distance -islands need special considerations -After establishing neighbors, you assign spatial weights (W weghts, binary) -can examine spatial lags -test for spatial autocorrelation- assume that the mean model of the data removes systemic spatial patterning (ignoring covariates may say you have spatial autocorrelation when you don't actually- Type I error- reject null accidently) --Use Moran's I (global test): see text "The approach taken most generally is to stan- dardise the observed value by subtracting the analytical expected value, and dividing the difference by the square root of the analytical variance for the spatial weights used, for a set of assumptions. The result is a standard deviate, and is compared with the Normal distribution to find the probability value of the observed statistic under the null hypothesis of no spatial dependence for the chosen spatial weights – most often the test is one-sided, with an alter- native hypothesis of the observed statistic being significantly greater than its expected value." -Randomization assumption- "the randomisation assumption, which differsfrom the simpler normality assumption by introducing a correction term based on the kurtosis of the variable of interest" -Could also use MCMC to mix up neighbors -Empirical rates Can also use local tests of spatial autocorrelation- this would detect clusters or hotspots}, author = {Bivand, Roger S. and Pebesma, Edzer J. and Gomez-Rubio, Virgilio}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bivand, Pebesma, Gomez-Rubio - 2008 - Applied Spatial Data Analysis with R.pdf:pdf}, isbn = {9780387781709}, pages = {374}, publisher = {Springer}, title = {{Applied Spatial Data Analysis with R}}, year = {2008} } @article{Orzack2005, author = {Orzack, Steven Hecht}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Orzack - 2005 - Discussion What , If Anything , Is “ The Strategy of Model Building in Population Biology” A Comment on Levins ( 19.pdf:pdf}, number = {July}, pages = {479--485}, title = {{Discussion : What , If Anything , Is “ The Strategy of Model Building in Population Biology?” A Comment on Levins ( 1966 ) and Odenbaugh ( 2003 )*}}, volume = {72}, year = {2005} } @book{James2013, address = {New York, NY}, annote = {Chapter 2: Different methods exist for situations in which you want to understand what is happening (inference) versus being able to predict -e.g. non linear may predict well but may be difficult to explain why Parametric vs non-parametric -parametric- assume f in linear in X and fit model with the data to estimate B1, B2,.. -non-parametric - do not make explicit assumptions about the form of f, need a large numer of observations typically Overfitting- bad because it is hard to make any accurate predictions about new data or data not in the training set Supervised (most of what we do- predictors and responses) versus unsupervised learning (make measurements but lack a response variable e.g. cluster analysis) Bias (inherhet bias in statistical technique) and variance (amount sample will very if selected again and again)- there is a tradeoff between the two -in a classification setting you would worry about the training error rate (look at a Bayes classifier or the K-Nearest Neighbor approach) instead of minmizing MSE Chapter 3: R{\^{}}2 measures the proportion of variability in Y that can be explained using X}, author = {James, Gareth and Witten, Daniela and Hastie, Trevor and Tibshirani, Robert}, doi = {10.1007/978-1-4614-7138-7}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/James et al. - 2013 - An Introduction to Statistical Learning.pdf:pdf}, isbn = {978-1-4614-7137-0}, pages = {436}, publisher = {Springer New York}, series = {Springer Texts in Statistics}, title = {{An Introduction to Statistical Learning}}, volume = {103}, year = {2013} } @article{Edgar2004, abstract = {Analysis of ecological baseline data collected for key resource species within the Galapagos Marine Reserve indicates that variation in animal density associated with the location of fully protected zones can be comparable to protected area effects. Even with a high level of interspersion between conservation, tourism and fishing management zones, major differences in densities of economically important species were evident between zone types prior to enforcement of fishing restrictions. Densities of the most valuable fishery resource, sea cucumbers, were three times higher in zones that remained open to fishing compared to ‘no-take' conservation zones, and densities of sharks were five times higher in tourism zones than fishing or conservation zones. These results highlight bias in the socio-political processes that can accompany selection of marine protected areas, where fishers attempt to minimize perceived impacts on their livelihood by locating large protected zones in resource-poor areas, and tourism operators and sport divers argue for protection of areas containing atypically-interesting features. Bias in the location of fully protected zones can seriously confound ‘control-impact' field investigations when data prior to prohibitions on fishing are lacking, including meta-analyses, which are dominated by such potentially systematically biased studies.}, author = {Edgar, GJ and Bustamante, RH and Farina, JM and Calvopina, M and Martinez, C and Toral-Granda, MV}, doi = {10.1017/S0376892904001584}, issn = {0376-8929}, journal = {Environmental Conservation}, pages = {212--218}, title = {{Bias in evaluating the effects of marine protected areas: the importance of baseline data for the Galapagos Marine Reserve}}, url = {http://journals.cambridge.org/abstract{\_}S0376892904001584}, volume = {31}, year = {2004} } @article{Meyer2009, abstract = {Shark cage diving is both popular and controversial, with proponents citing educational value and non-extractive use of natural resources and opponents raising concerns about public safety and ecological impacts. Logbook data collected 2004-2008 from two Oahu (Hawaii) shark cage diving operations were analysed to determine whether such voluntary records provide useful insights into shark ecology or ecotourism impacts. Operators correctly identified common shark species and documented gross seasonal cycles and long-term trends in abundance of Galapagos (Carcharhinus galapagensis), sandbar (Carcharhinus plumbeus) and tiger sharks (Galeorcerdo cuvier). Annual cycles in shark abundance may indicate seasonal migrations, whereas long-term trends suggest gradual exclusion of smaller sandbar sharks from cage diving sites. Numerically dominant ({\textgreater} 98{\%}) Galapagos and sandbar sharks are rarely implicated in attacks on humans. Negligible impact on public safety is supported by other factors such as: (1) remoteness of the sites, (2) conditioning stimuli that are specific to the tour operations and different from inshore recreational stimuli and (3) no increase in shark attacks on the north coast of Oahu since cage diving started. Tracking studies are required to validate logbook data and to determine whether sharks associated with offshore cage diving travel into inshore areas used for in-water recreation.}, author = {Meyer, Carl G. and Dale, Jonathon J. and Papastamatiou, Yannis P.. and Whitney, Nicholas M. and Holland, Kim N.}, doi = {10.1017/S0376892909990038}, isbn = {0376-8929}, issn = {0376-8929}, journal = {Environmental Conservation}, pages = {104}, title = {{Seasonal cycles and long-term trends in abundance and species composition of sharks associated with cage diving ecotourism activities in Hawaii}}, volume = {36}, year = {2009} } @article{McClintock2012, author = {McClintock, Brett T. and King, Ruth and Thomas, Len and Matthiopoulos, Jason and McConnell, Bernie J. and Morales, Juan M.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McClintock et al. - 2012 - A general discrete-time modeling framework for animal movement using multistate random walks.pdf:pdf}, journal = {Ecological Monographs}, keywords = {animal location data,bayesian model selection,biased correlated random walk,carlo,grey seal,halichoerus grypus,model,movement model,north sea,reversible-jump markov chain monte,state-space,switching behavior,telemetry}, number = {3}, pages = {335--349}, title = {{A general discrete-time modeling framework for animal movement using multistate random walks}}, volume = {82}, year = {2012} } @article{Hueter2013, abstract = {Whale sharks, Rhincodon typus, aggregate by the hundreds in a summer feeding area off the northeastern Yucatan Peninsula, Mexico, where the Gulf of Mexico meets the Caribbean Sea. The aggregation remains in the nutrient-rich waters off Isla Holbox, Isla Contoy and Isla Mujeres, Quintana Roo for several months in the summer and then dissipates between August and October. Little has been known about where these sharks come from or migrate to after they disperse. From 2003-2012, we used conventional visual tags, photo-identification, and satellite tags to characterize the basic population structure and large-scale horizontal movements of whale sharks that come to this feeding area off Mexico. The aggregation comprised sharks ranging 2.5-10.0 m in total length and included juveniles, subadults, and adults of both sexes, with a male-biased sex ratio (72{\%}). Individual sharks remained in the area for an estimated mean duration of 24-33 days with maximum residency up to about 6 months as determined by photo-identification. After leaving the feeding area the sharks showed horizontal movements in multiple directions throughout the Gulf of Mexico basin, the northwestern Caribbean Sea, and the Straits of Florida. Returns of individual sharks to the Quintana Roo feeding area in subsequent years were common, with some animals returning for six consecutive years. One female shark with an estimated total length of 7.5 m moved at least 7,213 km in 150 days, traveling through the northern Caribbean Sea and across the equator to the South Atlantic Ocean where her satellite tag popped up near the Mid-Atlantic Ridge. We hypothesize this journey to the open waters of the Mid-Atlantic was for reproductive purposes but alternative explanations are considered. The broad movements of whale sharks across multiple political boundaries corroborates genetics data supporting gene flow between geographically distinct areas and underscores the need for management and conservation strategies for this species on a global scale.}, author = {Hueter, Robert E. and Tyminski, John P. and de la Parra, Rafael}, doi = {10.1371/journal.pone.0071883}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hueter, Tyminski, de la Parra - 2013 - Horizontal movements, migration patterns, and population structure of whale sharks in the Gulf of.pdf:pdf}, issn = {19326203}, journal = {PloS one}, pmid = {23991000}, title = {{Horizontal movements, migration patterns, and population structure of whale sharks in the Gulf of Mexico and Northwestern Caribbean Sea}}, volume = {8}, year = {2013} } @article{Pauly1995, abstract = {Mention of Shifting Baseline Syndrome, suggesting to include anecdotal evidence in systematizing baselines.}, author = {Pauly, D}, doi = {10.1016/S0169-5347(00)89171-5}, isbn = {0169-5347}, issn = {01695347}, journal = {Trends in ecology {\&} evolution (Personal edition)}, pages = {430}, pmid = {21237093}, title = {{Anecdotes and the shifting baseline syndrome of fisheries.}}, volume = {10}, year = {1995} } @article{Stuart-Smith2015, annote = {-Agree that evenness is of limited value for conservation -State that evenness patterns were presented to provide context to FD patterns (however, in the paper they claim this evenness pattern is a new discovery) -reconginize that constraits on evennness are well known -make a good point about the simulations that had species counts higher than number of individuals counted -Claim out assumption of a SAD shape being universally consistent hurts our case --We held the SAD shape constant witihin each set of simulations -Feel Robinson et al have no clear evidence to support idea that methods were flawed b/c of poor detectability --Robinson et al used data from papers that used different sampling sizes --Robinson's evidence that video surveys increase diversity measures is rebutted -Agree that areas in polar regions may never reach threshold identified by Robinson et al --{\textgreater} this seems to support some of our point}, author = {Stuart-Smith, Rick D. and Bates, Amanda E. and Lefcheck, Jonathan S. and {Emmett Duffy}, J. and Baker, Susan C. and Thomson, Russell J. and Stuart-Smith, Jemina F. and Hill, Nicole a. and Kininmonth, Stuart J. and Airoldi, Laura and Becerro, Mikel a. and Campbell, Stuart J. and Dawson, Terence P. and Navarrete, Sergio a. and Soler, German and Strain, Elisabeth M.a. and Willis, Trevor J. and Edgar, Graham J.}, doi = {10.1016/j.marpol.2014.07.002}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stuart-Smith et al. - 2015 - The potential of trait-based approaches to contribute to marine conservation.pdf:pdf}, issn = {0308597X}, journal = {Marine Policy}, keywords = {Evenness,Functional diversity,Macroecology,Marine fish,Reef ecosystems,Underwater visual census (UVC),evenness,functional diversity,uvc}, mendeley-tags = {evenness,functional diversity,uvc}, month = {jan}, pages = {148--150}, publisher = {Elsevier}, title = {{The potential of trait-based approaches to contribute to marine conservation}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0308597X14001766}, volume = {51}, year = {2015} } @article{Levins1966, annote = {We cannot study complicated, realistic models as they end up telling us very little. There are some alternative strategies: 1) "sacrifice generality to realism and precision" 2) "sacrifice realism to generality and precision" 3) "sacrifice precision to realism and generality"- more converned with qualitive results - a super complicated model would have too many parameters to estimate and the results would be meaningless -does not view models as a hypothesis nor a theory - it cannot be directly verified by experiment -we don't care if a model is true, only that is generates good testable hypotheses -How sensitive are the results to the model specifications?}, author = {Levins, Richard}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levins - 1966 - The strategy of model building in population biology.pdf:pdf}, journal = {American Scientist}, keywords = {model,population}, mendeley-tags = {model,population}, number = {4}, pages = {421--431}, title = {{The strategy of model building in population biology}}, volume = {54}, year = {1966} } @article{Arias2014, author = {Arias, Adrian and Pressey, Robert L. and Jones, Rhondda E. and Alvarez-Romero, Jorge G. and Cinner, Joshua E.}, doi = {10.1017/S0030605314000337}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Arias et al. - 2014 - Optimizing enforcement and compliance in offshore marine protected areas a case study from Cocos Island, Costa Ric.pdf:pdf}, journal = {Oryx}, keywords = {cocos,cocos island,conservation,costa rica,elasmobranch,illegal fi shing,lining,long-,lunar phase,marine reserve,mpa,patrol,poaching}, mendeley-tags = {cocos,conservation,elasmobranch,mpa}, pages = {1--9}, title = {{Optimizing enforcement and compliance in offshore marine protected areas: a case study from Cocos Island, Costa Rica}}, year = {2014} } @article{Lea2000, abstract = {From mid-1997 through 1998, anomalously warm water occurred off the California coast as part of the more global El Niiio phenomenon of 1997-98. Warm- water periods of comparable magnitude were observed in 1957-59 and 1982-84; this most recent event may in fact be the strongest of the three. Biological evidence supporting the impact of this phenomenon was noted in a northern latitudinal shift in the range of a number of eastern tropical Pacific fishes into the warni-temper- ate waters of southern California. Families of fishes rep- resented include Carcharhinidae, Sphyrnidae, Elopidae, Albulidae, Ophichthidae, Clupeidae, Synodontidae, Fistulariidae, Scorpaenidae, Triglidae, Serranidae, Apogo- nidae, Carangidae, Lobotidae, Mulbdae, Chaetodontidae, Pomacanthidae, Pomacentridae, Sphyraenidae, Polyne- midae, Labridae, Scaridae, Blenniidae, Callionymidae, Gobiidae, Trichiuridae, Bothidae, Tetraodontidae, and Diodontidae. Of particular significance are the follow- ing new California records of Panamic species: Fistularia covneta, deepwater cornetfish; Diplectvum maximum, greater sand perch; Apogon paclficus, pink cardinalfish; Caranx vinctus, cocinero; Sphyraena ensis, Mexican barracuda; Decodon melasma, blackspot wrasse; Nicholsina denticulata, loosetooth parrotfish; Plagiotremus azaleus, sabertooth blenny; Synchiropus atrilabiatus, blacklip dragonet; and Engyophrys sanctilaurentii, speckled-tail flounder. Several species taken had not been reported since the Pacific Railroad Survey of the 1850s or the early 1900s (e.g., threebanded butterflyfish and longtail goby). Addtionally, several species heretofore known from single or a few records were taken on multiple occasions and in some numbers. Differences between the 1997-98 and previ- ous El Niiio events and a measure of the intensity of this event are discussed. Changes in the ichthyofauna of California during the most recent El Niiio were perhaps the most dramatic of the twentieth century.}, author = {Lea, Robert N. and Rosenblatt, Richard H.}, isbn = {0575-3317}, issn = {0575-3317}, journal = {CalCOFI Reports}, pages = {117--129}, title = {{Observations on fishes associated with the 1997-98 El Nino off California}}, volume = {41}, year = {2000} } @book{Hastie, author = {Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome}, edition = {2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hastie, Tibshirani, Friedman - Unknown - The Elements of Statisitical Learning.pdf:pdf}, title = {{The Elements of Statisitical Learning}} } @techreport{NationalOceanicandAtmosphericAdministration2014, author = {NOAA}, institution = {National Oceanic and Atmospheric Administration}, pages = {38213 --38242}, title = {{Endangered and threatened wildlife and plants; threatened and endangered status for distinct population segments of scalloped hammerhead sharks}}, url = {https://federalregister.gov/a/2014-15710}, year = {2014} } @misc{Norman2007, address = {Australia}, author = {Norman, Brad and Catlin, James}, booktitle = {Report for the international fund for animal welfare (IFAW)}, publisher = {Report for the international fund for animal welfare (IFAW)}, title = {{Economic importance of conserving whale sharks}}, year = {2007} } @article{Dulvy2014, author = {Dulvy, Nicholas K. and Pardo, Sebastian A. and Simpfendorfer, Colin A. and Carlson, John K.}, journal = {PeerJ}, pages = {e400}, title = {{Diagnosing the dangerous demography of manta rays using life history theory}}, volume = {2}, year = {2014} } @article{Heithaus2001, abstract = {Tiger sharks, Galeocerdo cuvier, are apex predators in a variety of nearshore ecosystems throughout the world. This study investigates the biology of tiger sharks in the shallow seagrass ecosystem of Shark Bay, Western Australia. Tiger sharks (n D 252) were the most commonly caught species (94{\%}) compared to other large sharks. Tiger sharks ranged from 148–407 cm TL. The overall sex ratio was biased towards females (1.8 : 1), but the sex ratio of mature animals ({\textgreater} 300 cm TL) did not differ from 1 : 1. Contrary to previous accounts, tiger sharks were caught more often in all habitats during daylight hours than at night. Tiger shark catch rates were highly correlated with water temperature and were highest when water temperatures were above 19 C. The seasonal abundance of tiger sharks is correlated to both water temperature and the occurrence of their main prey: sea snakes and dugongs, Dugong dugon. Stomach contents analysis indicated that sea turtles and smaller elasmobranchs were also common prey. The importance of major seagrass grazers (dugongs and green sea turtles, Chelonia mydas) in the diet of tiger sharks suggests the possibility that these sharks are keystone predators in this ecosystem.}, author = {Heithaus, Michael R.}, doi = {10.1023/A:1011021210685}, isbn = {0378-1909}, issn = {03781909}, journal = {Environmental Biology of Fishes}, keywords = {Dugong,Keystone predator,Predation,Predator-prey interactions,Prey availability,Sea turtle}, pages = {25--36}, title = {{The biology of tiger sharks, Galeocerdo cuvier, in Shark Bay, Western Australia: Sex ratio, size distribution, diet, and seasonal changes in catch rates}}, volume = {61}, year = {2001} } @article{Goffredo2010, abstract = {Institutes often lack funds and manpower to perform large-scale biodiversity monitoring. Citizens can be involved, contributing to the collection of data, thus decreasing costs. Underwater research requires specialist skills and SCUBA certification, and it can be difficult to involve volunteers. The aim of this study was to involve large numbers of recreational divers in marine biodiversity monitoring for increasing the environmental education of the public and collecting data on the status of marine biodiversity. Here we show that thousands of recreational divers can be enrolled in a short time. Using specially formulated questionnaires, nonspecialist volunteers reported the presence of 61 marine taxa encountered during recreational dives, performed as regular sport dives. Validation trials were carried out to assess the accuracy and consistency of volunteer-recorded data, and these were compared to reference data collected by an experienced researcher. In the majority of trials (76{\%}) volunteers performed with an accuracy and consistency of 50-80{\%}, comparable to the performance of conservation volunteer divers on precise transects in other projects. The recruitment of recreational divers involved the main diving and tour operators in Italy, a popular scientific magazine, and mass media. During the four-year study, 3825 divers completed 18757 questionnaires, corresponding to 13539 diving hours. The volunteer-sightings-based index showed that in the monitored area the biodiversity status did not change significantly within the project time scale, but there was a significant negative correlation with latitude, suggesting improved quality in the southernmost areas. This trend could be related to the presence of stressors in the northern areas and has been supported by investigations performed by the Italian Ministry of the Environment. The greatest limitation with using volunteers to collect data was the uneven spatial distribution of samples. The benefits were the considerable amounts of data collected over short time periods and at low costs. The successful development of citizen-based monitoring programs requires open-mindedness in the academic community; advantages of citizen involvement in research are not only adding large data sets to the ecological knowledge base but also aiding in the environmental education of the public.}, author = {Goffredo, Stefano and Pensa, Francesco and Neri, Patrizia and Orlandi, Antonio and Gagliardi, Maria Scola and Velardi, Angela and Piccinetti, Corrado and Zaccanti, Francesco}, doi = {10.1890/09-1546.1}, isbn = {1051-0761}, issn = {1051-0761}, journal = {Ecological Applications}, pages = {2170--2187}, pmid = {21265450}, title = {{Unite research with what citizens do for fun: "recreational monitoring" of marine biodiversity}}, volume = {20}, year = {2010} } @misc{Skaug2012, author = {Skaug, H and Fournier, D and Nielsen, A and Magnusson, A and Bolker, B}, publisher = {R package version 0.7.7}, title = {{Generalized linear mixed models using AD Model Builder}}, year = {2012} } @article{Gallagher2014a, abstract = {In many fisheries, some component of the catch is usually released. Quantifying the effects of capture and release on fish survival is critical for determining which practices are sus- tainable, particularly for threatened species. Using a standardized fishing technique, we studied sublethal (blood physiology and reflex impairment assessment) and lethal (post-release mortality with satellite tags) outcomes of fishing stress on 5 species of coastal sharks (great hammerhead, bull, blacktip, lemon, and tiger). Species-specific differences were detected in whole blood lactate, partial pressure of carbon dioxide, and pH values, with lactate emerging as the sole parameter to be significantly affected by increasing hooking duration and shark size. Species-spe- cific differences in reflex impairment were also found; however, we did not detect any significant relationships between reflex impairment and hooking duration. Taken together, we ranked each species according to degree of stress response, from most to least disturbed, as follows: hammer- head shark {\textgreater} blacktip shark {\textgreater} bull shark {\textgreater} lemon shark {\textgreater} tiger shark. Satellite tagging data revealed that nearly 100{\%} of all tracked tiger sharks reported for at least 4 wk after release, which was significantly higher than bull (74.1{\%}) and great hammerhead (53.6{\%}) sharks. We discuss which mechanisms may lead to species-specific differences in sensitivity to fishing and suggest that observed variation in responses may be influenced by ecological and evolutionary phenom- ena. Moreover, our results show that certain species (i.e. hammerhead sharks in this study) are inherently vulnerable to capture stress and mortality resulting from fisheries interactions and should receive additional attention in future conservation strategies.}, author = {Gallagher, AJ and Serafy, JE and Cooke, SJ and Hammerschlag, N}, doi = {10.3354/meps10490}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, keywords = {Stress {\textperiodcentered} Physiology {\textperiodcentered} Vulnerability {\textperiodcentered} Fishing {\textperiodcentered} An}, pages = {207--218}, title = {{Physiological stress response, reflex impairment, and survival of five sympatric shark species following experimental capture and release}}, url = {http://www.int-res.com/abstracts/meps/v496/p207-218/}, volume = {496}, year = {2014} } @article{Hayes2009, author = {Hayes, Christopher G. and Jiao, Yan and Cort{\'{e}}s, Enric}, journal = {North American Journal of Fisheries Management}, number = {5}, pages = {1406--1417}, title = {{Stock assessment of scalloped hammerheads in the western North Atlantic Ocean and Gulf of Mexico}}, volume = {29}, year = {2009} } @article{Simpfendorfer2001, abstract = {Stomach contents from tiger sharks, Galeocerdo cuvier, caught on lines off the central coast of Western Australia were analysed to investigate variations in the diet due to sex, size and geographic location. Stomachs from 84 specimens contained food, while 26 had empty stomachs and 66 had regurgitated.Twelve prey groups were identified, the most common being turtles, sea snakes, teleost fishes, dugongs and sea birds. Dietary overlap was high between males and females. An ontogenetic shift was observed in the diet. Smaller prey (e.g. cephalopods, teleosts and sea snakes) were more common in small individuals, while the occurrence of larger prey (e.g. turtles, dugongs and elasmobranchs) increased with increasing shark size. Differences in the diet were observed between four regions along the centralWestern Australian coast. The ability to catch and consume large prey, prey availability, prey density, and prey profitability were identified as factors influencing the diet. The high level of occurrence of dugongs and turtles in the diet of G. cuvier, relative to their abundance, suggests that shark predation may play an important role in regulating populations of these species.}, author = {Simpfendorfer, Colin A. and Goodreid, Adrian B. and Mcauley, Rory B.}, doi = {10.1023/A:1011021710183}, isbn = {0378-1909}, issn = {03781909}, journal = {Environmental Biology of Fishes}, keywords = {Dugong,Fishery interaction,Ontogenetic dietary shift,Prey diversity,Turtle}, pages = {37--46}, title = {{Size, sex and geographic variation in the diet of the tiger shark, Galeocerdo cuvier, from Western Australian waters}}, volume = {61}, year = {2001} } @misc{Barton2013, author = {Barto{\'{n}}, Kamil}, title = {{MuMIn: Multi-model inference. R package version 1.9.13}}, year = {2013} } @article{Friedlander2012, author = {Friedlander, Alan M and Zgliczynski, Brian J and Ballesteros, Enric and Aburto-Oropeza, Octavio and Bola{\~{n}}os, Allan and Sala, Enric}, journal = {Revista de Biologia Tropical}, pages = {321--338}, title = {{The shallow-water fish assemblage of Isla del Coco National Park, Costa Rica: structure and patterns in an isolated, predator-dominated ecosystem}}, volume = {60}, year = {2012} } @article{Bradshaw2008, author = {Bradshaw, Corey J.A. and Fitzpatrick, Ben M. and Steinberg, Craig C. and Brook, Barry W. and Meekan, Mark G.}, journal = {Biological Conservation}, number = {7}, pages = {1894--1905'}, title = {{Decline in whale shark size and abundance at Ningaloo Reef over the past decade: the world's largest fish is getting smaller}}, volume = {141}, year = {2008} } @techreport{Baum2007, author = {Baum, J. and Clarke, S. and Domingo, A. and Ducrocq, M. and Lam{\'{o}}naca, A.F. and Gaibor, N. and Graham, R. and Jorgensen, S. and Kotas, J.E. and Medina, E. and Martinez-Ortiz, J. and {Monzini Taccone di Sitizano}, J. and Morales, M.R. and Navarro, S.S. and P{\'{e}}rez-Jim{\'{e}}nez, J.C. and {Ruiz, C., Smith}, W. and Valenti, S.V. and Vooren, C.M.}, title = {{Sphyrna lewini. The IUCN Red List of Threatened Species. Version 2014.1}}, year = {2007} } @article{Costa2012, author = {Costa, Daniel P. and Breed, Greg A. and Robinson, Patrick W.}, journal = {Annual Review of Ecology, Evolution, and Systematics}, pages = {73--96}, title = {{New insights into pelagic migrations: implications for ecology and conservation}}, volume = {43}, year = {2012} } @article{Speed2010a, author = {Speed, Conrad W. and Field, Iain C. and Meekan, Mark G. and Bradshaw, Corey}, journal = {Marine Ecology Progress Series}, pages = {275--293}, title = {{Complexities of coastal shark movements and their implications for management}}, volume = {408}, year = {2010} } @incollection{Hoyt2014, address = {New York}, author = {Hoyt, Erich}, booktitle = {Sharks: Conservation, Governance and Management}, editor = {Techera, Erika J. and Klein, Natalie}, pages = {263}, publisher = {Routledge}, title = {{The role of marine protected areas and sanctuaries}}, year = {2014} } @article{Heupel2010, author = {Heupel, Michelle R. and Simpfendorfer, Colin A. and Fitzpatrick, Richard}, journal = {PloS One}, number = {3}, pages = {e9650}, title = {{Large-scale movement and reef fidelity of grey reef sharks}}, volume = {5}, year = {2010} } @article{Musick2000, author = {Musick, J.A. and Buggess, G. and Cailliet, G. and Camhi, M. and Fordham, S.}, journal = {Fisheries}, number = {3}, pages = {9--13}, title = {{Management of sharks and their relatives (Elasmobranchii)}}, volume = {25}, year = {2000} } @book{Allan1996, author = {Allan, R. and Lindesay, J. and Parker, D.}, pages = {416}, publisher = {CSIRO Publishing}, title = {{El Nino: Southern Oscillation and Climatic Variability}}, year = {1996} } @article{Dulvy2013a, author = {Dulvy, Nicholas K.}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, number = {3}, pages = {357--362}, title = {{Super-sized MPAs and the marginalization of species conservation}}, volume = {23}, year = {2013} } @phdthesis{Stump2013, author = {Stump, Kristine L}, pages = {173}, school = {University of Miami}, title = {{The effects of nursery habitat loss on juvenile lemon sharks, Negaprion brevirostris}}, year = {2013} } @article{Gallagher2014, author = {Gallagher, a. J. and Hammerschlag, N. and Shiffman, D. S. and Giery, S. T.}, doi = {10.1093/biosci/biu071}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Gallagher et al. - 2014 - Evolved for Extinction The Cost and Conservation Implications of Specialization in Hammerhead Sharks.pdf:pdf}, issn = {0006-3568}, journal = {BioScience}, keywords = {2011,and these removals can,anthropogenic disturbance,apex predator,argued that the loss,consumers is the most,estes et al,evolution,of apex,on,pervasive impact of humankind,specialization,t has recently been,the natural world,vulnerability}, month = {may}, number = {X}, pages = {1--6}, title = {{Evolved for Extinction: The Cost and Conservation Implications of Specialization in Hammerhead Sharks}}, url = {http://bioscience.oxfordjournals.org/cgi/doi/10.1093/biosci/biu071}, volume = {XX}, year = {2014} } @article{Cortes2012, author = {Cort{\'{e}}s, Jorge}, journal = {Revista de Biologia Tropical}, pages = {131--185}, title = {{Marine biodiversity of an Eastern Tropical Pacific oceanic island, Isla del Coco, Costa Rica}}, volume = {60}, year = {2012} } @book{Glynn1990, author = {Glynn, Peter W.}, publisher = {Elsevier}, title = {{Global ecological consequences of the 1982-83 El Nino-southern oscillation}}, year = {1990} } @article{DeMartini2008, abstract = {biodiversity, pristine, cocos}, annote = {On pristine coral reefs in the northern Line Islands, large-bodied predators are higher in abundance compared to exploitated reefs. }, author = {DeMartini, Edward E and Friedlander, Alan M and Sandin, Stuart A and Sala, Enric}, doi = {10.3354/meps07501}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/DeMartini et al. - 2008 - Differences in fish-assemblage structure between fished and unfished atolls in the northern Line Islands, cent.pdf:pdf}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, keywords = {apex predation,biodiversity,body size at sex,change,cocos,fisheries extraction,inverted biomass,latitudinal gradient,of the publisher,parrotfishes,permitted without written consent,prey body size distribution,pristine,pyramid,resale or republication not,upwelling}, mendeley-tags = {biodiversity,cocos,pristine}, month = {aug}, pages = {199--215}, title = {{Differences in fish-assemblage structure between fished and unfished atolls in the northern Line Islands, central Pacific}}, url = {http://www.int-res.com/abstracts/meps/v365/p199-215/}, volume = {365}, year = {2008} } @article{Sandin2008, abstract = {Effective conservation requires rigorous baselines of pristine conditions to assess the impacts of human activities and to evaluate the efficacy of management. Most coral reefs are moderately to severely degraded by local human activities such as fishing and pollution as well as global change, hence it is difficult to separate local from global effects. To this end, we surveyed coral reefs on uninhabited atolls in the northern Line Islands to provide a baseline of reef community structure, and on increasingly populated atolls to document changes associated with human activities. We found that top predators and reef-building organisms dominated unpopulated Kingman and Palmyra, while small planktivorous fishes and fleshy algae dominated the populated atolls of Tabuaeran and Kiritimati. Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy). In contrast, the biomass pyramid at Tabuaeran and Kiritimati exhibited the typical bottom-heavy pattern. Reefs without people exhibited less coral disease and greater coral recruitment relative to more inhabited reefs. Thus, protection from overfishing and pollution appears to increase the resilience of reef ecosystems to the effects of global warming.}, annote = {Baseline data are lacking in most systems. Pristine areas, or aras that have been protected, may provide baseline data that can be used to see the effect of humans on other areas. The Northern Line Islands present at opportunity to study pristine and non-pristine coral reefs. Apex predators were particuraly high in abundance at pristine reefs. }, author = {Sandin, Stuart A and Smith, Jennifer E and Demartini, Edward E and Dinsdale, Elizabeth A and Donner, Simon D and Friedlander, Alan M and Konotchick, Talina and Malay, Machel and Maragos, James E and Obura, David and Pantos, Olga and Paulay, Gustav and Richie, Morgan and Rohwer, Forest and Schroeder, Robert E and Walsh, Sheila and Jackson, Jeremy B C and Knowlton, Nancy and Sala, Enric}, doi = {10.1371/journal.pone.0001548}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sandin et al. - 2008 - Baselines and degradation of coral reefs in the Northern Line Islands.pdf:pdf}, issn = {1932-6203}, journal = {PloS ONE}, keywords = {Animals,Anthozoa,Biomass,Conservation of Natural Resources,Ecosystem,Eukaryota,Fishes,Geography,Greenhouse Effect,Water Pollutants}, month = {jan}, number = {2}, pages = {e1548}, pmid = {18301734}, title = {{Baselines and degradation of coral reefs in the Northern Line Islands.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2244711{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {3}, year = {2008} } @book{Ambrose2010, address = {San Francisco, CA}, annote = {Introduction Chapter 1: Student's Prior Knowledge: -There is often a mismatch between what students know and what professors expect them to know -Prior knowledge, that is incorrect, can also hurt a student's ability to learn something new -Therefore, student's prior knowledge ca either help or hinder learning -Prior knowledge (that is accurate and relvent) can be leveraged by an instructor to allow students to make new connections, this allows them to learn and retain more information -different types of knowledge --declarative knowledge- knowledge of facts or concepts that can be stated --procedural knowledge- knowing how and when to apply different procedures, theories, or styles -difference between knowing what versus how or when- important for instructors to keep this in mind -prior information, even when accurate, can hinder if it is not used in the correct context -inaccruate information or misconceptions may make students less willing to accept to evidence -a number of tools/approaches are available to overcome or use prior knowledge of students Chapter 2 (Organizing knowledge): -if you don't have a organizing structure for the material you are learning it impedes learning -difficult to learn with many isolated facts -need many connections between facts and ideas -want to organize book or course according to a framework designed around your learning objectives -Experts organize their knowledge according to a density of connections among different facts or skills -{\textgreater} allows knowledge to be accessed and used more effiently -need to be able to recongnize meaningful patterns -it can help a student if future problems if they can expalin how an already solved problem was derived Strategies: -create a concept map to organize your own knowledge -ask students different types of tasks or questions to see how many ways they have organized the material -provide students with the organizational structure of the course (and refer back to the material- could even go back to the same slide multiple times in the semester) -can help to explain the deeper connections or relationships between ideas -ask students to draw concept maps Chapter 3 (Motivation in learning): -students are not always motivated the same way as their professors -two key components to motivation: 1) subjective value of a goal 2) expecations for success of that goal -goals serve as a compass for actions and reasons for motivation or lack there of -often a mismatch of goals for students versus professors expectations of them -learning versus performance (grade) goals -if an acitivty satisfies more than one goal-{\textgreater} may result in better motivation -Value- a goal's importance (attainment value- satiffaction from mastery or accomplishment, intrinisic value- satisfaction one gains from simply doing a given task regardless of outcome, instrumental value- degree to which goal may help in accomplishing other important goals) -Expectancies- people want some idea that they can actually achieve the goals set forth for them --e.g. Gould said if you work hard, you will get an A, he was right. Kostelich was also encouraging --Need to believe you can do it (that is why early success is so important) --it is also important to identify the reasons for past success of failures -Classroom has to be a supportive and approachable place for students to be motivated -Three important components of motivation (value, expectations, the environment) -Combinations of these three switches may work better or worse for different students, but you do need all three in order for students to have success Strategies: For adding value: -connect material to students interests -provide authentic, real-world tasks -connect material to other courses or other material -explain how a particular skill can help in a student's future profession (explain why writing ability is important in lab reports) -identifiy and reward what you value as an instructor -share you own passion and enthusiasm!!!! For expectations: -ensure alignment of objectives and assessements of those objectives -need challenging but attainable goals -tell your students your expectations of them -provide feedback that is constructive -desribe effective study strategies -allow students to choose among many options (they can own it then) -make sure students have chance to reflect Chapter 4: developing mastery - students must develop component skills, practice integrating them, and know when to apply the skills}, author = {Ambrose, Susan A and Bridges, Michael W and Dipietro, Michele and Lovett, Marsha C and Norman, Marie K}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ambrose et al. - 2010 - How Learning Works 7 Research-Based Principles for Smart Teaching.pdf:pdf}, isbn = {9780470484104}, keywords = {education,software carpentry}, mendeley-tags = {education,software carpentry}, pages = {301}, publisher = {John Wiley and Sons}, title = {{How Learning Works: 7 Research-Based Principles for Smart Teaching}}, year = {2010} } @misc{Team2013, address = {Vienna, Austria}, author = {{R Development Core Team}}, publisher = {R Foundation for Statistical Computing}, title = {{R: A language and environment for statistical computing}}, url = {http://www.r-project.org/}, year = {2013} } @article{Garla2006, abstract = {The movement patterns and long-term site-fidelity of primarily juvenile Caribbean reef sharks, Carcharhinus perezi, were investigated using tag-recapture and automated telemetry at an insular nursery area, the Fernando de Noronha Archipelago, Brazil. Of the 143 externally tagged juvenile sharks ({\textless} 110 cm), 22 (15.3{\%}) were recaptured between 0 and 5 km from the site of tagging after 5-800 days at liberty, suggesting some site-fidelity in young individuals of this species. Site-fidelity and movement patterns of ten juvenile sharks ranging from 78 to 110 cm total length (TL) and one opportunistically captured adult female (224 cm TL) were also investigated for periods of up to 2 years with an array of automated telemetry receivers. Tagging and telemetry data from both inside and outside a marine protected area (MPA) show that shark abundance and activity is greatest along the part of the archipelago's coastline least disturbed by human activity. Telemetry tracking also showed that juvenile reef sharks demonstrated a high degree of site-fidelity and occupied specific locations along the coast throughout the year, with some evidence of an increase in activity space with ontogeny. Sharks appeared to range more widely at night and there were no seasonal variations in habitat use. Our results suggest that MPAs may be a useful conservation tool to protect young C. perezi and potentially other reef-dwelling carcharhinid sharks during their early life history.}, author = {Garla, Ricardo C. and Chapman, Demian D. and Wetherbee, Bradley M. and Shivji, Mahmood}, doi = {10.1007/s00227-005-0201-4}, isbn = {0025-3162}, issn = {00253162}, journal = {Marine Biology}, pages = {189--199}, pmid = {9027588}, title = {{Movement patterns of young Caribbean reef sharks, Carcharhinus perezi, at Fernando de Noronha Archipelago, Brazil: The potential of marine protected areas for conservation of a nursery ground}}, volume = {149}, year = {2006} } @article{Lucifora2011, annote = {-describe a new database for sharks around the world and show distributions of richness, functional diversity, and endemism to identify shark hotspots}, author = {Lucifora, Luis O and Garc{\'{i}}a, Ver{\'{o}}nica B and Worm, Boris}, doi = {10.1371/Citation}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lucifora, Garc{\'{i}}a, Worm - 2011 - Global Diversity Hotspots and Conservation Priorities for Sharks.pdf:pdf}, journal = {PloS ONE}, keywords = {conservation,diversity,elasmobranch}, mendeley-tags = {conservation,diversity,elasmobranch}, number = {5}, pages = {e19356}, title = {{Global Diversity Hotspots and Conservation Priorities for Sharks}}, volume = {6}, year = {2011} } @book{Compagno2005, address = {Princeton, New Jersey}, author = {Compagno, Leonard J V and Dando, Marc and Fowler, Sarah}, keywords = {elasmobranch}, mendeley-tags = {elasmobranch}, pages = {268}, publisher = {Princeton University Press}, title = {{Sharks of the World}}, year = {2005} } @article{Prugh2009, author = {Prugh, Laura R. and Stoner, Chantal J. and Epps, Clinton W. and Bean, William T. and Ripple, William J. and Laliberte, Andrea S. and Brashares, Justin S.}, doi = {10.1525/bio.2009.59.9.9}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Prugh et al. - 2009 - The Rise of the Mesopredator.pdf:pdf}, issn = {0006-3568}, journal = {BioScience}, keywords = {indirect effects,intraguild predation,mesocarnivore,mesocarnivore release,predation,trophic cascades}, mendeley-tags = {predation}, month = {oct}, number = {9}, pages = {779--791}, title = {{The Rise of the Mesopredator}}, url = {http://www.jstor.org/stable/27735987}, volume = {59}, year = {2009} } @misc{IUCN2013, author = {IUCN}, pages = {Version 2013.2}, title = {{The IUCN Red List of Threatened Species}}, url = {http://www.iucnredlist.org}, year = {2013} } @misc{Lockhart, author = {Lockhart, Paul}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lockhart - Unknown - A Mathematician's Lament.pdf:pdf}, title = {{A Mathematician's Lament}} } @article{Watson2009, abstract = {Bycatch--the incidental catch of nontarget species--is a principal concern in marine conservation and fisheries management. In the eastern Pacific Ocean tuna fishery, a large fraction of nonmammal bycatch is captured by purse-seine gear when nets are deployed around floating objects. We examined the spatial distribution of a dominant species in this fishery's bycatch, the apex predator silky shark (Carcharhinus falciformis), from 1994 to 2005 to determine whether spatial closures, areas where fishing is prohibited, might effectively reduce the bycatch of this species. We then identified candidate locations for fishery closures that specifically considered the trade-off between bycatch reduction and the loss of tuna catch and evaluated ancillary conservation benefits to less commonly captured taxa. Smoothed spatial distributions of silky shark bycatch did not indicate persistent small areas of especially high bycatch for any size class of shark over the 12-year period. Nevertheless, bycatch of small silky sharks ({\textless}90 cm total length) was consistently higher north of the equator during all years. On the basis of this distribution, we evaluated nearly 100 candidate closure areas between 5°N and 15°N that could have reduced, by as much as 33{\%}, the total silky shark bycatch while compromising only 12{\%} of the tuna catch. Although silky sharks are the predominant species of elasmobranchs caught as bycatch in this fishery, closures also suggested reductions in the bycatch of other vulnerable taxa, including other shark species and turtles. Our technique provides an effective method with which to balance the costs and benefits of conservation in fisheries management. Spatial closures are a viable management tool, but implementation should be preceded by careful consideration of the consequences of fishing reallocation.}, author = {Watson, Jordan T and Essington, Timothy E and Lennert-Cody, Cleridy E and Hall, Martin A}, doi = {10.1111/j.1523-1739.2008.01121.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Watson et al. - 2009 - Trade-offs in the design of fishery closures management of silky shark bycatch in the eastern Pacific Ocean tuna.pdf:pdf}, issn = {1523-1739}, journal = {Conservation Biology}, keywords = {Animals,Conservation of Natural Resources,Conservation of Natural Resources: methods,Demography,Fisheries,Fisheries: methods,Fisheries: statistics {\&} numerical data,Geography,Models,Pacific Ocean,Sharks,Sharks: growth {\&} development,Species Specificity,Theoretical,Tuna}, month = {jun}, number = {3}, pages = {626--35}, pmid = {19040650}, title = {{Trade-offs in the design of fishery closures: management of silky shark bycatch in the eastern Pacific Ocean tuna fishery}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19040650}, volume = {23}, year = {2009} } @article{Ward-Paige2010a, abstract = {BACKGROUND: In recent decades, large pelagic and coastal shark populations have declined dramatically with increased fishing; however, the status of sharks in other systems such as coral reefs remains largely unassessed despite a long history of exploitation. Here we explore the contemporary distribution and sighting frequency of sharks on reefs in the greater-Caribbean and assess the possible role of human pressures on observed patterns. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed 76,340 underwater surveys carried out by trained volunteer divers between 1993 and 2008. Surveys were grouped within one km2 cells, which allowed us to determine the contemporary geographical distribution and sighting frequency of sharks. Sighting frequency was calculated as the ratio of surveys with sharks to the total number of surveys in each cell. We compared sighting frequency to the number of people in the cell vicinity and used population viability analyses to assess the effects of exploitation on population trends. Sharks, with the exception of nurse sharks occurred mainly in areas with very low human population or strong fishing regulations and marine conservation. Population viability analysis suggests that exploitation alone could explain the large-scale absence; however, this pattern is likely to be exacerbated by additional anthropogenic stressors, such as pollution and habitat degradation, that also correlate with human population. CONCLUSIONS/SIGNIFICANCE: Human pressures in coastal zones have lead to the broad-scale absence of sharks on reefs in the greater-Caribbean. Preventing further loss of sharks requires urgent management measures to curb fishing mortality and to mitigate other anthropogenic stressors to protect sites where sharks still exist. The fact that sharks still occur in some densely populated areas where strong fishing regulations are in place indicates the possibility of success and encourages the implementation of conservation measures.}, annote = {Data are lacking for shark species that are reef-associated as these areas are often not exploitated by commercial fisheries but artisinal fisheries instead dominate. Diver collectd data is a reliable technique to examine trends in relative shark abundance. Using a large diver collected data set, the authors show how shark species are more rare in the Caribbean than they should be. -good citations -intrinsic rate of increase calculations}, author = {Ward-Paige, Christine A and Mora, Camilo and Lotze, Heike K and Pattengill-Semmens, Christy and McClenachan, Loren and Arias-Castro, Ery and Myers, Ransom A}, doi = {10.1371/journal.pone.0011968}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ward-Paige et al. - 2010 - Large-scale absence of sharks on reefs in the greater-Caribbean a footprint of human pressures.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {Animals,Anthozoa,Caribbean Region,Data Collection,Human Activities,Population Density,Sharks,citizen science,cocos,elasmobranch,extinction}, mendeley-tags = {citizen science,cocos,elasmobranch,extinction}, month = {jan}, number = {8}, pages = {e11968}, pmid = {20700530}, title = {{Large-scale absence of sharks on reefs in the greater-Caribbean: a footprint of human pressures}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2916824{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {5}, year = {2010} } @article{Davidson2012, author = {Davidson, Lindsay N. K.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Davidson - 2012 - Shark sanctuaries substance or spin.pdf:pdf}, journal = {Science}, pages = {1538}, title = {{Shark sanctuaries: substance or spin?}}, volume = {334}, year = {2012} } @article{Graham2010, annote = {Although many declines of sharks and rays have been reported, few studies have examined remote coral reef locations. It is often assumed that these areas represent pristine areas and are often compared to heavily exploited areas. However, temporal analyses are needed to actually assess the status of many shark and ray populations. Graham et al 2010 use a time series from 1975 to 2006 at a remote island in the central Indian Ocean. The data consists of five scientific expeditions in which reef shark abundance was estimated per dive. The relative abundnace of reef sharks at the island has declined by 90{\%} since 1975. Trends about specific species have been noted since 1996. In that time silvertip sharks increased, gray reef sharks increased and then decreased, both the tawny nurse and blacktip reef sharks saw similar declines, and the whitetip reef shark was recorded at low abundance in all years. There was also no significant difference between counts for the four observers. -a number of good citations for research on sharks and ray at remote coral reefs -reef associated species declined which indicates inshore poaching -information on baselines being appropriate -discuss need for enforcement and compliance -discuss reef shark populations in countries where enforcement and monitoring is not strong}, author = {Graham, Nicholas A. J. and Spalding, Mark D. and Sheppard, Charles R. C.}, doi = {10.1002/aqc.1116}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Graham, Spalding, Sheppard - 2010 - Reef shark declines in remote atolls highlight the need for multi-faceted conservation action.pdf:pdf}, issn = {10527613}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, month = {mar}, number = {5}, pages = {543--548}, title = {{Reef shark declines in remote atolls highlight the need for multi-faceted conservation action}}, url = {http://doi.wiley.com/10.1002/aqc.1116}, volume = {20}, year = {2010} } @article{Werry2014, abstract = {Knowledge of the habitat use and migration patterns of large sharks is important for assessing the effectiveness of large predator Marine Protected Areas (MPAs), vulnerability to fisheries and environmental influences, and management of shark-human interactions. Here we compare movement, reef-fidelity, and ocean migration for tiger sharks, Galeocerdo cuvier, across the Coral Sea, with an emphasis on New Caledonia. Thirty-three tiger sharks (1.54 to 3.9 m total length) were tagged with passive acoustic transmitters and their localised movements monitored on receiver arrays in New Caledonia, the Chesterfield and Lord Howe Islands in the Coral Sea, and the east coast of Queensland, Australia. Satellite tags were also used to determine habitat use and movements among habitats across the Coral Sea. Sub-adults and one male adult tiger shark displayed year-round residency in the Chesterfields with two females tagged in the Chesterfields and detected on the Great Barrier Reef, Australia, after 591 and 842 days respectively. In coastal barrier reefs, tiger sharks were transient at acoustic arrays and each individual demonstrated a unique pattern of occurrence. From 2009 to 2013, fourteen sharks with satellite and acoustic tags undertook wide-ranging movements up to 1114 km across the Coral Sea with eight detected back on acoustic arrays up to 405 days after being tagged. Tiger sharks dove 1136 m and utilised three-dimensional activity spaces averaged at 2360 km³. The Chesterfield Islands appear to be important habitat for sub-adults and adult male tiger sharks. Management strategies need to consider the wide-ranging movements of large (sub-adult and adult) male and female tiger sharks at the individual level, whereas fidelity to specific coastal reefs may be consistent across groups of individuals. Coastal barrier reef MPAs, however, only afford brief protection for large tiger sharks, therefore determining the importance of other oceanic Coral Sea reefs should be a priority for future research.}, annote = {Understanding the movement of large, marine megafauna is important in determining the effectiveness of MPAs or the impacts of fishing. Werry et al (2014) tagged 33 tiger sharks at both a populated island and a more remote island system. At the remote island, sub-adults and one male adult tiger displayed year-round residency where as females showed longer range movement. -paper has good information on movement and relevence to MPAs for sharks -cite Barnett 2012}, author = {Werry, Jonathan M and Planes, Serge and Berumen, Michael L and Lee, Kate A and Braun, Camrin D and Clua, Eric}, doi = {10.1371/journal.pone.0083249}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Werry et al. - 2014 - Reef-fidelity and migration of tiger sharks, i Galeocerdo cuvier i, across the Coral Sea.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {movement,shark,telemetry}, mendeley-tags = {movement,shark,telemetry}, month = {jan}, number = {1}, pages = {e83249}, pmid = {24421879}, title = {{Reef-fidelity and migration of tiger sharks, {\textless}i{\textgreater} Galeocerdo cuvier {\textless}/i{\textgreater}, across the Coral Sea}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3885424{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {9}, year = {2014} } @article{Minami2007, abstract = {The zero-inflated negative binomial (ZINB) regression model with smoothing is introduced for modeling count data with many zero-valued observations, and its use is illustrated with shark bycatch data from the eastern Pacific Ocean tuna purse-seine fishery for 1994-2004. Based on the generalized information criterion, the ZINB regression model provided a better fit to the data than either Poisson, negative binomial or zero-inflated Poisson regression models. To demonstrate the utility of the ZINB regression model for the standardization of catch data, standardized temporal trends in bycatch rates estimated with the ZINB regression model are computed and compared to those obtained from fits of the other three types of models to the same data. With the exception of the negative binomial, estimated temporal trends were more similar among models than would have been inferred from an analysis of model fit. Comparison of trends among models suggests that the negative binomial regression model may overestimate model coefficients when fitted to data with many zero-valued observations. ?? 2006 Elsevier B.V. All rights reserved.}, archivePrefix = {arXiv}, arxivId = {hep-th/0512172}, author = {Minami, M. and Lennert-Cody, C. E. and Gao, W. and Rom{\'{a}}n-Verdesoto, M.}, doi = {10.1016/j.fishres.2006.10.019}, eprint = {0512172}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Minami et al. - 2007 - Modeling shark bycatch The zero-inflated negative binomial regression model with smoothing.pdf:pdf}, isbn = {0165-7836}, issn = {01657836}, journal = {Fisheries Research}, keywords = {CPUE,EM algorithm,GAM,GLM,Negative binomial,Shark,Spline smoothing,Zero-inflated}, pages = {210--221}, primaryClass = {hep-th}, title = {{Modeling shark bycatch: The zero-inflated negative binomial regression model with smoothing}}, volume = {84}, year = {2007} } @article{Vellend2013, abstract = {Global biodiversity is in decline. This is of concern for aesthetic and ethical reasons, but possibly also for practical reasons, as suggested by experimental studies, mostly with plants, showing that biodiversity reductions in small study plots can lead to compromised ecosystem function. However, inferring that ecosystem functions will decline due to biodiversity loss in the real world rests on the untested assumption that such loss is actually occurring at these small scales in nature. Using a global database of 168 published studies and {\textgreater}16,000 nonexperimental, local-scale vegetation plots, we show that mean temporal change in species diversity over periods of 5-261 y is not different from zero, with increases at least as likely as declines over time. Sites influenced primarily by plant species' invasions showed a tendency for declines in species richness, whereas sites undergoing postdisturbance succession showed increases in richness over time. Other distinctions among studies had little influence on temporal richness trends. Although maximizing diversity is likely important for maintaining ecosystem function in intensely managed systems such as restored grasslands or tree plantations, the clear lack of any general tendency for plant biodiversity to decline at small scales in nature directly contradicts the key assumption linking experimental results to ecosystem function as a motivation for biodiversity conservation in nature. How often real world changes in the diversity and composition of plant communities at the local scale cause ecosystem function to deteriorate, or actually to improve, remains unknown and is in critical need of further study.}, annote = {It is well-known that global biodiversity is in decline.}, author = {Vellend, Mark and Baeten, Lander and Myers-Smith, Isla H and Elmendorf, Sarah C and Beaus{\'{e}}jour, Robin and Brown, Carissa D and {De Frenne}, Pieter and Verheyen, Kris and Wipf, Sonja}, doi = {10.1073/pnas.1312779110}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vellend et al. - 2013 - Global meta-analysis reveals no net change in local-scale plant biodiversity over time.pdf:pdf}, issn = {1091-6490}, journal = {PNAS}, keywords = {20th Century,21st Century,Biodiversity,Conservation of Natural Resources,Conservation of Natural Resources: statistics {\&} nu,Ecosystem,History,Plants,Plants: genetics}, month = {nov}, number = {48}, pages = {19456--9}, pmid = {24167259}, title = {{Global meta-analysis reveals no net change in local-scale plant biodiversity over time}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24167259}, volume = {110}, year = {2013} } @article{OHara2010, author = {O'Hara, Robert B. and Kotze, D. Johan}, doi = {10.1111/j.2041-210X.2010.00021.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/O'Hara, Kotze - 2010 - Do not log-transform count data.pdf:pdf}, issn = {2041210X}, journal = {Methods in Ecology and Evolution}, month = {mar}, number = {2}, pages = {118--122}, title = {{Do not log-transform count data}}, url = {http://doi.wiley.com/10.1111/j.2041-210X.2010.00021.x}, volume = {1}, year = {2010} } @book{Garrison2005, address = {Heredia, Costa Rica}, author = {Garrison, Ginger}, edition = {2}, pages = {430}, publisher = {InBio}, title = {{Peces de la Isla del Coco}}, year = {2005} } @article{Vianna2014, abstract = {Citizen science is promoted as a simple and cost-effective alternative to traditional approaches for the monitoring of populations of marine megafauna. However, the reliability of datasets collected by these initiatives often remains poorly quantified. We compared datasets of shark counts collected by professional dive guides with acoustic telemetry data from tagged sharks collected at the same coral reef sites over a period of five years. There was a strong correlation between the number of grey reef sharks (Carcharhinus amblyrhynchos) observed by dive guides and the telemetry data at both daily and monthly intervals, suggesting that variation in relative abundance of sharks was detectable in datasets collected by dive guides in a similar manner to data derived from telemetry at these time scales. There was no correlation between the number or mean depth of sharks recorded by telemetry and the presence of tourist divers, suggesting that the behaviour of sharks was not affected by the presence of divers during our study. Data recorded by dive guides showed that current strength and temperature were important drivers of the relative abundance of sharks at monitored sites. Our study validates the use of datasets of shark abundance collected by professional dive guides in frequently-visited dive sites in Palau, and supports the participation of experienced recreational divers as contributors to long-term monitoring programs of shark populations.}, annote = {Increasingly, citizen science datasets are being used to monitor marine megafauna, but not without criticism. Linking these datasets with independent movement data can help validate the citizen science approach. Vianna et al 2014 use data collected by dive companies at a series of sites in Palau over a period of five years. They find a strong correlation between telemetry data and divemaster count data. They are found that the presence of divers had little effect on the behavior of sharks. The study also examined the effect environmental variables have on shark abundance (using multiple linear regression). -lots of good citations -filtered out dives based on diver experience and site information Issues with paper: -innaccurate citation of Dulvy 2014 paper -log transform of count data}, author = {Vianna, Gabriel M S and Meekan, Mark G and Bornovski, Tova H and Meeuwig, Jessica J}, doi = {10.1371/journal.pone.0095565}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Vianna et al. - 2014 - Acoustic telemetry validates a citizen science approach for monitoring sharks on coral reefs.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {citizen science,shark,telemetry}, mendeley-tags = {citizen science,shark,telemetry}, month = {jan}, number = {4}, pages = {e95565}, pmid = {24760081}, title = {{Acoustic telemetry validates a citizen science approach for monitoring sharks on coral reefs}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24760081}, volume = {9}, year = {2014} } @article{Dornelas2014, abstract = {The extent to which biodiversity change in local assemblages contributes to global biodiversity loss is poorly understood. We analyzed 100 time series from biomes across Earth to ask how diversity within assemblages is changing through time. We quantified patterns of temporal $\alpha$ diversity, measured as change in local diversity, and temporal $\beta$ diversity, measured as change in community composition. Contrary to our expectations, we did not detect systematic loss of $\alpha$ diversity. However, community composition changed systematically through time, in excess of predictions from null models. Heterogeneous rates of environmental change, species range shifts associated with climate change, and biotic homogenization may explain the different patterns of temporal $\alpha$ and $\beta$ diversity. Monitoring and understanding change in species composition should be a conservation priority.}, author = {Dornelas, Maria and Gotelli, Nicholas J and McGill, Brian and Shimadzu, Hideyasu and Moyes, Faye and Sievers, Caya and Magurran, Anne E}, doi = {10.1126/science.1248484}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dornelas et al. - 2014 - Assemblage time series reveal biodiversity change but not systematic loss.pdf:pdf}, issn = {1095-9203}, journal = {Science}, month = {apr}, number = {6181}, pages = {296--9}, pmid = {24744374}, title = {{Assemblage time series reveal biodiversity change but not systematic loss}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24744374}, volume = {344}, year = {2014} } @article{Hutchings2012, abstract = {elasmobranch; conservation; body size; life history}, author = {Hutchings, Jeffrey A and Myers, Ransom A and Garc{\'{i}}a, Ver{\'{o}}nica B and Lucifora, Luis O and Kuparinen, Anna}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hutchings et al. - 2012 - Life-history correlates of extinction risk and recovery potential.pdf:pdf}, journal = {Ecological Applications}, keywords = {age at maturity,body size,chondrichthyes,conservation,elasmobranch,life history,marine,population growth rate}, mendeley-tags = {body size,conservation,elasmobranch,life history}, number = {4}, pages = {1061--1067}, title = {{Life-history correlates of extinction risk and recovery potential}}, volume = {22}, year = {2012} } @article{Molina2012, abstract = {Over the last few decades, much effort has been devoted towards quantifying and reducing bycatch in marine fisheries. Of late, there has been a particular focus on sharks given that bycatch is a frequently listed threat for sharks on the International Union for the Conservation of Nature Red List. However, currently there are no quantitative reviews or syntheses that explore the issue of shark bycatch globally which is problematic given that such a synthesis could inform conservation actions and identify pressing research gaps. We performed a qualitative and quantitative survey of the peer- reviewed literature to characterize trends in shark bycatch research with a particular goal of identifying research needs and opportunities. Using a structured literature review we identified 103 search criteria, with the first one published in 1993. Early research efforts focused on documenting the scope of bycatch (i.e., determining that sharks were indeed captured as bycatch), but more recently there have been increased efforts devoted to developing and evaluating bycatch reduction strategies for sharks. Research activity was most common in the North Atlantic (*40 {\%} of the total articles analysed) with comparatively less research in other areas such as the Indo-Pacific region where shark bycatch is regarded as particularly common and problematic. Most studies were observational with comparatively fewer exper- imental and modeling studies, and even fewer that combined research approaches. Gear modifications (e.g., hook size and type for long lines, net size and mesh design for nets) were the most commonly evaluated strategy for reducing shark bycatch; how- ever, development and use of techniques like repel- lents, or seasonal area closures, or a combination of strategies, offer interesting possibilities that require further study. In addition, although many sharks are discarded, little is known about post-release survival or sub-lethal consequences of fisheries interactions, or evaluations of different fish handling strategies, mak- ing it difficult to quantify the true cost of bycatch or to recommend handling strategies to fishers. Although there are some inherent challenges with developing and testing shark bycatch reduction strategies, there is an urgent need to do so and this would be best achieved through interdisciplinary research that spans field, laboratory, and modeling realms. papers that met our}, annote = {Through a literature review, the authors examined trends in shark bycatch research. Gaps in our knowledge were evident including few studies from certain parts of the world or developing new bycatch reduction technologies. Most research has also focused on large indutrial-scale fisheries. Recently, more studies have examined sublethal effects in sharks from fisheries interactions. Could we estimate sublethal effects by looking at Jupiter data?}, author = {Molina, Juan M. and Cooke, Steven J.}, doi = {10.1007/s11160-012-9269-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Molina, Cooke - 2012 - Trends in shark bycatch research current status and research needs.pdf:pdf}, isbn = {1116001292}, issn = {0960-3166}, journal = {Reviews in Fish Biology and Fisheries}, keywords = {bycatch,fisheries,review,shark}, mendeley-tags = {bycatch,fisheries,review,shark}, month = {jun}, number = {3}, pages = {719--737}, title = {{Trends in shark bycatch research: current status and research needs}}, url = {http://link.springer.com/10.1007/s11160-012-9269-3}, volume = {22}, year = {2012} } @book{Sagan1996, abstract = {Casting a wide net through history and culture, Sagan examines and authoritatively debunks such celebrated fallacies as witchcraft, faith healings, demons, and UFOs. And yet, disturbingly, in today's so.called information age, pseudoscience is burgeoning, with stories of alien abduction, "Channeling" past lives, and communal hallucinations commanding growing attention and respect. As Sagan demonstrates with lucid eloquence, the siren song of unreason is not just a culturatl wrong turn but a dangerous plunge into darkness that threatens our most basic freedoms.}, address = {New York}, annote = {-Story of how Sagan got interested in science -so much pseudo science out there -balony detection kit -US education system -Jefferson as a scientist and early us {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} Overall, I really enjoyed reading Carl Sagan's Demon Haunted World. Although long, at 450 pages, I read through it extremely quickly. I couldn't believe how well read he must have been. He cited everything from ancient Greek scholars to magazines and from political leaders to famous scientists. At some points his quoting of other sources did go on for pages and pages—probably unnecessarily. A few of the chapters certainly seem to meander and they felt like they did not have a clear topic. This was particularly true in the beginning of the book when Sagan discusses many examples of pseudoscience like UFO, government coverups, witchcraft, and alternative medicines. Consequently, I enjoyed the last 2/3 of the book much more. Here Sagan talked more about skepticism in general and the need for a strong education system. The first chapter of this type was the Balony Detection Kit—which reminded me a lot of Nagy's class of course. IN this chapter, Sagan lays out why a Balony Detection Kit is important not just in science, but also in politics, business, and everyday life. Sagan runs through a list of all the important tools in this Balony Detection Kit. I can see why Nagy referenced it so much in his class. Sagan feels very strongly about the need to educate not just future scientists but all citizens. He felt the most effective way to do this was through television.  Chapter 1: lat scientifically literate president may have been Thomas Jefferson Chapter 2: Science and Hope Face in the moon, canals on Mars, photos from Apollo missions pg 26: "We've arranged a global civilization in which most critical elements—transportation, communications, and all other industries; agriculture, medicine, education, entertainment, protecting the environment; and even the key democratic instrutionof voting—profoudly depend on science and technology" pg 27: “Science is far from a perfect instrument of knowledge. It's just the best we have." pg 27: “One of the reasons for its success is that science has built-in, error-correcting machinery at its very heart" pg 37: 4 reasons to convery science to every citizen: science can be a golden road out of poverty for emerging nations and people. The converse is also true science provides a early warning system into a changing world science teaches us about the deepest issues in the world values of science and values of democracy are very similar Chapter 4: Aliens -when he learned about process of science, how science actually works, while he was in college (pg 67) -Need more skepticism, especially in cases which seem extradinaroy or if we really want to believe they are true -pg 77: for most people the tools of skepticism are never taught or they are out of reach Chapter 5-11 Sagan discussed a number of issues related to UFO, abductions, government coverups, and the importance of being skeptical. he also discusses ghosts, hallucinations, how therapy can make you believe things that aren't true—providing you with false visions of the past, how ideas have to be testable Chapter 12: The Fine Art of Balony Detection Sagan begins this chapter by discussing mediums and the stories we tell our kids to make them feel good (e.g. Santa) “A sucker is born every minute” - P.T. Barnum pg 210 Tools of the Baloney Detection Kit independent confirmation of facts debate on a topic reject argument from authortiy examine multiple hypotheses don't get to attached to one hypothesis quantify if there is a chain argunement all links must work occam's razor always ask whether a hypothesis can be falsifiable Need carefully designed and controlled experiments Kit also includes things we must not do: ad hominem- attacking the arguer and not the argument argument from authority argument from adverse consequences appeal to ignorance - an idea not proved false but then be true special pleading begging the question observational selection - counting the hits and forgetting the misses statistics of small numbers misunderstanding the nature of statistics - half of people are below average for instance is not alarming inconsistency  non sequitor - Latin for “it doesn't follow”  post hoc “it happened after, so it was caused by" meaningless question  excluded middle or false dichtonmy- considering only two extremes short term vs long term - we can't afford to spend money on space (long term) if we have a budget crisis (short term) slippery slope - if we allow any abortion there is nothing preventing killing of infants correlation and causation straw man - caricaturing a position to make it easier to attack (shrimp on trendmills is crazy) suprressed evidence or half-truths weasel words - no boots on ground just "military advisors" pg 217 tobacco industry history of companies suppressing evidence CHapter 13: discusses James Randi and debunking pseudoscience Chapter 14 Antiscience science is also facing attack not from just pseudoscience but from antiscience Some see science as too subjective, like history Scientists recongnize they make mistakes, they learn from them, and move on because of error-correcting machinery and the ability to do experiments pg 256: Sagan explains a few times in his career where he was wrong: atmospheric pressure of Venus, clouds made of water on Venus, plate tectonics on Mars, and so forth  It is often difficult to judge people in the past without placing them in correct context (e.g. Washington owned slave) Sagan feels Thomas Paine is a bit of an exceptional in that he was far ahead of his time Goes on to discuss situations where science or information in general has ben suppressed (e.g. Soviet Union) Chapter 16: When scientists know sin In this chapter Sagan discusses how science can be misused—like the atomic and thermonuclear bombs. He discussed Oppenheimer and Edward Teller's conflicts during the Manahtten project. It was interesting to hear how badly Teller wanted a thermonuclear bomb—to a disturbing level. Teller was also a big proponent of the Star Wars project during the Reagan administration Chapter 17: the marriage of skepticism and wonder pg 300: Sagan discusses that in the skeptic movement it is often a us versus them type of attitude. That skeptics are right of course. He argues this is not constructive. We have to show compassion to these individuals.  Chapter 18: The wind makes dust He begins the chapter by asking, “ Why should so many people find science hard to learn and hard to teach?” - some have suggested it is hard b/c it is new. Science is not something that was helpful evolutionarily  Scientists always build on the work of others Sagan believes “A proclivity for science in embedded deeply within us, in all times, places and cultures. It has been the means of our survival. It is our birthright. When, through indifference, inattention, incompetence, or fear of skepticism, we discourage children from science, we are disenfranchising them, taking from them the tools needed to manage their future" Chapter 19: No such thing as a dumb question “In a world in transition, students and teachers both need to teach themselves one essential skill—learning how to learn" Felt children were natural-born scientists — somehow this changes by high school in which students no longer ask questions as they don't want to be embarrased Feels adults often put down children's curiosity but not responding to their questions “Bright, curious children are a national and world resource. They need to be cared for, cherished and encourage. But mere envoraement isn't enough. We must also give them the essential tools to think with." Goes on to discuss how the US has fallen behind much of the world Feels we do not spend enough on education and that students do not spend enough time in class or on homework - apparently research now doesn't really support this idea. Maybe it depends on which subjects you are interested in Also discussed how minority students are still behind Sagan believes at the university level we need imaginative, inspiring curricula dn textbooks from leading faculty. Feels scientists should spend more time engaging with public though textbooks, lectures, newspapers, magazines, and TV appearances, also feels all university students should have to take a class in skeptical thinking Argues scientists have to speak to general public more Chapter 20: House on fire}, author = {Sagan, Carl}, booktitle = {Nature Medicine}, doi = {10.1038/nm0996-1042}, isbn = {0307801047}, issn = {1078-8956}, keywords = {science education}, pages = {1042--1042}, pmid = {3506635}, publisher = {Random House Publishing Group}, title = {{The Demon-Haunted World: Science as a Candle in the Dark}}, volume = {2}, year = {1996} } @book{Darwin1859, abstract = {On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life.}, address = {London}, author = {Darwin, Charles}, booktitle = {Darwin}, issn = {00335770}, keywords = {evolution}, pages = {386}, title = {{On the Origin of the Species}}, volume = {5}, year = {1859} } @article{Byers2007, abstract = {Marine reserves are promoted as an effective supplement to traditional fishery management techniques of harvest quotas and effort limitation. However, quantitative fishery models have ignored the impact of noncompliance (poaching). Here we link a model of a harvested fish population to a game-theoretic representation of fisherman behavior to quantify the effect of poaching on fishery yield and the enforcement effort required to maintain any desired level of reserve effectiveness. Although higher fish densities inside reserves will typically entice fishermen to poach, we show that the initial investment in enforcement efforts provides the greatest return on maintaining the benefits of the reserve to the fishery. Furthermore, we find that poaching eliminates the positive effect of fish dispersal on yield that is predicted by traditional models that ignore fisherman behavior. Our results broaden a fundamental insight from previous models of marine reserves, the effective equivalence of the harvest quota and reserve fraction, to the more realistic scenario in which fishermen attempt to maximize their economic payoffs.}, annote = {Typically, fishing models ignore noncompliance on the part of fishermen. Results of these types of models cannot be used if poaching is high from low enforcement efforts. This paper using game theory and fishery models to predict the consequences of not enforcing marine reserves.}, author = {Byers, James E and Noonburg, Erik G}, doi = {10.1890/07-0067.1}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Byers, Noonburg - 2007 - Poaching, enforcement, and the efficacy of marine reserves.pdf:pdf}, isbn = {1051-0761}, issn = {1051-0761}, journal = {Ecological Applications}, keywords = {conservation,mpa,policy}, mendeley-tags = {conservation,mpa,policy}, number = {7}, pages = {1851--1856}, pmid = {17974326}, title = {{Poaching, enforcement, and the efficacy of marine reserves}}, volume = {17}, year = {2007} } @article{Whoriskey2011, annote = {Mahi-mahi has emerged as a highly productive fishery in the last half-century. However, little is known regarding the population status of Mahi-mahi or bycatch associated wiith the fishery. Using FAO data, authors report large increases in mahi-mahi catch and document the bycatch of several species. They model catch of each species using a GLM with a negative binomial error distribution and log link with {\#} of hooks as an offset. From 1999 to 2008, silky sharks catch dropped from 4.7 to {\textless}1 shark per 1000 hooks. Catch of Silky sharks was primarily in offshore longlines. A time area closure may work well to protect silky sharks. Turtles were often released alive after being caught with high survivability. Sharks were usually retained by fishermen for their fins. -Present interesting way to show models outcomes For Costan Rican fisheries data look at IATTC 2010 and Pretoma 2010}, author = {Whoriskey, Sophie and Arauz, Randall and Baum, Julia K.}, doi = {10.1016/j.biocon.2011.03.021}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Whoriskey, Arauz, Baum - 2011 - Potential impacts of emerging mahi-mahi fisheries on sea turtle and elasmobranch bycatch species.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {bycatch,cocos,fisheries,shark}, mendeley-tags = {bycatch,cocos,fisheries,shark}, month = {jun}, number = {6}, pages = {1841--1849}, publisher = {Elsevier Ltd}, title = {{Potential impacts of emerging mahi-mahi fisheries on sea turtle and elasmobranch bycatch species}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006320711001157}, volume = {144}, year = {2011} } @article{Ketchum2014a, author = {Ketchum, James T and Hearn, Alex and Klimley, A Peter and Pe{\~{n}}aherrera, C{\'{e}}sar and Espinoza, Eduardo and Bessudo, Sandra and Soler, Germ{\'{a}}n and Arauz, Randall}, doi = {10.1007/s00227-014-2393-y}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ketchum et al. - 2014 - Inter‑island movements of scalloped hammerhead sharks (Sphyrna lewini) and seasonal connectivity in a marine p.pdf:pdf}, journal = {Marine Biology}, keywords = {MPA,cocos,elasmobranch,movement}, mendeley-tags = {MPA,cocos,elasmobranch,movement}, number = {4}, pages = {939--951}, title = {{Inter‑island movements of scalloped hammerhead sharks (Sphyrna lewini) and seasonal connectivity in a marine protected area of the eastern tropical Pacific}}, volume = {61}, year = {2014} } @article{Arauz2005, author = {Arauz, Randall and Antoniou, Alex}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Arauz, Antoniou - 2005 - Movements of scalloped hammerhead sharks (iSphyrna lewinii) tagged in Cocos Island National Park, Costa Rica.pdf:pdf}, pages = {2}, title = {{Movements of scalloped hammerhead sharks ({\textless}i{\textgreater}Sphyrna lewini{\textless}/i{\textgreater}) tagged in Cocos Island National Park, Costa Rica}}, year = {2005} } @article{DeSanto2013, abstract = {International targets for marine protected areas (MPAs) and networks of MPAs set by the World Summit on Sustainable Development and United Nations Convention on Biological Diversity failed to meet their 2012 deadline and have been extended to 2020. Whilst targets play an important role in building momentum for conservation, they are also responsible for the recent designation of several extremely large no-take MPAs, which pose significant long-term monitoring and enforcement challenges. This paper critically examines the effectiveness of MPA targets, focusing on the underlying risks to achieving Millennium Development Goals posed by the global push for quantity versus quality of MPAs. The observations outlined in this paper have repercussions for international protected area politics with respect to (1) the science-policy interface in environmental decision-making, and (2) social justice concerns in global biodiversity conservation.}, annote = {Large marine protected areas are increasingly used as a conservation or management tool. However, calling for more and more MPAs of larger size may undermine real conservation efforts. More focus should go into implentation and management of MPAs. "MPAs have increasingly become a key tool for marine conservation despite the fact that they are often implemented without a firm understanding of both the ecological and socioeconomic considerations of conservation (Agardy et al., 2003)." Monitoring and enforcing large or remote MPAs is difficult.}, author = {{De Santo}, Elizabeth M}, doi = {10.1016/j.jenvman.2013.01.033}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/De Santo - 2013 - Missing marine protected area (MPA) targets How the push for quantity over quality undermines sustainability and socia.pdf:pdf}, issn = {1095-8630}, journal = {Journal of environmental management}, keywords = {Conservation of Natural Resources,Marine Biology,Social Justice,United Nations}, month = {jul}, pages = {137--46}, pmid = {23582739}, publisher = {Elsevier Ltd}, title = {{Missing marine protected area (MPA) targets: How the push for quantity over quality undermines sustainability and social justice}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23582739}, volume = {124}, year = {2013} } @article{Claudet2010, abstract = {Marine reserves are assumed to protect a wide range of species from deleterious effects stemming from exploitation. However, some species, due to their ecological characteristics, may not respond positively to protection. Very little is known about the effects of life history and ecological traits (e.g., mobility, growth, and habitat) on responses of fish species to marine reserves. Using 40 data sets from 12 European marine reserves, we show that there is significant variation in the response of different species of fish to protection and that this heterogeneity can be explained, in part, by differences in their traits. Densities of targeted size-classes of commercial species were greater in protected than unprotected areas. This effect of protection increased as the maximum body size of the targeted species increased, and it was greater for species that were not obligate schoolers. However, contrary to previous theoretical findings, even mobile species with wide home ranges benefited from protection: the effect of protection was at least as strong for mobile species as it was for sedentary ones. Noncommercial bycatch and unexploited species rarely responded to protection, and when they did (in the case of unexploited bentho-pelagic species), they exhibited the opposite response: their densities were lower inside reserves. The use of marine reserves for marine conservation and fisheries management implies that they should ensure protection for a wide range of species with different life-history and ecological traits. Our results suggest this is not the case, and instead that effects vary with economic value, body size, habitat, depth range, and schooling behavior.}, annote = {Ecological and life history traits are imporant in MPA success or failures. MPAs are often assumed to protect a wide range of species. However, some species--- based on their life history--- may not respond to MPA protection. More information on MPA success and life history traits of fish is needed. Using data from European MPAs, Claudet and others examining these questions. MPAs increased density of fish, were more effective in protecting fish with larger max body size and those that are not obligate schoolers. In addition, mobile predators benefited from protection (MPA may offer some benefit not included in previous modeling studies). Further MPA effect also depended on the commerical value and bycatch status of a particular species. Time of protection (time since MPA inception also had a strong effect on larger species compared to smaller ones).}, author = {Claudet, J and Osenberg, C W and Domenici, P and Badalamenti, F and Milazzo, M and Falc{\'{o}}n, J M and Bertocci, I and Benedetti-Cecchi, L and Garc{\'{i}}a-Charton, J A and Go{\~{n}}i, R and Borg, J A and Forcada, A and {De Lucia}, G A and Perez-Ruzafa, A and Afonso, P and Brito, A and Guala, I and {Le Dir{\'{e}}ach}, L and Sanchez-Jerez, P and Somerfield, P J and Planes, S}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Claudet et al. - 2010 - Marine reserves fish life history and ecological traits matter.pdf:pdf}, issn = {1051-0761}, journal = {Ecological Applications}, keywords = {Animal,Animals,Behavior,Biological,Body Size,Conservation of Natural Resources,Ecosystem,Europe,Fisheries,Fishes,Models,Population Density,Territoriality}, month = {apr}, number = {3}, pages = {830--9}, pmid = {20437967}, title = {{Marine reserves: fish life history and ecological traits matter}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20437967}, volume = {20}, year = {2010} } @article{Claudet2010a, annote = {There needs to be more assessment of MPA effectivness. Assessments would be improved if they included: 1) enforcement level 2) choice of indicators to MPA objectives 3) habitat structure 4) age and size of MPA and 5) fishing pressure outside the MPA. If these components are left out, MPAs may be regarded as an effective management tool by mistake. Paper reviews MPAs or marine reserves located in the Mediterranean. They acknowledge the fact that scientists cannot always have an ideal experimental design when it comes to studying MPAs. "In a recent, well-designed study, where no significant effects of protection were found, the authors recognized that protection was not enforced and fishing continued to occur within the MPA (Lipej et al., 2003). Without enforcement and compliance, an MPA is just a paper park and no protection effects should be expected. Actual enforcement and compliance, and not the formal MPA establishment, must be considered as the true starting point of protection (Guidetti et al., 2008)." Measures of success for MPAs depend on what the original objectives of the MPA were.}, author = {Claudet, Joachim and Guidetti, Paolo}, doi = {10.1002/aqc}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Claudet, Guidetti - 2010 - Improving assessments of marine protected areas.pdf:pdf}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, keywords = {enforcement and compliance,fishing effort,habitat features,historical standpoint,indicator,marine reserve age and,sampling design,size}, pages = {239--242}, title = {{Improving assessments of marine protected areas}}, volume = {242}, year = {2010} } @article{Lester2009, annote = {Through a metaanalysis of marine reserves, a number of positive effects of marine reserves were shown: biomass, density, richness, and organism size. The results indicate that these trends are not driven by: reserves being placed in more productive areas or displacement of fishing effort. Tropical vs temperate reserves do not differe in their benefits or success. Small reserves can still produce biological responses. Not all species increase in response to rserves because of differences in life history traits. The context of a marine reserve also plays a large effect in determining the reserve's success. Many parts of the world have reserves in place but with inadequate data to judge the effect of implementation or enforcement efforts. These parks may simply be paper parks. "If you do not invest time and money into enforcement and assessement, the park looks like a positive thing."- ME. It is rare to have data for before and after MPA implementation (more common to simply compare MPA vs non-MPA water).}, author = {Lester, S E and Halpern, B S and Grorud-Colvert, K and Lubchenco, J and Ruttenberg, B I and Gaines, S D and Airam{\'{e}}, S and Warner, R R}, doi = {10.3354/meps08029}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lester et al. - 2009 - Biological effects within no-take marine reserves a global synthesis.pdf:pdf}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, keywords = {algae,conservation,fishes,invertebrates,marine,marine reserves,of the publisher,permitted without written consent,protected area,resale or republication not,temperate,tropical}, month = {may}, pages = {33--46}, title = {{Biological effects within no-take marine reserves: a global synthesis}}, url = {http://www.int-res.com/abstracts/meps/v384/p33-46/}, volume = {384}, year = {2009} } @article{Hooker2004, annote = {Marine megafauna are often the driving force behind marine conservation projects and management efforts. Hooker and Gerber review marine megafauna's role in reserve implementation and success. They also argue that pelagic marine reserves need to be implemented. "Marine reserves are often simply paper parks which provide false sense of conservation success (Duffus and Dearden 1995)." They also stress the importance of using demographic modeling to examine how MPAs may affect species with different life histories. Can use these paper as citation for the delay in MPA success for long-lived species like predators. Can also use paper to discuss enforcement needed to avoid simply having "paper parks" In the MPA design stage, determine what a successful MPA will look like}, author = {Hooker, Sascha K. and Gerber, Leah R.}, doi = {10.1641/0006-3568(2004)054[0027:MRAATF]2.0.CO;2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hooker, Gerber - 2004 - Marine Reserves as a Tool for Ecosystem-Based Management The Potential Importance of Megafauna.pdf:pdf}, issn = {0006-3568}, journal = {BioScience}, keywords = {but they are,conservation,humanity discovered them,indicator species,marine predators,marine reserves,modeling,no means dead,the seas are by,they were when,unquestionably less alive than}, number = {1}, pages = {27}, title = {{Marine Reserves as a Tool for Ecosystem-Based Management: The Potential Importance of Megafauna}}, url = {http://bioscience.oxfordjournals.org/cgi/doi/10.1641/0006-3568(2004)054[0027:MRAATF]2.0.CO;2}, volume = {54}, year = {2004} } @article{Dulvy2006, abstract = {A recent study for the first time unravels a complete Hox regulatory network sufficient for the specification of a simple organ in Drosophila, linking Hox output to one specific group of executive genes, the realisators. As these genes have a direct effect on cellular functions and are required in most cell types, Hox genes may ultimately execute their function in controlling segmental fate by fine-tuning the spatial and temporal expression levels of these realisators.}, annote = {editorial of Robbins et al 2006 Robbins 2006 documented the decline of two reef shark species through UVC. They found that densities of whitetip and grey reef sharks were lower in fished zones.  McClanahan 2006 and Sale 2005 for citations about MPAs in general}, author = {Dulvy, Nicholas K}, doi = {10.1016/j.cub.2006.10.044}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dulvy - 2006 - Strict Marine Protected Areas Prevent Reef Shark Declines.pdf:pdf}, issn = {0960-9822}, journal = {Current biology}, keywords = {Animals,Cadherins,Cadherins: physiology,Cell Adhesion,Cell Polarity,Drosophila,Drosophila Proteins,Drosophila Proteins: genetics,Drosophila: embryology,Drosophila: genetics,Genes,Homeobox,Homeobox: physiology,Homeodomain Proteins,Homeodomain Proteins: genetics,Organogenesis}, month = {dec}, number = {23}, pages = {R988--9}, pmid = {17141603}, title = {{Strict Marine Protected Areas Prevent Reef Shark Declines}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17141603}, volume = {16}, year = {2006} } @article{Chuenpagdee2013, annote = {By reviewing MPAs in Spain and Mexico, the paper argues that MPA failures can be largely attributed to the initial MPA design and development stage. Paper does not discuss enforcement very much}, author = {Chuenpagdee, Ratana and Pascual-Fern{\'{a}}ndez, Jose J. and Szeli{\'{a}}nszky, Emese and {Luis Alegret}, Juan and Fraga, Julia and Jentoft, Svein}, doi = {10.1016/j.marpol.2012.10.016}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chuenpagdee et al. - 2013 - Marine protected areas Re-thinking their inception.pdf:pdf}, issn = {0308597X}, journal = {Marine Policy}, keywords = {marine protected areas}, month = {may}, pages = {234--240}, title = {{Marine protected areas: Re-thinking their inception}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0308597X12002151}, volume = {39}, year = {2013} } @article{Knip2012a, author = {Knip, Danielle M and Heupel, Michelle R and Simpfendorfer, Colin A}, doi = {10.1016/j.biocon.2012.01.008}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Knip, Heupel, Simpfendorfer - 2012 - Evaluating marine protected areas for the conservation of tropical coastal sharks.pdf:pdf}, issn = {0006-3207}, journal = {Biological Conservation}, keywords = {MPA,conservation,elasmobranch}, mendeley-tags = {MPA,conservation,elasmobranch}, number = {1}, pages = {200--209}, publisher = {Elsevier Ltd}, title = {{Evaluating marine protected areas for the conservation of tropical coastal sharks}}, url = {http://dx.doi.org/10.1016/j.biocon.2012.01.008}, volume = {148}, year = {2012} } @article{Robbins2006, abstract = {Marine ecosystems are suffering severe depletion of apex predators worldwide [1-4]; shark declines are principally due to conservative life-histories and fisheries overexploitation [5-8]. On coral reefs, sharks are strongly interacting apex predators and play??a key role in maintaining healthy reef ecosystems [9-11]. Despite increasing fishing pressure, reef shark catches are rarely subject to specific limits, with management approaches typically depending upon no-take marine reserves to maintain populations [12-14]. Here, we reveal that this approach is failing by documenting an ongoing collapse in two of the most abundant reef shark species on the Great Barrier Reef (Australia). We find an order of magnitude fewer sharks on fished reefs compared to no-entry management zones that encompass only 1{\%} of reefs. No-take zones, which are more difficult to enforce than no-entry zones, offer almost no protection for shark populations. Population viability models of whitetip and gray reef sharks project ongoing steep declines in abundance of 7{\%} and 17{\%} per annum, respectively. These findings indicate that current management of no-take areas is inadequate for protecting reef sharks, even in one of the world's most-well-managed reef ecosystems. Further steps are urgently required for protecting this critical functional group from ecological extinction. ?? 2006 Elsevier Ltd. All rights reserved.}, author = {Robbins, William D. and Hisano, Mizue and Connolly, Sean R. and Choat, J. Howard}, doi = {10.1016/j.cub.2006.09.044}, isbn = {0025-326X}, issn = {09609822}, journal = {Current Biology}, keywords = {EVO{\_}ECOL}, pages = {2314--2319}, pmid = {17141612}, title = {{Ongoing collapse of coral-reef shark populations}}, volume = {16}, year = {2006} } @article{Rife2013, annote = {Creating MPAs without proper monitoring or enforcement may lead to a false sense of conservation success. Funding for enforcement of MPAs may be a major hurdle. When MPAs are simply decreed without sufficient design, management, or enforcement, they simply become "paper parks" (White and Courtney 2004). Byers and Noonburg 2007- lack of enforcement Lots of good citations on MPA}, author = {Rife, Alexis N. and Erisman, Brad and Sanchez, Alexandra and Aburto-Oropeza, Octavio}, doi = {10.1111/j.1755-263X.2012.00303.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rife et al. - 2013 - When good intentions are not enough {\ldots} Insights on networks of “paper park” marine protected areas.pdf:pdf}, issn = {1755263X}, journal = {Conservation Letters}, keywords = {environmental policy,environmental threats,fisheries,gulf of california,management,marine protected areas}, month = {jun}, number = {3}, pages = {200--212}, title = {{When good intentions are not enough {\ldots} Insights on networks of “paper park” marine protected areas}}, url = {http://doi.wiley.com/10.1111/j.1755-263X.2012.00303.x}, volume = {6}, year = {2013} } @article{Friedrich2014, abstract = {With increasing evidence of the destructive impacts of human activities on the ocean there is a growing call for stronger public engagement in marine governance. An understanding of marine issues and pro- environmental values are key elements that influence an individual's engagement in conservation and pro-environmental behaviour. This paper presents a study on public perceptions of sharks and shark conservation in the UK. The study investigated knowledge of and attitudes towards sharks of a group of individuals with a clear interest in the marine environment, as well as possible factors that might influence their perceptions of sharks, in order to make recommendations on how to foster engagement in shark conservation. The key finding was that important prerequisites for engagement in shark conservation exist among parts of the UK public. However, this does not seem to be enough to motivate actual engagement. The study discusses a number of specific challenges with regard to sharks which might be influencing theway in which society connects to shark related issues. It concludes with priority recommendations for further investigation into potential catalysts for public engagement in shark conservation.}, annote = {     This study did interviews of aquarium guests to gauge public knowledge on shark conservation and management. They found that their sample group had a high knowledge about sharks. Knowledge correlated with living near the sea, visiting the aquarium regularly, or diving/swimming with sharks.  }, author = {Friedrich, Laura A. and Jefferson, Rebecca and Glegg, Gillian}, doi = {10.1016/j.marpol.2014.02.003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Friedrich, Jefferson, Glegg - 2014 - Public perceptions of sharks Gathering support for shark conservation.pdf:pdf}, issn = {0308597X}, journal = {Marine Policy}, keywords = {Public engagement,Public perception,Shark conservation,Shark fisheries,elasmobranch,public}, mendeley-tags = {elasmobranch,public}, month = {jul}, pages = {1--7}, publisher = {Elsevier}, title = {{Public perceptions of sharks: Gathering support for shark conservation}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0308597X14000360}, volume = {47}, year = {2014} } @article{Dudley2006, abstract = {Shark nets have been set off the beaches of KwaZulu–Natal, South Africa, since 1952 to reduce the risk of shark attack. The nets fish in fixed localities 400m from shore and both directly affect local shark populations and act as fisheries-independent monitoring devices. Reliable catch information at the species level was available for the period 1978–2003. Trends in catch rate and size were used to assess the population status of 14 commonly caught shark species. In addition, a demographic modelling approach was used in conjunction with the catch information to assess the potential effect of the nets on populations. Catch rates of four species (Carcharhinus leucas, C. limbatus, Sphyrna lewini and S. mokarran) showed a significant decline, as did the mean or median length of three species (Carcharhinus amboinensis, C. limbatus and female Carcharodon carcharias). For three species that showed declining catch rates or length the potential effect of the shark nets was assessed to be low, suggesting that other sources of catchwere responsible for the declining status.The potential effect of the shark nets was assessed to be high for two species (Carcharhinus obscurus and Carcharias taurus, neither of which showed declines in catch rate or length), because of very low intrinsic rates of population increase}, author = {Dudley, Sheldon F. J. and Simpfendorfer, Colin A.}, doi = {10.1071/MF05156}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dudley, Simpfendorfer - 2006 - Population status of 14 shark species caught in the protective gillnets off KwaZulu–Natal beaches, So.pdf:pdf}, issn = {1323-1650}, journal = {Marine and Freshwater Research}, keywords = {conservation,elasmobranch,fisheres,model}, mendeley-tags = {conservation,elasmobranch,fisheres,model}, number = {2}, pages = {225}, title = {{Population status of 14 shark species caught in the protective gillnets off KwaZulu–Natal beaches, South Africa, 1978–2003}}, url = {http://www.publish.csiro.au/?paper=MF05156}, volume = {57}, year = {2006} } @article{Garcia2008, abstract = {We compared life-history traits and extinction risk of chondrichthyans (sharks, rays and chimaeras), a group of high conservation concern, from the three major marine habitats (continental shelves, open ocean and deep sea), controlling for phylogenetic correlation. Deep-water chondrichthyans had a higher age at maturity and longevity, and a lower growth completion rate than shallow-water species. The average fishing mortality needed to drive a deep-water chondrichthyan species to extinction (Fextinct) was 38-58{\%} of that estimated for oceanic and continental shelf species, respectively. Mean values of Fextinct were 0.149, 0.250 and 0.368 for deep-water, oceanic and continental shelf species, respectively. Reproductive mode was an important determinant of extinction risk, while body size had a weak effect on extinction risk. As extinction risk was highly correlated with phylogeny, the loss of species will be accompanied by a loss of phylogenetic diversity. Conservation priority should not be restricted to large species, as is usually suggested, since many small species, like those inhabiting the deep ocean, are also highly vulnerable to extinction. Fishing mortality of deep-water chondrichthyans already exploited should be minimized, and new deep-water fisheries affecting chondrichthyans should be prevented.}, annote = {The paper looks at chondrichthyans species found in the three major marine habiatas: continental shelves, open ocean, and deep sea. They found that deep-water chondrichthyans are much more susceptible to overfishing. This is primarily because of deep-water chondrichtyands having more K-selected life history traits. Reproductive mode and body size were correlated with extinction risk. It only takes about half the amount of fishing pressure required for continental and oceanic species to drive deep sea species to extinction. Use F{\_}extinct, which is the fishing mortality neccessary to drive a species to extinction, as a measure of extinction risk. We could do something similar in the Cocos paper and compare F{\_}extinct versus species decline or increase. Use F{\_}extinct as a reponse variable in a series of models that correct for phylogeny}, author = {Garc{\'{i}}a, Ver{\'{o}}nica B and Lucifora, Luis O and Myers, Ransom A}, doi = {10.1098/rspb.2007.1295}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Garc{\'{i}}a, Lucifora, Myers - 2008 - The importance of habitat and life history to extinction risk in sharks, skates, rays and chimaeras.pdf:pdf}, issn = {0962-8452}, journal = {Proceedings of the Royal Society B}, keywords = {Age Factors,Animals,Biological,Body Size,Conservation of Natural Resources,Conservation of Natural Resources: methods,Ecosystem,Elasmobranchii,Elasmobranchii: genetics,Elasmobranchii: physiology,Extinction,Longevity,Oceans and Seas,Phylogeny,Reproduction,Reproduction: physiology,Risk Assessment,Species Specificity,conservation,elasmobranch,extinction,life history}, mendeley-tags = {conservation,elasmobranch,extinction,life history}, month = {jan}, number = {1630}, pages = {83--9}, pmid = {17956843}, title = {{The importance of habitat and life history to extinction risk in sharks, skates, rays and chimaeras.}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2562409{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {275}, year = {2008} } @article{Barraquand2014, abstract = {Proficiency in mathematics and statistics is essential to modern ecological science, yet few studies have assessed the level of quantitative training received by ecologists. To do so, we conducted an online survey. The 937 respondents were mostly early-career scientists who studied biology as undergraduates. We found a clear self-perceived lack of quantitative training: 75{\%} were not satisfied with their understanding of mathematical models; 75{\%} felt that the level of mathematics was “too low” in their ecology classes; 90{\%} wanted more mathematics classes for ecologists; and 95{\%} more statistics classes. Respondents thought that 30{\%} of classes in ecology-related degrees should be focused on quantitative disciplines, which is likely higher than for most existing programs. The main suggestion to improve quantitative training was to relate theoretical and statistical modeling to applied ecological problems. Improving quantitative training will require dedicated, quantitative classes for ecology-related degrees that contain good mathematical and statistical practice.}, annote = {The paper conducted a survey of early-career scientists and asked questions relating to their math backgrounds and proficiency and understanding of mathematical models. The authors advocate for more math and stats being integrated in ecology classes. In addition, a two semester course in Calculus (and linear algebra) and a course in statistics is important for undergrads. At the graduate level a course in probability and advanced statistics is important.}, author = {Barraquand, Fr{\'{e}}d{\'{e}}ric and Ezard, Thomas H G and J{\o}rgensen, Peter S and Zimmerman, Naupaka and Chamberlain, Scott and Salguero-G{\'{o}}mez, Roberto and Curran, Timothy J and Poisot, Timoth{\'{e}}e}, doi = {10.7717/peerj.285}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barraquand et al. - 2014 - Lack of quantitative training among early-career ecologists a survey of the problem and potential solutions.pdf:pdf}, journal = {PeerJ}, keywords = {ecology,education,quantitative,science metrics}, mendeley-tags = {ecology,education,quantitative,science metrics}, number = {e285}, title = {{Lack of quantitative training among early-career ecologists: a survey of the problem and potential solutions}}, volume = {2}, year = {2014} } @phdthesis{Eckert2013, annote = {Marine protected areas are often used as a conservation and management tool. However, it is unclear if MPAs are an effective tool for protected highly migratory animals like many species of sharks. This thesis examines the overlap of species ranges and MPAs on a global scale. The work finds that species are obviously seen outside of known MPAs quite often. Biases do exist in this type of analysis as most people are near continental MPAs or dive in MPAs compared to pelagic areas. There are a number of good citations}, author = {Eckert, Sara}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Eckert - 2013 - The value of the global marine protected area network in the conservation of migratory, endangered sharks.pdf:pdf}, keywords = {MPA,conservation,elasmobranch}, mendeley-tags = {MPA,conservation,elasmobranch}, number = {September}, pages = {77}, school = {Imperial College London}, title = {{The value of the global marine protected area network in the conservation of migratory, endangered sharks}}, type = {MSc}, year = {2013} } @article{Carr2013, author = {Carr, Lindsey A. and Stier, Adrian C. and Fietz, Katharina and Montero, Ignacio and Gallagher, Austin J. and Bruno, John F.}, doi = {10.1016/j.marpol.2012.12.005}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Carr et al. - 2013 - Illegal shark fishing in the Gal{\'{a}}pagos Marine Reserve.pdf:pdf}, issn = {0308597X}, journal = {Marine Policy}, keywords = {Conservation,Enforcement,Gal{\'{a}}pagos,Illegal,Marine reserves,Shark fishing}, month = {may}, pages = {317--321}, publisher = {Elsevier}, title = {{Illegal shark fishing in the Gal{\'{a}}pagos Marine Reserve}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0308597X12002461}, volume = {39}, year = {2013} } @article{Nadon2012, abstract = {Sharks and other large predators are scarce on most coral reefs, but studies of their historical ecology provide qualitative evidence that predators were once numerous in these ecosystems. Quantifying density of sharks in the absence of humans (baseline) is, however, hindered by a paucity of pertinent time-series data. Recently researchers have used underwater visual surveys, primarily of limited spatial extent or nonstandard design, to infer negative associations between reef shark abundance and human populations. We analyzed data from 1607 towed-diver surveys ({\textgreater}1 ha transects surveyed by observers towed behind a boat) conducted at 46 reefs in the central-western Pacific Ocean, reefs that included some of the world's most pristine coral reefs. Estimates of shark density from towed-diver surveys were substantially lower ({\textless}10{\%}) than published estimates from surveys along small transects ({\textless}0.02 ha), which is not consistent with inverted biomass pyramids (predator biomass greater than prey biomass) reported by other researchers for pristine reefs. We examined the relation between the density of reef sharks observed in towed-diver surveys and human population in models that accounted for the influence of oceanic primary productivity, sea surface temperature, reef area, and reef physical complexity. We used these models to estimate the density of sharks in the absence of humans. Densities of gray reef sharks (Carcharhinus amblyrhynchos), whitetip reef sharks (Triaenodon obesus), and the group "all reef sharks" increased substantially as human population decreased and as primary productivity and minimum sea surface temperature (or reef area, which was highly correlated with temperature) increased. Simulated baseline densities of reef sharks under the absence of humans were 1.1-2.4/ha for the main Hawaiian Islands, 1.2-2.4/ha for inhabited islands of American Samoa, and 0.9-2.1/ha for inhabited islands in the Mariana Archipelago, which suggests that density of reef sharks has declined to 3-10{\%} of baseline levels in these areas.}, annote = {There has been few studies on reef sharks because of a paucity of data (most data would normally come from fisheries logbooks). Using towed-diver surveys can help fill this gap. After accounting for environemntal factors, population trends can be estimated. In addition, original baselines for population size can be estimated by setting the human population term in a model to zero.}, author = {Nadon, Marc O and Baum, Julia K and Williams, Ivor D and McPherson, Jana M and Zgliczynski, Brian J and Richards, Benjamin L and Schroeder, Robert E and Brainard, Russell E}, doi = {10.1111/j.1523-1739.2012.01835.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nadon et al. - 2012 - Re-creating missing population baselines for Pacific reef sharks.pdf:pdf}, issn = {1523-1739}, journal = {Conservation Biology}, keywords = {Animals,Biological,Conservation of Natural Resources,Coral Reefs,Environment,Fisheries,Food Chain,Humans,Models,Pacific Ocean,Population Density,Reference Values,Seasons,Sharks,Sharks: physiology,Species Specificity,Water Pollution,Water Pollution: adverse effects}, month = {jun}, number = {3}, pages = {493--503}, pmid = {22536842}, title = {{Re-creating missing population baselines for Pacific reef sharks}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3494310{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {26}, year = {2012} } @article{Hampton2013, abstract = {The need for sound ecological science has escalated alongside the rise of the information age and “big data” across all sectors of society. Big data generally refer to massive volumes of data not readily handled by the usual data tools and practices and present unprecedented opportunities for advancing science and inform- ing resource management through data-intensive approaches. The era of big data need not be propelled only by “big science” – the term used to describe large-scale efforts that have had mixed success in the individual-driven culture of ecology. Collectively, ecologists already have big data to bolster the scientific effort – a large volume of distributed, high-value information – but many simply fail to contribute. We encourage ecologists to join the larger scientific community in global initiatives to address major scientific and societal problems by bringing their distributed data to the table and harnessing its collective power. The scientists who contribute such information will be at the forefront of socially relevant science – but will they be ecologists?}, author = {Hampton, Stephanie E and Strasser, Carly A and Tewksbury, Joshua J and Gram, Wendy K and Budden, Amber E and Batcheller, Archer L and Duke, Clifford S and Porter, John H}, doi = {10.1890/120103}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hampton et al. - 2013 - Big data and the future of ecology.pdf:pdf}, journal = {Front Ecol Environ}, keywords = {data,ecology,open science,review}, mendeley-tags = {data,ecology,open science,review}, number = {3}, pages = {156--162}, title = {{Big data and the future of ecology}}, volume = {11}, year = {2013} } @article{Roemer2002, annote = {Exotic species have open been implicated in altering community dynamics through direct effects. However, indirect effects of exotic species are less well understood. In a eagle-pig-fox-skunk system, the introduction of pigs may have led to the extinction of the island fox. In turn, this led to a competitive release of skunks. The study combines the predation and competition Lotka-Volterra models. These models were parameterized from field studies, stable isotope diet analysis, and metabolic requirements of each species. When pigs are included in the model, there is enough food for golden eagles to colonize the island. This causes a decrease in foxes and a increase in skunks. Without pigs, eagles are not able to colonize the island. Incorporating stochasticity in the model would be interesting}, author = {Roemer, Gary W and Donlan, C Josh and Courchamp, Franck}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Roemer, Donlan, Courchamp - 2002 - Golden eagles, feral pigs, and insular carnivores How exotic species turn native predators into prey.pdf:pdf}, journal = {PNAS}, keywords = {invasive species,model,predation}, mendeley-tags = {invasive species,model,predation}, number = {2}, pages = {791--796}, title = {{Golden eagles, feral pigs, and insular carnivores: How exotic species turn native predators into prey}}, volume = {99}, year = {2002} } @article{Edgar2014, abstract = {In line with global targets agreed under theConvention on Biological Diversity, the number of marine protected areas (MPAs) is increas- ing rapidly, yet socio-economic benefits generated byMPAsremain difficult topredictandunder debate1,2 .MPAsoftenfail to reachtheir full potential as a consequence of factors such as illegal harvesting, regulations that legally allow detrimental harvesting, or emigration of animals outside boundaries because of continuous habitat or inadequate size of reserve3–5 . Here we show that the conservation benefits of 87MPAsinvestigated worldwide increase exponentially with the accumulation of five key features: no take, well enforced, old(.10years), large (.100km2),andisolatedbydeepwateror sand. Using effective MPAs with four or five key features as an unfished standard, comparisonsofunderwatersurveydatafromeffectiveMPAs with predictions based on survey data from fished coasts indicate that total fish biomass has declinedabout two-thirds fromhistorical baselines as a result of fishing. EffectiveMPAs also had twice asmany large (.250mmtotal length) fish species per transect, five timesmore large fish biomass, and fourteen times more shark biomass than fished areas. Most (59{\%}) of the MPAs studied had only one or two key features and were not ecologically distinguishable from fished sites. Our results show that global conservation targets based on area alonewillnot optimize protectionofmarine biodiversity.More emphasis is needed on better MPA design, durable management andcomplianceto ensure thatMPAs achieve their desiredconserva- tion}, annote = {MPAs have been used around the world as a conservation and management tool. However, many MPAs fail to meet their objectives. The reason why MPAs fail is not always clear. Five key features have been identified for a MPA to be successful: no take, enforcement, old ({\textgreater}10year), large ({\textgreater}100km{\^{}}2), and isolated. Edgar et al 2014 used MPAs that fulfilled 4 to 5 of these features to unfished standards, including Cocos Island. MPA isolation was the strongest predictor of increased fish biomass. The study acknowledges that impact estimates are probably conservation because of the assumption that MPAs with 4 to 5 NEOLI features were considered to be unfished baselines. Compared measurements at MPA to predictions for MPA locations if fishing was allowed.}, author = {Edgar, Graham J. and Stuart-Smith, Rick D. and Willis, Trevor J. and Kininmonth, Stuart and Baker, Susan C. and Banks, Stuart and Barrett, Neville S. and Becerro, Mikel a. and Bernard, Anthony T. F. and Berkhout, Just and Buxton, Colin D. and Campbell, Stuart J. and Cooper, Antonia T. and Davey, Marlene and Edgar, Sophie C. and F{\"{o}}rsterra, G{\"{u}}nter and Galv{\'{a}}n, David E. and Irigoyen, Alejo J. and Kushner, David J. and Moura, Rodrigo and Parnell, P. Ed and Shears, Nick T. and Soler, German and Strain, Elisabeth M. a. and Thomson, Russell J.}, doi = {10.1038/nature13022}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Edgar et al. - 2014 - Global conservation outcomes depend on marine protected areas with five key features.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Edgar et al. - 2014 - Global conservation outcomes depend on marine protected areas with five key features(2).pdf:pdf}, issn = {0028-0836}, journal = {Nature}, keywords = {cocos,conservation,mpa}, mendeley-tags = {cocos,conservation,mpa}, month = {feb}, number = {0}, pages = {216--220}, title = {{Global conservation outcomes depend on marine protected areas with five key features}}, url = {http://www.nature.com/doifinder/10.1038/nature13022 evernote:///view/68547643/s399/44b4d47e-acc3-4eb9-8641-802b608955e3/44b4d47e-acc3-4eb9-8641-802b608955e3/}, volume = {506}, year = {2014} } @article{Brunnschweiler2014, abstract = {Diving with sharks, often in combination with food baiting/provisioning, has become an important product of today's recreational dive industry. Whereas the effects baiting/provisioning has on the behaviour and abundance of individual shark species are starting to become known, there is an almost complete lack of equivalent data from multi-species shark diving sites. In this study, changes in species composition and relative abundances were determined at the Shark Reef Marine Reserve, a multi-species shark feeding site in Fiji. Using direct observation sampling methods, eight species of sharks (bull shark Carcharhinus leucas, grey reef shark Carcharhinus amblyrhynchos, whitetip reef shark Triaenodon obesus, blacktip reef shark Carcharhinus melanopterus, tawny nurse shark Nebrius ferrugineus, silvertip shark Carcharhinus albimarginatus, sicklefin lemon shark Negaprion acutidens, and tiger shark Galeocerdo cuvier) displayed inter-annual site fidelity between 2003 and 2012. Encounter rates and/or relative abundances of some species changed over time, overall resulting in more individuals (mostly C. leucas) of fewer species being encountered on average on shark feeding dives at the end of the study period. Differences in shark community composition between the years 2004-2006 and 2007-2012 were evident, mostly because N. ferrugineus, C. albimarginatus and N. acutidens were much more abundant in 2004-2006 and very rare in the period of 2007-2012. Two explanations are offered for the observed changes in relative abundances over time, namely inter-specific interactions and operator-specific feeding protocols. Both, possibly in combination, are suggested to be important determinants of species composition and encounter rates, and relative abundances at this shark provisioning site in Fiji. This study, which includes the most species from a spatially confined shark provisioning site to date, suggests that long-term provisioning may result in competitive exclusion among shark species.}, annote = {The effect of shark provisioning dive operations on elasmobranch community structure is not well known. In Fiji, a particular baited shark feeding site (Shark Reef Marine Reserve) sees up to eight species of sharks. A single dive company has conducted trips to the site 3-4 times a week, since 2003. Over the course of the study, more individuals of fewer species were seen. The authors suggest that either inter-specific interactions among species or operator-specific feeding protocals may be the reasons for this. The paper suggests that C. leucas excluded the smaller reef sharks from the provisoining site. Strong seasonal trends were also seen for most species. Paper discusses a number of important points for comparing to Cocos: -increase of larger species compared to small species -some species are migratory while others are not -strong seasonal trends -change in elasmobranch community assemblage Meyer et al found that increasing abundance of Galapagos and tiger sharks eventually ecluded smaller sandbar sharks at a provisioning dive site in Hawaii. Clarke et al found that at a baited dive site, silky sharks increased significantly while grey reef sharks saw a large decline. Shortly therafter, silky sharks also declined.}, author = {Brunnschweiler, Juerg M and Abrantes, K{\'{a}}tya G and Barnett, Adam}, doi = {10.1371/journal.pone.0086682}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brunnschweiler, Abrantes, Barnett - 2014 - Long-term changes in species composition and relative abundances of sharks at a provisioning.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {conservation,elasmobranch,shark}, mendeley-tags = {conservation,elasmobranch,shark}, month = {jan}, number = {1}, pages = {e86682}, pmid = {24466197}, title = {{Long-term changes in species composition and relative abundances of sharks at a provisioning site}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3900589{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {9}, year = {2014} } @article{Baum2010, abstract = {We estimate recent (1992–2005) trends in relative abundance for Northwest Atlantic oceanic and large coastal sharks, using generalized linear mixed models to standardize catch rates of eight species groups as recorded by U.S. pelagic longline fishery observers. Models suggest precipitous (76{\%}) declines in ham- merhead (Sphyrna species) and large coastal (dusky, night, and silky shark, genus Carcharhinus) species, and moderate declines (53{\%}) in blue and oceanic whitetip sharks over this period. In contrast, mako and thresher sharks appear to have stabilized, and the tiger shark population appears to be increasing. A comparison of nominal shark catch rates from this fleet's observer and logbook data (to evaluate the veracity of trends previously estimated from the latter) showed a high degree of concordance for each species group, both in individual sub-areas and overall. Models of these two datasets for the common time period (1992–2000) show that compared to the observer data the logbook data indicate greater declines for some species, but lesser declines for others. Signs of recovery for some shark species are encouraging, but must also be set in the context of the significant declines that occurred in previous decades.}, author = {Baum, Julia K. and Blanchard, Wade}, doi = {10.1016/j.fishres.2009.11.006}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Baum, Blanchard - 2010 - Inferring shark population trends from generalized linear mixed models of pelagic longline catch and effort dat.pdf:pdf}, issn = {01657836}, journal = {Fisheries Research}, keywords = {bycatch,cpue,glmm,shark}, mendeley-tags = {bycatch,glmm,shark}, month = {mar}, number = {3}, pages = {229--239}, title = {{Inferring shark population trends from generalized linear mixed models of pelagic longline catch and effort data}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0165783609003087}, volume = {102}, year = {2010} } @article{Barnett2012, abstract = {Although marine protected areas (MPAs) are a common conservation strategy, these areas are often designed with little prior knowledge of the spatial behaviour of the species they are designed to protect. Currently, the Coral Sea area and its seamounts (north-east Australia) are under review to determine if MPAs are warranted. The protection of sharks at these seamounts should be an integral component of conservation plans. Therefore, knowledge on the spatial ecology of sharks at the Coral Sea seamounts is essential for the appropriate implementation of management and conservation plans. Acoustic telemetry was used to determine residency, site fidelity and spatial use of three shark species at Osprey Reef: whitetip reef sharks Triaenodon obesus, grey reef sharks Carcharhinus amblyrhynchos and silvertip sharks Carcharhinus albimarginatus. Most individuals showed year round residency at Osprey Reef, although five of the 49 individuals tagged moved to the neighbouring Shark Reef (,14 km away) and one grey reef shark completed a round trip of ,250 km to the Great Barrier Reef. Additionally, individuals of white tip and grey reef sharks showed strong site fidelity to the areas they were tagged, and there was low spatial overlap between groups of sharks tagged at different locations. Spatial use at Osprey Reef by adult sharks is generally restricted to the north-west corner. The high residency and limited spatial use of Osprey Reef suggests that reef sharks would be highly vulnerable to targeted fishing pressure and that MPAs incorporating no-take of sharks would be effective in protecting reef shark populations at Osprey and Shark Reef. Citation:}, annote = {My summary:      MPAs are often used as a conservation strategy without knowledge on the spatial movement of species the MPA is supposed to protect. This paper is the first to provide information on shark movement in a proposed MPA (as opposed to an MPA already in place). To examine these questions, they tagged sharks and set up an array of Vemco monitors. They found that both whitetip reef sharks and silver tips showed high site fidelity and limited spatial use. Because the study was done an isolated oceanic island, I can use some of the results in the Cocos paper. They argue that because of the limited spatial use among sharks at the reef, that a MPA would be an effective conservation tool.}, author = {Barnett, Adam and Abrantes, K{\'{a}}tya G and Seymour, Jamie and Fitzpatrick, Richard}, doi = {10.1371/journal.pone.0036574}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Barnett et al. - 2012 - Residency and spatial use by reef sharks of an isolated seamount and its implications for conservation.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {Animals,Conservation of Natural Resources,Sharks,Sharks: physiology,cocos,elasmobranch}, mendeley-tags = {cocos,elasmobranch}, month = {jan}, number = {5}, pages = {e36574}, pmid = {22615782}, title = {{Residency and spatial use by reef sharks of an isolated seamount and its implications for conservation}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3353940{\&}tool=pmcentrez{\&}rendertype=abstract evernote:///view/68547643/s399/6a72bf9a-2f34-415c-9e65-1717b6516072/6a72bf9a-2f34-415c-9e65-1717b6516072/}, volume = {7}, year = {2012} } @article{Hooper2012, annote = {It is well understood that biodiversity loss will impact ecosystem processes. It is less clear how biodiversity loss compares to other environmental changes (e.g. CO2, pollution) changing ecosystem processes and function. This paper finds that biodiversity loss can have as much impact on productivity and decompsition as other environmental changes. The biodiversity loss the more pronouced it's effect on ecosystem processes. Specifically, it less than 20{\%} of species were loss in a community, little change would result. With species loss greater than 40{\%}, diversity loss will play as large of a role in ecosystem funciton as warming, ozone and acidification. -productivity increases with invasive species}, author = {Hooper, David U and Adair, E Carol and Cardinale, Bradley J and Byrnes, Jarrett E K and Hungate, Bruce A and Matulich, Kristin L and Gonzalez, Andrew and Duffy, J Emmett and Gamfeldt, Lars and Connor, Mary I O}, doi = {10.1038/nature11118}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hooper et al. - 2012 - A global synthesis reveals biodiversity loss as a major driver of ecosystem change.pdf:pdf}, issn = {0028-0836}, journal = {Nature}, keywords = {Biodiversity,biodiversity,review}, mendeley-tags = {biodiversity,review}, number = {7401}, pages = {105--108}, publisher = {Nature Publishing Group}, title = {{A global synthesis reveals biodiversity loss as a major driver of ecosystem change}}, url = {http://dx.doi.org/10.1038/nature11118}, volume = {486}, year = {2012} } @article{Whatmough2011, abstract = {Humanvalues, perceptions, attitudes and interactions with the natural environment have been found to change over time, with social and economic information used to inform management decisions and actions. Content analysis is applied here to a 53-year long collection of the popular dive magazine, SportDiving, to identify recreational divers' experiences with regard to sharks and rays, the Great Barrier Reef (GBR) and marine protected areas (MPAs). This analysis suggests there has been a diversification of diver activities with the emergence of passive-observational activities such as SCUBA diving. Attitudes towards sharks and rays have changed significantly, with recreational divers changing from a group that could be described as adventure-seeking hunters to a group that can be described as nature-appreciating observers, suggesting an increase in conservation awareness. TheGBRcontinues to be a highly regarded dive destination, with divers perceiving positive effects of protection within MPAs. However, declines in the abundance of large fish and sharks and rays were occasionally reported throughout the 53 year period. Collectively, these types of data can show changes in resource-use patterns, perceptions and attitudes and provide information that supplements scientific monitoring data. These data may be valuable where scientific data is scarce, historical records difficult to obtain, and where attitudinal change}, author = {Whatmough, Sally and {Van Putten}, Ingrid and Chin, Andrew}, doi = {10.1071/MF10142}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Whatmough, Van Putten, Chin - 2011 - From hunters to nature observers a record of 53 years of diver attitudes towards sharks and rays an.pdf:pdf}, issn = {1323-1650}, journal = {Marine and Freshwater Research}, keywords = {scuba,shark}, mendeley-tags = {scuba,shark}, number = {6}, pages = {755}, title = {{From hunters to nature observers: a record of 53 years of diver attitudes towards sharks and rays and marine protected areas}}, url = {http://www.publish.csiro.au/?paper=MF10142 evernote:///view/68547643/s399/1f4a388d-eaf3-490b-a43f-4b4f24723572/1f4a388d-eaf3-490b-a43f-4b4f24723572/}, volume = {62}, year = {2011} } @article{Jeyasingh2014, abstract = {Understanding the ecological consequences of evolutionary change is a central challenge in contemporary biology. We propose a framework based on the {\~{}}25 elements represented in biology, which can serve as a conduit for a general exploration of poorly understood evolution-to-ecology links. In this framework, known as ecological stoichiometry, the quantity of elements in the inorganic realm is a fundamental environment, while the flow of elements from the abi- otic to the biotic realm is due to the action of genomes, with the unused ele- ments excreted back into the inorganic realm affecting ecological processes at higher levels of organization. Ecological stoichiometry purposefully assumes dis- tinct elemental composition of species, enabling powerful predictions about the ecological functions of species. However, this assumption results in a simplified view of the evolutionary mechanisms underlying diversification in the elemental composition of species. Recent research indicates substantial intraspecific varia- tion in elemental composition and associated ecological functions such as nutri- ent excretion. We posit that attention to intraspecific variation in elemental composition will facilitate a synthesis of stoichiometric information in light of population genetics theory for a rigorous exploration of the ecological conse- quences of evolutionary change.}, annote = {Paper notes: Seminar notes: -ranna's research eco-evo dynamics of guppies in lakes with and without predators -how life history traits evolve -she found that 90{\%} of so of variability in elemental compensation is due to the environent (i.e. river) instead of prescence of predators -need more info on interspecific variability -do elemental ratios change over lifetime -do elemental ratios actually vary with certain life history traits? -could plot life history traits (age at maturity) versus elemental ratios -}, author = {Jeyasingh, Punidan D. and Cothran, Rickey D. and Tobler, Michael}, doi = {10.1002/ece3.950}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Jeyasingh, Cothran, Tobler - 2014 - Testing the ecological consequences of evolutionary change using elements.pdf:pdf}, issn = {20457758}, journal = {Ecology and Evolution}, keywords = {consumer-driven nutrient recycling,eco loop,eco-evo-,eco-evolutionary dynamics,ecological stoichiometry,evolution,intraspecific,review,stoichiometry}, mendeley-tags = {evolution,review,stoichiometry}, month = {jan}, pages = {n/a--n/a}, title = {{Testing the ecological consequences of evolutionary change using elements}}, url = {http://doi.wiley.com/10.1002/ece3.950}, year = {2014} } @article{White2007, abstract = {Body size is perhaps the most fundamental property of an organism and is related to many biological traits, including abundance. The relationship between abun- dance and body size has been extensively studied in an attempt to quantify the form of the relationship and to understand the processes that generate it. However, progress has been impeded by the underappreciated fact that there are four distinct, but interrelated, relation- ships between size and abundance that are often con- fused in the literature. Here, we review and distinguish between these four patterns, and discuss the linkages between them.Weargue that a synthetic understanding of size–abundance relationships will result from more detailed analyses of individual patterns and from careful consideration of how and why the patterns are related.}, author = {White, Ethan P and Ernest, S K Morgan and Kerkhoff, Andrew J and Enquist, Brian J}, doi = {10.1016/j.tree.2007.03.007}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/White et al. - 2007 - Relationships between body size and abundance in ecology.pdf:pdf}, journal = {TRENDS in Ecology and Evolution}, keywords = {body size,review,scale}, mendeley-tags = {body size,review,scale}, number = {6}, pages = {323--330}, title = {{Relationships between body size and abundance in ecology}}, volume = {22}, year = {2007} } @article{Schindler2010, abstract = {One of the most pervasive themes in ecology is that biological diversity stabilizes ecosystem processes and the services they provide to society, a concept that has become a common argument for biodiversity conservation. Species-rich communities are thought to produce more temporally stable ecosystem services because of the complementary or independent dynamics among species that perform similar ecosystem functions. Such variance dampening within communities is referred to as a portfolio effect and is analogous to the effects of asset diversity on the stability of financial portfolios. In ecology, these arguments have focused on the effects of species diversity on ecosystem stability but have not considered the importance of biologically relevant diversity within individual species. Current rates of population extirpation are probably at least three orders of magnitude higher than species extinction rates, so there is a pressing need to clarify how population and life history diversity affect the performance of individual species in providing important ecosystem services. Here we use five decades of data from Oncorhynchus nerka (sockeye salmon) in Bristol Bay, Alaska, to provide the first quantification of portfolio effects that derive from population and life history diversity in an important and heavily exploited species. Variability in annual Bristol Bay salmon returns is 2.2 times lower than it would be if the system consisted of a single homogenous population rather than the several hundred discrete populations it currently consists of. Furthermore, if it were a single homogeneous population, such increased variability would lead to ten times more frequent fisheries closures. Portfolio effects are also evident in watershed food webs, where they stabilize and extend predator access to salmon resources. Our results demonstrate the critical importance of maintaining population diversity for stabilizing ecosystem services and securing the economies and livelihoods that depend on them. The reliability of ecosystem services will erode faster than indicated by species loss alone.}, annote = {In ecology, the portfolio effect refers to the notion that stability would increase in a more species-rich community because variance in population size of different species would level out. However, the portfolio effect has rarely been examined within an individual species contet. This could be at a population, indivudal, or genetic level. In this study, the authors examine a number of different salmon stocks of the same species. They find that individual stocks are much less stable than the entire population. They found that if the stocks were examined as a single group variability would be 2.2 times lower than when they are managed per stock. Class discussion:}, author = {Schindler, Daniel E and Hilborn, Ray and Chasco, Brandon and Boatright, Christopher P and Quinn, Thomas P and Rogers, Lauren a and Webster, Michael S}, doi = {10.1038/nature09060}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Schindler et al. - 2010 - Population diversity and the portfolio effect in an exploited species.pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {Alaska,Animal Migration,Animals,Biodiversity,Biological,Extinction,Fisheries,Fisheries: economics,Food Chain,Geography,Models,Population Dynamics,Probability,Rivers,Salmon,Salmon: classification,Salmon: physiology,Species Specificity,biodiversity,ecology,fisheries}, mendeley-tags = {biodiversity,ecology,fisheries}, month = {jun}, number = {7298}, pages = {609--12}, pmid = {20520713}, publisher = {Nature Publishing Group}, title = {{Population diversity and the portfolio effect in an exploited species}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20520713}, volume = {465}, year = {2010} } @book{Otto2007, address = {Princeton, New Jersey}, annote = {Chapter 1:}, author = {Otto, Sarah P. and Day, Troy}, edition = {1}, keywords = {mathematics,model}, mendeley-tags = {mathematics,model}, pages = {732}, publisher = {Princeton University Press}, title = {{A Biologist's Guide to Mathematical Modeling in Ecology and Evolution}}, url = {evernote:///view/68547643/s399/18585437-ea5b-4bc9-950d-defbb60675db/18585437-ea5b-4bc9-950d-defbb60675db/}, year = {2007} } @article{Desjardins-Proulx2013, abstract = {open science; public}, annote = {There is typically a long delay between the completion of a manuscript and it{\&}{\#}039;s official publication. Preprints are used in many fields (e.g. physics and mathematics) but are not widely accepted in biology. Preprints have four primary advantages: 1) quicker dissemntation of work; 2) visibility for early-career scientists; 3) improved peer review; 4) a fair way to credit discoveries. A number of jounals (mostly non-Bristish) have no problem with manuscripts uploaded to preprint services. }, author = {Desjardins-Proulx, Philippe and White, Ethan P and Adamson, Joel J and Ram, Karthik and Poisot, Timoth{\'{e}}e and Gravel, Dominique}, doi = {10.1371/journal.pbio.1001563}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Desjardins-Proulx et al. - 2013 - The Case for Open Preprints in Biology.pdf:pdf}, issn = {1545-7885}, journal = {PLoS Biology}, keywords = {Biology,Humans,Internet,Publications,Publications: trends,Publishing,Publishing: trends}, month = {jan}, number = {5}, pages = {e1001563}, pmid = {23690752}, title = {{The Case for Open Preprints in Biology}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3653830{\&}tool=pmcentrez{\&}rendertype=abstract evernote:///view/68547643/s399/9b778233-77d2-44f3-befa-f4ac45a7cbc6/9b778233-77d2-44f3-befa-f4ac45a7cbc6/}, volume = {11}, year = {2013} } @article{Wilson2014, annote = {Scientists spend 30{\%} of their time developing software yet only 10{\%} have any formal training in typical software practices. This paper reviews a number of "best practices" for scientists: -write programs for people, not computers -let the computer do the work -make incremental changes -don't repeat yourself -plan for mistakes -optimize software only after you know it works correctly -document design and purpose (versus mechanics of script) -collaborate The paper provides further examples and points to programs like Software Carpentry. Wilson G (2013). Software carpentry: lessons learned. arXiv:1307.5448. Available: http://arxiv.org/abs/1307.5448.}, author = {Wilson, Greg and Aruliah, D a and Brown, C Titus and {Chue Hong}, Neil P and Davis, Matt and Guy, Richard T and Haddock, Steven H D and Huff, Kathryn D and Mitchell, Ian M and Plumbley, Mark D and Waugh, Ben and White, Ethan P and Wilson, Paul}, doi = {10.1371/journal.pbio.1001745}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Wilson et al. - 2014 - Best practices for scientific computing.pdf:pdf}, issn = {1545-7885}, journal = {PLoS Biol}, keywords = {model,open science,statistics}, mendeley-tags = {model,open science,statistics}, month = {jan}, number = {1}, pages = {e1001745}, pmid = {24415924}, title = {{Best practices for scientific computing}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3886731{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {12}, year = {2014} } @article{Sutherland2013, annote = {Paper looks at the history of Ecology over the past 100 years to identify 100 fundamental questions. -Issues with how they surveyed people and selected questions -Questions are still fairly general Read War of Wounds- Paul Elictch}, author = {Sutherland, William J and Freckleton, Robert P and Godfray, H Charles J and Beissinger, Steven R and Benton, Tim and Cameron, Duncan D and Carmel, Yohay and Coomes, David A and Coulson, Tim and Emmerson, Mark C and Hails, Rosemary S and Hays, Graeme C and Hodgson, Dave J and Hutchings, Michael J and Johnson, David and Jones, Julia P G and Keeling, Matt J and Kokko, Hanna and Kunin, William E and Lambin, Xavier and Lewis, Owen T and Malhi, Yadvinder and Mieszkowska, Nova and Milner-Gulland, E J and Norris, Ken and Phillimore, Albert B and Purves, Drew W and Reid, Jane M and Reuman, Daniel C and Thompson, Ken and Travis, Justin M J and Turnbull, Lindsay A and Wardle, David A and Wiegand, Thorsten}, doi = {10.1111/1365-2745.12025}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sutherland et al. - 2013 - Identification of 100 fundamental ecological questions.pdf:pdf}, journal = {Journal of Ecology}, keywords = {ecology,history,open science,review}, mendeley-tags = {ecology,history,open science,review}, pages = {58--67}, title = {{Identification of 100 fundamental ecological questions}}, volume = {101}, year = {2013} } @article{Rooney2006, abstract = {Untangling the influence of human activities on food-web stability and persistence is complex given the large numbers of species and overwhelming number of interactions within ecosystems. Although biodiversity has been associated with stability, the actual structures and processes that confer stability to diverse food webs remain largely unknown. Here we show that real food webs are structured such that top predators act as couplers of distinct energy channels that differ in both productivity and turnover rate. Our theoretical analysis shows that coupled fast and slow channels convey both local and non-local stability to food webs. Alarmingly, the same human actions that have been implicated in the loss of biodiversity also directly erode the very structures and processes that we show to confer stability on food webs.}, annote = {Class discussion: -fast (strong interactions) and slow energy channels between nodes in a food web}, author = {Rooney, Neil and McCann, Kevin and Gellner, Gabriel and Moore, John C.}, doi = {10.1038/nature04887}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Rooney et al. - 2006 - Structural asymmetry and the stability of diverse food webs.pdf:pdf}, issn = {1476-4687}, journal = {Nature}, keywords = {Animals,Biodiversity,Biological,Food Chain,Humans,Marine Biology,Models,Predatory Behavior,Predatory Behavior: physiology,Soil,diversity,model}, mendeley-tags = {diversity,model}, month = {jul}, number = {7100}, pages = {265--9}, pmid = {16855582}, title = {{Structural asymmetry and the stability of diverse food webs}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16855582}, volume = {442}, year = {2006} } @article{Cahill2013, abstract = {Anthropogenic climate change is predicted to be a major cause of species extinctions in the next 100 years. Butwhatwill actually cause these extinctions? For example, will it be limited physiological tolerance to high temperatures, changing biotic interactions or other factors? Here, we systematically review the proximate causes of climate-change related extinctions and their empirical support. We find 136 case studies of climatic impacts that are potentially rel- evant to this topic. However, only seven identified proximate causes of demonstrated local extinctions due to anthropogenic climate change. Among these seven studies, the proximate causes vary widely. Surprisingly, none showa straightforward relationship between local extinction and limited toler- ances to high temperature. Instead,many studies implicate species interactions as an important proximate cause, especially decreases in food availability.We find very similar patterns in studies showing decreases in abundance associ- ated with climate change, and in those studies showing impacts of climatic oscillations. Collectively, these results highlight our disturbingly limited knowledge of this crucial issue but also support the idea that changing species interactions are an important cause of documented population declines and extinctions related to climate change. Finally, we briefly outline general research strategies for identifying these proximate causes in future studies. 1.}, author = {Cahill, Abigail E and Aiello-lammens, Matthew E and Fisher-reid, M Caitlin and Hua, Xia and Karanewsky, Caitlin J and Ryu, Hae Yeong and Sbeglia, Gena C and Spagnolo, Fabrizio and Waldron, John B and Warsi, Omar and John, J and Wiens, John J}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Cahill et al. - 2013 - How does climate change cause extinction.pdf:pdf}, journal = {Proceedings of the Royal Society B}, keywords = {biodiversity,climate change}, mendeley-tags = {biodiversity,climate change}, number = {20121890}, pages = {1--9}, title = {{How does climate change cause extinction?}}, volume = {280}, year = {2013} } @article{Dapp2013, abstract = {We used data collected by an observer program to assess the impact of the Costa Rican longline fishery on numbers, capture locations, seasonality and body sizes of silky sharks (Carcharhinus falciformis), pelagic thresher sharks (Alopias pelagicus), olive ridley turtles (Lepidochelys olivacea) and other bycatch species in the Central American Pacific. The longline fishery caught a large number of mahi-mahi (Coryphaena sp.) and silky sharks, but also caught a large number of olive ridley turtles and pelagic stingrays (Pteroplatytrygon violacea). We esti- mated that longline fisheries caught 699,600 olive ridleys, including 92,300 adult females, from 1999 to 2010. These captureswere associatedwith a decline of nesting populations atnearby arribada beaches. Therewere sta- tistically significant size decreases from1999 to 2010 inmature olive ridley turtles and from2003 to 2010 in silky sharks. Average fork length of silky sharks in 2010 was 97.3 cm, which was far below observed fork length at maturity, 144 cm. Pelagic thresher sharks were small and fluctuated in size over the study period. Capture of large numbers of juvenile blacktip sharks (Carcharhinus limbatus) indicated a nursery area near the Osa Peninsula. Geospatial analysis indicated shifts inmahi-mahi abundanceona temporal scalebutfishing efforts didnot shiftwith the shift in mahi-mahi abundance. Yellowfintuna(Thunnus albacares), Indo-Pacific bluemarlin (Makairamazara) and Indo-Pacificsailfish (Istiophorus platypterus) catches varied seasonally and were most abundant out to sea and south of Panama. Marine protected areas and/or time area closures are needed to reduce the impact of the Costa Rican longline fishery on sea turtles and sharks.}, annote = {-study looks at Costa Rican longline data from 1999-2010 -see declines in population numbers and the size of the fish {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -citations for longline fishing, trophic cascades}, author = {Dapp, Derek and Arauz, Randall and Spotila, James R. and O'Connor, Michael P.}, doi = {10.1016/j.jembe.2013.07.014}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dapp et al. - 2013 - Impact of Costa Rican longline fishery on its bycatch of sharks, stingrays, bony fish and olive ridley turtles (Lep.pdf:pdf}, isbn = {2158951273}, issn = {00220981}, journal = {Journal of Experimental Marine Biology and Ecology}, keywords = {Geospatial analysis,Longline fishery,Marine conservation,Marine protected areas,Observer program,Populations}, month = {oct}, pages = {228--239}, publisher = {Elsevier B.V.}, title = {{Impact of Costa Rican longline fishery on its bycatch of sharks, stingrays, bony fish and olive ridley turtles (Lepidochelys olivacea)}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0022098113002852}, volume = {448}, year = {2013} } @article{Kraft2011, abstract = {Understanding spatial variation in biodiversity along environmental gradients is a central theme in ecology. Differences in species compositional turnover among sites ($\beta$ diversity) occurring along gradients are often used to infer variation in the processes structuring communities. Here, we show that sampling alone predicts changes in $\beta$ diversity caused simply by changes in the sizes of species pools. For example, forest inventories sampled along latitudinal and elevational gradients show the well-documented pattern that $\beta$ diversity is higher in the tropics and at low elevations. However, after correcting for variation in pooled species richness ($\gamma$ diversity), these differences in $\beta$ diversity disappear. Therefore, there is no need to invoke differences in the mechanisms of community assembly in temperate versus tropical systems to explain these global-scale patterns of $\beta$ diversity.}, annote = {This study tries to determine what the actual drivers of beta diversity gradients are. They find that beta diversity gradients (both in latitude and elevation) disappear when accounting for gamma diversity using a null modeling approach. This implies that beta diversity gradients is more likely driven by gamma diversity rather than mechanisms of small scale community assembly.}, author = {Kraft, Nathan J.B. and Comita, Liza S. and Chase, Jonathan M. and Sanders, Nathan J. and Swenson, Nathan G. and Crist, Thomas O. and Stegen, James C. and Vellend, Mark and Boyle, Brad and Anderson, Marti J. and Cornell, Howard V. and Davies, Kendi F. and Freestone, Amy L. and Inouye, Brian D. and Harrison, Susan P. and Myers, Jonathan A.}, doi = {10.1126/science.1208584}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kraft et al. - 2011 - Disentangling the drivers of $\beta$ diversity along latitudinal and elevational gradients.pdf:pdf}, issn = {1095-9203}, journal = {Science}, keywords = {Altitude,Biodiversity,Biological,Climate,Ecosystem,Environment,Geography,Models,Plants,Trees,biodiversity,global}, mendeley-tags = {biodiversity,global}, month = {sep}, number = {6050}, pages = {1755--8}, pmid = {21940897}, title = {{Disentangling the drivers of $\beta$ diversity along latitudinal and elevational gradients}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21940897}, volume = {333}, year = {2011} } @incollection{Kingsland1991, abstract = {none}, address = {Chicago}, annote = {A good review of the field of ecology. The paper puts ecology in the context of evolutionary theory and details the contributions of all the major players. -first work on populations by Malthus 1798 --realized that populations would grow indefinitely if left unchecked --Darwin turned this logic around to animals and realized that overproduction would lead to competition and mortality ---this within species idea of competition was key -a lot of early work in ecology was connected to agriculture -ESA started in 1914/15 -early ecology work was put into the context of evolutionary theory -Grinnell connected competetive exclusion principle and the idea of a niche in 1917 -Russian ecologist, Georgii F. Gause did experimental and mathematical work on the competetive exclusion principle, also tested ideas of Pearl, Lotka and Volterra -first work in mathematical ecology was by Raymond Pearl studying human populations- developed Logisitic curve (discovered by Verhulst a century earlier), also used by Volterra to study competition -Lotka-Volterra models soon followed -Lotkas work influenced Patrick H. Leslie -Georgii F. Gause also tested ideas of Pearl, Lotka and Volterra -Lack, Hutchinson and MacArthur continued work in niches and competition -Nicholson and Bailey developed series of mathematial models to study host-parasite interactions, density effects -work on Genetics by Haldane, Fisher and Wright -Idea of an ecosystem was a key organizing principle}, author = {Kingsland, Sharon E.}, booktitle = {Foundations of Ecology: Classic Papers with Commentaries}, editor = {Brown, Leslie A. Real and Brown, James H.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kingsland - 1991 - Defining Ecology as a Science.pdf:pdf}, keywords = {classic,ecology,review}, mendeley-tags = {classic,ecology,review}, pages = {1--23}, publisher = {The University of Chicago Press}, title = {{Defining Ecology as a Science}}, year = {1991} } @article{McCann2000, abstract = {There exists little doubt that the Earth's biodiversity is declining. The Nature Conservancy, for example, has documented that one-third of the plant and animal species in the United States are now at risk of extinction. The problem is a monumental one, and forces us to consider in depth how we expect ecosystems, which ultimately are our life-support systems, to respond to reductions in diversity. This issue--commonly referred to as the diversity-stability debate--is the subject of this review, which synthesizes historical ideas with recent advances. Both theory and empirical evidence agree that we should expect declines in diversity to accelerate the simplification of ecological communities.}, annote = {Ecologists have long been interested in the relationship between diversity and stability in an ecosystem. A lot of early work hinted at the idea that diversity and stability are in fact poistively correlated. Other modeling and emphircal work found an opposite relationship. Recent work suggests that diversity does give rise to ecosystem stability. This relationship is may be primariuly driven by funcitonal diversity. The connections in a food web may be an important driver in this relationship as well. Class discussion: -good review for time period -conservation relevence at end of article --resistance and resiliance more important for conservation Why should there be high diversity? Ecosystems don't evolve, species do. Does high biodiversity help individual species by making the community more diverse thus stable. Field has gone along two lines -relationship between diversity (various metrics) and stability -mechanisms}, author = {McCann, K. S.}, doi = {10.1038/35012234}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McCann - 2000 - The diversity-stability debate.pdf:pdf}, issn = {0028-0836}, journal = {Nature}, keywords = {Animals,Ecosystem,Food Chain,Plants,biodiversity,review,stability}, mendeley-tags = {biodiversity,review,stability}, month = {may}, number = {6783}, pages = {228--33}, pmid = {10821283}, title = {{The diversity-stability debate.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/10821283}, volume = {405}, year = {2000} } @incollection{McCarthyPossingham2012, address = {Chichester, United Kingdom}, author = {McCarthy, Michael A and Possingham, Hugh P}, booktitle = {Encyclopedia of Environmetrics}, chapter = {Population}, edition = {2}, editor = {El-Shaarawi, A H and Piegorsch, W}, keywords = {book; review; pva}, pages = {2016--2020}, publisher = {John Wiley and Sons}, title = {{Encyclopedia of Environmetrics}}, year = {2012} } @article{Srivastava2004, abstract = {Several recent, high-impact ecological studies feature natural microcosms as tools for testing effects of fragmentation, metacommunity theory or links between biodiversity and ecosystem processes. These studies combine the microcosm advantages of small size, short generation times, contained structure and hierarchical spatial arrangement with advantages of field studies: natural environmental variance, 'openness' and realistic species combinations with shared evolutionary histories. This enables tests of theory pertaining to spatial and temporal dynamics, for example, the effects of neighboring communities on local diversity, or the effects of biodiversity on ecosystem function. Using examples, we comment on the position of natural microcosms in the roster of ecological research strategies and tools. We conclude that natural microcosms are as versatile as artificial microcosms, but as complex and biologically realistic as other natural systems. Research to date combined with inherent attributes of natural microcosms make them strong candidate model systems for ecology.}, annote = {{\textless}m:note{\textgreater}In ecology, few model systems exist for studying questions of interest. There are many benefits to working with models systems: tractability, generality and realism. Natural microcosms may represent an middle-ground between artificial experiments and large-scale studies. Microcosms may be well-suited to study metacommunity theory as multiple microcosms can be located near each other and search as 'patches'. It seems that microcosms are as useful as any experiment or theory-approach. They can elucidate potential mechanisms but if they do not compare to the real world, then our understanding of the system is incorrect. Artifical and natural systems need to be used with theoretical approaches to get a real understanding of ecological questions. {\textless}/m:note{\textgreater}}, author = {Srivastava, Diane S. and Kolasa, Jurek and Bengtsson, Jan and Gonzalez, Andrew and Lawler, Sharon P. and Miller, Thomas E. and Munguia, Pablo and Romanuk, Tamara and Schneider, David C. and Trzcinski, M. Kurtis}, doi = {10.1016/j.tree.2004.04.010}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Srivastava et al. - 2004 - Are natural microcosms useful model systems for ecology.pdf:pdf}, issn = {0169-5347}, journal = {Trends in ecology {\&} evolution}, keywords = {experiment,microcosm,review}, mendeley-tags = {experiment,microcosm,review}, month = {jul}, number = {7}, pages = {379--84}, pmid = {16701289}, title = {{Are natural microcosms useful model systems for ecology?}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/16701289}, volume = {19}, year = {2004} } @article{Speed2010, author = {Speed, C.W. and Field, I.C. and Meekan, M.G. and Bradshaw, C.J.A.}, doi = {10.3354/meps08581}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Speed et al. - 2010 - Complexities of coastal shark movements and their implications for management.pdf:pdf}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, keywords = {depth range,extinction risk,habitat loss,habitat partitioning,harvest,home range,horizontal range,life history,of the publisher,ontogeny,permitted without written consent,resale or republication not,segregation,site fidelity,vertical migration}, month = {jun}, pages = {275--293}, title = {{Complexities of coastal shark movements and their implications for management}}, url = {http://www.int-res.com/abstracts/meps/v408/p275-293/}, volume = {408}, year = {2010} } @article{Hutchinson1959, annote = {-begins with story of species collection that led him to ask why there are so many different species In examining food chains, it is possible to make predictions on the population size or body size of species in each level of the food chain using energy and scaling calculations. Selective forces can lead to the shortening of food chains (e.g. whales on plankton). Body size capabilities also affects the length of a food chain. Terrestrial systems are likely so diverse because of the huge number of plant species. Food chains are, of course, in fact food webs. Invasive species may have different levels of success depending on how stable the community already is (i.e. can invade when the system is weak). Diversity may be limited by primary productivity of the system or the number of niches. It is difficult to figure out how much difference must exist for two similar species to conexist. The mosaic nature of the environment is another way of stating that species colonize areas with different local diversity and different trophic structures. This may also imply that because in differences in trophic position and body size, large and small species may evolve differently. }, author = {Hutchinson, G.E.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hutchinson - 1959 - Homage to Santa Rosalia or Why Are There So Many Kinds of Animals.pdf:pdf}, journal = {American Naturalist}, keywords = {biodiversity,review}, mendeley-tags = {biodiversity,review}, number = {870}, pages = {145--159}, title = {{Homage to Santa Rosalia or Why Are There So Many Kinds of Animals}}, volume = {93}, year = {1959} } @incollection{Real1991, address = {Chicago}, annote = {-General review on the role of theory in ecology over the past 50 years Six main questions from 1950-1990 1) number and relrtive abundance of species in a community 2) niche theory 3) demography and pop dyn of single species 4) multi-species interations 5) population structure- spatial and scale 6) individual behavior 1) -Fisher, Corbet, and Williams on the hollow curve, extended by Preston around 1950, then MacArthur, then May, then Sugihara 2) niche theory being cornerstone of ecology, Huthinson's formal understanding of a niche 3) demography: Life history traits- David Lack, Cole Pop. dyn: Mayr- showed that more comlicated models arent always neccessary, chaos in ecolgoy 5) Multispecies interactions -ross and thompson, furthered my Lotka and Volterra - May 6) space and time A.S. Watt 1947, Skellam 1951,}, author = {Real, Leslie A. and Levin, Simon A.}, booktitle = {Foundations of Ecology: Classic Papers with Commentaries}, edition = {1}, editor = {Real, Leslie A. and Brown, James H.}, keywords = {Ecology,review,theoretical ecology}, pages = {177--191}, publisher = {The University of Chicago Press}, title = {{The Role of Theory in the Rise of Modern Ecology}}, year = {1991} } @article{Ketchum2014, abstract = {Movements and habitat preferences of sharks rel- ative to a central location are widely documented for many species; however, the reasons for such behaviors are cur- rently unknown. Do movements vary spatially or temporally or between individuals? Do sharks have seasonal habitat and environmental preferences or simply perform movements at random at any time of the year? To help understand require- ments for the designation of critical habitats for an endan- gered top predator and to develop zoning and management plans for key habitats, we examined vertical and horizon- tal movements, and determined habitat and environmental preferences of scalloped hammerhead sharks (Sphyrna lewini). We tracked seven hammerheads for 19–96 h at Wolf Island (1.38{\textordmasculine}N, 91.82{\textordmasculine}W) between 2007 and 2009 using ultra- sonic transmitters with depth and temperature sensors, and we profiled temperature through the water column. Move- ments of individual hammerheads fell in two classes: con- strained (remaining near the island) and dispersive (moving offshore to pelagic environments). The central activity space or kernel off the southeast side of Wolf Island was small and common to most, but the area varied among individuals (mean ± SE 0.25 ± 0.2 km2), not exceeding 0.6 km2 for any of the sharks, and not changing significantly between sea- sons. In general, hammerheads showed preference for the up- current habitat on the eastern side of Wolf Island in both the warm and cold seasons. However, the depth of sharks varied with season, apparently in response to seasonal changes in the vertical structure of temperature. Hammerheads performed frequent vertical excursions above the thermocline during offshore movements and, in general, were observed to pre- fer temperatures of 23–26 °C found above the thermocline. At times, though individuals moved into the thermocline and made brief dives below it. Our results provided evidence that hammerheads (1) are highly selective of location (i.e., habitat on up-current side of island) and depth (i.e., top of the ther- mocline) while refuging, where they may carry out essential activities such as cleaning and thermoregulation, and (2) per- form exploratory vertical movements by diving the width of the mixed layer and occasionally diving below the thermo- cline while moving offshore, most likely for foraging.}, annote = {-paper tries to understand short-term movement of scalloped hammerheads and discusses implications for management -seven sharks tagged at Wolf Island for a few days at a time -appear to be highly selective of thier location depending on season and behavior they are performing -good citations for cocos paper -use a series of regressions to compare movement and habitat preference to explanatory variables --upcurrent was most preferred habitat -sharks make pelagic excursions away from the island near dusk -discuss diet of cephalopods and pelagic fish -thermocline determines a lot of their vertical movement It will be interesting to reexamine this paper with more focus on the statistical methods. Their data is inherently correlated in space and time.}, author = {Ketchum, James T. and Hearn, Alex and Klimley, A. Peter and Espinoza, Eduardo and Pe{\~{n}}aherrera, C{\'{e}}sar and Largier, John L.}, doi = {10.1007/s00227-013-2375-5}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ketchum et al. - 2014 - Seasonal changes in movements and habitat preferences of the scalloped hammerhead shark (iSphyrna lewinii) while.pdf:pdf}, issn = {0025-3162}, journal = {Marine Biology}, month = {jan}, title = {{Seasonal changes in movements and habitat preferences of the scalloped hammerhead shark ({\textless}i{\textgreater}Sphyrna lewini{\textless}/i{\textgreater}) while refuging near an oceanic island}}, url = {http://link.springer.com/10.1007/s00227-013-2375-5}, year = {2014} } @article{Heupel2013, abstract = {The decline of predators in a variety of ecosystems has transformed community struc- ture through mesopredator release and trophic cascades. Elasmobranch fishes, one of the earth's most ubiquitous and diverse clade of predatory species, provide a model group for defining mar- ine predator roles. We consider whether the ecological predatory role of sharks is adequately defined by terrestrial-derived notions of apex- and mesopredation. Indeterminate growth and ontogenetic diet shifts may mean species-level classification of predatory roles is inadequate. We propose that examining the trophic level and body size of species might be the most pragmatic and informative way to define the ecological roles of predators. KEY}, annote = {Review paper discussing top-down control exerted by sharks. How does their role compare to terrestrial predators. -need a better definition of a shark's role in an ecosystem, what kind of predator and its role in the system -apex vs mesopredators -stable isotype and diet analyses only account for direct predation. Would it be possible to combine that with other information to see what is more important- direct or indirect effects of predation -body size is important (e.g. similar sized sharks are similar in diet regardless of species) -other changes as animal gets larger: larger home range, energy requirements.. -apex size classes instead of species -argue that most species would probably be mesopredators and therefore provide diffuse predation instead of concentrated -papper by Kitchell 2002 showed that simulated shark removal in open ocean ecosystem affected very litle -make prediction on the effects of an MPA on a reef- where diffuse predation probably dominates }, author = {Heupel, Michelle R. and Knip, Danielle M. and Simpfendorfer, Colin A. and Dulvy, Nicholas K.}, doi = {10.3354/meps10597}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Heupel et al. - 2013 - Sizing up the ecological role of sharks as predators.pdf:pdf}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, keywords = {home range,predation,predation risk,predator,predator-prey interactions,review,shark,top-down control}, mendeley-tags = {predation,predator,review,shark}, pages = {291--298}, title = {{Sizing up the ecological role of sharks as predators}}, url = {http://www.int-res.com/prepress/m10597.html}, volume = {495}, year = {2013} } @article{McGill2010, abstract = {none}, annote = {{\textless}m:note{\textgreater}McGill (2010) discusses the role of scale in ecology. Unlike other sciences (e.g. physics), ecology is scale-dependent. Ecologists have only recently been able to test the theoretical predictions of taking scaling into account. One example involves the seemingly minuscule role competition plays on a continental scale. Scaling is time may or may not be inherently linked to scaling in space. Four main factors are said to affect the distribution of species: climate, species interactions, habitat, and dispersal. Other factors?{\textless}/m:note{\textgreater}}, author = {McGill, Brian J.}, doi = {10.1126/science.1188528}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McGill - 2010 - Matters of scale.pdf:pdf}, issn = {1095-9203}, journal = {Science}, keywords = {Animals,Birds,Climate,Competitive Behavior,Demography,Denmark,Ecosystem,Population Density,Time Factors,review,scale}, mendeley-tags = {review,scale}, month = {apr}, number = {5978}, pages = {575--576}, pmid = {20431001}, title = {{Matters of scale.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/20431001}, volume = {328}, year = {2010} } @article{Carpenter1996, annote = {Microcosm experiments are common and can be extremely useful but they have serious limitations. It is important to remember the scale at which microcosms are able to represent. The onl y way to test the effectiveness of microcosms is by comparing there outputs to larger scale experiments. "It is irresponsible for academic eclogy to produce larval microcosmologists by canalizing graduate students into careers of small-scale experimentation." See Feynman 1985}, author = {Carpenter, Stephen R.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Carpenter - 1996 - Microcosm Experiments have Limited Relevance for Community and Ecosystem Ecology.pdf:pdf}, journal = {Ecology}, keywords = {ecology,experiment,microcosm,review}, mendeley-tags = {ecology,experiment,microcosm,review}, number = {3}, pages = {677--680}, title = {{Microcosm Experiments have Limited Relevance for Community and Ecosystem Ecology}}, volume = {77}, year = {1996} } @article{Mittelbach2007, abstract = {A latitudinal gradient in biodiversity has existed since before the time of the dinosaurs, yet how and why this gradient arose remains unresolved. Here we review two major hypotheses for the origin of the latitudinal diversity gradient. The time and area hypothesis holds that tropical climates are older and historically larger, allowing more opportunity for diversification. This hypothesis is supported by observations that temperate taxa are often younger than, and nested within, tropical taxa, and that diversity is positively correlated with the age and area of geographical regions. The diversification rate hypothesis holds that tropical regions diversify faster due to higher rates of speciation (caused by increased opportunities for the evolution of reproductive isolation, or faster molecular evolution, or the increased importance of biotic interactions), or due to lower extinction rates. There is phylogenetic evidence for higher rates of diversification in tropical clades, and palaeontological data demonstrate higher rates of origination for tropical taxa, but mixed evidence for latitudinal differences in extinction rates. Studies of latitudinal variation in incipient speciation also suggest faster speciation in the tropics. Distinguishing the roles of history, speciation and extinction in the origin of the latitudinal gradient represents a major challenge to future research.}, annote = {The latitudal gradient in biodiversity has remained unexplained. There are two current hypotheses to why it may exist. The time and area hypothesis says the gradient arises from the fact that tropical climates are older and larger which allows for more diversity. The diversification rate hypothesis argues that speciation rates are faster in the tropics. Evolutionary and historical explanations have reemerged because of the lack of support for ecological hypotheses to explain the gradient. Longer durations in the tropical habitats of the world do not seem to explain all of the diversity gradient observed. Therefore speciation rates might be what differs on the globe. Dispersal rates should be higher in species at higher latitudes? Interesting Higher temps may also drive higher extinction rates. }, author = {Mittelbach, Gary G. and Schemske, Douglas W. and Cornell, Howard V. and Allen, Andrew P. and Brown, Jonathan M. and Bush, Mark B. and Harrison, Susan P. and Hurlbert, Allen H. and Knowlton, Nancy and Lessios, Harilaos A. and McCain, Christy M. and McCune, Amy R. and McDade, Lucinda A. and McPeek, Mark A. and Near, Thomas J. and Price, Trevor D. and Ricklefs, Robert E. and Roy, Kaustuv and Sax, Dov F. and Schluter, Dolph and Sobel, James M. and Turelli, Michael}, doi = {10.1111/j.1461-0248.2007.01020.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Mittelbach et al. - 2007 - Evolution and the latitudinal diversity gradient speciation, extinction and biogeography.pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {Animals,Biodiversity,Biological,Biological Evolution,Extinction,Geography,Paleontology,Phylogeny,Plants,biodiversity,evolution,review}, mendeley-tags = {biodiversity,evolution,review}, month = {apr}, number = {4}, pages = {315--31}, pmid = {17355570}, title = {{Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17355570}, volume = {10}, year = {2007} } @article{Gourley2004, abstract = {A Stage Structured Predator-Prey mo del and its Dep endence on Through-Stage Dela y and Death Rate Stephen A. Gourley {\{}$\backslash$S{\}} Y ang Kuang y August 6, 2003 Abstract The w ork of Aiello and F reedman on a single sp ecies gro wth with stage structure has receiv ed m uc h atten tion in the literature in recen t y ears. Their mo del predicts a p ositiv e steady state as the global attractor and th us suggests that stage structure do es not generate the sustained oscillations frequen tly observ ed in nature. This w ork inevitably stirred some con tro v ersy . Subsequen t w orks b y other authors suggest that the time dela y to adultho o d should b e state dep enden t and careful form ulation of suc h state dep enden t time dela y can lead to mo dels that pro duce p erio dic solutions. W e review this w ork from a fresh biological angle: gro wth is a com bined result of birth and death pro cesses, b oth of whic h are closely link ed to the resource supply whic h is dynamic in nature. F rom this basic standp oin t, w e form ulate a general and robust predator-prey mo del with stage structure with constan t maturation time dela y (through-stage time dela y) and p erform a systematic mathematical and computational study . Our w ork indicates that if the juv enile death rate (through-stage death rate) is nonzero, then for small and large v alues of maturation time dela ys, the p opulation dynamics tak es the simple form of a globally attractiv e steady state. Our linear stabilit y w ork sho ws that if the resource is dynamic, as in nature, there is a windo w in maturation time dela y parameter that generates sustainable oscillatory dynamics}, author = {Gourley, Stephen A and Kuang, Yang}, journal = {Journal of Mathematical Biology}, keywords = {predation; stochastic}, number = {2}, pages = {188--200}, title = {{A stage structured predator-prey model and its dependence on maturation delay and death rate}}, volume = {49}, year = {2004} } @article{OvaskainenMeerson2010, author = {Ovaskainen, Otso and Meerson, Baruch}, journal = {Trends in Ecology and Evolution}, keywords = {shark; population model; stochastic}, number = {11}, pages = {643--652}, title = {{Stochastic models of population extinction}}, volume = {25}, year = {2010} } @article{NeubertCaswell2000, author = {Neubert, Michael G and Caswell, Hal}, journal = {Journal of Mathematical Biology}, keywords = {stochastic; population model}, number = {2}, pages = {103--121}, title = {{Density-dependent vital rates and their population dynamic consequences}}, volume = {41}, year = {2000} } @article{Wirsing2008, abstract = {The notion that predators can affect their prey without killing them is widely supported in the ecological literature yet rarely applied by marine mammal studies. We present three case studies in which patterns of time allocation by individual marine mammal foragers were used to index the sublethal effects of predators on bottlenose dolphins ( Tursiops sp.), harbor seals ( Phoca vitulina ), and dugongs ( Dugong dugon ). In each case, foraging individuals optimized energy gain and safety from predators by spending less time in more profitable but dangerous patches or de- creasing their use of risky feeding tactics that would increase net energy gain. By implication, marine mammals are subject to the non consumptive effects of their predators ( i.e. , to intimidation), and fear can mediate their impacts on their resources. We suggest, therefore, that future studies quantify patterns of time allocation to measure sublethal effects of predators on marine mammals, as well as the capacity of arine mammals to have sublethal effects on their own prey. We argue that such an approach is important because non consumptive effects may be of greater magnitude than lethal effects of predators, and information on sublethal effects of predators can inform conservation plans and studies of community structure. }, author = {Wirsing, Aaron J and Heithaus, Michael R and Frid, Alejandro and Dill, Lawrence M}, journal = {Marine Mammal Science}, keywords = {predation; bimini; sharks}, number = {1}, pages = {1--15}, title = {{Seascapes of fear: evaluating sublethal predator effects experienced and generated by marine mammals}}, volume = {24}, year = {2008} } @article{Crouse1987, author = {Crouse, Deborah T and Crowder, Larry B and Caswell, Hal}, journal = {Ecology}, keywords = {population model,sea turtles,shark}, number = {5}, pages = {1412--1423}, title = {{A stage-based population model for loggerhead sea turtles and implications for conservation}}, volume = {68}, year = {1987} } @article{Jenouvrier2012, author = {Jenouvrier, St{\'{e}}phanie and Holland, Marika and Str$\backslash$oeve, Julienne and Barbraud, Christophe and Weimerskirch, Henri and Serreze, Mark and Caswell, Hal}, journal = {Global Change Biology}, keywords = {stochastic; environmental stochasticity}, number = {9}, pages = {2756--2770}, title = {{Effects of climate change on an emperor penguin population: analysis of coupled demographic and climate models}}, volume = {18}, year = {2012} } @book{BrauerCastillo-Chavez2012, author = {Brauer, Fred and Castillo-Ch{\'{a}}vez, Carlos}, keywords = {population model}, publisher = {Springer}, series = {Texts in Applied Mathematics}, title = {{Mathematical models in population biology and epidemiology}}, year = {2012} } @article{Tsai2010, author = {Tsai, Wen-Pei and Liu, Kwang-Ming and Joung, Shoou-Jeng}, journal = {Marine and Freshwater Research}, keywords = {shark; population model}, number = {9}, pages = {1056--1066}, title = {{Demographic analysis of the pelagic thresher shark, $\backslash$emph{\{}Alopias pelagicus{\}}, in the northwestern Pacific using a stochastic stage-based model}}, volume = {61}, year = {2010} } @book{Mills2012, author = {Mills, L Scott}, edition = {2}, keywords = {population model}, publisher = {John Wiley and Sons}, title = {{Conservation of wildlife populations: demography, genetics, and management}}, year = {2012} } @article{Wang2009, abstract = {Population cycles in small mammals have attracted the attention of several generations of theoretical and experimental biologists and continue to generate controversy. Top-down and bottom-up trophic regulations are two recent competing hypotheses. The principal purpose of this paper is to explore the relative contributions of a variety of ecological factors to predator--prey population cycles. Here we suggest that for some species -- collared lemmings, snowshoe hares and moose in particular -- maturation delay of predators and the functional response of predation appear to be the primary determinants. Our study suggests that maturation delay alone almost completely determines the cycle period, whereas the functional response greatly affects its amplitude and even its existence. These results are obtained from sensitivity analysis of all parameters in a mathematical model of the lemming--stoat delayed system, which is an extension of Gilg's model. Our result may also explain why lemmings have a 4-year cycle whereas snowshoe hares have a 10-year cycle. Our parameterized model supports and extends May's assertion that time delay impacts cycle period and amplitude. Furthermore, if maturation periods of predators are too short or too long, or the functional response resembles Holling Type I, then population cycles do not appear; however, suitable intermediate predator maturation periods and suitable functional responses can generate population cycles for both prey and predators. These results seem to explain why some populations are cyclic whereas others are not. Finally, we find parameterizations of our model that generate a 38-year population cycle consistent with the putative cycles of the moose--wolf interactions on Isle Royale, Michigan.}, author = {Wang, Hao and Nagy, John D and Gilg, Olivier and Kuang, Yang}, journal = {Mathematical Biosciences}, keywords = {predation; sharks}, number = {1}, pages = {1--10}, title = {{The roles of predator maturation delay and functional response in determining the periodicity of predator--prey cycles}}, volume = {221}, year = {2009} } @article{Dulvy2013, abstract = {The rapid expansion of human activities threatens ocean-wide biodiversity loss. Numerous marine animal populations have declined, yet it remains unclear whether these trends are symptomatic of a chronic accumulation of global marine extinction risk. We present the first systematic analysis of threat for a globally-distributed lineage of 1,041 chondrichthyan fishes – sharks, rays, and chimaeras. We estimate that one-quarter are threatened according to IUCN Red List criteria due to overfishing (targeted and incidental). Large-bodied, shallow-water species are at greatest risk and five out of the seven most threatened families are rays. Overall chondrichthyan extinction risk is substantially higher than for most other vertebrates, and only one-third of species are considered safe. Population depletion has occurred throughout the world's ice-free waters, but is particularly prevalent in the Indo-Pacific Biodiversity Triangle and Mediterranean Sea. Improved management of fisheries and trade is urgently needed to avoid extinctions and promote population recovery}, annote = {-estimate 1/4 of species are threatened -point our that coastal species are more threatened than pelgaic species -caribbean has most Data Deficient species -use GLMs to compare threat status of species to life history and ecological correlates (max length and depth weere important) -list of laws and policies put into place}, author = {Dulvy, Nicholas K. and Fowler, Sarah L. and Musick, John A. and Cavanagh, Rachel D. and Peter, M. and Harrison, Lucy R. and Carlson, John K. and Davidson, Lindsay N. K. and Sonja, V. and Francis, Malcolm P. and Pollock, Caroline M. and Simpfendorfer, Colin A. and Burgess, H. and Carpenter, Kent E. and Compagno, Leonard J. V. and Ebert, David A. and Stevens, John D. and Valenti, Sarah and White, William T.}, doi = {http://dx.doi.org/10.7554/eLife.00590}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dulvy et al. - 2014 - Extinction risk and conservation of the world's sharks and rays.pdf:pdf}, journal = {eLife}, keywords = {Conservation,conservation,fisheries,shark}, mendeley-tags = {conservation,fisheries,shark}, number = {e00590}, title = {{Extinction risk and conservation of the world's sharks and rays}}, volume = {3}, year = {2014} } @article{Chase2013, abstract = {There is little consensus about how natural (e.g. productivity, disturbance) and anthropogenic (e.g. invasive species, habitat destruction) ecological drivers influence biodiversity. Here, we show that when sampling is standardised by area (species density) or individuals (rarefied species richness), the measured effect sizes depend critically on the spatial grain and extent of sampling, as well as the size of the species pool. This compromises comparisons of effects sizes within studies using standard statistics, as well as among studies using meta-analysis. To derive an unambiguous effect size, we advocate that comparisons need to be made on a scale-independent metric, such as Hurlbert's Probability of Interspecific Encounter. Analyses of this metric can be used to disentangle the relative influence of changes in the absolute and relative abundances of individuals, as well as their intraspecific aggregations, in driving differences in biodiversity among communities. This and related approaches are necessary to achieve generality in understanding how biodiversity responds to ecological drivers and will necessitate a change in the way many ecologists collect and analyse their data.}, annote = {-paper reviews how biodiversity measures can be bias even if standardized by area or with rarefied estimates -adovocate Hurlberts Probablity of Interspecific Encounter (complement of Inverse Simpsons) -ENS versus simpsons or other indexes {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -implications of nonlinear SAC -can get different results depending on sampling grain (area sampled) and number of samples -cannot simply standardize sampling if comparing amongst different communities -the diffeent species pools found in different communties greatly hinders fair comparisons}, author = {Chase, Jonathan M. and Knight, Tiffany M.}, doi = {10.1111/ele.12112}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chase, Knight - 2013 - Scale-dependent effect sizes of ecological drivers on biodiversity why standardised sampling is not enough.pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {biodiversity,distribution,distributions,ecology letters,effect size,intraspecific aggregation,probability of interspecific encounter,rarefaction,species abundance,species-accumulation curve}, mendeley-tags = {biodiversity,distributions}, month = {may}, pages = {17--26}, pmid = {23679009}, title = {{Scale-dependent effect sizes of ecological drivers on biodiversity: why standardised sampling is not enough}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23679009}, year = {2013} } @article{Botta-Dukat2005, author = {Botta-Dukat, Zoltan}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botta-Dukat - 2005 - Rao's quadratic entropy as a measure of functional diversity based on multiple traits.pdf:pdf}, journal = {Journal of Vegetation Science}, keywords = {biodiversity,functional,functional diversity,functional group}, mendeley-tags = {biodiversity,functional diversity}, pages = {533--540}, title = {{Rao's quadratic entropy as a measure of functional diversity based on multiple traits}}, volume = {16}, year = {2005} } @article{Chao2012, abstract = {We propose an integrated sampling, rarefaction, and extrapolation methodology to compare species richness of a set of communities based on samples of equal completeness (as measured by sample coverage) instead of equal size. Traditional rarefaction or extrapolation to equal-sized samples can misrepresent the relationships between the richnesses of the communities being compared because a sample of a given size may be sufficient to fully characterize the lower diversity community, but insufficient to characterize the richer community. Thus, the traditional method systematically biases the degree of differences between community richnesses. We derived a new analytic method for seamless coverage-based rarefaction and extrapolation. We show that this method yields less biased comparisons of richness between communities, and manages this with less total sampling effort. When this approach is integrated with an adaptive coverage-based stopping rule during sampling, samples may be compared directly without rarefaction, so no extra data is taken and none is thrown away. Even if this stopping rule is not used during data collection, coverage-based rarefaction throws away less data than traditional size-based rarefaction, and more efficiently finds the correct ranking of communities according to their true richnesses. Several hypothetical and real examples demonstrate these advantages.}, annote = {-paper explains how traditional rarefraction (which depends on equal-sized samples) is inappropriate and should instead be replaced by sample coverage -coverage-based rarefraction is a better estimator of comparing richnesses across different communities {\_}{\_}{\_}{\_}{\_}{\_}{\_} -final slope of rarefraction curve must be small for community to be sampled well. Slope of this curve is the prob. the next individual sampled will be from a new species -traditional rarefraction estimates lead to large biases in richness values even at larger sample sizes -sample coverage can be estimated simply by knowing the {\#} of individuals sampled and the number of species that are found by detecting just one or two individuals of that particular species -can take multiple communities and read off richness values for any desired coverage level}, author = {Chao, Anne and Jost, Lou}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chao, Jost - 2012 - Coverage-based rarefaction and extrapolation standardizing samples by completeness rather than size.pdf:pdf}, issn = {0012-9658}, journal = {Ecology}, keywords = {Algorithms,Animals,Biological,Ecosystem,Environmental Monitoring,Environmental Monitoring: methods,Genetic Speciation,Models, Biological,Orchidaceae,Orchidaceae: genetics,Population Density,Selection Bias,Species Specificity}, month = {dec}, number = {12}, pages = {2533--47}, pmid = {23431585}, title = {{Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23431585}, volume = {93}, year = {2012} } @article{Botsford2011, annote = {-explore why specific age-structured models may be needed instead of simple ecosystem models -focus on models of fishing and climate change -explain importance of age structure in predicting dynamics in salmon and cod -incldude berveton-holt egg-recruiits relationship in the models (density effects) -try model where adults are lumped into one class to see what happens when age is not explicent -fishing pressure increase variance }, author = {Botsford, L. W. and Holland, M. D. and Samhouri, J. F. and White, J. W. and Hastings, a.}, doi = {10.1093/icesjms/fsr042}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Botsford et al. - 2011 - Importance of age structure in models of the response of upper trophic levels to fishing and climate change.pdf:pdf}, issn = {1054-3139}, journal = {ICES Journal of Marine Science}, keywords = {age structure,climate,fisheries,population modelling,upper trophic levels}, month = {apr}, number = {6}, pages = {1270--1283}, title = {{Importance of age structure in models of the response of upper trophic levels to fishing and climate change}}, url = {http://icesjms.oxfordjournals.org/cgi/doi/10.1093/icesjms/fsr042}, volume = {68}, year = {2011} } @techreport{Kyne2012a, address = {Vancouver, Canada}, annote = {-{\textperiodcentered}       Lemon shark is listed as Near Threatened globally (Sundstrom 2000 and this report) -Broad regional- scale studies are only recently becoming available such as the compiled observations from recreational divers suggesting very low abundance of sharks throughout the Caribbean with the exception of the Bahamas (Ward-Paige et al. 2010). -The Bahamas banned longline fishing in 1993. In 2011, the Bahamas banned commercial shark fishing, sale, and trade. A limited number of sharks from incidental and artisanal catches may be kept and consumed. Permits can be granted for retention and export of sharks for scientific and educational purposes. Sport fishing for sharks is limited to catch and release -information on species from Cocos and nearby sites}, author = {Kyne, Peter M. and Carlson, John K. and Ebert, David A. and Fordham, Sonja V. and Bizzarro, Joseph J. and Graham, Rachel T. and Kulka, David W. and Tewes, Emily E. and Harrison, Lucy R. and Dulvy, Nicholas K.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kyne et al. - 2012 - The Conservation Status of North American, Central American, and Caribbean Chondrichthyans.pdf:pdf}, institution = {IUCN Species Survival Commission Shark Specialist Group}, isbn = {9780956106322}, pages = {148}, title = {{The Conservation Status of North American, Central American, and Caribbean Chondrichthyans}}, year = {2012} } @article{Sutherland2011, abstract = {There is a widely recognized gap between the data generated by researchers and the information required by policy makers. In an effort to bridge the gap between conservation policy and science, we have convened in several countries multiple groups of policy makers, practitioners and research- ers to identify priority information needs that can be met by new research in the social and natural sciences. 2. The exercises we have coordinated included identification of priority policy-relevant research questions in specific geographies (UK, USA, Canada); questions relating to global conservation; questions relating to global agriculture; policy opportunities in the United Kingdom; and emerging global conservation issues or ‘horizon scanning'. 3. We outline the exercises and describe our methods, which are based on principles of inclusivity, openness and democracy. Methods to maximize inclusiveness and rigour in such exercises include solicitation of questions and priorities from an extensive community, online collation of material, repeated voting and engagement with policy networks to foster uptake and application of the results. 4. These methods are transferable to a wide range of policy or research areas within and beyond the conservation}, annote = {-try to identify key questions/problems in conservation work -in UK, Canada, and the US -top priority questions, horizon scanning, }, author = {Sutherland, William J. and Fleishman, Erica and Mascia, Michael B. and Pretty, Jules and Rudd, Murray A.}, doi = {10.1111/j.2041-210X.2010.00083.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sutherland et al. - 2011 - Methods for collaboratively identifying research priorities and emerging issues in science and policy.pdf:pdf}, issn = {2041210X}, journal = {Methods in Ecology and Evolution}, keywords = {collaboration,horizon scanning,participation,policy makers,priority setting}, month = {jun}, number = {3}, pages = {238--247}, title = {{Methods for collaboratively identifying research priorities and emerging issues in science and policy}}, url = {http://doi.wiley.com/10.1111/j.2041-210X.2010.00083.x}, volume = {2}, year = {2011} } @article{Bird2013, abstract = {Networks of citizen scientists (CS) have the potential to observe biodiversity and species distributions at global scales. Yet the adoption of such datasets in conservation science may be hindered by a perception that the data are of low quality. This perception likely stems from the propensity of data generated by CS to contain greater levels of variability (e.g., measurement error) or bias (e.g., spatio-temporal clustering) in comparison to data collected by scientists or instruments. Modern analytical approaches can account for many types of error and bias typical of CS datasets. It is possible to (1) describe how pseudo-replica- tion in sampling influences the overall variability in response data using mixed-effects modeling, (2) inte- grate data to explicitly model the sampling process and account for bias using a hierarchical modeling framework, and (3) examine the relative influence of many different or related explanatory factors using machine learning tools. Information from these modeling approaches can be used to predict species dis- tributions and to estimate biodiversity. Even so, achieving the full potential from CS projects requires meta-data describing the sampling process, reference data to allow for standardization, and insightful modeling suitable to the question of interest.}, annote = {-paper discusses how to overcome issues typically associated with citizen science data -different types of models to account for pseaudo-replicaiton, sampling bias, explantatory variables -some applicaitons to the jupiter and cocos papers {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -common problem is non-random distribution of effort (i.e. people survey where it is easy or comfortable for them) - in Cocos they survey where the diving is good -machine learning is useful when large numbers of predictors are used -false vs. true zeros -observers and sites as random variables -Arab et al 2008- zero inflated models -use of machine learning algorithems -dscuss how to account for variation in sampling and detectability variance weighting model for clustered data like the shark paper}, author = {Bird, Tomas J. and Bates, Amanda E. and Lefcheck, Jonathan S. and Hill, Nicole a. and Thomson, Russell J. and Edgar, Graham J. and Stuart-Smith, Rick D. and Wotherspoon, Simon and Krkosek, Martin and Stuart-Smith, Jemina F. and Pecl, Gretta T. and Barrett, Neville and Frusher, Stewart}, doi = {10.1016/j.biocon.2013.07.037}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bird et al. - 2013 - Statistical solutions for error and bias in global citizen science datasets.pdf:pdf}, issn = {00063207}, journal = {Biological Conservation}, keywords = {biodiversity,citizen science}, mendeley-tags = {biodiversity,citizen science}, month = {sep}, publisher = {Elsevier Ltd}, title = {{Statistical solutions for error and bias in global citizen science datasets}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0006320713002693}, year = {2013} } @article{Heithaus2008a, abstract = {Recent studies document unprecedented declines in marine top predators that can initiate trophic cascades. Predicting the wider ecological consequences of these declines requires understanding how predators influence communities by inflicting mortality on prey and inducing behavioral modifications (risk effects). Both mechanisms are important in marine communities, and a sole focus on the effects of predator-inflicted mortality might severely underestimate the importance of predators. We outline direct and indirect consequences of marine predator declines and propose an integrated predictive framework that includes risk effects, which appear to be strongest for long-lived prey species and when resources are abundant. We conclude that marine predators should be managed for the maintenance of both density- and risk-driven ecological processes, and not demographic persistence alone.}, annote = {-consequences of marine predator declines -information on how top predators specifically affect ecosystemsi is limited citations 1-4 for marine predator declines citations 5,11 for mesopredator elasmobranch release, 45, 13 citations for role of top predators 32, this paper,38-41 -both direct predation and the ability of top predators to induce behavioral changes are important -if prey population numbers don't change they may simply change their behavior which could affect the next level down (predators increase, prey stays same-{\textgreater} prey may switch behavior) -connection between resource availability and predation }, author = {Heithaus, Michael R. and Frid, Alejandro and Wirsing, Aaron J. and Worm, Boris}, doi = {10.1016/j.tree.2008.01.003}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Heithaus et al. - 2008 - Predicting ecological consequences of marine top predator declines.pdf:pdf}, issn = {0169-5347}, journal = {Trends in ecology {\&} evolution}, keywords = {Animals,Biodiversity,Conservation of Natural Resources,Ecosystem,Fishes,Food Chain,Population Dynamics,Predatory Behavior,Risk Assessment,Seawater,Sharks,Shellfish,Turtles,ecosystem,marine,predator,sharks}, mendeley-tags = {ecosystem,marine,predator,sharks}, month = {apr}, number = {4}, pages = {202--10}, pmid = {18308421}, title = {{Predicting ecological consequences of marine top predator declines}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18308421}, volume = {23}, year = {2008} } @article{Stuart-Smith2013, abstract = {Species richness has dominated our view of global biodiversity patterns for centuries. The dominance of this paradigm is reflected in the focus by ecologists and conservation managers on richness and associated occurrence-based measures for understanding drivers of broad-scale diversity patterns and as a biological basis for management. However, this is changing rapidly, as it is now recognized that not only the number of species but the species present, their phenotypes and the number of individuals of each species are critical in determining the nature and strength of the relationships between species diversity and a range of ecological functions (such as biomass production and nutrient cycling). Integrating these measures should provide a more relevant representation of global biodiversity patterns in terms of ecological functions than that provided by simple species counts. Here we provide comparisons of a traditional global biodiversity distribution measure based on richness with metrics that incorporate species abundances and functional traits. We use data from standardized quantitative surveys of 2,473 marine reef fish species at 1,844 sites, spanning 133 degrees of latitude from all ocean basins, to identify new diversity hotspots in some temperate regions and the tropical eastern Pacific Ocean. These relate to high diversity of functional traits amongst individuals in the community (calculated using Rao's Q), and differ from previously reported patterns in functional diversity and richness for terrestrial animals, which emphasize species-rich tropical regions only. There is a global trend for greater evenness in the number of individuals of each species, across the reef fish species observed at sites ('community evenness'), at higher latitudes. This contributes to the distribution of functional diversity hotspots and contrasts with well-known latitudinal gradients in richness. Our findings suggest that the contribution of species diversity to a range of ecosystem functions varies over large scales, and imply that in tropical regions, which have higher numbers of species, each species contributes proportionally less to community-level ecological processes on average than species in temperate regions. Metrics of ecological function usefully complement metrics of species diversity in conservation management, including when identifying planning priorities and when tracking changes to biodiversity values.}, annote = {-want to examine functional diversity instead of just number of species -for them functional diversity is number and which species, phenotypes of those species and the particular individuals -look at 4357 underwater transects- this is not a lot of data --record eight traits that relate to functional position -richness of functional groups follows pattern in species density -functional diversity reveals different patterns compared to abundance of species -abundance-weighted functional diversity more accuratly reflects community functional structure E=species diversity/ species density (or richness) density={\#} of species per 500m{\^{}}2}, author = {Stuart-Smith, Rick D and Bates, Amanda E and Lefcheck, Jonathan S and Duffy, J Emmett and Baker, Susan C and Thomson, Russell J and Stuart-Smith, Jemina F and Hill, Nicole a and Kininmonth, Stuart J and Airoldi, Laura and Becerro, Mikel a and Campbell, Stuart J and Dawson, Terence P and Navarrete, Sergio a and Soler, German a and Strain, Elisabeth M a and Willis, Trevor J and Edgar, Graham J}, doi = {10.1038/nature12529}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stuart-Smith et al. - 2013 - Integrating abundance and functional traits reveals new global hotspots of fish diversity.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stuart-Smith et al. - 2013 - Integrating abundance and functional traits reveals new global hotspots of fish diversity(2).pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Stuart-Smith et al. - 2013 - Integrating abundance and functional traits reveals new global hotspots of fish diversity(3).pdf:pdf}, issn = {1476-4687}, journal = {Nature}, month = {sep}, number = {7468}, pages = {539--42}, pmid = {24067714}, publisher = {Nature Publishing Group}, title = {{Integrating abundance and functional traits reveals new global hotspots of fish diversity.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24067714}, volume = {501}, year = {2013} } @article{Locey2013, abstract = {The species abundance distribution (SAD) is one of the most intensively studied distributions in ecology and its hollow-curve shape is one of ecology's most general patterns. We examine the SAD in the context of all possible forms having the same richness (S) and total abundance (N), i.e. the feasible set. We find that feasible sets are dominated by similarly shaped hollow curves, most of which are highly correlated with empirical SADs (most R(2) values {\textgreater} 75{\%}), revealing a strong influence of N and S on the form of the SAD and an a priori explanation for the ubiquitous hollow curve. Empirical SADs are often more hollow and less variable than the majority of the feasible set, revealing exceptional unevenness and relatively low natural variability among ecological communities. We discuss the importance of the feasible set in understanding how general constraints determine observable variation and influence the forms of predicted and empirical patterns.}, annote = {-examine how the species abundance distribution changes as richnes and total abundance change -find that richness and abundance have strong efffects on SAD -exceptional unevenness and low natural variability in most systems {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -read McGill 2007, White 2012 -feasible set= parameter space -macrostate=particualar pt in param sp. -microstate=unique dist of individuals among species -look at dataset of birds, mammals, tress, prokaryotes and fungi -use integer partionaing to find combos of N and S -unevenness increases as Species {\#} increases- of course as average abundance approaches 1.0 the SAD becomes even -"evennnesss can be expected purely on differences in the feasible set" }, author = {Locey, Kenneth J. and White, Ethan P.}, doi = {10.1111/ele.12154}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Locey, White - 2013 - How species richness and total abundance constrain the distribution of abundance.pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {constraints,distribution of wealth,feasible set,functional diversity,hollow curve,macroecology,maxent,species abundance}, mendeley-tags = {functional diversity}, month = {sep}, number = {9}, pages = {1177--85}, pmid = {23848604}, title = {{How species richness and total abundance constrain the distribution of abundance.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23848604}, volume = {16}, year = {2013} } @article{King2012, abstract = {Traditionally, state-space models are fitted to data where there is uncertainty in the observation or measurement of the system. State-space models are partitioned into an underlying system process describing the transitions of the true states of the system over time and the observation process linking the observations of the system to the true states. Open population capture-recapture-recovery data can be modelled in this framework by regarding the system process as the state of each individual observed within the study in terms of being alive or dead, and the observation process the recapture and/or recovery process. The traditional observation error of a state-space model is incorporated via the recapture/recovery probabilities being less than unity. The models can be fitted using a Bayesian data augmentation approach and in standard BUGS packages. Applying this state-space framework to such data permits additional complexities including individual heterogeneity to be fitted to the data at very little additional programming effort. We consider the efficiency of the state-space model fitting approach by considering a random effects model for capture-recapture data relating to dippers and compare different Bayesian model-fitting algorithms within WinBUGS.}, annote = {-review of state space models and how they can be applied to capture-recapture studies -state-space models can seperate an observed process into biological info and measurement error -can use Bayesian approach to check how good a model is by simulating data from a given model and comparing that with observed values -}, author = {King, Ruth}, doi = {10.1098/rsfs.2011.0078}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/King - 2012 - A review of Bayesian state-space modelling of capture-recapture-recovery data.pdf:pdf}, issn = {2042-8901}, journal = {Interface focus}, keywords = {bayesian approach,bugs,data augmentation,hierarchical model,individual heterogeneity,mixed effects,mixed effects models,statistics}, mendeley-tags = {mixed effects,statistics}, month = {apr}, pages = {190--204}, pmid = {23565333}, title = {{A review of Bayesian state-space modelling of capture-recapture-recovery data}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3293198{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {2}, year = {2012} } @article{Alvarado2012, abstract = {With 51 100km2 of terrestrial area and 589 000km2 of national waters, Costa Rica is considered one of the countries with the greatest biodiversity. It has approximately 3.5{\%} of the world marine species. In the last four decades, Costa Rica has done a considerable effort to create a representative system of Protected Areas (PA), mainly terrestrial. We present an assessment of the current situation of the Marine Protected Areas (MPA) in Costa Rica, through an historical analysis, and an evaluation of their distribution, coverage and management categories. Costa Rica has 166 protected areas covering 50{\%} of the coastline; of these 20 are MPAs, classified as National Parks (90.6{\%}), National Wildlife Refuges (6.6{\%}), Wetlands (1.5{\%}), Biological Reserves (1{\%}), and one Absolute Natural Reserve (0.3{\%}). According to IUCN criteria, 93.7{\%} correspond to category II, 5{\%} to IV and 1.3{\%} to I. The marine protected surface is 5 296.5km2, corresponding to 17.5{\%} of the territorial waters and 0.9{\%} of the Exclusive Economic Zone. The median distance between MPAs is 22.4km in the Pacific and 32.9km along the Caribbean. The median size is close to 54km2. The main threats to MPAs are the lack of coordination between governmental agencies, limited economic resources, restricted patrolling and control, poor watershed management, and rampant coastal alteration. Rev. Biol. Trop. 60 (1): 129-142. Epub 2012 March 01.}, annote = {-paper examines the history of protected areas in Costa Rica and discussed Cocos a bit -look at data on protected area size and connectivity -MPAs vary in size quite a bit in Costa Rica -lack of coordination between multiple groups -some training of park rangers actually occurs at Coco Island -only one half of MPAs have at least one good patrolling boat {\_}{\_}{\_}{\_}{\_} -often MPAs were established after a land territory nearby was established (this was the case for Coco Island) -Coco Island was declared a World Heritage Area by UNESCO in 1997 Timeline: 1978- Coco is declared protected area (land area only) 1984- Coco has MPA established to 5km offshore (78.5km{\^{}}2) 1991- expansion of Coco MPA with 629km2 2001- another expansion of Coco MPA with 1 287km2 1997- Coco Island was declared a World Heritage Area by UNESCO Current- Coco Island MPA is 1 994.69km2}, author = {Alvarado, Juan Jos{\'{e}} and Cort{\'{e}}s, Jorge and Esquivel, Mar{\'{i}}a Fernanda and Salas, Eva}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Alvarado et al. - 2012 - Costa Rica's marine protected areas status and perspectives.pdf:pdf}, journal = {Revista de Biologia Tropical}, keywords = {cocos,conservation,exclusive economic zone,management categories,marine conservation,marine protected area,review}, mendeley-tags = {cocos,conservation,review}, number = {1}, pages = {129--142}, title = {{Costa Rica's marine protected areas: status and perspectives}}, volume = {60}, year = {2012} } @book{Zuur2009, address = {New York}, author = {Zuur, Alain F. and Ieno, Elena N. and Walker, Neil J. and Saveliev, Anatoly A. and Smith, Graham M.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Zuur et al. - 2009 - Mixed Effects Models and Extensions in Ecology with R.pdf:pdf}, isbn = {9780387874579}, pages = {574}, publisher = {Springer}, title = {{Mixed Effects Models and Extensions in Ecology with R}}, year = {2009} } @article{Martin2005, abstract = {A common feature of ecological data sets is their tendency to contain many zero values. Statistical inference based on such data are likely to be inefficient or wrong unless careful thought is given to how these zeros arose and how best to model them. In this paper, we propose a framework for understanding how zero-inflated data sets originate and deciding how best to model them. We define and classify the different kinds of zeros that occur in ecological data and describe how they arise: either from 'true zero' or 'false zero' observations. After reviewing recent developments in modelling zero-inflated data sets, we use practical examples to demonstrate how failing to account for the source of zero inflation can reduce our ability to detect relationships in ecological data and at worst lead to incorrect inference. The adoption of methods that explicitly model the sources of zero observations will sharpen insights and improve the robustness of ecological analyses.}, annote = {-paper reviews techniques to handle the various types of zeros that arise in ecological data {\_}{\_}{\_}{\_}{\_} -zero-inflated refers to data that has so many zeros it does not fit standard distributions -discusses differences between true and false zeors -false zeros make interpretations hard b/c a change in pop size may be real or b/c of change in detection True zeros-use a two-part or mixture model False zeros- use a mixture modelling aproach -could also just leave zeros out of data and analyze it Examples: -bird count data (true zeros) --}, author = {Martin, Tara G. and Wintle, Brendan A. and Rhodes, Jonathan R. and Kuhnert, Petra M. and Field, Scott A. and Low-Choy, Samantha J. and Tyre, Andrew J. and Possingham, Hugh P.}, doi = {10.1111/j.1461-0248.2005.00826.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Martin et al. - 2005 - Zero tolerance ecology improving ecological inference by modelling the source of zero observations.pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {GLM,bayesian inference,detectability,ecology letters,error,excess zeros,false negative,mixture model,observation,sampling error,statistics,zero inflation,zero-inflated binomial,zero-inflated poisson}, mendeley-tags = {GLM,statistics}, month = {nov}, number = {11}, pages = {1235--1246}, pmid = {21352447}, title = {{Zero tolerance ecology: improving ecological inference by modelling the source of zero observations.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/21352447}, volume = {8}, year = {2005} } @article{Laurance2013, annote = {-study reviews what may predict publicaiton success for scientists -pre-PhD publications were the strongest predictor -gender and language had some effect -univesity prestige had no effect {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -only successful scientists (ones with jobs in science ten years later) could be interviewed}, author = {Laurance, William F. and Useche, D. Carolina and Laurance, Susan G. and Corey, J. A.}, doi = {10.1525/bio.2013.63.10.9}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Laurance et al. - 2013 - Predicting Publication Success for Biologists.pdf:pdf}, issn = {00063568}, journal = {BioScience}, keywords = {academic performance,gender,language,publication success,science metrics,university ranking}, mendeley-tags = {publication success,science metrics}, month = {oct}, number = {10}, pages = {817--823}, title = {{Predicting Publication Success for Biologists}}, url = {http://www.jstor.org/stable/info/10.1525/bio.2013.63.10.9}, volume = {63}, year = {2013} } @article{Edgar2011, annote = {-paper examines survey data from a series of MPAs in the Eastern Pacific -examine both 'no-take' and openly fished sites {\_}{\_}{\_}{\_}{\_}{\_} -series of papers looked at trophic cascade at the galapagoes island -note that strong policing of regulations occurs at Coco and Malpelo with little enforcement elsewhere Isla del Coco- 1997km2 MPA Malpelo history: -MPA declared in 1997 -expanded to 25 mile distance in 2006 -8575km2 total MPA -simply break species up into five trophic level instead of diet matrix {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -northern Galapagos Islands were more similar to Coco and Malpelo than other areas of the galapagos -discuss effect of El Nino -as expected, there are more large fish in well-protected MPAs -argue the need for temporal data in determining role of MPA in relation to ecological effects -little is know regarding specifics of having a good MPA established}, author = {Edgar, Graham J. and Banks, Stuart A. and Bessudo, Sandra and Cort{\'{e}}s, Jorge and Guzm{\'{a}}n, Hector M. and Henderson, Scott and Martinez, Camilo and Rivera, Fernando and Soler, German and Ruiz, Diego and Zapata, Fernando A.}, doi = {10.1111/j.1466-8238.2010.00642.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Edgar et al. - 2011 - Variation in reef fish and invertebrate communities with level of protection from fishing across the Eastern Tropi.pdf:pdf}, issn = {1466822X}, journal = {Global Ecology and Biogeography}, keywords = {cocos,colombia,coral reef,correspondence,costa rica,ecuador,edgar,effects of fishing,galapagos,graham j,malpelo,marine,mpa,panama,reserve,review,tasmanian,unesco world heritage}, mendeley-tags = {cocos,malpelo,mpa,review}, month = {sep}, number = {5}, pages = {730--743}, title = {{Variation in reef fish and invertebrate communities with level of protection from fishing across the Eastern Tropical Pacific seascape}}, url = {http://doi.wiley.com/10.1111/j.1466-8238.2010.00642.x}, volume = {20}, year = {2011} } @article{Baum2004a, author = {Baum, Julia K. and Myers, Ransom a.}, doi = {10.1111/j.1461-0248.2003.00564.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Baum, Myers - 2004 - Shifting baselines and the decline of pelagic sharks in the Gulf of Mexico.pdf:pdf}, issn = {1461023X}, journal = {Ecology Letters}, keywords = {135,145,2004,7,ecology letters,fisheries,generalized linear model,marine,overexploitation,pelagic shark assemblage,population,predator,restoration}, month = {feb}, number = {2}, pages = {135--145}, title = {{Shifting baselines and the decline of pelagic sharks in the Gulf of Mexico}}, url = {http://doi.wiley.com/10.1111/j.1461-0248.2003.00564.x evernote:///view/68547643/s399/18f138c4-8dca-4ee6-8c3b-708602f3f650/18f138c4-8dca-4ee6-8c3b-708602f3f650/}, volume = {7}, year = {2004} } @article{Kuparinen2007, abstract = {Exploitation of fish populations can induce evolutionary responses in life histories. For example, fisheries targeting large individuals are expected to select for early maturation at smaller sizes, leading to reduced fecundity and thus also reduced fisheries yield. These predicted phenotypic shifts have been observed in several fish stocks, but disentangling the environmental and genetic causes behind them has proved difficult. Here, we review recent studies investigating phenotypic shifts in exploited populations and strategies for minimizing fisheries-induced evolution. Responses to selective harvesting will depend on species-specific life-history traits, and on community-level and environmental processes. Therefore, the detection of fisheries-induced evolution and successful fish stock management requires routine population monitoring, and a good understanding of genetics, relevant ecological processes and changing environmental conditions.}, annote = {-paper reviews recent studies that have looked at fisheries-induced evolution -difficult to seperate environmental effects from selection -also have to distinguish evolutionary resopnses from phenotypic plasticity -past study did selection experiments on guppies -most data are time series with life-history traits- few include genotype frequencies --suggest that indiret measures can be used -probabilistic reaction norms are functions that determine size specific prob. of maturation for individual s of a given age -slow-graowing, late-aturing species would be at the higest risk for fisheries-induced evolution -we could look at this in the bimini data set- what selection would be acting?}, author = {Kuparinen, Anna and Meril{\"{a}}, Juha}, doi = {10.1016/j.tree.2007.08.011}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kuparinen, Meril{\"{a}} - 2007 - Detecting and managing fisheries-induced evolution.pdf:pdf}, issn = {0169-5347}, journal = {Trends in ecology {\&} evolution}, keywords = {Animals,Biological Evolution,Conservation of Natural Resources,Conservation of Natural Resources: methods,Fisheries,Fishes,Fishes: genetics,evolution,fisheries,life history,selection}, mendeley-tags = {evolution,fisheries,life history,selection}, month = {dec}, number = {12}, pages = {652--9}, pmid = {17981361}, title = {{Detecting and managing fisheries-induced evolution}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/17981361}, volume = {22}, year = {2007} } @book{Brockwell2002, address = {New York}, annote = {-book discusses how to conduct various time series analysis -important citation for Jupiter paper as the book explains that AICC can be used to test different time lags to find an optimal one}, author = {Brockwell, Peter J. and Davis, Richard A.}, edition = {2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Brockwell, Davis - 2002 - Introduction to Time Series and Forecasting.pdf:pdf}, isbn = {0387953515}, keywords = {statistics,time series}, mendeley-tags = {statistics,time series}, pages = {434}, publisher = {Springer}, title = {{Introduction to Time Series and Forecasting}}, year = {2002} } @article{Zuur2010, annote = {-paper reviews common statisitcal mistakes they see in ecology papers -stress importance of better data exploration {\_}{\_}{\_}{\_}{\_}{\_} Usual steps 1) look for outliers 2) homogeneity of variance 3) normal data? 4) number of zeros --e.g. count data with lots of zeros- cannot run an ordinay Poisson or negative binomial GLM because this will bias parameter estimates (need to use zero-inflated GLMs instead (Cameron and Trivedi 1998) --another problem of double zeros for multiple species analyses simply happening by chance 5) collinearity -lots of collinearity can make a model that appears to have no siginicant parameters 6) relationship between Y and X variables 7) considering interactions 8) are obserations independent -lagged response variables (Brockwell {\&} Davis 2002) -ignoring auto-correlation may give P-values that are 400{\%} inflated (Ostrom 1990) -need to check for dependence in raw data and in the residuals {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}}, author = {Zuur, Alain F. and Ieno, Elena N. and Elphick, Chris S.}, doi = {10.1111/j.2041-210X.2009.00001.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Zuur, Ieno, Elphick - 2010 - A protocol for data exploration to avoid common statistical problems.pdf:pdf}, issn = {2041210X}, journal = {Methods in Ecology and Evolution}, keywords = {GLMM,collinearity,data exploration,independence,statistics,transformations,type I and II errors,zero inflation}, mendeley-tags = {statistics}, month = {mar}, pages = {3--14}, title = {{A protocol for data exploration to avoid common statistical problems}}, url = {http://doi.wiley.com/10.1111/j.2041-210X.2009.00001.x}, volume = {1}, year = {2010} } @article{Bessudo2011a, abstract = {Sixty nine hammerhead sharks, Sphyrna lewini, were tagged at Malpelo Island (Colombia) with ultrasonic transmitters during March 2006, 2007 and 2008, as part of a study to understand their residency at the island and their horizontal and vertical movements. Five sharks visited Cocos Island, 627 km distant from Malpelo. One of the sharks that appeared at Cocos Island also visited the Galapagos Islands, 710 km from Cocos, a month later. There is connectivity of Sphyrna lewini between Malpelo, Cocos and the Galapagos Islands, but the frequency of movements between the islands appears to be relatively low ({\textless}7{\%} of the tagged sharks). The most common depth at which the sharks swam coincided with the thermocline (rs=0.72, p{\textless}0.01). The depth of the thermocline varied depending on the time of the year. Nocturnal detections of the sharks were more frequent during the cold season than during the warm season (W=60, p{\textless}0.01). We also found that hammerheads spent significantly more time on the up-current side of the island (Kruskal-Wallis=31.1008; p{\textless}0.01). This study contributes to the knowledge of hammerhead sharks not only in Malpelo Island but also at a regional level in the Eastern Tropical Pacific.}, annote = {-study looked at 69 tahhed sharks at Malpelo and tracked their movement during 2006-2008 *paper has some insight for out project -found that hammerheads do move between Malpelo, Cocos, and the Galapagoes --however, only 7{\%} of sharks were actually seen to do this -sharks swam at a depth that coincided with the thermocline -sharks spent more time on up-current side of island (this might affect our analyses) {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -lots of detail and citations about Malpelo -some detail on range testing as well -use environmental data from DIVERSITY Project (Themis) at resolution of 4km -examine depth of thermocline vs. depth of shark --back this data up with scuba observation surveys -also have data on number of fished individuals and how many were pregnant at various time during the year -sharks had specific diel pattern, seasonal trend and spent more time at particular sites than others -also fish abundance surveys from Malpelo Foundation (unpubished) Boom: suggest that hammerheads may be using environmental cues to know when to migrate each year}, author = {Bessudo, Sandra and Soler, German Andres and Klimley, A. Peter and Ketchum, James T. and Hearn, Alex and Arauz, Randall}, doi = {10.1007/s10641-011-9769-3}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bessudo et al. - 2011 - Residency of the scalloped hammerhead shark (Sphyrna lewini) at Malpelo Island and evidence of migration to othe.pdf:pdf}, isbn = {1064101197693}, issn = {0378-1909}, journal = {Environmental Biology of Fishes}, keywords = {cocos,malpelo,marine protected areas,sharks,telemetry}, mendeley-tags = {cocos,malpelo,sharks,telemetry}, month = {feb}, number = {2}, pages = {165--176}, title = {{Residency of the scalloped hammerhead shark (Sphyrna lewini) at Malpelo Island and evidence of migration to other islands in the Eastern Tropical Pacific}}, url = {http://link.springer.com/10.1007/s10641-011-9769-3}, volume = {91}, year = {2011} } @book{Klimley2013, address = {Chicago and London}, annote = {So far the book does a pretty good job at hitting all the major points one would expect. The author has some nice stories and gives a bit of historical context. However, so far some of the chapters have felt a bit wordy. By this, I mean the text would desribe anatomy or some topic and would simply write out a list of terms. Most of this could have fit nicely within some figures instead of in the text. I like the idea of starting with a story to set up each chapter. Klimley then proceeds to hit the major topics of the chapter with good comparisons between the three groups in chondrithyans. Needs to do a better job at pointing to future sources. Book Review journal options: Fish and Fisheries Journal of FIsh Biology Chapter 1: Chapter 2: Chapter 3: Chapter 4: Osmoregulation chapter- lots of focus on the classic examples of extreme osmoregulation. Desribing role of Urea and TMAO Chapter 5: Warming of the Body Begins by discussing the heating ability of the order Lamniformes in comparison to most sharks. The families Lamnidae, Alopiidae and Mobulidae have evolved similar abilities to generate heat. Goes into physiology of countercurrent heat exchangers. He also discussed differences within group of elasmobranchs that can raise their body temps. Mistake? in blacktail vs. blacktip reef shark (pg. 117) Chapter 6: Chemoreception             Klimley begins this chapter by discussing sharks in popular culture and shark repellent history from WWII. He emphasizes that shark species may be more or less sensitive to blood or amino acids based on their diet. Klimley presents a study that looked at how a white shark responded to an odor trail. In general, the author puts more emphasis on how experiments were carried out and the results from them. The author then shifts his attention to the anatomy and physiology of chemoreception. He begins by describing the nares along with the incurrent and excurrent nostrils. He also explains the differences in nare structure between different elasmobranch species: benthic (wide circular nares) and neritic (slit-like nares). There is quite a bit of variance in the number of lamellae and the surface area of those lamellae in the olfactory organs of sharks and rays. In general, neritic species depend more on olfaction compared to epibenthic groups. The author goes on to describe how experiments on chemical sensitivity are conducted and the results from those experiments. He also discusses the ability of sharks to detect changes in salinity. Amino acids and amines were the chemicals most attractive to sharks. Sharks are actually attracted to the chemical metabolites given off by their favored prey items. Conversely, some chemicals, like those produced from sea cucumbers, can produce a negative response from a shark. Klimley ends the chapter describing the various ways chemicals can be detected by animals in the water (e.g. swimming straight for the chemical or a sinosodial pattern) and the various species that use these different strategies. There are two Spotlight sections in this chapter. The first discusses the history, development and current use of shark repellent. The second Spotlight examines a recent study that looked at the ability of sharks with a laterally elongated rostrum (i.e. hammerheads) to detect chemicals in the water. The study found that, because of their head structure, hammerheads are able to sample more water for chemicals as they swim. Chapter 7: Mechanoreception -some poor figures chosen -lots of detail that you can get lost in -never goes over sharks being able to produce sounds themselves or using it for communication Chapter 8: Vision -discussing shark vision ability, eye anatomy,pigments, day/night vision -Lots on Gruber's work of course -i like comparison to human sense Chapter 9: Electromagnetic fields Chapter 10: Chapter 11: Reproduction -story of nurse sharks mating -goes through reproductive anatomy, maturation, paturation reproductive cycle, sexual segregation, courtship- no need to desribe it in detail with pictures there, better evidence can be presented in spots, exact wording in summary of chapter -weird figure setup on page 294 Chapter 12: feeding -story of great whites, feeding strategies, anatomy/phsiology of jaws, lots of detail of feeding biomechanics, teeth -rows of teeth shed in 8-10 days for lemon shark Chapter 13: Diet and growth -story about extracting vertebrae from great white,sharks in the food chain, tropic level table, diet- a number of papers, digestion anatomy, growth rate (w/ table), life span, -juvenile lemons eat 1.5-2.1 percent of body weight per day Chapter 14: Movement -tagging of hammerheads stories,}, author = {Klimley, A. Peter}, edition = {1}, keywords = {review,shark}, pages = {512}, publisher = {The University of Chicago Press}, title = {{The Biology of Sharks and Rays}}, year = {2013} } @article{Ward-Paige2011, abstract = {BACKGROUND: Around the world, researchers are using the observations and experiences of citizens to describe patterns in animal populations. This data is often collected via ongoing sampling or by synthesizing past experiences. Since elasmobranchs are relatively rare, obtaining data for broad-scale trend analysis requires high sampling effort. Elasmobranchs are also relatively large and conspicuous and therefore it may be possible to enlist recreational divers to collect data on their occurrence and relative abundance from daily dive activities. For this, however, a good understanding of the value of data collected by recreational divers is essential. METHODOLOGY/PRINCIPAL FINDINGS: Here, we explore the value of recreational divers for censusing elasmobranchs using a diverse set of data sources. First, we use a simulation experiment to explore detection rates of the roving diver technique, used by recreational divers, across a range of fish densities and speeds. Next, using a field survey, we show that inexperienced recreational divers detect and count elasmobranchs as well as experienced recreational divers. Finally, we use semi-structured interviews of recreational dive instructors to demonstrate the value of their recollections in terms of effort and their descriptions of spatial and temporal distributions of sharks in Thailand. CONCLUSIONS/SIGNIFICANCE: Overall, this study provides initial ground-work for using recreational divers for monitoring elasmobranch populations. If used appropriately, citizen-collected data may provide additional information that can be used to complement more standardized surveys and to describe population trends across a range of spatial and temporal scales. Due to the non-extractive nature of this data, recreational divers may also provide important insight into the success of conservation initiatives, such as shark sanctuaries and no-take zones.}, annote = {-used simulation (AnimDens) and survey data to determine if scuba diver data can be used -find that both inexperienced and experienced divers count elasmobranhcs equally well -focus on sites in Thailand and the Andaman Sea {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -use a GLM with a poisson distribution and log link to model the number of shark species at each site as a function of the log of the number of dives -roving technique works fine for large, fast-moving fish (in comparison to more scientific techniques)}, author = {Ward-Paige, Christine A. and Lotze, Heike K.}, doi = {10.1371/journal.pone.0025609}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ward-Paige, Lotze - 2011 - Assessing the value of recreational divers for censusing elasmobranchs.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {Animals,Data Collection,Diving,Elasmobranchii,Observation,Population Density,Population Dynamics,Time Factors,scuba,sharks}, mendeley-tags = {scuba,sharks}, month = {jan}, number = {10}, pages = {e25609--e25609}, pmid = {22016771}, title = {{Assessing the value of recreational divers for censusing elasmobranchs}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3189927{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {6}, year = {2011} } @article{Chave2013, abstract = {Over the past 20 years, major advances have clarified how ecological patterns inform theory, and how in turn theory informs applied ecology. Also, there has been an increased recognition that the problem of scale at which ecological processes should be considered is critical if we are to produce general predictions. Ecological dynamics is always stochastic at small scales, but variability is conditional on the scale of description. The radical changes in the scope and aims of ecology over the past decades reflect in part the need to address pressing societal issues of environmental change. Technological advances in molecular biology, global positioning, sensing instrumentation and computational power should not be overlooked as an explanation for these radical changes. However, I argue that conceptual unification across ecology, genetics, evolution and physiology has fostered even more fertile questions. We are moving away from the view that evolution is played in a fixed ecological theatre: the theatre is being rapidly and relentlessly redesigned by the players themselves. The maintenance of ecosystem functions depends on shifts in species assemblages and on cellular metabolism, not only on flows of energy and matter. These findings have far reaching implications for our understanding of how ecosystem function and biodiversity will withstand (or not) environmental changes in the 21st century.}, annote = {-review examines how patterns inform theory and how theory turns into application -scale is an important factor -argues that unification of different fields has resulted in most change in ecology --evolution is something to study for applied scientists as well {\_}{\_}{\_}{\_} -begin by citing Levins (1992)- scale and pattern in ecology --led to interdisiplinary work *patterns can emerge at one scale generated by another -advances in computing, molecular biology, environmental sensing, knowledge sharing have all been important in ecology over the past 20 years -feedbacks between environment, populations, and individuals -even animals living in same environment may not experience same spatial scale (plakton and whales) -four areas of ecology where pattern and scale are focused: 1)bridging ecology and evolution 2)bringing ecosystem science into evolutionary and pop bio 3)frontiers of an organism 4)spatial patterns in ecology {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} 1)-impact of evolution on ecology ---rotifer ecperiments- predator-prey oscillations changed depending on if evolution could take place ---Dawin's finch example of beak size changing very quickly ---can study using Fisher's covariance equation -ecosystem consequences of evolution ---example of experiments with guppies and predators- change in trait of guppies (e.g. age at maturity) ----then examined how different groups of evolved guppies affected their environment differently 2)-scales at global scale ---need a common currency ---can look at ensemble averages on a larger scale to study something on a smaller scale ---study of allometry (body size related to other features) ---metabolic rate and environmental conditions 3)-modualarity in interaction networks ---biological systems are heirachial and modular ---modularity-"the degree to which the nodes of a system can be decoupled into relatively discrete components" (May et al 2008) ---allows redundancy -individual variation and interaction networks -individual behavior can lead to patterns at larger scale --slime moulds 4)-spatial patterns ---tree clumping or plankton blooms ---local dispersal and large scale patterns ---latitude gradient of species diversity}, author = {Chave, J{\'{e}}r{\^{o}}me}, doi = {10.1111/ele.12048}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Chave - 2013 - The problem of pattern and scale in ecology what have we learned in 20 years.pdf:pdf}, issn = {1461-0248}, journal = {Ecology letters}, keywords = {2013,eco-evolutionary dynamics,ecology letters,global change,modularity,pattern,scale,spatial ecology}, month = {may}, pages = {1--13}, pmid = {23351093}, title = {{The problem of pattern and scale in ecology: what have we learned in 20 years?}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23351093}, volume = {16 Suppl 1}, year = {2013} } @article{Clarke2013, abstract = {Accurate assessment of shark population status is essential for conservation but is often constrained by limited and unreliable data. To provide a basis for improved management of shark resources, we analyzed a long-term record of species-specific catches, sizes, and sexes of sharks collected by onboard observers in the western and central Pacific Ocean from 1995 to 2010. Using generalized linear models, we estimated population-status indicators on the basis of catch rate and biological indicators of fishing pressure on the basis of median size to identify trends for blue (Prionace glauca), mako (Isurus spp.), oceanic whitetip (Carcharhinus longimanus), and silky (Carcharhinus falciformis) sharks. Standardized catch rates of longline fleets declined significantly for blue sharks in the North Pacific (by 5{\%} per year [CI 2{\%} to 8{\%}]), for mako sharks in the North Pacific (by 7{\%} per year [CI 3{\%} to 11{\%}]), and for oceanic whitetip sharks in tropical waters (by 17{\%} per year [CI 14{\%} to 20{\%}]). Median lengths of silky and oceanic whitetip sharks decreased significantly in their core habitat, and almost all sampled silky sharks were immature. Our results are consistent with results of analyses of similar data sets. Combined, these results and evidence of targeted fishing for sharks in some regional fisheries heighten concerns for sustainable utilization, particularly for oceanic whitetip and North Pacific blue sharks. Regional regulations that prohibit shark finning (removal of fins and discarding of the carcass) were enacted in 2007 and are in many cases the only form of control on shark catches. However, there is little evidence of a reduction of finning in longline fisheries. In addition, silky and oceanic whitetip sharks are more frequently retained than finned, which suggests that even full implementation of and adherence to a finning prohibition may not substantially reduce mortality rates for these species. We argue that finning prohibitions divert attention from assessing whether catch levels are sustainable and that the need for management of sharks should not be addressed by measures that are simple to implement but complex to enforce and evaluate.}, author = {Clarke, Shelley C. and Harley, Shelton J. and Hoyle, Simon D. and Rice, Joel S.}, doi = {10.1111/j.1523-1739.2012.01943.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Clarke et al. - 2013 - Population trends in Pacific Oceanic sharks and the utility of regulations on shark finning.pdf:pdf}, issn = {1523-1739}, journal = {Conservation Biology}, keywords = {Animals,Conservation of Natural Resources,Conservation of Natural Resources: legislation {\&} j,Endangered Species,Linear Models,Pacific Ocean,Physiological,Population Density,Population Dynamics,Sharks,Sharks: anatomy {\&} histology,Sharks: physiology,Species Specificity,Stress,cocos,conservation,finning,sharks}, mendeley-tags = {cocos,conservation,finning,sharks}, month = {feb}, number = {1}, pages = {197--209}, pmid = {23110546}, title = {{Population trends in Pacific Oceanic sharks and the utility of regulations on shark finning}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23110546}, volume = {27}, year = {2013} } @article{Reyier, annote = {-examine juvenile lemon shark movement off of Cape Canaveral -show that several sharks moved rapidly with quick drops in water temp -long distance movement instead of natal site fidelity -lots of good references to stats models used Model -want to see which enivironmental parameters predict lemon shark presence -rank models with AIC -individual sharks were a random effect to account for individual heterogeneity (GLMM) -Study year was a random effect because array size changed each year* -"Month crossed with year was a random effect to account for temporal patterns not explained by any fixed effects" -filtered out hits and infrequently seen sharks -accounted for temporal autocorrelation --looked at residuals for full model for individual sharks --created new variables to account for pres/abs over the past 1-6 days --found optimal correlation structure than ran all combinations of fixed effects -test correlation structure 3 different ways -nearshore waters of Cape Canaveral are a winter nursery under Heupel's criteria -suggest that growing day length provides initial cue for coastal migrations- as ssen in sandbar sharks Citations: Snellson and Williams 1981 Morissey and Gruber 1993 Brown and Gruber 1988 Feldheim 2002 Morrissey and Gruber 1993 (different) Chapman 2009 Murcjie et al 2010 Franks 2007 Guttridge 2012 Stats: 46-53 Zuur AF, Ieno EN, Walker NJ, Saveliev AA, Smith GM (2009) Mixed Effects Models and Extensions in Ecology with R. New York: Springer. 574 p.47. Pinheiro J, Bates D, DebRoy S, Sarkar D, Team RC (2012) nlme: Linear and Nonlinear Mixed Effects Models. 48. Schielzeth H (2010) Simple means to improve the interpretability of regression coefficients. Methods in Ecology and Evolution 1: 103-113. 49. Hosmer DW, Lemeshow T (2000) Applied logistic regression. New York: John Wiley and Sons. 50. Burnham KP, Anderson DR (2002) Model selection and multimodel inference : a practical information-theoretic approach. New York: Springer. xxvi, 488 p. p. 51. Anderson DR (2008) Model based inference in the life sciences: A primer on evidence. New York: Springer. 52. Hamel S, Yoccoz NG, Gaillard JM (2012) Statistical evaluation of parameters estimating autocorrelation and individual heterogeneity in longitudinal studies. Methods in Ecology and Evolution 3: 731-742. }, author = {Reyier, Eric A and Franks, Bryan R and Chapman, Demian D and Scheidt, Douglas M and Stolen, Eric D and Gruber, Samuel H}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Reyier et al. - Unknown - Title Regional-Scale Migrations and Habitat Use of Juvenile Lemon Sharks (Negaprion brevirostris) in the US So.pdf:pdf}, number = {2}, pages = {1--30}, title = {{Title Regional-Scale Migrations and Habitat Use of Juvenile Lemon Sharks (Negaprion brevirostris) in the US South Atlantic}}, volume = {32899} } @article{Ward-Paige2013, abstract = {Despite being the world's largest rays and providing significant revenue through dive tourism, little is known about the population status, exploitation and trade volume of the Mobulidae (mobulids; Manta and Mobula spp.). There is anecdotal evidence, however, that mobulid populations are declining, largely due to the recent emergence of a widespread trade for their gill rakers, which is reflected in increasing Food and Agriculture Organization landings trends. Here, we present results from two dedicated diver surveys, one from the eManta project, which includes summary observations from ninety 10ux10u regions with ,200–62,000 dives per region, and the other from the Reef Environmental Education Foundation, which includes spatially more detailed observations from 3 regions with ,4,000–118,000 dives per region. We show that mobulids as a group, which includes eleven species, have globally and regionally restricted distributions, typically have low sighting frequency (,1{\%} of dives) and aggregate in only a few locations. Of the regions surveyed by divers, almost half (47{\%}) report declining mobulid sightings over the last decade. Divers indicate that although mobulid ecotourism occurs in many regions (45{\%} of those reported, n = 41) they are considered protected in only 32{\%} of the regions. Mobulids being fished or sold in local markets were reported from 16{\%} and 12{\%} of regions, respectively, with most being adjacent to mobulid abundance hotspot and ecotourism regions (e.g. Sri Lanka, Indonesia, east Africa). Identification of regions where ecotourism and exploitation are at odds could help prioritize conservation efforts. Vulnerability analysis, using life history characteristics, indicates that Manta spp. are vulnerable to exploitation, tolerating only low fishing mortality rates; data limitations prohibited such analysis for Mobula spp. Our analyses support previous studies in showing the need for improved conservation and monitoring efforts, and suggest that international and enforceable management policies are required to prevent further population decline.}, annote = {-study using scuba survey data (from two sources) to investigate the global trends of the Mobulidae subfamily (Manta and Mobula spp) -half of surveyed sights report a decline in last decade QUESTION: are dives biased b'c of there stake in what is happening? - we should assess life history characterisitcs to look at explotation risks {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -a number of good sources for scuba diving observation data use -created their own survey (questionairre) and used data from REEF www.reef.org {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} 16. Couturier LIE, Jaine FRA, Townsend KA, Weeks SJ, Richardson AJ, et al. (2011) Distribution, site affinity and regional movements of the manta ray, Manta alfredi (Krefft, 1868), along the east coast of Australia. Mar. Freshwat. Res. 62: 628–637.17. Bansemer CS, Bennett MB (2010) Retained fishing gear and associated injuries in the east Australian grey nurse sharks (Carcharias taurus): implications for population recovery. Mar. Freshwat. Res. 61: 97–103. 18. Ward-Paige CA, Mora C, Lotze HK, Pattengill-Semmens C, McClenachan L, et al. (2010) Large-scale absence of sharks on reefs in the greater-Caribbean: A footprint of human pressures. PLoS ONE 5: e11968. 19. Ward-Paige CA, Pattengill-Semmens C, Myers RA, Lotze HK (2011) Spatial and temporal trends in yellow stingray abundance: evidence from diver surveys. Environ. 20. Arzoumanian Z, Holmberg J, Norman B (2005) An astronomical pattern- matching algorithm for computer-aided identification of whale sharks Rhincodon typus. J. App. Ecol. 42: 999–1011.21. Ward-Paige CA, Lotze HK (2011) Assessing the value of recreational divers for censusing elasmobranchs. PLoS ONE 6: e25609. {\_}{\_}{\_}{\_}{\_}{\_} -looked at size of schools over time (is this valide metric?)}, author = {Ward-Paige, Christine A. and Davis, Brendal and Worm, Boris}, doi = {10.1371/journal.pone.0074835}, editor = {Stergiou, Konstantinos I.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ward-Paige, Davis, Worm - 2013 - Global Population Trends and Human Use Patterns of Manta and Mobula Rays.pdf:pdf}, issn = {1932-6203}, journal = {PLoS one}, keywords = {Population Dynamics,cocos,elasmobranch,scuba,sharks,survey}, mendeley-tags = {sharks,survey}, month = {sep}, number = {9}, pages = {e74835--e74835}, title = {{Global Population Trends and Human Use Patterns of Manta and Mobula Rays}}, url = {http://dx.plos.org/10.1371/journal.pone.0074835}, volume = {8}, year = {2013} } @article{Levin1992, annote = {Scaling is interface between theory and emphirisism and ecosystem with populaiton biology Ideas: review on time and spatial scale of studies in ecology (like fig 2) {\_}{\_}{\_}{\_}{\_}{\_} Scale underlies the study of ecology and arguarably all of science. There is no "correct" scale to look at in ecology - it depends on the context and problem. There are often properties that emerge from one level to affect the next level. How do you construct simple models to elucidate patterns in the real world? The evolution of life history traits is driven by different processes at different scales. Often, it is best to study processes on a different scale than the one of true interest. For example, small scale studies are often driven by stochastic variation where analysis is difficult. If you use a larger scale, ensemble averages can become useful for studying the phenomenon of interest. Pattern formation and scale are inheriently linked together. Often patterns emerges from one scale to affect another. Mechanisms need to be understood so as to allow real predictive power istead of simply correlation. Theory creates a set of possible mechanisms and experimentation must weed through this set. In one example, it was shown that krill movement dynamics differed depending on what scale the phenomenon was measured at. Therefore two different processes were driving the dynamics. The focus is on why are organisms distributed the way they are. Use random walk and diffusion models for dispersal models. Can ignore the individuals and use the law of large numbers. Apply models of phyics to examples in biology. Phytoplankton. Spread of invasive species. Methods from aquatic systems can also be applied in the terrestrial realm. It is not always possible to delineate scales easily... Metapopulation models have been a centerpiece of theoretical ecology. These models have been important in conservation, evolution, and epidemiology. A lot of work has been done in analyzing food webs from a mathematical (i.e. graph theory) viewpoint. Linking scales between GCC and ecological models in a continual challenge. Scaling is also important in understanding evolution. How do forces on individuals affect patterns seen on community and ecosystem levels? It is important to figure out which level of detail to include.}, author = {Levin, Simon A.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Levin - 1992 - The Problem of Pattern and Scale in Ecology.pdf:pdf}, journal = {Ecology}, keywords = {heterogeneity,patchiness,pattern,review,scale,variability}, mendeley-tags = {pattern,review,scale}, number = {6}, pages = {1943--1967}, title = {{The Problem of Pattern and Scale in Ecology}}, volume = {73}, year = {1992} } @article{Ward-Paige2010, abstract = {BACKGROUND: Increasingly, underwater visual censuses (UVC) are used to assess fish populations. Several studies have demonstrated the effectiveness of protected areas for increasing fish abundance or provided insight into the natural abundance and structure of reef fish communities in remote areas. Recently, high apex predator densities ({\textgreater}100,000 individuals x km(-2)) and biomasses ({\textgreater}4 tonnes x ha(-1)) have been reported for some remote islands suggesting the occurrence of inverted trophic biomass pyramids. However, few studies have critically evaluated the methods used for sampling conspicuous and highly mobile fish such as sharks. Ideally, UVC are done instantaneously, however, researchers often count animals that enter the survey area after the survey has started, thus performing non-instantaneous UVC. METHODOLOGY/PRINCIPAL FINDINGS: We developed a simulation model to evaluate counts obtained by divers deploying non-instantaneous belt-transect and stationary-point-count techniques. We assessed how fish speed and survey procedure (visibility, diver speed, survey time and dimensions) affect observed fish counts. Results indicate that the bias caused by fish speed alone is huge, while survey procedures had varying effects. Because the fastest fishes tend to be the largest, the bias would have significant implications on their biomass contribution. Therefore, caution is needed when describing abundance, biomass, and community structure based on non-instantaneous UVC, especially for highly mobile species such as sharks. CONCLUSIONS/SIGNIFICANCE: Based on our results, we urge that published literature state explicitly whether instantaneous counts were made and that survey procedures be accounted for when non-instantaneous counts are used. Using published density and biomass values of communities that include sharks we explore the effect of this bias and suggest that further investigation may be needed to determine pristine shark abundances and the existence of inverted biomass pyramids. Because such studies are used to make important management and conservation decisions, incorrect estimates of animal abundance and biomass have serious and significant implications.}, annote = {-use simulation to evaluate the success of various diving survey techniques -indicate that factors (e.g. fish speed) can bias survey results {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -bias of shark sampling more than an order of magnitude -need to use instananeous visual surveys (don't count fish that enter the survey data)}, author = {Ward-Paige, Christine and {Mills Flemming}, Joanna and Lotze, Heike K}, doi = {10.1371/journal.pone.0011722}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ward-Paige, Mills Flemming, Lotze - 2010 - Overestimating fish counts by non-instantaneous visual censuses consequences for population a.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {Animals,Biomass,Fishes,Fishes: growth {\&} development,Models,Theoretical,scuba,sharks}, mendeley-tags = {scuba,sharks}, month = {jan}, number = {7}, pages = {e11722--e11722}, pmid = {20661304}, title = {{Overestimating fish counts by non-instantaneous visual censuses: consequences for population and community descriptions}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2908695{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {5}, year = {2010} } @article{Hamel2012, abstract = {1. Autocorrelation and individual heterogeneity are now considered to reflect biological processes rather than simply being a nuisance requiring to be accounted for.Before using parameter estimates that represent autocorrelation and individual heterogeneity to infer biological processes, a statistical evaluation of their precision and accuracy is required to validate their use. 2. Using simulated data, we evaluated accuracy and precision of temporal autocorrelation and individual heterogeneity estimates provided by different statistical models. We compared estimates across different intensity of individual variation and life histories, and sampling effort. We focused on recurrent binary variables because statistical evaluations of models describing binary processes have often been overlooked although several evolutionary and ecological processes are expressed as binary variables (e.g. probability of annual reproduction, plant annual flowering and detection, seasonal migration decision). 3. Our results showed that autocorrelation and individual heterogeneity were generally better esti- mated using a ‘time series' modelling approach, but that a ‘state dependence' modelling approach also provided fair estimates in most cases. The latter method was even more robust when data sets included missing values. Data sets including missing values or consisting of very short times series resulted in important bias in someinstances. 4. Models ignoring either individual heterogeneity or autocorrelation performed poorly, illustrat- ing the fundamental association between these two processes, and demonstrating that the complex structure of autocorrelation and individual heterogeneity patterns is difficult to tackle using simple models. 5. Ourwork'smajor finding is the demonstration that autocorrelation and individual heterogeneity need to be both accounted for to provide reliable estimates even in studies focusing on only one of these processes. Our study also offers a set of practical recommendations for helping researchers modelling these two processes depending on their scientific aims and the structure of their data. Finally, our results illustrate that more research is required for estimating individual heterogeneity when positive temporal autocorrelation is expected because none of the models evaluated provided suitable estimates}, annote = {-develop models that incorporate both individual heterogeneity and autocorrelation -look at state dependence and time series models --state dependence (previous time step/time lag one/first-order autocorrelation) -}, author = {Hamel, Sandra and Yoccoz, Nigel G. and Gaillard, Jean-Michel}, doi = {10.1111/j.2041-210X.2012.00195.x}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hamel, Yoccoz, Gaillard - 2012 - Statistical evaluation of parameters estimating autocorrelation and individual heterogeneity in longitu.pdf:pdf}, issn = {2041210X}, journal = {Methods in Ecology and Evolution}, keywords = {GLMM,accuracy,first-order autocorrelation,generalized linear mixed models,individual heterogeneity,precision,random intercept model,sharks,time series}, mendeley-tags = {GLMM,sharks,time series}, month = {aug}, number = {4}, pages = {731--742}, title = {{Statistical evaluation of parameters estimating autocorrelation and individual heterogeneity in longitudinal studies}}, url = {http://doi.wiley.com/10.1111/j.2041-210X.2012.00195.x}, volume = {3}, year = {2012} } @book{McCullagh1989, address = {London, UK}, author = {McCullagh, Peter and Nelder, John A.}, edition = {2}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/McCullagh, Nelder - 1989 - Generalized Linear Models (Monogaphs on statistics and applied probability 37).pdf:pdf}, pages = {511}, publisher = {Chapman Hall}, title = {{Generalized Linear Models (Monogaphs on statistics and applied probability 37)}}, year = {1989} } @article{Worm2013, abstract = {Adequate conservation and management of shark populations is becoming increasingly important on a global scale, especially because many species are exceptionally vulnerable to overfishing. Yet, reported catch statistics for sharks are incomplete, and mortality estimates have not been available for sharks as a group. Here, the global catch and mortality of sharks from reported and unreported landings, discards, and shark finning are being estimated at 1.44 million metric tons for the year 2000, and at only slightly less in 2010 (1.41 million tons). Based on an analysis of average shark weights, this translates into a total annual mortality estimate of about 100 million sharks in 2000, and about 97 million sharks in 2010, with a total range of possible values between 63 and 273 million sharks per year. Further, the exploitation rate for sharks as a group was calculated by dividing two independent mortality estimates by an estimate of total global biomass. As an alternative approach, exploitation rates for individual shark populations were compiled and averaged from stock assessments and other published sources. The resulting three independent estimates of the average exploitation rate ranged between 6.4{\%} and 7.9{\%} of sharks killed per year. This exceeds the average rebound rate for many shark populations, estimated from the life history information on 62 shark species (rebound rates averaged 4.9{\%} per year), and explains the ongoing declines in most populations for which data exist. The consequences of these unsustainable catch and mortality rates for marine ecosystems could be substantial. Global total shark mortality, therefore, needs to be reduced drastically in order to rebuild depleted populations and restore marine ecosystems with functional top predators.}, annote = {-paper looks to estimate the total number of sharks taken per year worldwide -estimate that 97 million sharks were taken in 2010 -global shark mortality between 63 and 273 million sharks per year {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -combine various data sources and convert biomass to number of sharks caught -examine repound potential of various species studied -Jennings et al estimated the global biomass of elasmobranchs before modern fishing at 86 260 000 tons -find exploitation rate of 6.7 percent per year -no leveling off of global fin trade since 2000}, author = {Worm, Boris and Davis, Brendal and Kettemer, Lisa and Ward-Paige, Christine A. and Chapman, Demian and Heithaus, Michael R. and Kessel, Steven T. and Gruber, Samuel H.}, doi = {10.1016/j.marpol.2012.12.034}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Worm et al. - 2013 - Global catches, exploitation rates, and rebuilding options for sharks.pdf:pdf}, issn = {0308597X}, journal = {Marine Policy}, keywords = {Conservation,Ecosystem management,Fishing mortality,Shark finning,Sharks}, month = {jul}, pages = {194--204}, publisher = {Elsevier}, title = {{Global catches, exploitation rates, and rebuilding options for sharks}}, url = {http://linkinghub.elsevier.com/retrieve/pii/S0308597X13000055}, volume = {40}, year = {2013} } @article{Bessudo2011, annote = {{\textless}m:note{\textgreater}-examined horizonatal and vertical movements of S. lewini{\textless}m:linebreak/{\textgreater} {\textless}m:linebreak/{\textgreater} {\textless}/m:note{\textgreater}}, author = {Bessudo, Sandra and Soler, Germ{\'{a}}n A and Klimley, Peter A and Ketchum, James and Arauz, Randall and Hearn, Alex and Guzmán, Adriana and Calmettes, Beatriz}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bessudo et al. - 2011 - Vertical and horizontal movements of the scalloped hammerhead shark (Sphyrna lewini) around Malpelo and Cocos Is.pdf:pdf}, journal = {Environmental Biology of Fishes}, keywords = {cocos,malpelo,satellite telemetry,sharks,sphyrna lewini,telemetry,vertical and horizontal movements}, mendeley-tags = {cocos,sharks,telemetry}, number = {2}, pages = {165--176}, title = {{Vertical and horizontal movements of the scalloped hammerhead shark (Sphyrna lewini) around Malpelo and Cocos Islands (tropical Eastern Pacific) using satellite telemetry}}, volume = {91}, year = {2011} } @article{Bolker2009, abstract = {How should ecologists and evolutionary biologists analyze nonnormal data that involve random effects? Nonnormal data such as counts or proportions often defy classical statistical procedures. Generalized linear mixed models (GLMMs) provide a more flexible approach for analyzing nonnormal data when random effects are present. The explosion of research on GLMMs in the last decade has generated considerable uncertainty for practitioners in ecology and evolution. Despite the availability of accurate techniques for estimating GLMM parameters in simple cases, complex GLMMs are challenging to fit and statistical inference such as hypothesis testing remains difficult. We review the use (and misuse) of GLMMs in ecology and evolution, discuss estimation and inference and summarize 'best-practice' data analysis procedures for scientists facing this challenge.}, author = {Bolker, Benjamin M and Brooks, Mollie E and Clark, Connie J and Geange, Shane W and Poulsen, John R and Stevens, M Henry H and White, Jada-Simone S}, doi = {10.1016/j.tree.2008.10.008}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bolker et al. - 2009 - Generalized linear mixed models a practical guide for ecology and evolution.pdf:pdf}, issn = {0169-5347}, journal = {Trends in ecology {\&} evolution}, keywords = {Bayes Theorem,Biological Evolution,Data Interpretation, Statistical,Ecology,Likelihood Functions,Linear Models,Software}, month = {mar}, number = {3}, pages = {127--35}, pmid = {19185386}, title = {{Generalized linear mixed models: a practical guide for ecology and evolution.}}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19185386}, volume = {24}, year = {2009} } @article{Moore2009, abstract = {This paper reviews the available information (observer programs, estimates, statutes, regulations) for bycatch of marine mammals, sea turtles, and seabirds in fisheries of the United States. Goals of the review were to evaluate the state of knowledge of bycatch and the role of existing protective legislation in shaping bycatch management for different taxa. Pressing issues are identified, as well as knowledge gaps and policy limitations that hinder multi-species bycatch reduction. The USA has made important progress toward reducing bycatch in its fisheries, but the efficacy of its management has been limited somewhat by a focus on taxon- and fishery-specific regulation and the lack of consistent mandate across taxa for taking a cumulative perspective on bycatch. Applying consistent criteria across taxa for setting bycatch limits (e.g., extending the approach used for marine mammals to sea turtles and seabirds) would be the first step in a multi-species approach to bycatch reduction. A population-based multi- species multi-gear approach to bycatch would help identify priority areas where resources are needed most and can be used most effectively.}, annote = {REVIEW-lots of good management citations -review paper that looks to investigate by catch in the US but focuses on policy that drives any conservation efforts -identifies knowledge gaps and policy limitations -calls for more consistent by catch management strategies across multiple taxa {\_}{\_}{\_}{\_} -FAO 2008, reports that USA has larges exclusive economic zone of greater than 11 million square kilometers which span 8 different marine ecosystems -discuss four main acts relevant to marine mammals, birds and turtles: Migratory Bird Treaty Act, Marine Mammal Protection Act, Endagered Species Act, Magnuson-Stevens Fishery Conservation and Management Act --laws are often different on state and federal levels -sources that show observer programs provide the most reliable data -large data gaps in Alaska fisheries and in Southeast USA Process is clear for management and conservation: 1) estimate population stock size 2) determine cumulative by catch of all fisheries 3) determine if by catch numbers are biologically too high 4) account for uncertainty 5) develop and implement by catch reduction plans -currently most management is a population by population approach instead of an overarching comprehensive plan -also incidental take levels are often not well determined }, author = {Moore, Jeffrey E and Wallace, Bryan P and Lewison, Rebecca L and {\v{Z}}ydelis, Ram{\'{u}}nas and Cox, Tara M and Crowder, Larry B}, journal = {Marine Policy}, keywords = {extinction,fisheries,megafauna,vaquita}, pages = {435--451}, title = {{A review of marine mammal, sea turtle and seabird bycatch in USA fisheries and the role of policy in shaping management}}, volume = {33}, year = {2009} } @article{Bobadilla2011, abstract = {We retrospectively analyzed environmental policy instruments decreed by the Mexican federal government for the protection of marine species and ecosystems in the Upper Gulf of California. Totoaba (Totoaba macdonaldii) and the vaquita porpoise (Phocoena sinus) are two priority species in the national and international agendas for marine protection. We observe that while the measures taken by the State, since 1949, show a growing commitment to sustainable management of the region, there are limitations in the design and implementation of concrete actions for their protection. Some possible reasons the tools have proven to be ineffective are: there has been no consistency between the goals of fisheries and conservation sectors; the decrees are not clear on how they will achieve success; the fishers have not been sufficiently or appropriately informed about the harm done by their work practices and they only respond to their needs and interests; there is not enough honest inspection and surveillance, so illegal and improper practices occur. The case of totoaba has been handled in a way that is clearly ineffective, because the instruments have focused on the protection of adults without regard to juveniles. This is possibly because the decrees have tried not to interfere with shrimp fishing at sea.}, annote = {REVIEW -discuss management strategies and success/failures in regards to vaquita and totoaba in G of C -explain possible reasons for ineffectiveness of specific programs {\_}{\_}{\_} -specifically examine Upper Gulf of California and Colorado River Delta (UGCCRD) -detail on decrees in area my federal government -Mexican government invested 3 million US for conservation purposes to help compensate the fishing industry and eventually end fishing activities 1993- Biosphere reserve 1995-UGCCRD Reserve Management Plan 1997- International Committee for the Recovery of the Vaquita (CIRVA) declared gill nets were most hazardous factor 2000- Mexican National Fishers Chart reported to prevent extinction by catch rate should be under 0.2 percent per year {\~{}}2007- PACE- support individuals and families to not fish {\_}{\_}{\_}{\_} Three local problems 1) high fish production facing problems of population declines 2) MPA with convergent goals of conservation 3) Bycatch in commercial fisheries -Mexican fisheries have conducted many strategies and policies but have often been ineffective --no consistency between fisheries and conservation sectors --decrees have objectives but don't describe how to meet those objectives --fishers only respond to individual needs --not enough honest surveillance and enforcement }, author = {Bobadilla, Mariana and Alvarez-Borrego, Saul and Avila-Foucat, Sophie and Lara-Valencia, Francisco and Espejel, Ileana}, journal = {Environmental Science and Policy}, keywords = {fisheries,vaquita}, pages = {998--1007}, title = {{Evolution of environmental policy instruments implemented for the protection of totoaba and the vaquita porpoise in the Upper Gulf of California}}, volume = {14}, year = {2011} } @article{Pauly1980, abstract = {-looks at 175 different fish stocks at examines relationships between mortality, growth, and environmental temperature -examines these parameters through use of von Bertalanffy growth formula -argue three variables affect natural mortality: size of fish, growth rate of fish, and environmental temperature }, author = {Pauly, Daniel}, journal = {Journal du Conseil International pour l'Exploration de la Mer}, keywords = {environmental stochasticity,growth,mortality,shark}, pages = {175--192}, title = {{On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks}}, volume = {39}, year = {1980} } @book{Caswell2001, author = {Caswell, Hal}, edition = {second}, keywords = {demography,environmental stochasticity,leslie matrix,matrixes}, publisher = {Sinauer Associates, Inc.}, title = {{Matrix Population Models: Construction, Analysis, and Interpretation}}, year = {2001} } @article{HastingsBoettiger2013, author = {Boettiger, Carl and Hastings, Alan}, journal = {Nature}, keywords = {fisheries,projections,theoretical ecology}, number = {7431}, pages = {157--158}, title = {{From patterns to predictions}}, volume = {493}, year = {2013} } @article{Lawton1999, annote = {Argues not to study community ecology -like physics- no point in studying planets because you can't learn about the whole universe of planet theory that way/? -we cannot accuratly predict where a projectile will land but we can still make generalizations -we still have to merge theory of relativity and quatum field theory -there is a need to not do such pigeon-holed experiments and observations-what theory are you actually working at instead of "what can we measure" -local species richness mostly depends on regional species pool other useful sites http://www.nceas.ucsb.edu/nceas-web/projects/resources/ecoessay/brown/kareiva.html http://oikosjournal.wordpress.com/2011/04/21/synthesizing-ecology-revisiting-an-oikos-classic/}, author = {Lawton, John H.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Lawton - 1999 - Are There General Laws in Ecology.pdf:pdf}, journal = {Oikos}, keywords = {ecology,laws,scaling,theoretical ecology}, pages = {177--192}, title = {{Are There General Laws in Ecology?}}, volume = {84}, year = {1999} } @article{Sibaja-Cordero2008, abstract = {Data on several marine species collected over 15 years (1991 to 2007), by dive-masters of the diving company Undersea Hunter, at 27 sites around Isla del Coco (Cocos Island), Pacific Costa Rica, were analyzed. The goal was to create a base line of the pelagic species that live in the waters of the Island based on reports of their activity during tourist dives. A data matrix was generated and multivariate methods used to determine the patterns of temporal and spacial variation. variability in the occurrence of several species was high between sites. All sites presented a change in the asemblages during the 1991-92 and 1997-98 El Niño events. However, some sites had more influence by this climatic oscillation. El Niño event had stronger repercussion on the abundance and occurrence of particular species. Elasmobranchs such as the scalloped hammerhead sharks (Sphyrna lewini) and the marbled ray (Taeniura meyeni) showed a negative association with anomalous sea surface temperatures. Starting in 2000 there is a decrease in the average abundances and in the presence of the pelagic species, especially for economically important sharks. These variables reach similar values compared to those of El Niño years. A possible explanation is the increase of illegal fishing that took place around the Island or immediate waters. Some of these are species with great mobility. Nevertheless, some species had a small recovery in recent years. A collaborative program between the Government of Costa Rica and Marviva (a non governmental organization) in recent years has resulted in an improvement in the conservation of the marine fauna of Isla del Coco. Rev. Biol. Trop. 56 (Suppl. 2): 113-132. Epub 2008 August 29.}, annote = {Abstract: -15 years of data from Undersea Hunter group at Cocos Island -multivariate methods used to examine effects of time and space variation -change in populations during El Nino years of 1991-92 and 1997-98 -beginning in 2000 there was a decrease in abundance and presence of large sharks- illegal fishing increase? Translated notes: Number of dives over time would be useful plot Examine data not only on elasmobranchs byt also on dolphins, whales, and turtles Introduction: -past dive surveys by Reef Environmental Education Foundation -also see Wilson et al. 2001 -look at presence/absence as a ratio to number of dives --use Principal COmponent Analysis to look at time variation Results: -find signifcant changes in abundance during El nino years -hammerheads are seasonally from june to dec, decrease in overall abundance over time -whitetips are residents year round, decrease in overall abundance over time -Silky sharks have declined since 1998 -Blacktip shark presence was low for 2001/2002 but then began to increase -whitetip has become more common recently -eagle ray population has increased since 2001 (same trends for other rays-need to look into) -some data exists for other species: mackeral, barracuda, dolphins, humpbacks, false killer whales, pilot whales, lobsters and octopus -there is variation amongst dive sites (it would be useful to get habitat/depth info for each site) -sharks were 20 percent of Costa Rica biomass from 1988 to 1997 but fell to 16.7 between 1998-2005}, author = {Sibaja-Cordero, Jeffrey Alejandro}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sibaja-Cordero - 2008 - Tendencias espacio-temporales de los avistamientos de fauna marina en los buceos tur{\'{i}}sticos (Isla del Coco , Co.pdf:pdf}, journal = {Revista de Biologia Tropical}, keywords = {cetaceans,cocos,cocos island,costa rica,el ni{\~{n}}o,illegal fishing,isla del coco,movement,pelagic,sharks}, mendeley-tags = {cocos,movement,sharks}, number = {August}, pages = {113--132}, title = {{Tendencias espacio-temporales de los avistamientos de fauna marina en los buceos tur{\'{i}}sticos (Isla del Coco , Costa Rica)}}, volume = {56}, year = {2008} } @article{Coulson2012, abstract = {Replicated experiments at the level of the population are often not feasible for field systems. Despite this, population-level observational studies play a critical role in biology. For example, they have revealed how environmental change generates ecological and evolutionary change in free-living populations. When replicated experiments are impossible, construct- ing models and using these to conduct in silico experiments is the next best thing. Recent advances in the construction and analysis of integral projection models (IPMs) mean they offer a remarkably powerful tool to study ecological and evolutionary dynamics. IPMs can be parameterised using data frequently collected by ecologists, but the ease with which they can be constructed and analysed is perhaps not as widely appreciated as it could be. In this paper, which is loosely related to the talk I gave when receiving the Per Brinck Oikos Award in 2012, I show how easily IPMs can be constructed and analysed, and I argue they play an important role in posing and testing hypotheses in population biology.}, annote = {Personal note -could you modify this for a metapopulation and evolve traits (dispersal)??? {\_}{\_}{\_}{\_}{\_}{\_}{\_} -paper is a summary of integral projection model use and analysis -argues that these models use data often collected by field biologists {\_}{\_} -we cannot replicate many ecological and evolutionary setups so we need to construct models to run simulations -integral projection models allow the dynamics of continuous phenotypic traits to be tracked (ex. body size) --can generalize these models to include a mix of discrete and continuous traits -create a model using Soay sheep population data in Scotland (mark-recapture study) -describes methods for estimating each parameter Survival --generalized linear models to estimate ---can also incorporate density and climate effects Recruitment --is a function of reproducing female body size --then use similar analytic approach as was used for survival Development -body weight development function (describes how body weight changes for survivors) -fits function to actual data to find growth distribution -(lots of detail in paper) Inheritance -use same logic as development parameter -fits function of recruits size (weight) versus the size of their mothers {\_}{\_}{\_} -the constructed model then projects the distribution of body weight for the next year using a single integral -to commute the IPM the easiest way is to discretise the body weight distribution -can then set up a square matrices --each matrix will describe a different set of transition rate for survival, recruitment, development, and inheritance -can then run models that are density independent, density-dependent and/or stochastic models where transition rates vary with time independent of density, or a stochastic density-dependent model -can then measure: viability, fertility selection, parent-offspring phenotypic covariances, dist. of lifetime reproduction sucess, life expectancy, generation length, population growth and size {\_}{\_}{\_} -examines sensitivity of his parameter estimates -also finds that life history and associations between his four parameters vary significantly with the density of the system {\_}Future Work{\_} -incorporate age and sex-structure -environmental changes -different type of recruitment }, author = {Coulson, Tim}, journal = {Oikos}, keywords = {matrices,population model}, pages = {1337--1350}, title = {{Integral projections models, their construction and use in posing hypotheses in ecology}}, volume = {121}, year = {2012} } @article{McKaneNewman2004, author = {McKane, Alan J and Newman, Timothy J}, journal = {Physical Review Letters}, keywords = {demography,physics,population model,statistics}, number = {041902}, title = {{Stochastic models in population biology and their deterministic analogs}}, volume = {70}, year = {2004} } @article{Gallucci2006, abstract = {Abstract: Several life history traits of sharks result in juveniles being particularly vulnerable to exploitation. However, population level impacts of harvests on juvenile sharks have not been well quantified. This paper examines a range of harvest strategies, including those targeting juveniles. Reproductive value and yield per recruit are used to compare the harvests, which are represented by Leslie matrix models with a harvest matrix. Two species are used as examples: the short-lived Rhizoprionodon taylori and the long-lived Squalus acanthias. Harvests that maintain a stationary population size cause reproductive values to change in opposing ways, but they remove equal fractions of the population's repro- ductive potential. A new theorem gives population growth as a function of the fraction of reproductive potential re- moved by a harvest, a relationship useful for comparing harvests on juveniles and adults. Stochastic projections indicate that the risk of depletion is associated with the fraction of reproductive potential removed annually, a measure which encompasses the information in both the selectivity and the rate of fishing mortality. These results indicate the value of focusing conservation efforts on preserving reproductive potential.}, annote = {-paper is examining harvest strategies in different species of sharks based on reproductive value and yield per recruit -use a matrix harvest model and focus on effects of harvesting juveniles from a population {\_}{\_}{\_}{\_}{\_} -explains why age-structured models are much more useful when it comes to shark populations -examine reproductive value in depth --"RV is the relative contrition of individuals at each age to the long-term growth of the population" -reproductive potential simply extends the definition of RV to the population level (sum of all individuals) {\_}{\_}{\_}{\_}{\_} -assume constant mortality across age classes -reproductive value depends on linear function of length (age) -harvests were included as a diagonal matrix (H) -also use stochastic projections to evaluate the risks associated with different harvesting strategies -use lognormal random variables in survival, fecundity, and harvest parameters to incorporate stochasticity --all age classes were assumed to be effected equally based on environmental stochasticity -would run 1000 trials and calculated the probability that the population after 50 years decreased to 20 percent of the initial projection {\_}{\_}{\_}{\_}{\_}{\_} -show how harvesting different ages affects the reproductive value of individuals. Harvesting juveniles actually increases RV Theorem: The asymptotic annual growth of a harvested population lambda decreases linearly with the fraction of the reproductive potential harvested annually: -this allows a framework for evaluating how much of the reproductive potential may be removed from a population for sustainable harvest regardless of age -find that changes in reproductive value are not good indicators to the effect of harvest, especially in older age classes -instead reproductive potential summed across all individuals is a much better indicator because it includes information about age distributions -no matter what kind of fishery if you harvest juveniles and adults the population is likely to be in danger }, author = {Gallucci, Vincent F and Taylor, Ian G and Erzini, Karim}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, keywords = {juvenile,population model,shark}, pages = {931--942}, title = {{Conservation and management of exploited shark populations based on reproductive value}}, volume = {63}, year = {2006} } @article{Smith74a, annote = {-describes finding of: --patches not being fully saturated --extinction is related to patch size --recolonization is related to inter patch distance --300 m appears to be dispersal radius --at Bodie birth rate is higher, adult death rate (35 {\%}) is lower and juvenile death rate is higher juvenile mortality rate is very high {\_}{\_}{\_}{\_}{\_} -from 1969-72 they measured for each patch: number of pikas, island perimeter, and inter island distance to patches with 3 or more pikas (if they had less than 3 they could not be a source of recolonization -MacArthur found (as did Andrew) that time to extinction is related to patch size -if carrying capacity of path is equal to 4 then time to extinction would be 90 years -find dispersal of pikas is related to crowding of juveniles --feel in this study that there should be a mixed strategy for producing dispersers -argue dispersal is random so pikas have no sense of surrounding patch density if they choose to disperse -dispersal should affect bode greater than normal range because Bodie is on edge of range for princeps}, author = {Smith, Andrew T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith - 1974 - The distribution and dispersal of pikas Consequences of insular population structure.pdf:pdf}, journal = {Ecology}, keywords = {dispersal,pika}, number = {5}, pages = {1112--1119}, title = {{The distribution and dispersal of pikas: Consequences of insular population structure}}, volume = {55}, year = {1974} } @article{Jennings2012, abstract = {Abstract Coastal biodiversity is threatened worldwide by both direct and indirect anthropogenic activities. To more ef- fectively manage and protect coastal biodiversity, accurate assessments of genetic, species, and ecosystem level diversity are required. We present the results from an assessment of the aquatic species diversity of a small (3 km2), shallow, mangrove- fringed Bahamian lagoon (the North Sound) subject to ongoing anthropogenic development. The assessment was conducted through a collation of field observations and data in published literature. We found that eight angiosperm species, 30 macro- algal species, and 370 animal species (including 95 fishes, 69 arthropods, 56 birds, and 45 mollusks) were documented within the lagoon. At least 11 of these species are of conser- vation concern, such as the critically endangered smalltooth sawfish (Pristis pectinata) and hawksbill turtle (Eretmochelys imbricata). Comparisons of community similarity indicated that the North Sound has a relatively distinct fauna and flora, but available data suggest that the species found there are most similar to those found in nearby habitats in Cuba. The lagoon forms a key nursery habitat for many species, including lemon sharks (Negaprion brevirostris), Caribbean spiny lobsters (Panulirus argus), and queen conch (Strombas gigas). Recently, the lagoon was included as part of a new marine protected area (MPA), but much of the habitat has already experienced considerable anthropogenic disturbance and the MPA boundaries have yet to be established. We have therefore analyzed the lagoon biodiversity and expect the data presented here to serve as a baseline for future comparisons.}, annote = {REVIEW -this paper is a complete review on all the various research that has been conducted in the North Sound -looks at Biodiversity of species and species of conservation concern -puts results into a broader context with similar habitats found in nearby Cuba -hope data collected here will serve as a future baseline if anthropomorphic development continues {\_}{\_}{\_}{\_} -gives good information regarding the MPA and previous habitat destruction -408 total species found in the North Sound, 11 of which are endangered -56 of 140 bird species are said to be transient or permanent residents in the North Sound -three species of turtles and one species of snake (Bimini Boa) -eight species of chondrichthyans from four different orders have been documented in the NS -N. brevirostris, Dasyastis americana, Carcharhinus leucas, Sphyrna tiburo, Ginglymostoma cirratium, Aetobatus narinari, Urobatis jamaicensis, Pristis pectinata -compare diversity indices to similar sites in Florida, Cuba, Guadeloupe, and the US Virgin Islands --NS is similar to Cuba but in general the NS is more unique with given indices -discuss how Bimini qualifies as a nursery site under Heupel 2007 recommendations and criteria}, author = {Jennings, David E and DiBattista, Joseph D and Stump, Kristine L and Hussey, Nigel E and Franks, Bryan R and Grubbs, R Dean and Gruber, Samuel H}, journal = {Journal of Coastal Conservation}, keywords = {bimini,review,shark}, month = {may}, pages = {1--24}, title = {{Assessment of the aquatic biodiversity of a threatened coastal lagoon at Bimini, Bahamas}}, year = {2012} } @article{Caswell1986, annote = {-a lot of the same information as Caswell 2001 book (some parts word for word actually) -need to return to this paper or the book for deeper understanding of the mathematics behind some of the modeling attempts -begin by stating most models depend on only one sex -this is justified off life cycles of sexes are identical or dynamics of population can be completely determined by one sex independent of the abundance of the other sex {\_}{\_}{\_}{\_}{\_} -major differences can occur in female versus male mortality rates including: mortality, age at maturity, and fecundity -explains different models for different life cycles -defines marriage functions -discusses effects of chaos and oscillations that can emerge}, author = {Caswell, Hal and Weeks, Daniel E}, journal = {The American Naturalist}, keywords = {demography,sea lions,two-sex}, number = {5}, pages = {707--735}, title = {{Two-Sex Models: Chaos, Extinction, and Other Dynamic Consequences of Sex}}, volume = {128}, year = {1986} } @article{Hartig2011, abstract = {Abstract Statistical models are the traditional choice to test scientific theories when observations, processes or boundary conditions are subject to stochasticity. Many important systems in ecology and biology, however, are difficult to capture with statistical models. Stochastic simulation models offer an alternative, but they were hitherto associated with a major disadvantage: their likelihood functions can usually not be calculated explicitly, and thus it is difficult to couple them to well-established statistical theory such as maximum likelihood and Bayesian statistics. A number of new methods, among them Approximate Bayesian Computing and Pattern-Oriented Modelling, bypass this limitation. These methods share three main principles: aggregation of simulated and observed data via summary statistics, likelihood approximation based on the summary statistics, and efficient sampling. We discuss principles as well as advantages and caveats of these methods, and demonstrate their potential for integrating stochastic simulation models into a unified framework for statistical modelling.}, author = {Hartig, Florian and Calabrese, Justin M and Reineking, Bjorn and Wiegand, Thorsten and Huth, Andreas}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Hartig et al. - 2011 - Statistical inference for stochastic simulation models -- theory and application.pdf:pdf}, journal = {Ecology Letters}, keywords = {statistics}, pages = {816--827}, title = {{Statistical inference for stochastic simulation models -- theory and application}}, volume = {14}, year = {2011} } @article{Gislason2010, abstract = {The natural mortality of exploited fish populations is often assumed to be a species- specific constant independent of body size. This assumption has important implica- tions for size-based fish population models and for predicting the outcome of size- dependent fisheries management measures such as mesh-size regulations. To test the assumption, we critically review the empirical estimates of the natural mortality, M (year)1), of marine and brackish water fish stocks and model them as a function of von Bertalanffy growth parameters, L (cm) and K (year)1), temperature (Kelvin) and length, L (cm). Using the Arrhenius equation to describe the relationship between M and temperature, we find M to be significantly related to length, L and K, but not to temperature (R2 = 0.62, P {\textless} 0.0001, n = 168). Temperature and K are signif- icantly correlated and when K is removed from the model the temperature term becomes significant, but the resulting model explains less of the total variance (R2 = 0.42, P {\textless} 0.0001, n = 168). The relationships between M, L, L, K and temperature are shown to be in general accordance with previous theoretical and empirical investigations. We conclude that natural mortality is significantly related to length and growth characteristics and recommend to use the empirical formula: ln(M) = 0.55 ) 1.61ln(L) + 1.44ln(L) + ln(K), for estimating the natural mortality of marine and brackish water fish }, annote = {-examine 168 empirically tested marine fish stocks (few are shark species) to determine relationships between mortality and parameters of the von Bertalanffy growth curve -find that length, max length, K, but not temperature significantly affect natural mortality -give general equation that correlates with body size ln(M) = 0.55 -1.61*ln(L) +1.44*ln(L{\_}{\{}$\backslash$infy{\}}) + ln(K) {\_}{\_}{\_} -gives a number of references which describe how mortality should scale with body size -look deeply at literature to find empirical tests of natural mortality (367 publications screened with and only accepted data on 168 fish stocks) {\_}{\_}{\_} -find the temperature had little effect on mortality --however there is a relationship between K and temperature, stressing importance of K in estimating mortality }, author = {Gislason, Henrik and Daan, Niels and Rice, Jake C and Pope, John G}, journal = {Fish and Fisheries}, keywords = {demography,mortality,population model,shark}, pages = {149--158}, title = {{Size, growth, temperature and the natural mortality of marine fish}}, volume = {11}, year = {2010} } @article{Irwin2003, annote = {{\textless}m:note{\textgreater}-freezing of frogs causes locomotion impairment for at least 96 hours{\textless}m:linebreak/{\textgreater}-recovered with normal behavior and metabolites within 24 hours but it took the 96 hours to recover full endurance in locomotion{\textless}m:linebreak/{\textgreater} {\textless}m:linebreak/{\textgreater} {\textless}/m:note{\textgreater}}, author = {Irwin, Jason T and Costanzo, Jon P and {Richard E. Lee}, Jr.}, journal = {Physiological and Biochemical Zoology}, keywords = {frog,physiology}, number = {3}, pages = {331--338}, title = {{Postfreeze Reduction of Locomotor Endurance in the Freeze: Tolerant Wood Frog, $\backslash$emph{\{}Rana sylvatica{\}}}}, volume = {76}, year = {2003} } @article{Gruber2001, author = {Gruber, Samuel H and de Marignac, Jean R C and Hoenig, John M}, journal = {Transactions of the American Fisheries Society}, keywords = {bimini,juvenile,shark}, pages = {376--384}, title = {{Survival of Juvenile Lemon Sharks at Bimini, Bahamas, Estimated by Mark-Depletion Experiments}}, volume = {130}, year = {2001} } @misc{Rcitation, address = {Vienna, Austria}, annote = {citation for R}, author = {{R Development Core Team}}, institution = {R Foundation for Statistical Computing}, keywords = {math,population model,statistics}, title = {{R: A Language and Environment for Statistical Computing}}, year = {2011} } @article{MacKenzieKendall2002, abstract = {Determination of the relative abundance of two populations, separated by time or space, is of interest in many ecological situations. We focus on two estimators of relative abundance, which assume that the probability that an individual is detected at least once in the survey is either equal or unequal for the two populations. We present three methods for incorporating the collected information into our inference. The first method, proposed previously, is a traditional hypothesis test for evidence that detection probabilities are unequal. However, we feel that, a priori, it is more likely that detection probabilities are actually different; hence, the burden of proof should be shifted, requiring evidence that detection probabilities are practically equivalent. The second method we present, equivalence testing, is one approach to doing so. Third, we suggest that model averaging could be used by combining the two estimators according to derived model weights. These differing approaches are applied to a mark--recapture experiment on Nuttall's cottontail rabbit ($\backslash$emph{\{}Sylvilagus nuttallii{\}}) conducted in central Oregon during 1974 and 1975, which has been previously analyzed by other authors.}, author = {MacKenzie, Darryl I and Kendall, WIlliam L}, journal = {Ecology}, keywords = {fisheries}, number = {9}, pages = {2387--2393}, title = {{How should detection probability be incorporated into estimates of relative abundance?}}, volume = {83}, year = {2002} } @article{Baum2005, abstract = {NA}, annote = {-paper responding to Burgess et al. 2005 -address all size of criticisms and still find their results and conclusions to be robust {\_}{\_}{\_}{\_}{\_}{\_}{\_} -say they only used certain data sets because of the availability or the inadequate other data sets -don't feel it is appropriate to simply analyze contrasting data sets and averaging out the results is appropriate as seen in Cortes 2002 --excluded all sharks in shark fishery specifically as Burgess discusses before and after 1993 -they agree with criticism over change in fishing methods over 4 decades -point out how many other analyses found similar conclusions to their papers -still feel that all species previously discussed on in series need of high conservation priority}, author = {Baum, Julia K and Kehler, Daniel G and Myers, Ransom A}, journal = {Fisheries}, keywords = {fisheries,shark}, month = {oct}, number = {10}, pages = {27--29}, title = {{Robust estimates of decline for pelagic shark population in the northwest Atlantic and Gulf of Mexico}}, volume = {30}, year = {2005} } @article{Cortes1998, abstract = {The use of demographic analyses incorporating life history information on validated age and growth, reproduction, and natural mortality is proposed to gain insight into the population dynamics of sharks under a variety of scenarios and to assess their vulnerability to varying exploitation rates. This approach provides a useful framework for comparison with other currently used methods of assessment, especially those that rely only on fishery-dependent data, and thus can be helpful to stock assessments and to the rational exploitation and management of shark stocks. A review of demographic analyses of large coastal sharks on the east coast of the US indicates that the lemon and sandbar sharks have very low rates of population increase (r{\textless}1.2{\%} year-1) and are thus extremely vulnerable to exploitation. In contrast, one of the small coastal group species of lesser importance to the fisheries, the bonnethead shark, has some of the highest r values yet calculated for any shark. Preliminary demographic analyses using nonvalidated age estimates indicate that two other common and economically valuable large coastal species, the blacktip and dusky sharks, may also exhibit relatively slow rates of population change and be very vulnerable to overexploitation. Improved assessment of shark stocks requires increased collection of biological and fishery data, and a much better understanding of their population dynamics, especially stock$\backslash$pmrecruitment relationships. 5 1998 Elsevier Science B.V. All rights reserved}, annote = {-proposes using demographic analyses that utilize life history information for studying population dynamics and exploration rates -discusses how more models that operate as they would for marine mammals, using age structure, may be more appropriate for sharks because of their life history characteristics -models age structure for (lemons, sandbars, dusk's, blacktips atlantic sharp nose and bonnet head) -demographic analyses are advantageous for many reasons, one being that important life history traits can be examined. -used equation to estimate survivorship in a specific age based on length at north and annual growth rate Lemon shark parameters Max age= 26 Age{\_}mat=12 length at birth =6- First year survival = 0.39 Second year survival =0.63 Third year survival = 0.86 r= -.0085 * he includes another set of values that are slightly different -indicates that if the life history parameters are reasonable then the populations cannot even sustain moderate levels of harvesting -argues that density dependence in sharks probably exists it is much less dramatic then teleosts because of the difference in life history characteristics }, author = {Cort{\'{e}}s, Enric}, journal = {Fisheries Research}, keywords = {demography,mortality,shark}, pages = {199--208}, title = {{Demographic analysis as an aid in shark stock assessment and management}}, volume = {39}, year = {1998} } @article{Seppanen2012, abstract = {Question: How might global climate change affect American pika (Ochotona princeps) metapopulation dynamics in the Great Basin, and how would such effects impact evolutionary dynamics of dispersal? Mathematical methods: A structured, semi-discrete, mechanistic metapopulation model in which patch age is the structuring variable. We apply adaptive dynamics for the evolutionary analysis and derive an invasion fitness proxy for this model setting. Key assumptions: Global climate change potentially alters the probability of patch extinction, dispersal costs, mortality, and fecundity. Births and immigration occur at discrete points in time. Deaths and emigration occur continuously over time. We model `average' patch dynamics. Results: Potentially viable metapopulations nevertheless can be destined for extinction via evolutionary suicide driven by climatic forcing. Specifically, selection can drive down dispersal rates in viable metapopulations, degrading colonization rates and increasing extinction rates to the point where the metapopulation crashes. Conclusions: Exclusive reliance on ecological dynamics without this evolutionary perspective would miss the phenomenon identified here. This result arises in realistic ranges of parameters and therefore generates a testable hypothesis with potential applications to long-term metapopulation sustainability.}, annote = {-what to see what effect GCC might have on metapopulation dynamics and evolutionary dynamics of dispersal -use a metapopulation model structured by patch age, use adaptive dynamics -Assumptions: --GCC can affect a number of different parameters --discrete birth and immigration, continuous death and emigration -metapopulation can go extinct via evolutionary suicide by climate forcing -we must model evolutionary dynamics to get a clear picture {\_}{\_}{\_} -semi-discrete model with seasons Steps: 1) census -compete for territories in summer 2) continual time for disperses to enter global dispersal pool from $\tau${\_}1 to $\tau${\_}2 3) at $\tau${\_}2 pikas are randomly placed on patches from global dispersal pool and compete for territories once again 4) within-season dynamics are governed by set of odes --over winter adult mortality and catastrophes --established juveniles become adults}, author = {Sepp{\"{a}}nen, Anne and Parvinen, Kalle and Nagy, John D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Sepp{\"{a}}nen, Parvinen, Nagy - 2012 - Evolution of dispersal in {\{}A{\}}merican pika (emph{\{}Ochotona princeps{\}}) metapopulations.pdf:pdf}, journal = {Evolutionary Ecology Research}, keywords = {bodie,dispersal,evolution,metapopulation,pika}, pages = {1--29}, title = {{Evolution of dispersal in {\{}A{\}}merican pika ($\backslash$emph{\{}Ochotona princeps{\}}) metapopulations}}, volume = {14}, year = {2012} } @article{Ferretti2010, abstract = {Whereas many land predators disappeared before their ecological roles were studied, the decline of marine apex predators is still unfolding. Large sharks in particular have experienced rapid declines over the last decades. In this study, we review the documented changes in exploited elasmobranch communities in coastal, demersal, and pelagic habitats, and synthesize the effects of sharks on their prey and wider communities. We show that the high natural diversity and abundance of sharks is vulnerable to even light fishing pressure. The decline of large predatory sharks reduces natural mortality in a range of prey, contributing to changes in abundance, distribution, and behaviour of small elasmobranchs, marine mammals, and sea turtles that have few other predators. Through direct predation and behavioural modifications, top-down effects of sharks have led to cascading changes in some coastal ecosystems. In demersal and pelagic communities, there is increasing evidence of mesopredator release, but cascading effects are more hypothetical. Here, fishing pressure on mesopredators may mask or even reverse some ecosystem effects. In conclusion, large sharks can exert strong top-down forces with the potential to shape marine communities over large spatial and temporal scales. Yet more empirical evidence is needed to test the generality of these effects throughout the ocean.}, annote = {REVIEW-lots of good citations bascompte (2005) -review paper that looks at exploited elasmobranch populations and how it has effects both prey and wider communities -explain how vulnerable shark are even when exposed to light fishing pressure -discusses mesopredator releases and trophic cascades {\_}{\_}{\_} -in depth review of shark demography and vulnerability to fishing -show that undisturbed coastal areas almost always had higher levels of predators making up the fish biomass --has to do with coastal changes and overall human footprint -show how shark nets have provided a good measure for sharks CPUE and show significant declines in most shark species -give examples of large declines in pelagic elasmobranchs in particular -discuss how decline of large sharks causes direct and indirect mechanisms for inducing trophic cascades: direct predation and non-consumption mechanisms -also interesting to see if you remove one shark species and not another the different kind of effects and/ or trophic effects that can be induced -also show large increases in mesopredator elasmobranchs during declines of larger shark species }, author = {Ferretti, Francesco and Worm, Boris and Britten, Gregory L and Heithaus, Michael R and Lotze, Heike K}, journal = {Ecology Letters}, keywords = {fisheries,review,shark}, pages = {1055--1071}, title = {{Patterns and ecosystem consequences of shark declines in the ocean}}, volume = {13}, year = {2010} } @article{Ziemba2000, author = {Ziemba, Robert E and Myers, Michael T and Collins, James P}, journal = {Oecologia}, keywords = {cannibalism}, pages = {225--231}, title = {{Foraging under the risk of cannibalism leads to divergence in body size among tiger salamander larvae}}, volume = {124}, year = {2000} } @article{Fujitani2012, abstract = {Abstract. Changes in human behavior are a precursor to measurable impacts of no-take marine reserves. We investigated changes in recreational fishing site selection in response to the 2005 announcement of enforcement in a marine reserve in the Gulf of California, Mexico. We used a novel data set of daily self-reported boating destinations from emergency rescue logbooks for a recreational angling community from 2000 to 2008. Because the reserve system has no experimental control, we modeled the data two ways to test for robustness to model specification. We tested for changes in human fishing behavior with regression and fit a fleet- level discrete choice model to project a counterfactual scenario. The counterfactual is the statistically constructed ex post expectation of the human behavior we would have observed if the reserve never existed. We included month and year fixed effects in our models to account for seasonal and interannual fluctuations in fishing behavior and catch rates. We detected a decrease in reserve use compared to the counterfactual, indicating that the reserve rapidly experienced a decrease in visitation. However, the reserve's effect to reduce trips diminished with time. These results indicate that the reserve is unlikely to meet its ecological goals without institutional changes that enhance compliance. This illustrates the value of human use data to understanding the processes underlying marine reserve function. We suggest that managers should consider human use with the same frequency, rigor, and tools as they do fishery stocks. Marine reserves directly affect people, and understanding human behavioral responses to marine reserves is an important step in marine reserve management.}, annote = {-paper examines changes in recreational fishing behavior before and after the announcement of a no-take marine reserve --argue that human behavior is a good precursor to possible impacts {\_}{\_}{\_}{\_}{\_} -use data collected that fishermen report for safety reasons -cannot simply fit a data to a model and examine differences before and after the marine reserve --must fit data with a single model and models before and after the marine reserve to see if there is a major change in behavior (i.e. a 'break'') -also constructed a control for the experiment (statistically) {\_}{\_}{\_} -biological monitoring did not detect effect of reserve but this new analysis was able to detect a change in fleet-level behavior -marine reserve did not afford long-term protection --relative decrease in trips to reserve did not last long -need better enforcement or stronger disincentives to fish (no penalties have ever been enforced) -human monitoring can help determine if governing of a reserve area is actually working}, author = {Fujitani, Marie L and Fenichel, Eli P and Torre, Jorge and Gerber, Leah R}, journal = {Ecological Applications}, keywords = {fisheries,megafauna,mexico,reserve}, number = {2}, pages = {597--605}, title = {{Implementation of a marine reserve has a rapid but short-lived effect on recreational angler use}}, volume = {22}, year = {2012} } @book{Croft2008, address = {Princeton, New Jersey}, author = {Croft, Darren P and James, Richard and Krause, Jens}, keywords = {math,movement,network analysis,shark,statistics}, publisher = {Princeton University Press}, title = {{Exploring Animal Social Networks}}, year = {2008} } @article{Moritz2008, abstract = {We provide a century-scale view of small-mammal responses to global warming, without confounding effects of land-use change, by repeating Grinnell's early--20th century survey across a 3000-meter-elevation gradient that spans Yosemite National Park, California, USA. Using occupancy modeling to control for variation in detectability, we show substantial ({\~{}}500 meters on average) upward changes in elevational limits for half of 28 species monitored, consistent with the observed {\~{}}3$\backslash$,{\^{}}{\{}$\backslash$circ{\}}C increase in minimum temperatures. Formerly low-elevation species expanded their ranges and high-elevation species contracted theirs, leading to changed community composition at mid- and high elevations. Elevational replacement among congeners changed because species' responses were idiosyncratic. Though some high-elevation species are threatened, protection of elevation gradients allows other species to respond via migration.}, annote = {-set out to repeat an experiment that was originally conducted in early 20th century -conduct transect survey at 3000 m elevation in yosemite for small mammals -find that species have shifted their elevational limits with increase in temperature {\_}{\_}{\_}{\_} -find that elevation limits do shift upwards and this occurs more often at lower versus higher elevations **does depend on the particular species though -high elevation species typically endured range contractions -other traits like life history and ecological traits proved to be poor predictors in elevation changes -A lot of data missing for O. princeps but they experienced a range contraction of lower range limit change = 153 with an original elevation range of 2377-3871 -argue how important large-scale elevation gradients are to allow species to migrate in response to climate, vegetation change, or both}, author = {Moritz, Craig and Patton, James L and Conroy, Chris J and Parra, Juan L and White, Gary C and Beissinger, Steven R}, journal = {Science}, keywords = {climate,environmental stochasticity,pika}, month = {oct}, pages = {261--264}, title = {{Impact of a Century of Climate Change on Small-Mammal Communities in Yosemite National Park, USA}}, volume = {322}, year = {2008} } @article{Peterson1984, author = {Peterson, Ingrid and Wroblewski, J S}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, keywords = {fisheries,mortality,shark}, number = {7}, pages = {1117--1120}, title = {{Mortality Rate of Fishes in the Pelagic Ecosystem}}, volume = {41}, year = {1984} } @article{Grimm2005, abstract = {Agent-based complex systems are dynamic networks of many interacting agents; examples include ecosystems, financial markets, and cities. The search for general principles underlying the internal organization of such systems often uses bottom-up simulation models such as cellular automata and agent-based models. No general framework for designing, testing, and analyzing bottom-up models has yet been established, but recent advances in ecological modeling have come together in a general strategy we call pattern- oriented modeling. This strategy provides a unifying framework for decoding the internal organization of agent-based complex systems and may lead toward unifying algorithmic theories of the relation between adaptive behavior and system complexity.}, annote = {REVIEW -paper that examines the different methods of analyzing simulation models of individual agents. -in particular, utilizing bottom-up methods to evaluate success of such models {\_}{\_}{\_} -pattern-orientated modeling allows a proper analysis of bottom-up modeling -use patterns in data to decide what to include in models so they are not too simple nor too complex -multiple pattern matching allows for greater confidence that the models not only reproduces the real life patterns but also reflects how the real system potentially operates -build string inference my using multiple models and comparing them to actual data -use "inverse modeling" to fit parameter values by reproducing multiple patterns seen in real life and fine tuning the input values --give a number of examples of this but indicate how rarely it is utilized in ACS studies }, author = {Grimm, Volker and Revilla, Eloy and Berger, Uta and Jeltsch, Florian and Mooji, Wolf M and Railsback, Steven F and Thulke, Hans-Hermann and Weiner, Jacob and Wiegand, Thorsten and DeAngelis, Donald L}, journal = {Science}, keywords = {math,population model,theoretical}, number = {987}, pages = {987--991}, title = {{Pattern-Orientated Modeling of Agent-Based Complex Systems: Lessons from Ecology}}, volume = {310}, year = {2005} } @article{Heupel2002, abstract = {Abstract: A population of young blacktip sharks (Carcharhinus limbatus) was monitored over three years to determine their mortality rates using a series of acoustic listening stations. Based on these data it was possible to use several mortality estimators, including indirect life history based methods and direct methods such as the Kaplan-Meier and SURVIV methods, to estimate natural, fishing, and total mortality. Kaplan-Meier (61--91{\%}) and SURVIV (62--92{\%}) methods provided nearly identical total mortality rates during the first six months of life. This agreement suggests that these estimates are accurate for this population. All natural and fishing mortality occurred within the first 15 weeks of the study. This suggests that young sharks are most vulnerable to all types of mortality during this period. Sharks that survived beyond the first 15 weeks successfully left the nursery and were presumed to have migrated southward during fall months. These results provide critical information concerning the early life history of sharks and the importance of nursery areas to the survival of young animals.}, annote = {-used telemetry data to estimate mortality ---estimated mortality through life history based methods and direct methods like the Kaplan-Meier (61-91{\%}) and SURVIV (62-92{\%}) -suggests that young sharks are to all types of mortality during this early stage in life -tagged sharks with internal transmitters and followed them using an array of monitors -sharks were then grouped as (i) survivals, one's that left the study site (ii) natural mortalities (iii) removals- removed for factors other than natural mortality or swimming out -tagged a total of 92 C. limbatus and transmitted them over course of three years- all neonates with open umbilical scars -mortality was estimated between 0.35 and 0.45 per year -Peterson and Wroblewski (1984) showed a decline of 0.30 per year for newborns to 0.14 per year for the maximum age of 10 years -used six "equation methods" for estimated mortality -they also looked at mortality over time of the study (turned out to be that juveniles died a lot at first but these rates slowed over the course of the study }, author = {Heupel, M R and Simpfendorfer, C A}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, keywords = {juvenile,mortality,shark}, pages = {624--632}, title = {{Estimation of mortality of juvenile blacktip sharks, $\backslash$textit{\{}Carcharhinus limbatus{\}}, within a nursery area using telemetry data}}, volume = {59}, year = {2002} } @article{Dudgeon2013, abstract = {Site fidelity and migratory movements of vertebrate animals occur at many spatial and temporal scales. Larger migratory movements tend to occur in species that live in seasonal environments in which food supplies vary markedly, while species found in thermally stable environments are more site-attached. In the marine environment, seasonal migrations are often associated with predictable temporary aggre- gations that have largely been targeted for exploitation. We employed passive acoustic telemetry to investigate inter- and intraseasonal site fidelity of zebra sharks to an aggregation site in southeast Queensland, Australia, close to the southern latitudinal extent of this species' range. We tracked 10 zebra sharks over two aggregation seasons (21 months). We applied a generalized linear mixed-effects model to investigate the presence/absence of these zebra sharks with respect to several environmental vari- ables. We found that different environmental factors were associated with site fidelity of zebra sharks at different temporal levels and that these may be indicative of the mechanisms driving the movements. Seasonal patterns may be driven by endogenous systems, and cues such as photoperiod and water temperature are likely to be important. Intraseasonal patterns are more likely to be indicative of direct behavioural responses to changes in environmental conditions such as increased wave heights, as well as foraging bouts away from a core refuge. Understanding the relative contributions of these environmental parameters, as well as biological factors, will be important for making predictions of site fidelity and movements of migratory marine vertebrates under differing future scenarios such as increases in sea temperature.}, author = {Dudgeon, Christine L and Lanyon, Janet M and Semmens, Jayson M}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dudgeon, Lanyon, Semmens - 2013 - Seasonality and site fi delity of the zebra shark , Stegostoma fasciatum , in southeast Queensland , A.pdf:pdf}, journal = {Animal Behavior}, keywords = {GLMM,movement,shark,statistics,telemetry}, pages = {471--481}, title = {{Seasonality and site fidelity of the zebra shark, $\backslash$emph{\{}Stegostoma fasciatum{\}} in southeast {\{}Q{\}}ueensland, {\{}A{\}}ustralia}}, volume = {85}, year = {2013} } @article{Lutz1985, abstract = {The sea turtle is habitually submarine, surfacing only briefly to breathe. Aquat- ic respiration is negligible in the loggerhead (Caretta caretta), accounting for less than 2{\%}of the resting oxygen consumption. Unlike most marine mammals there are no special adaptations for increased oxygen capacity in blood or tissue. The lung, however, functions as the major oxygen store, and calculations indicate that it can supply sufficient oxygen for most routine dives (up to 20 min) to be aerobic. The respiratory properties of sea turtle blood are particularly well suited to lung-tissue transport during routine breathhold periods. Sea turtles survive prolonged dives of at least 3 h by having a high anaerobic capacity. Substantial changes in blood gas and pH levels are endured and special adaptations in brain energy metabolism are indicated.}, annote = {-studied the loggerhead turtle (Caretta caretta) -found that aquatic respiration accounted for only 2{\%} of the resting oxygen consumption -unlike marine mammals they have not evolved increased oxygen capacity in blood/tissue -lungs can supply enough oxygen for routine dives(20 min) *they survive long dives of 3 hours by high anaerobic activity -this obviously greatly affects good gas and pH levels {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -would place turtles in tanks and measure blood composition -also examined muscle tissue for myoglobin amount {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -only spend 1 percent of time at surface breathing -they have the same hematocrit and hemoglobin concentration and O2 capacities as non-diving reptiles as opposed to elevated levels like those seen in diving mammals -they also have a Bohr effect that is on the low end of the reptile range (diving mammals have increased Bohr values) -non bicarbonate blood buffer capacity is lower than other reptiles -do not have high myoglobin concentration like diving mammals -periphenal ischemia- conserves the circulation (oxygen stores as well) for the brain and heart while everything else goes anaerobic --if this is relaxed after the dive then the blood is flooded with lactate *in turtles this does not happen because all tissues become anaerobic during the dive Brain anoxia -unlike rats turtles were able to deoxidize their cytochrome (reverse effects of anoxia) }, author = {Lutz, Peter L and Bentley, Timothy B}, journal = {Copeia}, keywords = {physiology,turtle}, month = {aug}, number = {3}, pages = {671--679}, title = {{Respiratory Physiology of Diving in the Sea Turtle}}, year = {1985} } @article{McAuley2007, abstract = {Stochastic demographic models were developed for Carcharhinus obscurus and C. plumbeus populations off the west coast of Australia by resampling the input parameters for life tables from empirical biological data collected from commercial target fisheries and fishery-independent surveys. The models were used to examine the effects of multiple scenarios of age-specific survival, derived from the fishing mortality rates estimated from a tagging study on sharks and indirect estimates of natural mortality. In the absence of fishing, median estimates of the rates of intrinsic population increase (r) were 0.025 for both species. Inclusion of the age-specific fishing mortality rates estimated for C. obscurus recruits born in 1994 and 1995 resulted in the median estimates of r declining to 0.007 and 0.012, respectively, suggesting that recent harvest levels of mainly neonates by the target fishery were probably sustainable. However, the model also suggested that the population was more susceptible to exploitation of older sharks than was previously believed. The C. plumbeus model indicated that fishing mortality between 2001 and 2004 was probably unsustainable. The increasingly negative trend in median r estimates (from --0.032 to --0.049), and the population's apparently limited capacity for density-dependent compensation through changes in fecundity, somatic growth and longevity, suggests that management intervention is necessary to prevent continued stock depletion.}, annote = {-developed stochastic models for C. obscures and plumbeus populations off of Australia -wanted to examine age specific effects of fishing and natural mortality derived from tagging data -showed that at certain times and for certain populations that the fishing mortality rates were unsustainable {\_}{\_}{\_}{\_}{\_} -lot of fishing of these species, adults and juveniles -longline and gill net fishing -can't perform dynamic assessment techniques so demographic models is the next logical choice, however, demographic models have not been used widely in assessing fishing practices --also want to use stochastic models for more realistic estimates {\_}{\_}{\_}{\_} used demographic, age-structured models of females -incorporate stochasticity by running 1000 sets of estimates for age, growth, and reproduction parameters -have to estimate natural mortality from 7 previous studies for either density independent of dependent mortality -use von Bertalanffy growth equation for some parameters -obtained fishing mortality rates from tagging studies -even qualified rates at which shark fishers would report their kills of animals with tags {\_}{\_}{\_}{\_} -found natural mortality to be estimated between 0.098-0.137 for sandbar -also found fishing mortality rates for different age classes -fishing mortality varied between species and ages -estimate that only 7.5 percent of C. obscures born will reproduce {\_}{\_}{\_}{\_} -discuss importance of using local biological data -feel previous estimates overestimated realistic and viable harvest rates -used a Poisson distribution to estimate fishers that did not report caught sharks to factor that into the model -suggest only faction of juvenile sharks should be the only group harvested for k-selected shark species -discuss density dependence in sharks -say it is not possible to verify model measurements of natural mortality }, author = {McAuley, Rory B and Simpfendorfer, Colin A and Hall, Norm G}, journal = {Journal of Marine Science}, keywords = {shark}, pages = {1710--1722}, title = {{A method for evaluating the impacts of fishing mortality and stochastic influences on the demography of two long-lived shark stocks}}, volume = {64}, year = {2007} } @article{Rossmanith2007, abstract = {In population viability analysis we are often faced with a lack of knowledge of survival rates in animal populations. In particular, survival of recruits is usually hard to assess. However, data on population structure might be considered as patterns that contain valuable information to estimate missing parameters indirectly. As an example for this pattern-oriented modelling and parameterization, pre-breeding survival rate of the endangered Lesser Spot- ted Woodpecker (Picoides minor) was determined here using data on population structure (e.g. sex ratio) and reproductive success at the population level (e.g. nesting success). There- fore, an individual-based model was developed simulating the population dynamics for two different populations that had been empirically studied at Lake Mockeln, Sweden, and Taunus, Germany. For both populations, a small range for pre-breeding survival rates could be identified wherein all simulated patterns corresponded best to the empirical values. Pre- breeding survival rate was found to be higher in the German scenario than in the Swedish and geographical variation in life-history traits is discussed as a possible reason. It is concluded that the pattern-oriented approach is a valuable method for estimating missing demographic parameters, even when using weak patterns from empirical investigations. Furthermore, it was shown that the use of multiple patterns is necessary for this purpose.}, annote = {-Study looks at how to estimate pre-breeding survival rate using pattern-orientated modeling and parameterization -examines two woodpecker populations in Germany and Sweden {\_}{\_}{\_} -provide sources for why using data from other population of the same species is not always particularly helpful -use data on population structure and reproductive success as patterns to be evaluated {\_}{\_}{\_} -a stochastic individual-based model is used -determine if model fits actual data to see if a parameter combination is a good fit -11 step algorithm each year is simulated -make model stochastic by drawing from a normal distribution for each parameter with its given mean and standard deviation -five variable (patterns) are used that relate to the unknown parameter in some way --sex ration, pair ratio, breeding success, occupancy of territories, breeding success -throw out populations that went extinct or quasi-extinct **find mean value for all simulations and determine if it falls within the 95 percent CI of actual field data estimates, not the other way around -use nice plot of pattern matching versus unknown parameter value -also show which demographic patterns are the most useful (most sensitive if you will) }, author = {Rossmanith, Eva and Blaum, Niels and Grimm, Volker and Jeltsch, Florian}, journal = {Biological Conservation}, keywords = {aves,inverse modelling,parameter estimation}, pages = {555--564}, title = {{Pattern-oriented modelling for estimating unknown pre-breeding survival rates: The case of the Lesser Spotted Woodpecker ($\backslash$emph{\{}Picoides minor{\}})}}, volume = {135}, year = {2007} } @article{Nance2011, abstract = {Abstract Genetic diversity (h), effective population size (Ne), and contemporary levels of gene flow are important parameters to estimate for species of conservation concern, such as the globally endangered scalloped hammerhead shark, Sphyrna lewini. Therefore, we have reconstructed the demographic history of S. lewini across its Eastern Pacific (EP) range by applying classical and coalescent population genetic methods to a combination of 15 microsatellite loci and mtDNA control region sequences. In addition to significant population genetic structure and isolation-by-distance among seven coastal sites between central Mexico and Ecuador, the analyses revealed that all populations have experienced a bottleneck and that all current values of h are at least an order of magnitude smaller than ancestral h, indicating large decreases in Ne (h = 4Nem), where m is the mutation rate. Application of the isolation-with-migration (IM) model showed modest but significant genetic connectivity between most sampled sites (point estimates of Nm=0.1--16.7), with divergence times (t) among all populations significantly greater than zero. Using a conservative (i.e., slow) fossil-based taxon-specific phylogenetic calibration for mtDNA mutation rates, posterior probability distributions (PPDs) for the onset of the decline in Ne predate modern fishing in this region. The cause of decline over the last several thousand years is unknown but is highly atypical as a post-glacial demographic history. Regardless of the cause, our data and analyses suggest that S. lewini was far more abundant throughout the EP in the past than at present.}, annote = {-have found significant genetic structure and isolation between 7 costal sites between mexico and ecuador --two sites were La Paz and Mazatlan (collected samples from landed sharks in fisheries) -all the populations have experienced a bottleneck -population appears to have begun declining well before modern fishing. S. lewini was far more abundant in the eastern pacific in the past -decline appears to have started 3600 to 12 000 years ago --example of La Paz was current population size of 435.51 and historical at 39,627.80 with the decline beginning 8452.79 -genetic diversity is at least an order or magnitude small than ancestral populations -used several methods to try and estimate the population size -observed and expected heterozygosity across all loci and populations was 0.770 and 0.792 -only 3.7 percent of individuals per sample were full siblings -59.2 Percent were half siblings ***however they believe their sample size may be too small to really estimate this -microsatellite mutation rate was between 1.0E-5 and 2.0E-4 -rate of gene flow (migrants per generation) ranged from 0.1 to 16.7 migrants per generation **a lot of this may be underestimates because they could not sample every population obviously Big Results -this East pacific shark exists in series of separate and potentially small populations -not sure why population began declining so long ago S. lewini facts -reproduction- 15 years of age -23 pups = mean litter size }, author = {Nance, Holly A and Klimley, Peter and Galvan-Magana, Felipe and Martinez-Ortiz, Jimmy and Marko, Peter B}, journal = {PLoSONE}, keywords = {extinction,genetics,hammerhead,lewini,mexico,shark}, month = {jun}, number = {7}, title = {{Demographic Processes Underlying Subtle Patterns of Population Structure in the Scalloped Hammerhead Shark, $\backslash$textit{\{}Sphyrna lewini{\}}}}, volume = {6}, year = {2011} } @article{Booth2011, annote = {-conducted vertebral band-pair formation in spotted gully shark and compared data to wild sharks over 21 year period -estimated max length, k, and t{\_}0 using von Bertalanffy growth model -natural mortality was estimated at 0.17/yr -age at maturity 11 and 15 for males and females respectively -juvenile survival was most important in variability of population growth rate (revealed by elasticity analysis) -only know about reproduction and feeding behavior to go off of for management -they developed a leslie based matrix model to evaluate how the gully shark would respond to increased fishing pressure -from Caswell (2011) exactly Could find: --growth rate (lambda) --stable age distribution (w) --age-specific reproductive value (v) solved Aw=(lambda)*w and v*A=(lambda)*w -sensitivity= relative sensitivity to lambda for a given parameter -elasticity= absolute "{\{}{\ldots}{\}}{\{}{\ldots}{\}}{\{}{\ldots}{\}}{\{}{\ldots}{\}}{\{}{\ldots}{\}}" -injected sharks with OTC (antibiotic, oxytetracycline hydrochloride)- number of fluorescent rings are counted and calculations from time of capture are performed -also killed a number of sharks for the study -natural mortality was estimated from three sources: Pauly's (1980) Hoenig's (1983) Jensen's (1996)}, author = {Booth, Anthony J and Foulis, Alan J and {and Malcolm J. Smale}}, journal = {Fisheries Bulletin}, keywords = {growth,leslie matrix,mortality,shark}, pages = {101--112}, title = {{Age validation, growth, mortality, and demographic modeling of spotting gully shark ($\backslash$textit{\{}Triakis megalopterus{\}}) from the southeast coast of South Africa}}, volume = {109}, year = {2011} } @article{Kneebone2012, abstract = {The sand tiger shark Carcharias taurus is a large coastal species that has endured marked declines in its western North Atlantic population over the past 30 yr. In the face of these declines, identification of nursery areas for this species is of particular importance to ensure the implementation of protective measures that will maximize survival of young individuals to maturity. Passive acoustic telemetry was used to assess the emergence of Plymouth, Kingston, Duxbury (PKD) Bay, Massachusetts, USA, as a seasonal nursery for juvenile sand tigers that migrate north from southern parturition grounds. Seasonal residency, habitat use, and site fidelity of 73 acoustically tagged juvenile sand tigers (78 to 108 cm fork length) were monitored within PKD Bay during 4 seasonal periods from 2008 to 2011. Eight individuals were tracked in multiple years, with 2 individuals returning to PKD Bay in 3 consecutive years. Sand tigers remained in PKD Bay for periods of 1 to 124 d and displayed a high degree of site fidelity to 2 core habitats during each year of the study. Weekly activity space estimates were relatively constant throughout each yearly monitoring period, with a general increase prior to emigration of sharks from the embayment. Emigration of sharks from PKD Bay was significantly related to both day length and water temperature. Collectively, these results suggest that PKD Bay constitutes a seasonal nursery area for juvenile sand tigers and warrants the extension of juvenile sand tiger essential fish habitat north of Cape Cod, Massachusetts, USA.}, author = {Kneebone, Jeff and Chisholm, John and Skomal, Gregory B}, doi = {10.3354/meps09989}, journal = {Marine Ecology Progress Series}, keywords = {juvenile,nursery site,shark,statistics,telemetry}, month = {dec}, pages = {165--181}, title = {{Seasonal residency, habitat use, and site fidelity of juvenile sand tiger sharks $\backslash$emph{\{}Carcharias taurus{\}} in a {\{}M{\}}assachusetts estuary}}, volume = {471}, year = {2012} } @article{Botsford1997, abstract = {The global marine fish catch is approaching its upper limit. The number of overfished populations, as well as the indirect effects of fisheries on marine ecosystems, indicate that management has failed to achieve a principal goal, sustainability. This failure is primarily due to continually increasing harvest rates in response to incessant sociopo- litical pressure for greater harvests and the intrinsic uncertainty in predicting the harvest that will cause population collapse. A more holistic approach incorporating interspecific interactions and physical environmental influences would contribute to greater sustain- ability by reducing the uncertainty in predictions. However, transforming the manage- ment process to reduce the influence of pressure for greater harvest holds more im- mediate promise.}, annote = {-discuss both direct and indirect effects of overfishing -attribute this to pressures for heater harvests and uncertainties regarding viable harvest rates -need to incorporate multiple interactions and environmental stochasticity {\_}{\_}{\_}{\_} -200 million people employed by fisheries -half of all stocks are fully exploited, 22 percent overexploited -size selective fishing can have a large effect -trophic interactions and degradation of marine systems through fishing --predator releases -ENSO conditions have many effects -regime shifts occur every few decades -importance of spatial and temporal scales -need to move to ecosystem based management -challenge to MSY --did not account for spatial variability --single species --only benefits of fisheries considered -only way to stop overfishing is through better management and predictions are to decrease the pressure to produce ever-increasing harvests --second choice appears more feasible -shift to optimal sustained yield instead of MSY}, author = {Botsford, Louis W and Castilla, Juan Carlos and Peterson, Charles H}, journal = {Science}, keywords = {fisheries}, month = {jul}, pages = {509--515}, title = {{The Management of Fisheries and Marine Ecosystems}}, volume = {277}, year = {1997} } @article{Wiegand2003, abstract = {We suggest that the conscious use of information that is ``hidden'' in distinct structures in nature itself and in data extracted from nature (=pattern) during the process of modeling (=pattern-oriented modeling) can substantially improve models in ecological application and conservation. Observed patterns, such as time-series patterns and spatial patterns of presence/absence in habitat patches, contain a great deal of data on scales, site-history, parameters and processes. Use of these data provides criteria for aggregating the biological information in the model, relates the model explicitly to the relevant scales of the system, facilitates the use of helpful techniques of indirect parameter estimation with independent data, and helps detect underlying ecological processes. Additionally, pattern-oriented models produce com- parative predictions that can be tested in the field. We developed a step-by-step protocol for pattern-oriented modeling and illustrate the potential of this protocol by discussing three pattern-oriented population models: (1) a population viability analysis for brown bears (Ursus arctos) in northern Spain using time-series data on females with cubs of the year to adjust unknown model parame- ters; (2) a savanna model for detecting underlying ecological processes from spatial patterns of tree distribution; and (3) the incidence function model of metapopulation dynamics as an example of process integration and model generalization. We conclude that using the pattern-oriented approach to its full potential will require a major paradigm shift in the strategies of modeling and data collection, and we argue that more emphasis must be placed on observing and documenting relevant patterns in addition to attempts to obtain direct estimates of model parameters.}, annote = {REVIEW -review paper that examines the use of pattern-orientated modeling in ecology -examine three situations: PVA of brown bears in Spain, savanna model of tree distribution spatial patterns, and the incidence function model of a metapopulation {\_}{\_}{\_} -discuss the large growth in using models to study ecological systems over the past three decades but point out the chronic lack of data that is used to parameterize these models -patterns can include time-series data, spatial patterns, wave-like pattern of spread of disease, size-class distribution, and the likes --essentially a pattern is a trend observed in nature that is driven by underlying processes Four main steps for pattern-orientated modeling: 1) aggregation of biological information and scales 2) determination of parameter values 3) systemic comparison between the observed patterns and patterns predicted by the model --have to also determine what defines difference between observed pattern and that of the model ---need to make sure the model output is not a single output and the patterns cannot be matched with simple random combinations of parameters 4) secondary predictions -would determine which processes are most important for pattern-matching {\_}{\_}{\_}{\_} -first example is similar to the shark paper as it examines a bear population and using time-series data as the pattern in modeling attempts -describes implications for Hanski Incidence Function Model of metapopulations --used by Moilanen 1999 for the American Pika, compared model output of patch occupancy to that of presumably Bodie, also compare number of turnover events}, author = {Wiegand, Thorsten and Jeltsch, Florian and Hanski, Ilkka and Grimm, Volker}, journal = {OIKOS}, keywords = {math,metapopulation,population model,review,statistics}, pages = {209--222}, title = {{Using pattern-orientated modeling for revealing hidden information: a key for reconciling ecological theory and application}}, volume = {100}, year = {2003} } @article{Forrest2009, abstract = {Abstract: Deepwater dogsharks (Order Squaliformes) are thought to be particularly vulnerable to overfishing due to life history strategies that place them at the lower end of the shark productivity spectrum. Sharks frequently have relatively low value in multispecies fisheries, where management is usually aimed at maintaining harvest of more valuable and pro- ductive teleosts. This results in low priority being given to data collection for sharks and hampers identification of appro- priate harvest strategies. Here an age-structured model with maximum sustainable harvest rate (UMSY) as leading productivity parameter is systematically applied to show that for certain growth and reproductive schedules that apply to some sharks, the range of possible values that can be taken by UMSY can become very small. The model was applied to 12 Australian dogshark species and was used to show that UMSY is highly constrained under some selectivity schedules. Re- sults were consistent with estimates of the intrinsic rate of growth obtained using a demographic model, suggesting that there may be more certainty about UMSY than expected for many shark species, given uncertainty in recruitment parame- ters. The approach could be used to inform policy for some sharks and may be useful in the development of informative Bayesian priors for assessment models.}, annote = {-discusses a lot about low priority and productive of sharks in fisheries- causes little to be know about them and how to mange them -build an age structured model with maximum sustainable harvest -focus on squaliformes order in australian waters -use model from Forrest (2008) -also use model by McAllister 2001 for simple demographic analysis {\_}{\_}{\_} -good citations in the introduction -discuss productivity of different species in depth with dogfish sharks being on the low end of the spectrum -models looking at shark populations (Cortes 1998, Smith 1998, Heppell 1999) -McAllister 2001 and Cortes 1998 both found very very low rates of maximum sustainable harvest -discuss density mortality and sources for other papers in depth -a number of papers show evidence for density dependent mortality in juveniles (Walker 1994, Gruber 2001, Gedamke 2007, Wood 1979, Brander 1981, and Bonfil 1996) -density parameters can be shown to be related to maximum sustainable yield -discuss different estimates of mortality based on age and temperature -cut litter sizes in half as sharks give birth only every two years -treated significant parameters as random variables to incorporate uncertainty -also look at different possible maximum ages for testing Daley 2002 converts length to weight for sharks {\_}{\_}{\_}{\_}{\_}{\_}{\_} -use contour plots to represent the data well -generally MSYs of less than 0.1 were found --Less sensitive to max age, more sensitive age at maturity and litter sizes -also looked at same results across 12 species of australian dogfish -also examined r and MSY relationship {\_}{\_}{\_}{\_}{\_}{\_}{\_} -Beverton-Holt recruitment may be best method for density dependent mortality in elasmobranchs -MSY is more constrained in pops with late maturity, slower growth, and lower fecundity -could not see impact of max age in this study although Forrest 2008 sees that }, author = {Forrest, Robyn E and Walters, Carl J}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, keywords = {demography,juvenile,mortality,population model,shark}, pages = {2062--2080}, title = {{Estimating thresholds to optimal harvest rate for long-lived, low-fecundity sharks accounting for selectivity and density dependence in recruitment}}, volume = {66}, year = {2009} } @incollection{SmithGilpin1997, abstract = {none, book chapter}, address = {London, UK}, annote = {-populations on patches at Bodie demonstrated some equilibrium between extinction (inversely related to patch size) and recolonization (inversely related to inter patch distance) -this led to idea of implementing 2D "stepping stone" model- can look at interactions between neighbors -also discuss all relevant natural history for the model -Nagy- tagged 58 animals with only one adult moving 18 meters - two of five surviving juveniles dispersed -Peacock (1995)- only 1 of 105 adults dispersed -found 11 of 15 dispersing juveniles did so between patches -went an average of 132.5 meters (range 70-396) -sugarloaf hill went extinct in 80's presumably -Severaid (1955) observed they were never at carrying capacity -did dispersal experiments and saw how low recolonization was {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} Patch size= perimeter in meters Degree of isolation= measured by distance to nearest patch inhabited by 3+ pikas Percent saturation= number counted/ number possible model included patch locations, population change on patches, observations of extinction of patches and recolonizations -assumed a rectangular dispersal function -run for 100 years and repeated 20 times for each combination of both lambda and effects radius --lambda was a stochastic growth rate for a particular patch -three effects radius of 0.5, 1 and 2.0 km Quantified spatial autocorrelation of population-level events on patches by two methods: -looked at net population growth or decline in zones surrounding focal patch -positive autocorrelation indicated focal patch and area around did in fact increase -used Moran's I statistic to quantify the spatial autocorrelation of growth rates among neighbors -correlation occurred when occupancy depended significantly on nearby patches are occupied {\_}{\_}{\_}Results{\_}{\_}{\_}{\_}{\_} -vacant patches were always significantly smaller in size -same trends with inter island distance -looked at ratio of northern pikas to southern, may be inappropriate- measure other aspects instead -after 100 years though they did found that the north always did better under favorable conditions -model is most sensitive to the effects radius -find that the north is more vulnerable at intermediate parameters -nearest neighbor distance (North: 0.204 km) (South: 0.169 km) *model did not show the extinction of the South like our model {\_}{\_}Discussion{\_}{\_}{\_}{\_} There model includes size and location of patches, distance dependent recolonization Could not match dynamics using stepping stone model so felt that patially correlated events might be occuring}, author = {Smith, Andrew T and Gilpin, Michael}, booktitle = {Metapopulation Biology: ecology, genetics, and evolution}, chapter = {17}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Gilpin - 1997 - Spatially correlated dynamics in a pika metapopulation.pdf:pdf}, keywords = {demography,metapopulation,pika}, pages = {407--423}, publisher = {Academic Press}, title = {{Spatially correlated dynamics in a pika metapopulation}}, year = {1997} } @article{Minteer2010, annote = {-there are certainly ecological concerns about assisted migration but there are also ethical concerns --aggressive approach to conservation, the fact that managed relocation departs from past goals for ecological viability, ethical response specifically to climate change -authors feel a more "dynamic and pragmatic" approach is needed {\_}{\_}{\_} -one study found that up to 35 percent of world's species are on track from climate-driven extinction -climate change is indirect so our classic notions of stopping habitat loss and creating parks no longer works -proposal for managed relocation in situations where species or populations can not adapt or disperse quickly enough to escape their inhospitable natural ranges --debate over whether or not managed relocation can even be controlled -no guarantee that translocated species will even do well, many species can move nowhere new -could be shift for us from preservers to makes of novel ecosystems, change our focus and goals as a whole -many see this type of viewpoint as simply arrogant and that relocating species is a cop out from the real ecological, ethical problems -Key issues and questions: 1) candidate species 2) institutional context- relevance to zoos, aquaria, and botanical gardens 3) authorization and oversight 4) motive 5) environmental responsibility }, author = {Minteer, Ben A and Collins, James P}, journal = {Ecological Applications}, keywords = {climate,ethics}, number = {7}, pages = {1801--1804}, title = {{Move it or lose it? The ecological ethics of relocating species under climate change}}, volume = {20}, year = {2010} } @article{Mlot2013, annote = {-Short article reviewing current status of the Isle Royale wolf population -Explains debate on what to do next with three options: 1) do nothing 2) introduce new wolves asap 3) introduce new wolves once the current population dies off -a decision on what to do will be made by the park service in Fall 2013 -explain importance of random events in the Isle Royale system (ex. wolves crossing over ice bridge) -detail the genetic problems the wolves are facing -no pups were born this past year}, author = {Mlot, Christine}, journal = {Science}, keywords = {extinction,genetics,review,wolves}, number = {6135}, pages = {919--921}, title = {{Are Isle Royale's Wolves Chasing Extinction?}}, volume = {340}, year = {2013} } @article{Cheung2013, abstract = {Marine fishes and invertebrates respond to ocean warming through distribution shifts, generally to higher latitudes and deeper waters. Consequently, fisheries should be affected by `tropicalization' of catch (increasing dominance of warm-water species). However, a signature of such climate-change effects on global fisheries catch has so far not been detected. Here we report such an index, the mean temperature of the catch (MTC), that is calculated from the average inferred temperature preference of exploited species weighted by their annual catch. Our results show that, after accounting for the effects of fishing and large-scale oceanographic variability, global MTC increased at a rate of 0.19 degrees Celsius per decade between 1970 and 2006, and non-tropical MTC increased at a rate of 0.23 degrees Celsius per decade. In tropical areas, MTC increased initially because of the reduction in the proportion of subtropical species catches, but subsequently stabilized as scope for further tropicalization of communities became limited. Changes in MTC in 52 large marine ecosystems, covering the majority of the world's coastal and shelf areas, are significantly and positively related to regional changes in sea surface temperature. This study shows that ocean warming has already affected global fisheries in the past four decades, highlighting the immediate need to develop adaptation plans to minimize the effect of such warming on the economy and food security of coastal communities, particularly in tropical regions}, annote = {-marine ecosystems should be affected by "tropicalization" because of climate change -tropicalization simply means tropical species should be able to move to higher latitudes with climate change -propose new metric, mean temperature of the catch (MTC- average inferred temp preference for a given species), to evaluate these predictions -find positive correlation between sea surface temp and MTC {\_}{\_}{\_} -use a generalized additive mixed model to account for oceanographic variability and fishing effort -data from 990 species in 52 marine ecosystems from 1970 to 2006 {\_}{\_}{\_}{\_} -tropical areas showed asymptotic pattern of MTC over time -look at further data in the North Sea to see how catch data compares to survey data -bring up point that phenotypic or evolutionary changes would reduce the rate of change in MTC (which species are more plastic?) --tropical species evolve quicker so their asymptotic pattern of MTC could be due to evolution and not tropicalizaiton}, author = {Cheung, William W L and Watson, Reg and Pauly, Daniel}, doi = {10.1038/nature12156}, journal = {Nature}, keywords = {climate,fisheries}, number = {7449}, pages = {365--368}, title = {{Signature of ocean warming in global fisheries catch}}, volume = {497}, year = {2013} } @article{Smith74b, annote = {-paper looks more closely at how behavior and seasonality affect the distribution and dispersal of pikas -show that high temperatures are a major stress for pikas {\_}{\_}{\_} -again data from 1969-72 of high and low sites for O. princeps -show activity patterns during different times of year at high and low sites -seasonal activity was examined through onset of haying, timing of parturition, frequency of calling {\_}{\_}{\_} -animals at low site are much less active when it is hot in daytime during summer -much greater calling rates at low site during the nighttime -Caged animals died in 6 hours at low site with temperature of 25.5 and 29.4 -body temperature was high and varied very little for shot pikas -explains importance of behavior for not overheating -do in fact harvest certain plants over other based on protein content and water}, author = {Smith, Andrew T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith - 1974 - The distribution and dispersal of pikas influences of behavior and climate.pdf:pdf}, journal = {Ecology}, keywords = {behavior,climate,pika}, number = {6}, pages = {1368--1376}, title = {{The distribution and dispersal of pikas: influences of behavior and climate}}, volume = {55}, year = {1974} } @article{Hoenig1983, abstract = {-develop general equations to predict mortality rate for fish, cetacean and mollusk stocks ---do so all based on the maximum age -general equation is in the form ln(Z)=a+ b ln(t{\_}{\{}max{\}}) -different taxonomical groups have different least square solutions for a and b -equation has good predictive power with high r{\^{}}2, in addition it can predict well between species and within different stocks of a particular species -one issue with his technique is that sample size is not taken into account --discusses some papers at end that may take this into account}, author = {Hoenig, John M}, journal = {Fisheries Bulletin}, keywords = {demography,mortality,shark}, pages = {898--903}, title = {{Empirical use of longevity data to estimate mortality rates}}, volume = {82}, year = {1983} } @article{Brown1988, abstract = {Vertebral centra were removed from 55 tag-recaptured lemon sharks, Negaprion brevirostris, that had been injected intramuscularly with tetracycline hydrochloride at a dosage level of 12.5 mg/kg at the time of release. Tetracycline deposited at sites of active calcification on the vertebral centra served as a fluorescent marker along the periphery of each centrum at the time of injection. Thin growth zones, or circuli, were observed in ground and stained sections. A lunar periodicity of approx. 29 d was validated for circulus deposition. Precision of circulus counts was evaluated, with an index of average percent error of 3.4{\%} for a single reader. Age estimates were then obtained using circulus counts for a total of 110 sharks, with a plot of precaudal length against estimated age for both sexes fitting a von Bertalanffy growth curve with the parameters Loo = 317.65, k = 0.057, and to = -2.302. The predicted age at maturity for males is 11.6 yr and for females is 12.7 yr. These results show that this species is slow growing and long-lived.}, annote = {-removed vertebral centra from 55- tagged and recaptured lemon sharks -when originally tagged the sharks were injected with tetracycline hydrochloride so measurements could be made regarding their rate of growth -are able to fit a von Bertalanffy growth curve with L{\_}{\{}$\backslash$infty{\}} = 317.65, K=0.057 and t{\_}0 = -2.302 -also predict age at maturity for males to be 11.6 yr and 12.7 for females {\_}{\_}{\_}{\_}{\_}{\_} -their type of analysis can only be used on lemon sharks because of the differences in the degree of calcification between different species -unlike previous work involving tetracycline and band deposition they wanted to look at the temporal periodicity of circulus formation {\_}{\_}{\_}{\_}{\_}{\_} -circulus deposition appears to be related to lunar cycles with periods of 29 days -other species have relationships with tidal cycles at 14 and 28 days}, author = {Brown, Craig A and Gruber, Samuel H}, journal = {Copeia}, keywords = {bimini,growth,shark}, pages = {747--753}, title = {{Age Assessment of the Lemon Shark, $\backslash$emph{\{}Negaprion brevirostris{\}}, Using Tetracycline Validated Vertebral Centra}}, volume = {3}, year = {1988} } @article{Myers2007, abstract = {Impacts of chronic overfishing are evident in population depletions worldwide, yet indirect ecosystem effects induced by predator removal from oceanic food webs remain unpredictable. As abundances of all 11 great sharks that consume other elasmobranchs (rays, skates, and small sharks) fell over the past 35 years, 12 of 14 of these prey species increased in coastal northwest Atlantic ecosystems. Effects of this community restructuring have cascaded downward from the cownose ray, whose enhanced predation on its bay scallop prey was sufficient to terminate a century-long scallop fishery. Analogous top-down effects may be a predictable consequence of eliminating entire functional groups of predators.}, annote = {-point out little work has been done studying ecosystem effects of the removal of large predator -discuss how 11 species of sharks have declined 12 of 14 of their prey species have increases in the NW atlantic {\_}{\_}{\_}{\_} -a lot of literature about trophic cascades but not so for the ocean -use time series data to show the massive declines in many shark species from 1970-2004 -at the same time elasmobranch prey has increased --focus on cow nose ray which must have higher mortality rates in the past based on its life history and current population numbers --these large numbers are wiping out different species of bivalves -also used ray-exclusion experiments to see how much mortality the rays were causing on scallops --shows how bad they are wiping out bivalve populations--many bivalve fisheries have been closed -compare this result to the killer whale-sea lion-urchin-kelp trophic cascade (Science 1998)}, author = {Myers, Ransom A and Baum, Julia K and Shepherd, Travis D and Powers, Sean P and Peterson, Charles H}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Myers et al. - 2007 - Cascading effects of the loss of apex predatory sharks from a coastal ocean.pdf:pdf;:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Myers et al. - 2007 - Cascading effects of the loss of apex predatory sharks from a coastal ocean(2).pdf:pdf}, journal = {Science}, keywords = {fisheries,predation,shark}, month = {mar}, pages = {1846--1850}, title = {{Cascading effects of the loss of apex predatory sharks from a coastal ocean}}, volume = {315}, year = {2007} } @article{Sanz-Aguilar2011, abstract = {Fire and fire management are recognized as important factors in biodiversity conservation. Measuring species-level demographic, behavioural and population responses to different fire regimes is essential for designing adequate management policies. Here we assessed the impact of fire on survival rates, repro- duction and movement patterns in Testudo graeca, an endangered terrestrial tortoise inhabiting the Mediterranean region, a system in which fire plays a relevant role in the functioning of their ecosystems. Then we predicted the probabilities of quasi-extinction of T. graeca under several fire regimes and population sizes by means of stochastic population models. Our results showed that fire caused direct and delayed reductions in local survival, young individuals being the most affected. There were not differences in fecundity and movement patterns of tortoises between burned and unburned areas. Population models showed a strong variation in the probability of quasi-extinction of populations depending on the fire regime and the population size. Under fire frequencies similar to those occurring in the wild ({\textless}1 fire every 20--30 years) most tortoise populations seemed to buffer the effects of fires. However, when this threshold value of fire frequency was surpassed, the probability of quasi-extinction of populations exploded for all populations, except for those with the largest sizes. T. graeca populations may be able to cope with natural current fire frequencies, but the effects of more recurrent fires may severely threaten the species. Our results have straightforward applications for fire management pur- poses in those areas of the Mediterranean region where this endangered species is present.}, annote = {-paper focuses on the species and specific population of tortoises that Jose and I are studying -study is primarily interested examined the effects of a fire on the population --they assess how fire affects survival, reproduction, and movement patterns {\_}{\_}{\_} -reptiles are said to be especially susceptible to fire and other environmental factors because of their low movement capabilities -there has not been a lot of work to examine the effects of fire on demographic parameters -can be immediate and delayed effects of fire -use stochastic population models to predict how the population would respond after different fire regimes Study site -Cumbres de la Galera biological reserve (Sierra de la Carrasquilla, Murcia, Spain 37'32'N, 1'39'W) -20 individual tortoises per hectare (maybe 700 total in study area) -pop. monitored from 1999 to 2009 -mean rainfall of 295mm and temp of 18-19 degrees C -fire occurred in summer (August 1st) of 2004 and burned 31{\%} of study area -juveniles 1-4 years old -subadult 5-8 -adult {\textgreater}8 years old (only level at which you can sex animals) {\_}{\_}{\_}{\_}{\_} -estimate natural survival rates of 0.98, 0.79, and 0.20 for adult, subadult, and juveniles, respectively -number of clutches and total number of eggs was not different between burned and unburned areas --number of clutches= 1.83, 2.17 --number of eggs = 5.33, 6.83 -produce graph of extinction probability versus tortoise density and fire frequency {\_}{\_}{\_}{\_}{\_} -find that pop growth rates are more sensitive to variation in adult survival than fecundity parameters -fire has large effects on small or low-density tortoise populations -find that fire frequency needs to be around 1 fire every 20-30 years (this is the amount seen in their natural habitat) -indicates that frequent (planned or unplanned) fires would have a strong negative effect on these tortoise populations -54 percent of the species' populations occur at low density }, author = {Sanz-Anguilar, Ana and Anad{\'{o}}n, Jose Daniel and Gim{\'{e}}nez, Andr{\'{e}}s and Ballestar, Rub{\'{e}}n and Graci{\'{a}}, Eva and Oro, Daniel}, journal = {Biological Conservation}, keywords = {population model,stochastic,tortoise}, pages = {1040--1049}, title = {{Coexisting with fire: The case of the terrestrial totoise {\textless}i{\textgreater}Testudo graeca{\textless}/i{\textgreater} in Mediterranean shrublands}}, volume = {144}, year = {2011} } @article{Smith1978, abstract = {Abstract. The structure of 4 populations of a small boreal mammal,the pika(Ochotona princeps), is examined to explore the causal mechanisms of evolution of life-history features of the species. Litter size reflects potential and realized fecundity and is largest at Bodie (low latitude, low altitude), intermediate at Sierra and Colorado(low latitude,high altitude),and smallest at Alberta(high latitude). The age specificity of mortality largely determines the number of sites available for settlement by juveniles, which dictates the feedback to litter size. Populations are stable and habitats continuously saturated at Alberta; mortality of adults is predictable.The Sierra and Colorado sites possess unstable populations. At these sites, snow melt in spring(the harbinger of emergent vegetation and successful weaning)is relatively unpredictable compared to Alberta; adult mortality may be high in years of early or late snowmelt.The unpredictability also selects for asynchronous breeding such that more sites are available in any one year to offspring from certain successfully weaned litters. The habitat at Bodie is temporally and spatially unsaturated. Largely because of poor vagility of pikas, much of the habitat is vacant. Colonization is unable to completely offset extinction of populations on patches of habitat. Here,the selective factor determining litter size is juvenile production and not adult mortality}, annote = {-examined O. princeps in Colorado over three years and examined not only population data but also behavioral data. In particular, looked at interactions among pikas -most juveniles were in fact philopatric or settled nearby if they dispersed - presents reproductive timing data for Bodie (n=118), SIerra (n=40), Colorado (n=53), and Albera (n=253) - Alberta had the shortest breeding season, longest season at Bodie -mean data of partrition conincided with peak vegetative growth -apparently seasonal climate is most predicable at Alberta compared to Bodie and the Sierra {\_}{\_}{\_}{\_} -Performed focal and scan sampling surveys to examine behavior -each minute behavioral data was recording during 15 minute blocks --aggression defined as active chases and fights --affiliative behavior- mothers nursing young and social tolerance (animals w/n 3 meters of each other and do not fight even when they were aware of each other) -behavior measurements are expressed as mean rate per unit time that pikas were active -76 percent of established animals were local juveniles -most social tolerance occurred between a juvenile and their mother, father, or sibling -high numbers between same groups for aggressive behaviors -resident was almost always the aggressor -very similar results as above for animals that were artificially placed on a particular patch -dispersing juveniles tended to show up relatively late in the season -juveniles on patches that did not get a territory were not seen after winter time -most juvenile colonization is philopatric --this would lead to high inbreeding which agrees with genetic data *inbreeding would not be a big deal because any reduction in fitness due to inbreeding is probably much less than the reduction in fitness a juvenile endures if it can not establish a territory -alternatively, they may just not experience inbreeding depression --would mean that pikas went through a genetic bottleneck in which most deleterious alleles were eliminated from the gene pool -adults were typically only seen to disperse to increase mating success -found that behavior, spatial relationships and immigration rates were not influenced by density}, author = {Smith, Andrew T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith - 1978 - Comparative demography of pikas (emph{\{}Ochotona{\}}) Effect of spatial and temporal age-specific mortality.pdf:pdf}, journal = {Ecology}, keywords = {demography,mortality,pika}, number = {1}, pages = {133--139}, title = {{Comparative demography of pikas ($\backslash$emph{\{}Ochotona{\}}): Effect of spatial and temporal age-specific mortality}}, volume = {59}, year = {1978} } @phdthesis{Nagy1996, abstract = {The question of how dispersal evolved has a rich history, but the answer has certainly not been established. This dissertation addresses an important subsidiary question, how much information about the local environment (patch) should an organism living in a metapopulation use when 'deciding' whether or not to disperse? More precisely, what behavioral response to proximate cues for dispersal are evolutionary attracting? The first objective of the following study is to define precisely what an evolutionary attractor is. Then, three metapopulation dynamics models are derived and analyzed. A technique is developed which allows one to use these population dynamics models to investigate the properties of evolutionarily attracting dispersal strategies. THe results of this dissertation indicate that although density dependent dispersal strategies are often, but not always, superior tot the best density independent strategy, even moderate costs associated with the former strategy reverse the superiority. In some cases, the evolutionary mechanism has difficulty differentiating between a density dependent strategy and the best density independent one. In such cases the system possesses two stable evolutionary attractors. These results suggest that the best density independent strategy makes efficient use of the metapopulation resources in the form of vacant territories. As a result, basing dispersal on local resources confers little advantage, and may even be disadvantageous. Therefore, it is reasonable to expect to find density independent strategies in nature. Also, it is shown that the models obey a classical average individual fitness principle, but such a fitness concept is highly dependent on population dynamics. A more precise concept of fitness in the context of these models is the dominant Lyapunov exponent definition outlined in recent literature. It is shown that this concept retains the essential properties of the classical concept of fitness. In addition to these results, a comparison of the models implies that sufficient spatial or temporal variation in patch occupancy is necessary for the development and evolutionary maintenance of a nonzero dispersal strategy, and demographic stochasticity is sufficient to supply that variation only when patch sizes are small. The evolutionary attracting (EA) dispersal strategy is sensitive to variation in average patch size; as patches increase in size, EA dispersal fractions decrease rapidly. The EA dispersal strategy is also highly sensitive to direct costs of dispersal. Again, the EA dispersal fraction drops rapidly with probability of mortality during dispersal.}, author = {Nagy, John D}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Nagy - 1996 - Evolutionary Attracting Dispersal Strategies in Vertebrate Metapopulations.pdf:pdf}, keywords = {bodie,evolution,math,pika}, month = {may}, school = {Arizona State University}, title = {{Evolutionary Attracting Dispersal Strategies in Vertebrate Metapopulations}}, type = {Ph.D. diss.}, year = {1996} } @article{Avila-Forcada2012, abstract = {Vaquita marina, a small species of porpoise endemic to the Northern Gulf of California in Mexico, is the world's most endangered cetacean species. With the purpose of preserving vaquita, the Mexican govern- ment launched PACE-Vaquita in 2008. This voluntary program offers an innovative schedule of compensa- tions: as in a payment-for-conservation program, PACE-Vaquita compensates for temporary reductions in fishing effort; as in a program to accelerate technology adoption, PACE-Vaquita compensates for switching to vaquita-safe fishing methods; and as in a buyback program, PACE-Vaquita compensates fishermen for a permanent exit from fisheries. This paper seeks the factors explaining fishermen's participation in PACE- Vaquita during its first year of operation. Analysis is carried out through a multinomial logit specification on a data set collected one week after the enrollment deadline. This paper shows that fishermen with skills in alternative economic activities more likely quit fishing, and fishermen with relatively less productive vessels more likely switched to vaquita-safe fishing methods. Discussion of public policy implications is provided.}, annote = {-study examines PACE- Vaquita program and discusses how it has been and how it can continue to be a good way to reduce fishing capacity {\_}{\_}{\_} -in 2007, 2070 artisanal fishers from San Felipe, Penasco and Santa Clara -fisheries generate revenues US16.17 million each year -in 2008, fishermen had three alternatives within PACE-Vaquita: rent-out, switch-out, buy-out --rent-out- time contract for fishermen to stop all gill net fishing in Vaquita Refuge Area --switch-out- compensation for permanently switching to vaquita-safe harvesting gear --buy-out- compensates fishermen for permanently turning in permits and fishing boat/gear --vessels turned in 153,18 and 0 in 2008-2010 -in 2009/2010, more incentive was placed on rent-out instead of buy-out {\_}{\_}{\_} -also use theoretical model to determine which factors may be most significant in convincing fishermen to take an option in PACE -also conduct interviews of local fishermen to gather more information regarding fishermen backgrounds and incentives for participating in PACE {\_}{\_}{\_} -rent-out option is larger for owners of cooperative, fishermen with savings -switch-out- increases with the boats owned by fishermen and decreases with profits per boat -buy-out- increases with age, education, number of young kids, number of people in house, alternative skills, and number of boats owned by fishermen -other variables may be weakly correlated {\_}{\_}{\_} -buyouts need to now be used less and less as they only encourage near retirement fishers to accept -}, author = {Avila-Forcada, Sara and Mart{\'{i}}nez-Cruz, Ad{\'{a}}n L and Mu{\~{n}}oz-Pi{\~{n}}a, Carlos}, journal = {Marine Policy}, keywords = {fisheries,review,vaquita}, pages = {613--622}, title = {{Conservation of vaquita marine in the Northern Gulf of California}}, volume = {36}, year = {2012} } @article{Krakauer2011, abstract = {Scientific theories seek to provide simple explanations for significant empirical regularities based on fundamental physical and mechanistic constraints. Biological theories have rarely reached a level of generality and predictive power comparable to physical theories. This discrepancy is explained through a combination of frozen accidents, environmental heterogeneity, and widespread non-linearities observed in adaptive processes. At the same time, model building has proven to be very successful when it comes to explaining and predicting the behavior of particular biological systems. In this respect biology resembles alternative model-rich frameworks, such as economics and engineering. In this paper we explore the prospects for general theories in biology, and suggest that these take inspiration not only from physics, but also from the information sciences. Future theoretical biology is likely to represent a hybrid of parsimonious reasoning and algorithmic or rule-based explanation. An open question is whether these new frameworks will remain transparent to human reason. In this context, we discuss the role of machine learning in the early stages of scientific discovery. We argue that evolutionary history is not only a source of uncertainty, but also provides the basis, through conserved traits, for very general explanations for biological regularities, and the prospect of unified theories of life.}, annote = {REVIEW -a review of how theoretical biology has emerged, how it is similar/dissimilar to other fields, challenges, and future of the field -discuss simulation models including monte carlo methods and agent based models -one of the biggest challenges in theoretical biology is addressing the factor of scaling for different phenomena -possibility of using Einstein's work with differential geometry and special relativity in biology -in general the use of new mathematics to describe biological processes -"there has been a shift in model preferences, toward those frameworks that provide increasing predictive power and a loss of compressed explanatory insight" --this would lead to us being able to predict and control processes in biology but for reasons unknown as the necessary theory would not be in place }, author = {Krakauer, David C and Collins, James P and Erwin, Douglas and Flack, Jessica C and Fontana, Walter and Laubichler, Manfred and Prohaska, Sonja J and West, Geoffrey B and Stadler, Peter F}, journal = {Journal of Theoretical Biology}, keywords = {math,statistics,theoretical}, pages = {269--276}, title = {{The challenges and scope of theoretical biology}}, volume = {276}, year = {2011} } @article{Krebs, author = {Krebs, C J}, journal = {Science}, keywords = {predation,snowshoe hares}, pages = {1112--1115}, title = {{Impact of food and predation on the snowshoe hare cycle}}, volume = {269}, year = {1995} } @article{Carlson2012, abstract = {In the north-west Atlantic Ocean, stock assessments conducted for some commercially harvested coastal sharks indicate declines from 64 to 80{\%} with respect to virgin population levels. While the status of commercially important species is available, abundance trend information for other coastal shark species in the north-west Atlantic Ocean are unavailable. Using a generalized lin- ear modelling (GLM) approach, a relative abundance index was derived from 1994 to 2009 using observer data collected in a commercial bottom longline fishery. Trends in abundance and average size were estimated for bull shark Carcharhinus leucas, spinner shark Carcharhinus brevipinna, tiger shark Galeocerdo cuvier and lemon shark Negaprion brevirostris. Increases in relative abun- dance for all shark species ranged from 14{\%} for C. brevipinna, 12{\%} for C. leucas, 6{\%} for N. brevirostris and 3{\%} for G. cuvier. There was no significant change in the size at capture over the time period considered for all species. While the status of shark populations should not be based exclusively on abundance trend information, but ultimately on stock assessment mod- els, results from this study provide some cause for optimism on the status of these coastal shark species.}, annote = {-study looks at longline data in the atlantic of commercially harvested coastal shark species: bull, spinner, tiger, and lemon -study shows optimism as abundance has tended to increase for all species in study area from 1994 to 2009 {\_}{\_}{\_} -report that for others species declines of 64 to 80 percent have been seen -use two data sets of longline fishing consisting of 100 000 hours- independent monitoring programs -number of techniques for analyzing catch time series data (Maunder and Punt 2004) -GLM (Myers 2007, Baum and Blanchard 2010) -zero-inflated model (Minami 2007, Carlson 2009) -they utilize the delta method (essentially you fit two sub models to a given data set which standardizes the datasets) --first sub-model estimates probability of a nonzero catch (binomial error distribution) --second model assumed non-zero catch distribution as log normal (Poisson, negative-binomial, or gamma)- used in a number of other papers -examine a number of variables one by one to determine there effects on the model {\_}{\_}{\_}{\_} -find significant increases for all species studied -also were able to determine which model works best and what factors are in fact the most important in the model -also find that during time period shark size changed very little}, author = {Carlson, J K and Hale, L F and Morgan, A and Burgess, G}, journal = {Journal of Fish Biology}, keywords = {fisheries,shark}, pages = {1749--1764}, title = {{Relative abundance and size of coastal sharks derived from commercial shark longline catch and effort data}}, volume = {80}, year = {2012} } @techreport{Manire1993, abstract = {Determination of natural mortality rate is an important step in understanding and quantifying the population dynamics of a species. This is the first study using elasmo- branchs which directly measured the rate of natural mortality. An unexploited population oflemon sharks, Negaprion brevirostris, in Bimini, Bahamas, was and continues to be censused to determine natural mortality. Preliminary results indicate an instantaneous natural mor- tality rate (M) ranging from 0.60-1.01 for lemon sharks in their first year of life (equivalent to an annual mortality of as much as 64{\%}). The natural mortality rate must be highest in this age class and must be very low and possibly zero in subsequent age classes for the population to remain viable. }, annote = {pages 65-71 of technical report -study looked to determine what the natural mortality rate in age 0 sharks actually is and estimates ranged from 0.60-1.01 (annual mortality rate of 64 percent). -Study provides the groundwork for future studies on mortality and the procedures for confuting population censuses in Bimini {\_}{\_}{\_} -use multiple censuses throughout year to estimate changes in population size (number of individuals that die represent any change in population size because other factors are ignored)-mark recapture methods -discuss how abundance estimates must account for both learning abilities of shark and behavioral biases -discuss how they will only sample one time annually to help these biases }, author = {Manire, C A and Gruber, Samuel H}, institution = {NMFS}, keywords = {bimini,shark}, number = {115}, title = {{A preliminary estimate of natural mortality of age-0 lemon sharks, $\backslash$emph{\{}Negaprion brevirostris{\}}.}}, type = {NOAA Technical Report}, year = {1993} } @article{Gerber2010, abstract = {In polygynous mating systems, males often increase their fecundity via aggressive defense of mates and/or resources necessary for successful mating. Here we show that both male and female reproductive behavior during the breeding season (June--August) affect female fecundity, a vital rate that is an important determinant of population growth rate and viability. By using 4 years of data on behavior and demography of California sea lions (Zalophus californianus), we found that male behavior and spatial dynamics---aggression and territory size---are significantly related to female fecundity. Higher rates of male aggression and larger territory sizes were associated with lower estimates of female fecundity within the same year. Female aggression was significantly and positively related to fecundity both within the same year as the behavior was measured and in the following year. These results indicate that while male aggression and defense of territories may increase male fecundity, such interactions may cause a reduction in the overall population growth rate by lowering female fecundity. Females may attempt to offset male-related reductions in female fecundity by increasing their own aggression--- perhaps to defend pups from incidental injury or mortality. Thus in polygynous mating systems, male aggression may increase male fitness at the cost of female fitness and overall population viability.}, author = {Gerber, Leah R and Gonz{\'{a}}lez-Su{\'{a}}rez, Manuela and Hern{\'{a}}ndez-Camacho, Claudia J and Young, Julie K and Sabo, John L}, journal = {ecology}, keywords = {demography,evolution,sea lions}, number = {8}, pages = {1--8}, title = {{The Cost of Male Aggression and Polygyny in California Sea Lions ($\backslash$emph{\{}Zalophus californianus{\}})}}, volume = {5}, year = {2010} } @article{Knip2010, abstract = {ABSTRACT: Theoretical models of coastal shark popu- lations have remained largely unchanged since the 1960s despite limitations in applicability to many spe- cies. Smaller bodied coastal species are poorly repre- sented by the current models. A new theoretical model is proposed to represent those species that spend most or all of their life within nearshore waters but do not show use of discrete nursery areas. Description of this new model outlines the importance of nearshore areas to these smaller species. While all coastal shark popu- lations are susceptible to environmental and anthro- pogenic impacts, species that fit the new model are more vulnerable to varying coastal processes, habitat degradation, and fishing pressure than are species that use nearshore areas for only part of their life-span. The dynamic nature of nearshore areas and their proximity to human populations present all sharks that occur in them with a range of advantages and disadvantages. This paper reviews how different species utilise near- shore areas and how they overcome the challenges they face in inhabiting these areas. Improving and ex- panding theoretical models of coastal shark popula- tions will provide a better understanding of how sharks use nearshore environments and assist in making con- servation and management decisions for these regions.}, annote = {-look up model by Springer 1967 which describes same system as Bimini --this paper looks at nearshore species that utilize nursery sites as juveniles Knip et al. present a 2nd example shark species that spend there whole life nearshore and write a review of other similar papers that have nearshore sharks that don't utilize nursery areas (ex. Atlantic sharpnose Rhizoprionodon terraenovae and blacknose Carcharhinus acronotus) -this type of species is important because there whole population will be affected by activities not just a certain age class}, author = {Knip, Danielle M and Heupel, Michelle R and Simpfendorfer, Colin A}, journal = {Marine Ecology Progress Series}, keywords = {nearshore,population model,shark}, pages = {1--11}, title = {{Sharks in nearshore environments: models, importance, and consequences}}, volume = {402}, year = {2010} } @article{Beerkircher2002, annote = {-discuss difficulties of estimated natural mortality- argue demographic models can help estimate this -run Monte Carlo simulations to introduce variability in the parameters -run combinations of parameters for natural and fishing mortality impacts --discuss implications for gear selectivity {\_}{\_} -ran simulations and measured net reproductive rate, mean generation length, and intrinsic rate of population increase -found various results depending on specific model and gear selectivity abilities {\_}{\_}{\_}{\_} -find sensitivity of first few age classes to mortality as seen in other studies -show how slow population grows even at low natural mortality --could not handle even moderate fishing pressures -age dependent parameters dramatically affect results }, author = {Beerkircher, Lawrence and Shivji, Mahmood S and Cort{\'{e}}s, Enric}, journal = {Fisheries Bulletin}, keywords = {demography,shark}, month = {jul}, pages = {168--174}, title = {{A Monte Carlo demographic analysis of the silky shark ($\backslash$textit{\{}Carcharhinus falciformis{\}}): implications of gear selectivity}}, volume = {101}, year = {2002} } @article{loannou2012, abstract = {Movement in animal groups is highly varied and ranges from seemingly disordered motion in swarms to coordinated aligned motion in flocks and schools. These social interactions are often thought to reduce risk from predators, despite a lack of direct evidence. We investigated risk-related selection for collective motion by allowing real predators (bluegill sunfish) to hunt mobile virtual prey. By fusing simulated and real animal behavior, we isolated predator effects while controlling for confounding factors. Prey with a tendency to be attracted toward, and to align direction of travel with, near neighbors tended to form mobile coordinated groups and were rarely attacked. These results demonstrate that collective motion could evolve as a response to predation, without prey being able to detect and respond to predators}, author = {Loannou, C C and Guttal, V and Couzin, I D}, journal = {Science}, keywords = {adaptive dynamics,movement,predation}, pages = {1212--1215}, title = {{Predatory Fish Select for Coordinated Collective Motion in Virtual Prey}}, volume = {337}, year = {2012} } @book{Pastor2008, address = {Chichester, West Sussex, United Kingdom}, annote = {{\textless}m:note{\textgreater}see book for notes{\textless}/m:note{\textgreater}}, author = {Pastor, John}, keywords = {math,matrixes,population model}, publisher = {John Wiley and Sons}, title = {{Mathematical Ecology of Populations and Ecosystems}}, year = {2008} } @incollection{Dulvy2010, address = {Boca Raton, FL}, annote = {{\textless}m:note{\textgreater}see book for notes{\textless}/m:note{\textgreater}}, author = {Dulvy, Nicholas K and Forrest, Robyn E}, booktitle = {Sharks and Their Relatives}, editor = {Carrier, Jeffrey C and Musick, John A and Heithaus, Michael R}, keywords = {demography,nursery site,population model,review,shark}, pages = {639--679}, publisher = {CRC Press}, title = {{Life Histories, Population Dynamics, and Extinction Risks in Chondrichthyans}}, volume = {II}, year = {2010} } @book{MorrisDoak2002, address = {Sunderland, Massachusetts, USA}, author = {Morris, William F and Doak, Daniel F}, keywords = {leslie matrix,population model}, publisher = {Sinauer Associates, Inc.}, title = {{Quantitative conservation biology: theory and practice of population viability analysis}}, year = {2002} } @article{Heupel2007, abstract = {ABSTRACT: The concept of elasmobranch species using nursery areas was introduced in the early 1900s and has been an accepted aspect of shark biology and behavior for several decades. Despite several descriptions of how shark species use nursery areas and what types of regions nurseries may be found in, no explicit definition of what constitutes a shark nursery area has been presented. Here we evaluate the assumptions of the current shark nursery paradigm in light of available data. Based on examination of these assumptions and available methods of quantifying and accurately describing shark nursery areas, a new more quantitative definition of shark nursery areas is proposed. This def- inition requires 3 criteria to be met for an area to be identified as a nursery: (1) sharks are more com- monly encountered in the area than other areas; (2) sharks have a tendency to remain or return for extended periods; and (3) the area or habitat is repeatedly used across years. These criteria make the definition of shark nursery areas more compatible with those for other aquatic species. The improved definition of this concept will provide more valuable information for fisheries managers and shark biologists.}, annote = {REVIEW -paper examines past work on shark nursery sites to give a more precise definition of a shark nursery site by providing a more quantitative framework -three primary criteria: --sharks are more commonly encountered in particular area than others --sharks stay or return to site --used repeatedly across years -paper discusses how to use data in determining actual nursery site, validity of different assumptions, and future directions for research {\_}{\_}{\_} -point out past studies that argue for predation pressure instead of prey availability as primary driver in shark nursery sites (Branstetter 1990) -two types of studies in regards to nursery sites: simple mapping surveys and those that try to understand the function of nursery areas (lot of citations given) -point out that many studies simply regard the presence of juveniles at a site to conclude it is a nursery 4 assumptions of current definition of nursery area: 1) all sharks have nursery areas --if you assume that a nursery site simply has juveniles there then all species would have nursery sites --many tradeoffs between nursery site use and key life history strategies 2) nursery areas provide ample resources --give a number of examples that show the opposite --other studies show that juvenile blacktips distribute according the predator avoidance than prey resources (Heupel 2002, 2005) 3) nursery sites reduce predation risk and therefore have low mortality rates --studies show conflicting data for this assumption --also find that some "nursery sites" do in fact have a number of adult sharks associated with them --predator density manipulation studies would be interesting 4) primary nursery areas overlap with secondary nursery areas --authors find these definitions to be inadequate and propose not using the terms anymore {\_}{\_}{\_}{\_} }, author = {Heupel, Michelle R and Carlson, John K and Simpfendorfer, Colin A}, journal = {Marine Ecology Progress Series}, keywords = {nursery site,review,shark}, pages = {287--297}, title = {{Shark nursery areas: concepts, definition, characterization and assumptions}}, volume = {337}, year = {2007} } @article{DiBattista2011, abstract = {The level of genetic variation in natural populations influences evolutionary potential, and may therefore influence responses to selection in the face of future environmental changes. By combining long-term monitoring of marked individuals with genetic pedigree reconstruction, we assessed whether habitat loss influenced genetic variation in a lemon shark (Negaprion brevirostris) pop- ulation at an isolated nursery lagoon (Bimini, Bahamas). We also tracked changes in the strength and direction of natural selection. Contrary to initial expectations, we found that after the habitat loss neutral genetic variation increased, as did additive genetic variance for juvenile morphological traits (body length and mass). We hypothesize that these effects might result from philopatric behavior in females coupled with a possible influx of male geno- types from other nursery sites. We also found changes in the strength of selec- tion on morphological traits, which weakened considerably after the disturbance; habitat loss therefore changed the phenotypes favored by natural selection. Because such human-induced shifts in the adaptive landscape may be common, we suggest that conservation biologists should not simply focus on neutral genetic variation per se, but also on assessing and preserving evolution- ary parameters, such as additive genetic variation and selection.}, annote = {-examining effects of habitat loss on genetic variation in lemon sharks at Bimini -they found that habitat loss actually increased neutral genetic variation and genetic variance in juvenile morphological traits -habitat loss changed phenotypes favored by natural selection {\_}{\_}{\_}{\_} -believe that changes in habitat would effect population isolation, carrying capacity, increased environmental variance, and shifts in local trait optima -by looking at this genetic data they can acquire estimates for 3 variables: --number of breeding adults --mortality rate of juveniles --neutral genetic variation --quantitative genetic parameters --strength and form of natural selection {\_}{\_}{\_} -find the average number of females to give birth at Bimini each year was 16.08 +/- 1.19 SEM -more adults contributed to the juvenile shark population after the disturbance occurred -conflicting with previous genetic studies they found that neutral genetic variation actually increased after habitat loss- this did not happen at South Bimini during same time period in which there was no mangrove destruction -additive genetic variance also increased after disturbance -find that the disturbance definitely affected natural selection in regards to the size of juveniles and predation in some way although not completely clear}, author = {DiBattista, Joseph D and Feldheim, Kevin A and Garant, Dany and Gruber, Samuel H and Hendry, Andrew P}, journal = {Evolutionary Applications}, keywords = {bimini,evolution,habitat,shark}, month = {apr}, pages = {1--17}, title = {{Anthropogenic disturbance and evolutionary parameters: a lemon shark population experiencing habitat loss}}, volume = {4}, year = {2011} } @article{Fath2007, abstract = {Ecological network analysis (ENA) is a systems-oriented methodology to analyze within system interactions used to identify holistic properties that are otherwise not evident from the direct observations. Like any analysis technique, the accuracy of the results is as good as the data available, but the additional challenge is that the data need to characterize an entire ecosystem's flows and storages. Thus, data requirements are substantial. As a result, there have, in fact, not been a significant number of network models constructed and development of the network analysis methodology has progressed largely within the purview of a few established models. In this paper, we outline the steps for one approach to construct network models. Lastly, we also provide a brief overview of the algorithmic methods used to construct food web typologies when empirical data are not available. It is our aim that such an effort aids other researchers to consider the construction of such models as well as encourages further refinement of this procedure.}, annote = {REVIEW -paper outlines basic example of network analysis in ecological settings -here nodes nodes can be anywhere from 6 to numbering in the thousands {\_}{\_} -their study focusing on trophic systems and application of network analysis -look at energy flows through a system and different interactions -give an example of nutrient movement between tree ecosystem of island in Belize -discuss modeling framework Ecopath developed by Pauly in 1992, 2000, also discuss Ecosim -also discuss calculation of flow rates in a network with inverse modeling }, author = {Fath, Brian D and Scharler, Ursula M and Ulanowicz, Robert E and Hannon, Bruce}, journal = {Ecological Modelling}, keywords = {network analysis,population model}, pages = {49--55}, title = {{Ecological network analysis: network construction}}, volume = {208}, year = {2007} } @article{Whitehead2009, abstract = {SOCPROG is a set of programs which analyses data on animal associations. Data usually come from observations of the social behaviour of individually identifiable animals. Associations among animals, sampling periods, restrictions on the data and association indices can be defined very flexibly. SOCPROG can analyse data sets including 1,000 or more individuals. Association matrices are displayed using sociograms, principal coordinates analysis, multidimensional scaling and cluster analyses. Permutation tests, Mantel and related tests and matrix correlation methods examine hypotheses about preferred associations among individuals and classes of individual. Weighted network statistics are calculated and can be tested against null hypotheses. Temporal analyses include displays of lagged association rates (rates of reassocia- tion following an association). Models can be fitted to lagged association rates. Multiple association measures, including measures produced by other programs such as genetic or range use data, may be analysed using Mantel tests and principal components analysis. SOCPROG also performs mark-recapture population analyses and move- ment analyses. SOCPROG is written in the programming language MATLAB and may be downloaded free from the World Wide Web.}, author = {Whitehead, Hal}, journal = {Behav. Ecol. Sociobiol.}, keywords = {bimini,math,movement,network analysis,shark}, pages = {765--778}, title = {{SOCPROG programs: analysing animal social structures}}, volume = {63}, year = {2009} } @article{Reeve2009, abstract = {Prey preference of juvenile lemon sharks Negaprion brevirostris was examined in experiments conducted in field-based pens where the fish were offered meals of live teleosts: grey snapper Lutjanus griseus and yellow fin majorra Gerres cinereus in ratios of L. griseus:G. cinereus varying from 10:0 to 2:8. Relative electivity indices for each treatment showed that N. brevirostris preyed on G. cinereus rather than L. griseus. They showed a prey preference relating to density of G. cinereus (type II functional response) but not to L. griseus. }, annote = {-investigated how juvenile lemons preyed upon either grey snapper or yellow fin majorra during pen trials, prey was given live and in different densities -they find that the juvenile lemons prefer majorra (Gerres cinereus) and prey on them according to a type II functional response {\_}{\_}{\_}{\_} -discuss work by Cortes and Gruber on diets in the early 1990's -they perform stomach content analysis after releasing prey fish into juvenile shark pens in the NS -use relative electively index (Ivlev 1961, Vanderploeg and Scavia 1979) to determine prey selectivity {\_}{\_}{\_} -find that the lemons do in fact prefer and go after G. cinereus more often -also see a curvilinear rise in the mean number of G. cinereus eaten with increasing prey density (type II functional response)- these trends were not seen for L. griseus }, author = {Reeve, A and Handy, R D and Gruber, S H}, journal = {Journal of Fish Biology}, keywords = {bimini,predation,shark}, pages = {276--281}, title = {{Prey selection and functional response of juvenile lemon sharks $\backslash$emph{\{}Negaprion brevirostris{\}}}}, volume = {75}, year = {2009} } @article{Chapman2009, annote = {-through genetic analysis they analyzed how quickly sharks dispersed from nursery sites starting at about age 3. Also sample a number of sharks from age 3 to 11 years -find that sharks tend to disperse very slowly, usually years {\_}{\_}{\_} -find that less and less locally born sharks are found with increases in shark length --approximently half of the large immature sharks sampled were actually locally for ---these are conservative estimates and the actual number is probably higher than 1/2 -know that these sharks are gradually dispersing not at some threshold (bang bang strategy) -management wise this is important because MPAs around nursery sites will also protect critical age classes including subadults}, author = {Chapman, Demian D and Babcock, Elizabeth A and Gruber, Samuel H and DiBattista, Joseph D and Franks, Bryan R and Kessel, Steven T and Guttridge, Tristan and Pikitch, Ellen K and Feldheim, Kevin A}, journal = {Molecular Ecology}, keywords = {bimini,genetics,nursery site,shark}, pages = {3500--3507}, title = {{Long-term natal site-fidelity by immature lemon sharks ($\backslash$emph{\{}Negaprion brevirostris{\}}) at a subtropical island}}, volume = {18}, year = {2009} } @article{Payne2013, annote = {{\textless}m:note{\textgreater}-Article is a short comment in Nature discussing the Cheung et al. 2013 paper in the same issue{\textless}m:linebreak/{\textgreater}-explains the main findings of a change in spatial distribution of different fish that may be caused by climate change{\textless}m:linebreak/{\textgreater}-paper looks at catch composition and how it has changed over time{\textless}m:linebreak/{\textgreater} {\textless}/m:note{\textgreater}}, author = {Payne, Mark R}, journal = {Nature}, keywords = {climate,comment,fisheries}, number = {7449}, pages = {320--321}, title = {{Climate change at the dinner table}}, volume = {497}, year = {2013} } @article{Guttridge2012, abstract = { Non-consumptive or risk effects imposed by predators can influence prey behaviour over different spatio-temporal scales. Prey vulnerability to predation can also be dependent on abiotic conditions, such as tidal height. We conducted direct field observations of juvenile lemon sharks Negaprion brevirostris in a tidally influenced mangrove-inlet. We also used acoustic tracking to determine the movement patterns of juvenile lemon sharks and their predators (sub-adult lemon sharks) across the tidal cycle. Results showed that greater numbers of juvenile lemon sharks used the mangrove-inlet for longer time periods at deeper and warmer high tide depths. This coincided with an increased presence of potential predators (sub-adult lemon sharks) in the surrounding areas. Furthermore, in accordance with body-size dependent anti-predatory investment, smaller juvenile lemon sharks visited the mangrove inlet more often, spent longer there and left latest on average. Our acoustic tracking data also revealed a tidally-influenced pattern, with both juvenile and sub-adult lemon sharks detected at locations inshore over the high tide and offshore during the low tide. We concluded that the mangrove lake served as a refuge for juvenile lemon sharks over the high tide, providing safe habitat when inshore areas become accessible to large predators, such as sub-adult lemon sharks. We suggest that these decisions are updated through ontogeny and also with daily fluctuations in abiotic factors, such as water depth. This study provides evidence for how intra-specific predator-prey interactions in a top predator species influence juvenile habitat selection , with potential implications for population structure and regulation.}, annote = { -study assesses direct observations and acoustic tracking of juvenile and subadult lemon sharks in Bimini (a.k.a non-consumptive effects of predators) -they find that juveniles do utilize the inlet for longer periods at deeper and warmer depths --also show that the larger the juvenile the last time that is spent in area -sharks are also known to move with tidal fluctuations {\_}{\_}{\_}{\_} -cannibalism has been documented in lemon sharks by Morrissey and Gruber 1993 and Vorenberg 1962 -caught and tagged 24 subadult and adult lemons and gave them acoustic tags to examine movements, as well as 13 juvenile sharks, 9 acoustic receivers --give some information of the SURs in Bimini (and filtering) {\_}{\_}{\_}{\_} }, author = {Guttridge, Tristan L and Gruber, Samuel H and Franks, Brian and Kessel, Steven T and Gledhill, Katie S and Uphill, Jen and Krause, Jens and Sims, David W}, journal = {Marine Ecology Progress Series}, keywords = {bimini,cannibalism,habitat,shark}, pages = {279--291}, title = {{Deep danger: intra-specific predation risk influences habitat use and aggregation formation of juvenile lemon sharks $\backslash$emph{\{}Negaprion brevirostris{\}}}}, volume = {445}, year = {2012} } @article{SmithIvins1983, abstract = {Summary. Relative tendencies toward dispersal or philopatry in a marked population of alpine mammals, the pika (Ochotona princeps),were investigated over a 3-year period in the Rocky Mountains of Colorado. Home range size, distances between centers of activity of dyads, and weighted overlaps of home ranges of dyads were used to define space use patterns. Disappearance and establishment of individuals reflected the temporal component of space use. Social relationships among conspecifics were defined by agonistic and affiliative behaviors. Home ranges of resident adult males and fe- males were of equal size on talus, the obligate habitat of pikas. Adjacent home ranges were normally occupied by members of the opposite sex, and this spacing apparently results from the balance of agonistic and affiliative behaviors exhibited by nearest-neighbor heterosexual pairs. Most juveniles were philopatric. Throughout the summer they remained on their natal home range where they were involved in both agonistic and affiliative behaviors with their mother and putative father. Most animals that established residency were juveniles, and of these almost all settled within 50 m of their natal home range center. This pattern was independent of population density. Immigrants were met with extreme aggression by resident adults that was not balanced by affiliative behaviors. Few immigrants of either sex successfully established on the study area. Adults occasionally changed home ranges, probably to enhance their chances of mating. Intense aggression directed at unfamiliar animals coupled with the acceptance of spatial overlap of related young throughout the summer apparently promote philopatty in pikas. Philopatric settlement in pikas may lead to incestuous matings and contribute to their low intrapopulation genetic variability.}, annote = {-examined O. princeps in Colorado over three years and examined not only population data but also behavioral data. In particular, looked at interactions among pikas -most juveniles were in fact philopatric or settled nearby if they dispersed {\_}{\_}{\_}{\_} -Performed focal and scan sampling surveys to examine behavior -each minute behavioral data was recording during 15 minute blocks --aggression defined as active chases and fights --affiliative behavior- mothers nursing young and social tolerance (animals w/n 3 meters of each other and do not fight even when they were aware of each other) -behavior measurements are expressed as mean rate per unit time that pikas were active -76 percent of established animals were local juveniles -most social tolerance occurred between a juvenile and their mother, father, or sibling -high numbers between same groups for aggressive behaviors -resident was almost always the aggressor -very similar results as above for animals that were artificially placed on a particular patch -dispersing juveniles tended to show up relatively late in the season -juveniles on patches that did not get a territory were not seen after winter time -most juvenile colonization is philopatric --this would lead to high inbreeding which agrees with genetic data *inbreeding would not be a big deal because any reduction in fitness due to inbreeding is probably much less than the reduction in fitness a juvenile endures if it can not establish a territory -alternatively, they may just not experience inbreeding depression --would mean that pikas went through a genetic bottleneck in which most deleterious alleles were eliminated from the gene pool -adults were typically only seen to disperse to increase mating success -found that behavior, spatial relationships and immigration rates were not influenced by density territories over time}, author = {Smith, Andrew T and Ivins, Barbara L}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Ivins - 1983 - Colonization in a pika population dispersal vs. philopatry.pdf:pdf}, journal = {Behav. Ecol. Sociobiol.}, keywords = {pika}, pages = {37--47}, title = {{Colonization in a pika population: dispersal vs. philopatry}}, volume = {13}, year = {1983} } @book{Dawkins1976, address = {Great Clarendon Street, Oxford OX2 6DP}, author = {Dawkins, Richard}, edition = {3}, keywords = {evolution}, publisher = {Oxford University Press Inc}, title = {{The Selfish Gene}}, year = {1976} } @article{Burgess2005, abstract = {Increasingfishingpressureon sharksstocksover recentdecadeshasresultedin declinesof manypopulationsandledto increasingconcernfsortheirconservationT.heextentofthese declinesh,owever,hasbeenhighlyvariable--theresultoftheleveloffishing,oceancondi- tions,andthelifehistoryof individuaslpeciesT.worecentarticleshavedescribedthecollapse and possiblextirpationof sharkpopulationsin the northwestAtlanticOceanand Gulf of Mexico.Herein,we examinethe resultsof thesetwo paperscommentingon the data sets used,comparingthem to other availabledata sets,and criticallyevaluatingthe analysesand conclusionWs.e arguethat theseconclusionhsavebeenoverstatedbecause(:1)the analyses werebasedonalimitednumberofdatasets,(2)thedatasetsthemselvesareinadequateto describethe statusof all sharkpopulationsin the northwestAtlanticOceanand Gulf of Mexicoreportedinthesestudies(,3)availabledatasetsthat couldproducedifferentconclu- sionswere not utilized, (4) somefactorswere not taken into accountthat could have biased the results(,5) there were no alternatehypothesespresentedevaluatingother causesof the perceivedecline,and(6)theauthorsdidnotconsidearnycurrentstockassessmenwtsh,ich inseveraclasesreportthestatusofsharksto beconsiderablhyealthierthanasserted. }, annote = {-argue that the extent at which species have declined in NW Atlantic and Gulf of Mexico are highly variable -argue that conclusions by Baum et al. 2003 and Baum and Myers 2004 are overstated because: --limited amount of data sets --data themselves do not represent whole areas --did not use all available data sets --certain factors were not taken into account --no alternative hypotheses for the decline --authors did not consider any current stock assessments {\_}{\_}{\_}{\_} -begin by discussing modeling work that has assessed populations and has found that even some can be harvested properly -discuss conservation implications of the two papers in question with many species being protected following the publishing of the results -believe that the two papers make inferences based on results inappropriate for many shark species -don't feel using only one data set (longline fishing) is appropriate to cover all species -on these points misidentification of species may also have been very high --particularly true for white sharks -also changes in how shark landings were recorded before and after 1993 which could skew results --(i.e. less sharks would be reported after 1993) -trends can be quite different for different data sets used (use C. plumbeus as example) -also point out that bite off rates in monofilament are steel leader fishing gear will play a significant role in how many sharks are caught -type of fishing hook also appears more important than the two papers had pointed out -papers had analyzed depth but did not look at habitat preference for the shark species --depth should have had significant effect on catch rates -this paper cites study by ICCAT for sustainable shark populations{\{}{\ldots}{\}}..which could be bullshit as well }, author = {Burgess, George H and Beerkircher, Lawrence R and Calliet, Gregor M and Carlson, John K and Cort{\'{e}}s, Enric and Goldman, Kenneth J and Grubbs, R Dean and Musick, John A and Musyl, Michael K and Simpfendorfer, Colin A}, journal = {Fisheries}, keywords = {fisheries,shark}, number = {10}, pages = {19--26}, title = {{Is the collapse of shark populations in the Northwest Atlantic Ocean and Gulf of Mexico real?}}, volume = {30}, year = {2005} } @article{Allen, author = {Allen, D L}, journal = {The University of Michigan Press}, keywords = {isle royale,wolves}, title = {{Wolves of Minong: Isle Royales Wild Community.}}, year = {1979} } @book{vanKampen1992, address = {Amsterdam}, author = {van Kampen, Nicolaas G}, edition = {2nd}, keywords = {physics,population model,statistics,stochastic}, publisher = {Elsevier}, title = {{Stochastic processes in physics and chemistry}}, year = {1992} } @article{McCauley2012, abstract = {Abstract. Accurately surveying shark populations is critical to monitoring precipitous ongoing declines in shark abundance and interpreting the effects that these reductions are having on ecosystems. To evaluate the effectiveness of existing survey tools, we used field trials and computer simulations to critically examine the operation of four common methods for counting coastal sharks: stationary point counts, belt transects, video surveys, and mark and recapture abundance estimators. Empirical and theoretical results suggest that (1) survey method selection has a strong impact on the estimates of shark density that are produced, (2) standardizations by survey duration are needed to properly interpret and compare survey outputs, (3) increasing survey size does not necessarily increase survey precision, and (4) methods that yield the highest density estimates are not always the most accurate. These findings challenge some of the assumptions traditionally associated with surveying mobile marine animals. Of the methods we trialed, 8 3 50 m belt transects and a 20 m radius point count produced the most accurate estimates of shark density. These findings can help to improve the ways we monitor, manage, and understand the ecology of globally imperiled coastal shark populations.}, annote = {-used field trials and simulations to demonstrate effectiveness and accuracy of shark surveying methods -looked at stationary point counts, belt transects, video surveys, mark-recapture -most accurate were belt transects and radius point counts {\_}{\_}{\_}{\_}{\_} -simulation model used shark movement data and used the three different underwater survey methods to evaluate their different efficiencies. Works because the actual shark density is known in the model -also tested different ranges of belt transects and point counts {\_}{\_}{\_}{\_}{\_}{\_} -video and point surveys consistently generated the highest shark density and detection rates -belt transects always yielded the lowest amounts -daytime vs nighttime video did not differ -did not compare surveys to mark recapture but were able to estimate 661 sharks in their study area -in fished population simulations variability of method outputs grew significantly {\_}{\_}{\_}{\_}{\_} -even though video and point surveys produced high densities it appears that belt transects produce the most accurate though simulations -choosing to model density as volume instead of area would affect the results }, author = {McCauley, Douglas J and Mclean, Kevin A and Bauer, John and Young, Hillary S and Micheli, Fiorenza}, journal = {Ecological Applications}, keywords = {shark,survey techniques}, number = {2}, pages = {385--392}, title = {{Evaluating the performance of methods for estimating the abundance of rapidly declining coastal shark populations}}, volume = {22}, year = {2012} } @article{Feldheim2004, abstract = {Because sharks possess an unusual suite of reproductive characteristics, including internal fertilization, sperm storage, relatively low fecundity, and reproductive modes that range from oviparity to viviparity, they can provide important insight into the evolution of mating systems and sexual selection. Yet, to date, few studies have characterized behavioral and genetic mating systems in natural populations of sharks or other elasmobranchs. In this study, highly polymorphic microsatellite loci were used to examine breeding biology of a large coastal shark, the lemon shark, Negaplrion brevirostris, at a tropical lagoon nursery. Over six years, 910 lemon sharks were sampled and genotyped. Young were assigned into sibling groups that were then used to reconstruct genotypes of unsampled adults. We assigned 707 of 735 young sharks to one of 45 female genotypes (96.2{\%}), and 485 (66.0{\%}) were assigned to a male genotype. Adult female sharks consistently returned to Bimini on a biennial cycle to give birth. Over 86{\%} of litters had multiple sires. Such high levels of polyandry raise the possibility that polyandry evolved in viviparous sharks to reduce genetic incompatibilities between mother and embryos. We did not find a relationship between relatedness of mates and the number of offspring produced, indicating that inbreeding avoidance was probably not driving pre- or postcopulatory mate choice. Adult male sharks rarely sired more than one litter at Bimini and may mate over a broader geographic area.}, annote = {*discussing a lot of past work in detail that will be important in our introduction *Castro 1996 found the biennial reproductive pattern is expected for female but not male sharks -used micro satellite loci to study the breeding biology of lemon sharks in Bimini -were able to assign 707 of 735 sharks into one of 45 genotypes -discuss the two year cycle of returning females -found that inbreeding avoidance did not drive mate choice {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -very little work has been done examining shark mating systems, believe that genetic studies can chad some light on this -describes genetic techniques and programs used in the study -also looked at possible inbreeding by examining the micro satellites of mated individuals -estimated year of birth for most of the animals using biennial female patterns and growth rant of 5.2-7.1 cm -45 adult females and 84 males parented young from 1993 to 2001 -32 of 45 females returned multiple times and most on the 2 year cycle *more females used bimini in odd years than in even years -average litter size was 6.7 with a range of 1-18 -97 total litters, check this -84 male father genotypes were identified with a minimum of another 120 necessary -must be very good at inbreeding avoidance with a relatedness value between mated individuals of only 0.0109 (range= -.369 to 0.3707) -males may breed over large area indicating that they are responsible for any gene flow in the atlantic "Little is known about any of these factors in elasmobranchs, but our demonstration of high levels of polyandry in a viviparous shark species is consistent with the predictions of the genetic incompatibility avoidance hypothesis" }, author = {Feldheim, Kevin A and Gruber, Samuel H and Ashley, Mary V}, journal = {Evolution}, keywords = {bimini,genetics,juvenile,shark}, number = {10}, pages = {2332--2342}, title = {{Reconstruction of parental micro satellite genotypes reveals female polyandry and philopatry in the lemon shark, $\backslash$textit{\{}Negaprion brevirostris{\}}}}, volume = {58}, year = {2004} } @phdthesis{Kessel2010, abstract = {Coastal shark populations have been subject to increasing anthropogenic pressure over the past two decades. This study focused on two lemon shark (Negaprion brevirostris) populations, the site-attached maturing sub-adults at the Island of Bimini, Bahamas, threatened by a large-scale resort development, and adults forming winter aggregations off the coast of Jupiter, Florida, subject to direct fishing pressure. For the sub-adult population, analysis was carried out on the long-term temporal patterns in abundance and population structure, relative to potential driving factors, and the influence of variables affecting longline catch- rates used as the basis for stock assessment. For the aggregating adult population, life-history aspects of population structure and distribution were investigated for relative implications on the species vulnerability status. The following analysis and methodologies were utilised to investigate the two populations: longline catch records from 1982 -- 2008; monitoring of variables potentially affecting longline catch-rates; documentation of shark behavioural interactions with longline equipment using underwater video surveillance; aerial surveying for abundance estimates; comparison of spatial utilisation patterns with longline catch locations; external tagging; the utilisation of archival satellite tags; passive tracking with Vemco acoustic monitoring system and research collaborations with other scientific groups utilising the same acoustic monitoring system. The key findings of this study were that in the northwest Atlantic, N. brevirostris populations are experiencing considerable anthropogenic pressure at all life-stages. In Bimini, the effects of a large-scale resort development have resulted in a significant decline in abundance, to a level ({\~{}}52 individuals) well below the temporal average ({\~{}}158). On the U.S. east coast, seasonal aggregating behaviour has further increased vulnerability through increased catchability, beyond the highly vulnerable status already attributed to this species, and targeted N. brevirostris fisheries appear to be currently operating at unsustainable levels. Shark longline catchability was noted to be significantly influenced by multiple shark presence, resulting in greater susceptibility for N. brevirostris (and other similar species) that naturally exhibit this group behaviour. Incidental encounterability and predation risk significantly influenced longline catch-rates. Adult N. brevirostris exhibited large-scale seasonal migrations on the U.S. east coast, which, in addition to documented international transitions, supports existing evidence for genetic mixing across the distribution. Water temperature was found to be a significant driver of N. brevirostris behaviour at all life-stages, with an apparent adult temperature preference of {\~{}}24$\backslash$,{\^{}}{\{}$\backslash$circ{\}}C. This study represents the first long-term abundance assessment for sub-adult N. brevirostris, and the first in-depth study to focus on an adult N. brevirostris population. The results provide essential life-history information, revealing that at all life-stages N. brevirostris appear to be highly sensitive to anthropogenic activities, relative to other species, and therefore require enhanced management for species protection. It is therefore highly recommended that N. brevirostris be added to the U.S. prohibited species list.}, address = {United Kingdom}, annote = {-have only read work done at Bimini so far, nothing on Jupiter -study focuses on two lemon shark populations: subadults in bimini and adults along east coast of the united states -examined longline records from 1982-2008 (from multiple sources) -find that lemon sharks of all life stages are experiences significant anthropogenic effects -advise the N. brevirostris be to the U.S. prohibited species list {\_}{\_}{\_} -discusses lemon shark past research in detail, a lot of information on genetics database -also describes why Bimini is a great place to examine population dynamics -longlines caught 117 lemons (1982-1989) and 234 from other species (1984-1989) -202 (1992-2003) and 367 (surveys stopped intentional killings conducted in the 1980s -2003-2008 long lining was focused on a actual census instead of simply to catch specimens (much more detailed and examined many more variables affecting catch and population trends -needed to create a CPUE for all these databases -discusses predation by G. cuvier on lemon sharks {\_}{\_}{\_}{\_} -using CPUE and recapture data, Steve reconstructed what the total population size should be from 1982-2008 at Bimini{\{}{\ldots}{\}}.used Lincoln-Peterson Model to accomplish this N= (M*C/R)/Y **some of this data is tough to interpret because of a disproportionate percentage of age classes caught; however, after 2000 now juveniles were caught by longlines so from 2000 to 2008 a good estimate of combined subadult and adult population numbers can be found. These could be compared to model outputs in the juvenile shark paper -he also gives percentage of CPUE that each age group contributed to over 36 year time frame (these values vary wildly) }, author = {Kessel, Steven T}, keywords = {bimini,shark,survey techniques}, school = {Cardiff University}, title = {{An investigation into the behavior and population dynamics of the lemon shark ($\backslash$emph{\{}Negaprion brevirostris{\}})}}, type = {Ph.D. diss.}, year = {2010} } @article{Dulvy2008, abstract = {1. Fishing spans all oceans and the impact on ocean predators such as sharks and rays is largely unknown. A lack of data and complicated jurisdictional issues present particular challenges for assessing and conserving high seas biodiversity. It is clear, however, that pelagic sharks and rays of the open ocean are subject to high and often unrestricted levels of mortality from bycatch and targeted fisheries for their meat and valuable fins. 2. These species exhibit a wide range of life-history characteristics, but many have relatively low productivity and consequently relatively high intrinsic vulnerability to over-exploitation. The IUCN World Conservation Union Red List criteria were used to assess the global status of 21 oceanic pelagic shark and ray species. 3. Three-quarters (16) of these species are classified as Threatened or Near Threatened. Eleven species are globally threatened with higher risk of extinction: the giant devilray is Endangered, ten sharks are Vulnerable and a further five species are Near Threatened. Threat status depends on the interaction between the demographic resilience of the species and intensity of fisheries exploitation. 4. Most threatened species, like the shortfin mako shark, have low population increase rates and suffer high fishing mortality throughout their range. Species with a lower risk of extinction have either fast, resilient life histories (e.g. pelagic stingray) or are species with slow, less resilient life histories but subject to fisheries management (e.g. salmon shark). 5. Recommendations, including implementing and enforcing finning bans and catch limits, are made to guide effective conservation and management of these sharks and rays.}, annote = {-review paper on fishery practices and life history properties in regards to pelagic elasmobranch conservation -examine 21 species with the IUCN criteria -find trends of extinction risks related to life history and/or good fisheries practices {\_}{\_}{\_} -discuss previous work on finning and examining global fishing practices, provide detailed information on all 21 species they investigated {\_}{\_}{\_} -there are 30 oceanic pelagic species in total but they examined the 21 often caught in fisheries -this paper comes from the work done by the IUCN Shark Specialist Group over a number of years -notice a lot of variability in good data and difference in population assessment between regions and globally -the oceanic whitetip, bigeye thresher, silky, blue, other thresher species, and hammerhead sharks make up bulk of fin trade (Clarke et al., 2006) -ecosystem models have suggested that oceanic pelagic sharks are not in fact keystone predators {\_}{\_}{\_} -19 countries and the EU now ban having only fins aboard a fishing vessel -discuss current laws and policies in different countries -offer suggestions for fishing management for both managers and countries in general }, author = {Dulvy, Nicholas K and Baum, Julia K and Clarke, Shelley and Compagno, Leonard J V and Cort{\'{e}}s, Enric and Domingo, Andr{\'{e}}s and Fordham, Sonja and Fowler, Sarah and Francis, Malcolm P and Gibson, Claudine and Mart{\'{i}}nez, Jimmy and Musick, John A and Soldo, Alen and Stevens, John D and Valenti, Sarah}, journal = {Aquatic Conservation: Marine and Freshwater Ecosystems}, keywords = {fisheries,shark}, month = {may}, pages = {459--482}, title = {{You can swim but you can't hide: the global status and conservation of oceanic pelagic sharks and rays}}, volume = {18}, year = {2008} } @article{HanskiGilpin1991, abstract = {We review the early development of metapopulation ideas, which culminated in the well-known model by Levins in 1969. We present a survey of metapopulation terminology and outline the kinds of studies that have been conducted on single-species and multi species metapopulations. Metapopulation studies have important conceptual links with the equilibrium theory of island biogeography and with studies on the dynamics of species living in patchy environments. Metapopulation ideas play an increasingly important role in landscape ecology and conservation biology. }, annote = {Paper examines history of metapopulation dynamics research up until 1991 starting primarily with Levins (1969) Levins' model dp/dt= mp (1-p) - ep p=faction of patches occupied, m=rate of colonization, e= rate of extinction -discuss application to spotted owl conservation in the United States}, author = {Hanski, Ilkka and Gilpin, Michael}, journal = {Biological Journal of the Linnean Society}, keywords = {dispersal,metapopulation,population model,review}, pages = {3--16}, title = {{Metapopulation dynamics: brief history and conceptual domain}}, volume = {42}, year = {1991} } @article{Gutttridge2009, abstract = {The role of learning in behaviour is well known for many animal taxa, including teleost fishes, insects, birds and mammals. However, its importance to sharks in everyday behavioural processes has rarely been considered. Almost 50 years ago the first learning experiments on sharks were conducted; our first section discusses these studies and places them in a framework of associative and non-associative learning. These experiments showed that sharks were capable of different forms of learning, such as operant and classical conditioning and habituation. Sharks could learn associations as rapidly as other vertebrates and also remember training regimes for several months. However, much of this experimental evidence was based on small sample sizes and few shark orders, such as Carcharhiniformes and Orectobliformes, leaving large gaps in our knowledge of the general learning capabilities of other shark orders. We also examine recent research that has tested for, or inferred learning in behavioural processes. This section reveals that sharks, like teleost fishes use learning to improve prey search and capture to potentially navigate and orientate in their home range and recognize conspecifics, heterospecifics and mates. Learning is also discussed in relation to ecotourism and fisheries. Findings indicated that these activities may lead to conditioning of sharks and that considerable effort should go into investigating what impact this could have on the shark species involved. Finally, we discuss the importance of combining laboratory experiments with field studies, the use of new experimental techniques, the role of model species and research priorities for future work.}, annote = {-Review paper on shark learning abilities and how that affects shark behavior -discuss 50 years of research on learning, prey searching, navigation, ecotourism, and fisheries {\_}{\_}{\_} -two types of learning: associative and non-associative --associative-learning of association between two different events --non-associative- learning occurs because of result of single stimulus -gives examples of research from Sims on Basking sharks to the work on juvenile lemons in Bimini -often hard to identify if behaviors are truly learnt or genetic somehow -definitely learnt in Basking shark and plankton case -discuss Franks 2007 and the results at Bimini showing significantly different sizes in home ranges from South Bimini and North Sound sharks- different balances of energy costs and energy intake --idea is that sharks are able to learn about environment and adjust their behaviors accordingly --could also be adjusting behavior though based on predation risks, shape and bathymetry of nursery areas -discuss in detail studies looking at the effect ecotourism is having on elasmobranch populations and surrounding prey populations }, author = {Guttridge, Tristan L and Myrberg, Arthur A and Porcher, Ila F and Sims, David W and Krause, Jens}, journal = {Fish and Fisheries}, keywords = {behavior,bimini,movement,shark}, month = {jul}, pages = {1--20}, title = {{The role of learning in shark behavior}}, year = {2009} } @article{Cortes2002a, abstract = {I explored the effect of uncertainty in demographic traits on demographic analyses of sharks, an approach not used before for this taxon. I used age-structured life tables and Leslie matrices based on a pre- breeding survey and a yearly time step applied only to females to model the demography of 41 populations from 38 species of sharks representing four orders and nine families. I used Monte Carlo simulation to reflect uncertainty in the estimates of demographic traits and to calculate population statistics and elasticities for these populations; I used correlation analysis to identify the demographic traits that explained most of the variation in population growth rates (lambda). The populations I examined fell along a continuum of life-history characteristics that can be linked to elasticity patterns. Sharks characterized by early age at maturity, short lifespan, and large litter size had high lambda values and short generation times, whereas sharks that mature late and have long lifespans and small litters have low lambda values and long generation times. Sharks at the ``fast'' end of the spectrum tended to have comparable adult and juvenile survival elasticities, whereas sharks at the ``slow'' end of the continuum had high juvenile survival elasticity and low age--zero survival (or fertility) elasticity. Ratios of adult survival to fertility elasticities and juvenile survival to fertility elasticities suggest that many of the populations studied do not possess the biological attributes necessary to restore lambda to its original level after moderate levels of exploitation. Elasticity analysis suggests that changes in juvenile survival would have the greatest effect on lambda, and correlation analysis indicates that variation in juvenile survival, age at maturity, and reproduction account for most of the variation in lambda. In general, combined results from elasticity and correlation analyses suggest that research, conservation, and management efforts should focus on these demographic traits.}, annote = {-examines the effect of uncertainty (through monte carlo simulation) in demographic traits on specific demographic analyses of sharks- first time this has been done for sharks --leslie matrices are then used for analysis with elasticities -41 populations of 38 various species representing 4 orders and nine families -analysis of elasticity shows juvenile survival has the greatest effect on growth rate -Smith 1998 looked at sharks through modeling density dependence in early stages {\_}{\_}{\_}{\_}{\_}{\_} -incorporated uncertainty into the simulations and took means of 10000 trials -juvenile and adult elasticities were always higher than fertility elasticities -typically age at maturity accounted for the greatest effect on the variation in lambda -found that the growth rate is less than one for some surprising species thought to be abundant (C. limbatis, S. acanthi as, C. acronotus) -look at Cortes 98/99 and Walker 1998 for density dependence in sharks -density dependence survivorship in pre-adult stages can compensate for other things -elasticity ratios showed that harvesting of large, slow grow, long lived species is dangerous -can only compensate if there is increase in age-0 survival or fecundity- however a 10{\%} decrease in survival would require almost impossible levels of increase in age-0 survival or fecundity -future work should examine all possible ways a population could compensate -"decrease in fertility elasticity from the fast to slow end of the life history continuum" -increasing trend in juvenile survival elasticity also observed in mammals -decreasing trend in adult survival elasticity with generation time was different that that seen in other long lived vertebrates -feels that future work should gather more data on juvenile survival, age at maturity, and reproductive rates --conservation efforts should focus on these things }, author = {Cort{\'{e}}s, Enric}, journal = {Conservation Biology}, keywords = {demography,leslie matrix,mortality,shark}, month = {aug}, number = {4}, pages = {1048--1062}, title = {{Incorporating Uncertainty into Demographic Modeling: Application to Shark Populations and Their Conservation}}, volume = {16}, year = {2002} } @article{Newman2010, abstract = {ABSTRACT: Sharks are often regarded as opportunistic asynchronous predators that feed on the most abundant prey. In the present study, 2 populations of juvenile lemon sharks Negaprion brevi- rostris were investigated from Bimini, Bahamas, with well-defined home ranges facilitating the esti- mation of prey preference. Stomach contents were quantitatively analysed from 396 lemon sharks with data on prey species and abundance obtained from quantitative sampling of mangrove and sea- grass faunal communities to elucidate preferences with respect to prey type, prey size and location. Yellowfin mojarra Gerres cinereus dominated the diet of juvenile lemon sharks ({\textgreater}50{\%} by weight and percentage index of relative importance, {\%}IRI), even when present in lower abundances in the environment. Preference was determined and compared using abundance, {\%}IRI values and original weight of prey, with the latter preferred due to their close relationship with energetic intake. Juve- nile lemon sharks do not feed indiscriminately, but exhibit prey preference and size selection. Juve- nile lemon sharks at Bimini demonstrated a hierarchy of prey preference: parrotfish (Scaridae) {\textgreater} mojarra (Gerreidae) {\textgreater} toadfish (Batrachoididae) {\textgreater} filefish (Balistidae) {\textgreater} grunts (Haemulidae) {\textgreater} bar- racuda (Sphyraenidae). High overlap between shark diet and mangrove communities revealed the importance of mangroves to lemon sharks and their prey. Lemon sharks fed disproportionately on intermediate sized teleosts and crustaceans, with maximum prey size of nursery-bound sharks pri- marily limited by availability in the environment. We conclude that sharks can be highly plastic for- agers, capable of selective feeding, but will switch to more opportunistic foraging when environmen- tal conditions deteriorate. }, annote = {-paper investigates the general diet of juvenile lemon sharks in Bimini by examining stomach contents and nearby prey abundance in both the NS and SB -find that juvenile lemon's intake is over 50 percent Yellowfin mojarra (Gerres cinereus) -could also demonstrate hierarchy of prey preference -demonstrate how important mangrove communities are to juvenile lemon sharks {\_}{\_}{\_} -stomach content procedure is described by Schurdak and Gruber 1989 with a 1:20 000 dilution of tricaine in seawater Diet of shark and the seine prey population catches were analyzed with the following indices IRI= {\%}O x ({\%}N + {\%}W) {\_}{\_}{\_} -find that sharks in the NS have a wider range of diet than at SB but animals in SB had greater values of dietary breadth -mojarra was the main prey in both lagoons but NS sharks ate more crustaceans where as SB sharks ate more parrotfish -however toadfish, parrotfish, and barracuda were all preferred in both nurseries -also selectively hunt intermediate sized prey than the average size of prey found in the community }, author = {Newman, Steven P and Handy, Richard D and Gruber, Samuel H}, journal = {Marine Ecology Progress Series}, keywords = {bimini,juvenile,predation,shark}, month = {jan}, pages = {221--334}, title = {{Diet and prey preference of juvenile lemon sharks $\backslash$emph{\{}Negaprion brevirostris{\}}}}, volume = {398}, year = {2010} } @article{Gerrodette2011, abstract = {Bycatch in artisanal gill nets threatens the vaquita, Phocoena sinus, with extinction. In 2008 the Mexican government announced a conservation action plan for this porpoise, with three options for a protected area closed to gill net fishing. The probability of success of each of the three options was estimated with a Bayesian population model, where success was defined as an increase in vaquita abundance after 10 yr. The model was fitted to data on abundance, bycatch, and fishing effort, although data were sparse and imprecise. Under the first protected area option, the existing Refuge Area for the Protection of the Vaquita, bycatch was about 7{\%} of population size, and probability of success was 0.08. Under the second option with a larger protected area, the probability of success was 0.35. The third option was large enough to eliminate vaquita bycatch and had a probability of success {\textgreater}0.99. Probability of success was reduced if elimination of vaquita bycatch was delayed or incomplete. Despite considerable efforts by the Mexican government to support vaquita conservation, abundance will probably continue to decline unless additional measures to reduce vaquita bycatch are taken, such as banning gill nets within the vaquita's range and developing effective alternative fishing gear.}, annote = {-paper examines Mexican's governments plan for three different options of protection areas where gill net fishing would be illegal -using Bayesian methods the study depends which of the three options is optimal and there chance of success {\_}{\_}{\_} Timeline -1993 Biosphere reserve is established in vaquita area (Upper Gulf of California and Colorado River Delta Biosphere Reserve) -1997 government establishes vaquita recovery plan (International Committee for the Recovery of the Vaquita (CIRVA)) -2005 additional Refuge Area for Vaquitas was established -2008 plan be president of Mexico to prevent extinction (PACE Vaquita) --marked first time good enforcement actually occurred in the Refuge Area --a voluntary buyout program was also started which reduced number of net boats (1/3 of fishermen have accepted this) --plan describes three options for future area closures --describes economic consequences of the three options {\_}{\_}{\_} -determine success of program by having a growth rate over a ten year period to simply be greater than one -use a very simple population model to estimate future population size and effect of by catch -using same model to estimate success of three options by 2018 the researchers also examined the success of past protected areas, both protection plans still allowed significant decrease in population size -study also looks at effects of delaying conservation till after proposed 2010 starting date, if start data occurred after 2014 the population would almost certainly continue to decrease}, author = {Gerrodette, Tim and Rojas-Bracho, Lorenzo}, journal = {Marine Mammal Science}, keywords = {MPA,vaquita}, number = {2}, pages = {E101--E125}, title = {{Estimating the success of protected areas for the vaquita, $\backslash$emph{\{}Phocoena sinus{\}}}}, volume = {27}, year = {2011} } @article{Chirakkal2010, abstract = {Abstract. Conservation practitioners use demographic population viability analysis (PVA) to understand long-term effects of changing demographic rates on population growth rate. Sensitivities and elasticities of stage-specific survival and fertility rates provide managers with guidelines on the relative contributions of various life-history stages to long-term population growth. However, short-term patterns, especially single-year effects, of elasticity may be dramatically different from long-term effects, calling for caution in implementing management policies focusing entirely on only long- or short-term elasticities. Here we illustrate the temporal and spatial variation in elasticity patterns for four populations of California sea lions. Short-term stochastic elasticities were significantly different from long- term elasticities, and spatial patterns of short- and long-term elasticities varied across sites. These differences may be explained by transient effects in age structure and deviations from the stable age distribution, as well as environmental variation. Our results suggest that conservation practitioners should consider calculations of both short-and long-term elasticity in viability analyses that are used to guide management and should use caution in generalizing elasticity patterns across populations.}, annote = {-discuss how elasticity and sensitivity analysis can be very different for long term versus short term analysis -show example of sea lions at different sites in baja {\_}{\_}{\_} -find that short term elasticity analysis and long term very significantly -**show that short term elasticity analysis shows more pronounced effects for younger age classes -long term analysis affect vital rates of older age classes (as is typically seen) -**(make F and S beta variables and determine a, b for B(a,b) through quadratic programming (see Wood 1997 and Wielgus 2008) -average out 100 000 trials and computed lambdas for each {\_}{\_}{\_}{\_} -short term and long term elasticities always differed -point our that mating behavior will be important for management strategies }, author = {Chirakkal, Haridas and Gerber, Leah R}, journal = {Ecological Applications}, keywords = {PVA,demography,elasticity,sea lions}, number = {3}, pages = {783--788}, title = {{Short- and long-term population response to changes in vital rates: implications for population viability analysis}}, volume = {20}, year = {2010} } @article{McKaneetal2007, author = {McKane, Alan J and Nagy, John D and Newman, Timothy J and Stefanini, Marianne O}, journal = {Journal of Statistical Physics}, keywords = {demography,oscillations,physics,population model,statistics}, pages = {165--191}, title = {{Amplified Biochemical Oscillations in Cellular Systems}}, volume = {128}, year = {2007} } @article{MichaelisMenton1913, author = {Michaelis, Leonor and Menten, Maud}, journal = {Biochem. Z.}, keywords = {demography,math,statistics}, pages = {333--369}, title = {{Die Kinetik der Invertinwirkung}}, volume = {49}, year = {1913} } @article{Mollet2002, abstract = {Abstract. Results of demographic analyses of four species of elasmobranchs were compared by use of life-history tables, Leslie matrices, and several stage-based matrix models. Dasyatis violacea, with few age classes, was used to demonstrate the basics of Leslie-matrix and stage-based matrix model calculations. The demography for Carcharias taurus, with a 2-year reproductive cycle, produced higher potential population growth using actual fertility rather than effective annual fertility. The demography for Alopias pelagicus, with continuous reproduction, produced higher potential population growth for a birth-flow than a birth-pulse population. The Carcharodon carcharias example demonstrated only a small difference in potential population growth between step-like and logistic fertility functions. Stage-based models with fixed stage duration produced potential population growths identical to those obtained from a life-history table or Leslie matrix, but the net reproductive rates and generation times differed. Stage-based models with few stages had different dynamics with shorter recovery to the stable age distribution; they underestimated the elasticity of juvenile survival and overestimated the elasticity of adult survival, suggesting that interpretation should be cautious. Elasticity analyses were used to estimate the number of juvenile age classes that could be fished and have the same effect on potential population growth as fishing all the adult age classes.}, annote = {*paper discusses mortality functions in discussion -see hard copy for notes -studied four species of elasmobranchs and compared life-history tables, Leslie matrices, and several stage-based matrix models -stage based models produced population growths identical to life history tables or leslie matrices. However they differed in new reproductive rates and generation times -stage based models underestimated the elasticity of juvenile survival and overestimated that of adults -all four species were used to compare different questions within the species and their particular model construct --data for species was taken from previous studies (reproductive age, max age, natural mortality (estimated), and fertility) estimated mortality = -ln(0.01)/(max age) **this tis from (Campana et al. 2001) -used standard life-history table based on discrete Euler-Lotka equation (Caughley 1977) to find the solution e{\^{}}r = (lambda) -mention birth-pulse function a lot (just like Bimini, individuals born at certain time instead of continuous) -C taurus which they studied has similar birth every two years for females as lemon sharks -explains how 10 percent decrease in adult or juvenile survival would require a 50 percent increase in fertility in order to recover (we can do this for the Bimini model) -in great whites a step like maturity function (ex. age 12 equals adults) produced slightly biased results -suggest that a geometric distribution is not good for elasmobrancks as it produced different growth rates when compared to Leslie matrix or LHT -management should focus on combined results of elasticity (prospective) and correlation (retrospective) ****found that the importance in juvenile survival was reduced in 4 and 2 staged small models }, author = {Mollet, H F and Cailliet, G M}, journal = {Marine Freshwater Research}, keywords = {leslie matrix,mortality,population model,shark}, pages = {503--516}, title = {{Comparative population demography of elasmobranchs using life history tables, Leslie matrices and stage-based matrix models}}, volume = {53}, year = {2002} } @incollection{Heithaus2010, address = {Boca Raton, FL}, annote = {{\textless}m:note{\textgreater}see book for notes {\textless}/m:note{\textgreater}}, author = {Heithaus, Michael R and Frid, Alejandro and Vaudo, Jeremy J and Worm, Boris and Wirsing, Aaron J}, booktitle = {Sharks and Their Relatives}, editor = {Carrier, Jeffrey C and Musick, John A and Heithaus, Michael R}, keywords = {demography,nursery site,population model,review,shark}, pages = {611--637}, publisher = {CRC Press}, title = {{Unraveling the Ecological Importance of Elasmobranchs}}, volume = {II}, year = {2010} } @article{Squires2010, abstract = {Abstract Buybacks of fishing vessels, licences, access and other rights, and gear, sometimes called decommissioning schemes, have traditionally been a key policy tool to address overcapacity, overexploitation of fish stocks, and distributional issues in fisheries. Two more issues can be added, sustainable use of ecosystems and conservation of biodiversity (i.e. ecological public goods and services) and providing a transition to a more rationalized fishery. This study discusses reasons for buybacks; examines consequences; considers asymmetric information, design of buyback auctions and other design issues; buybacks as a transition to a rationalized industry with strong property rights and governance, financing and transnational fisheries; draws out key lessons from the international experience; and provides an overall evaluation.}, annote = {REVIEW -paper examines reasons for buybacks, consequences, asymmetric information, design, and buybacks as a transition to other fishery types, financing, and international problems {\_}{\_}{\_}{\_} -can buyback fishing vessels, licenses, access, or the fishing gear itself -used to address overcapacity, overexploitation of fish stocks and distribution problems in fisheries --now fisheries have started being applied in animal conservation and biodiversity tools -also used as tool to transition to more sustainable fisheries and fisheries practices {\_}{\_}{\_}{\_} Purpose: -address overcapacity, overfishing, and conservation issues Impacts: -affects different fishers and crew members in different ways -can restore profitability for remaining fishermen --however, the remaining fishermen then invest more in technology which increases fishing capacity once again Asymmetric Information: -often times costs and benefits can be overlooked when examining buyback authorities and fishers --many times fishers understand effectiveness of gear and vessels better then the buyback authorities --one group may withhold information from the other -fishers may only leave fishery b/c buyback can rescue an unprofitable business -investors have less risk when putting money into fishing vessels -can target wrong vessels for buyout programs --(i.e.) buying out old fishermen that may have retired soon anyway- happens in Mexico. The resulting fleet then consists of younger vessels that may be better at catching fish in the first place -to solve these problems, need better screening of vessels Conservation/biodiversity: -using buybacks to address these specific issues (loss of public goods) -discuss applications in Gulf of California with endangered vaquitas -also discusses Pacific leatherback fishery (fishermen were given a one time payment to switch from j hooks to circle hooks, however, the one time payment was not sufficient to make up losses on reduced dolphin-fish catch Programme design issues: -set clear goals (avoid contrasting goals) -clearly defined scope -must also fulfill 3 conditions before program start (proper license registration, communication between fishers and buyback group, measures to prevent new fishers/technology from entering) -decide what type of buyout to use -mandatory or voluntary buyouts -prevent increases in fishery capacity or spillover to other fisheries -limit reinvestment or new investment -determining payment type (i.e. one time payment, multiple payments) --important in areas that may not have strong alternatives to fisheries -limiting actual fishing time -can also associate buybacks with things other than property (i.e. quotas) Buyback prices and markets: -different methods to setting buyback prices, most common are fixed prices and auctions. Both have pros and cons. Auctions can reveal true market values -reverse auctions, reservation prices, releasing bits of information, eligibility requirements, ranking of bids by some metric, sealed vs. open bids, strike price auctions, single vs. multiple rounds Financing buybacks: -public vs. privately funded- depends on situation -either can produce wrong incentives or moral hazards Buybacks as transition: -addresses long-term career changes or displacing of vessels to new areas outside MPA -can user garner more support from fishers themselves Transnational fisheries: -problems with countries that do or do not put up necessary funds -need to address new vessels entering fisheries Guidelines: -must start early to achieve a more economic and successful outcome -buyback design is critical -more effective when fleets are smaller in number and somewhat homogenous -knowing which group of fishers to target -balance among incentives for different groups and fisheries -establishing necessary preconditions are in place -stakeholder involvement -reduce information asymmetry -funding of project and sources of funding -transnational endure a host of other concerns -buybacks cannot be only solution to problem Summary: -do not address "Tragedy of Commons" and can sometimes make situation worse}, author = {Squires, Dale}, journal = {Fish and Fisheries}, keywords = {buybacks,fisheries,megafauna,review,vaquita}, pages = {366--387}, title = {{Fisheries buybacks: a review and guidelines}}, volume = {11}, year = {2010} } @article{Anadon2012, abstract = {Abstract. Animal movement and behavior may respond to habitat modification or fragmentation in non trivial ways, thereby strongly conditioning the fate of populations. This study aims to understand movement patterns of non-dispersal animals in both natural and altered landscapes, using the endangered terrestrial tortoise Testudo graeca as example. We used individual-based simulation models representing competing hypotheses on tortoise movement. Model parameterization and selection was based on radiotracking data and an inverse approach that is able to deal with observation uncertainty, individual variability, and process stochasticity. We find that land use intensification had a strong impact on the movement and behavior of non-dispersing individuals of T. graeca. In natural landscapes, males and females showed a similar movement and behavior profile with a strong home behavior component, and little individual variability. However, in altered landscapes, movement and behavior greatly varied among individuals, particularly in females, and males and females showed different movement patterns. Females showed a wide range of movement patterns, from strong home behavior to an unbounded movement. Our study shows that population or movement models that assume single behavioral states for animals inhabiting different landscape structures can be strongly misleading and, furthermore, that the impact of landscape modification on movement and behavioral patterns can be strongly sex-biased. Flexible, individual-based movement models coupled with inverse parameterization and model selection approaches proved useful in understanding the mechanisms controlling animal movement patterns.}, annote = {-study tries to understand how movement patterns in both natural and altered landscapes can differ for an endangered species of tortoise -use individual-based simulation models that examine different hypotheses of tortoise movement -in parameterizing the model an inverse approach was used -study shows that in altered landscapes females move a lot more than males unlike in natural landscapes where they move in relatively equal proportions --implications of work show that single sex or single behavior state models can be inappropriate {\_}{\_}{\_}{\_} -use several summary statistics to determine if a particular parameter combination made sense -inverse pattern-orientated modeling approach (POM, Wiegand 2004, Grimm 2005, Hartig 2011) -tests 4 different movement models: random walk, correlated random walk, homing behavior, and habitat dependent random walk -he has observed turtle movements through active tracking every 2-3 hours each week. So in his modeling attempts he simply samples the turtles in the model every 2-3 hours each week as well so he can accurately compare the model measurements to the observed data (distance traveled, home range, and so forth) {\_}{\_}{\_} -are able to show that some movement models cannot match according the pattern-orientated modeling if certain parameters (i.e. home range) was not included -could also determine which models shared different parameter combinations -find that home behavior was the most relevant when simulating tortoise movement *or else the model cannot predict actually movement patterns very well (parametric combinations are rejected) -intensive land use is found to have a strong impact on the movement and behavior of these animals -also showed large differences between the sexes in altered environment (a.k.a females move more in these altered landscapes)- shows that there may actually be more connectivity in fragmented landscapes which is a bit counter-intuitive -show that the variability among males and females could suggest the memory plays an important role in the movements of these animals --this behavior has seldom been integrated in modeling of real biological systems}, author = {Anad{\'{o}}n, J.D. and Wiegand, T. and Gim{\'{e}}nez, A.}, journal = {Ecosphere}, keywords = {movement,turtle}, number = {7}, pages = {64}, title = {{Individual-based movement models reveals sex-biased effects of landscape fragmentation on animal movement}}, volume = {3}, year = {2012} } @article{Neubauer2013, abstract = {Recovery of overexploited marine populations has been slow, and most remain below target biomass levels. A key question is whether this is due to insufficient reductions in harvest rates or the erosion of population resilience. Using a global meta-analysis of overfished stocks, we find that resilience of those stocks subjected to moderate levels of overfishing is enhanced, not compromised, offering the possibility of swift recovery. However, prolonged intense overexploitation, especially for collapsed stocks, not only delays rebuilding but also substantially increases the uncertainty in recovery times, despite predictable influences of fishing and life history. Timely and decisive reductions in harvest rates could mitigate this uncertainty. Instead, current harvest and low biomass levels render recovery improbable for the majority of the world's depleted stocks.}, annote = {-study evaluates drivers of slow growth for recovering fish stocks {\_}{\_}{\_} -currently theoretical models predict overfished stocks should be able to bounce back quickly but data from the field suggests that is not happening -this study looked at others contributors to the recovery process: life history, exploration history, and other drivers {\_}{\_}{\_} -moderate levels of overexplotation before depletion seem to make populations more resilient and shorten recovery times -{\textgreater} this is caused by adaptations in life history traits -examples can include: --maturation schedules }, author = {Neubauer, Phillip and Jensen, Olaf P and Hutchings, Jeffrey A and Baum, Julia K}, doi = {10.1126/science.1230441}, journal = {Science}, keywords = {fisheries}, pages = {347--349}, title = {{Resilience and Recovery of Overexploited Marine Populations}}, volume = {340}, year = {2013} } @article{Hanski1991, abstract = {This paper outlines a conceptual and theoretical framework for single-species metapopulation dynamics based on the Levins model and its variants. The significance of the following factors to metapopulation dynamics are explored: evolutionary changes in colonization ability; habitat patch size and isolation; compensatory effects between colonization and extinction rates; the effect of immigration on local dynamics (the rescue effect); and heterogeneity among habitat patches. The rescue effect may lead to alternative stable equilibria in metapopulation dynamics. Heterogeneity among habitat patches may give rise to a bimodal equilibrium distribution of the fraction of patches occupied in an assemblage of species (the core-satellite distribution). A new model of incidence functions is described, which allows one to estimate species' colonization and extinction rates on islands colonized from mainland. Four distinct kinds of stochasticity affecting metapopulation dynamics are discussed with examples. The concluding section describes four possible scenarios of metapopulation extinction.}, annote = {Review paper of Levins' model and spinoff models -explains additions that can be made to Levins' model to make it more biologically realistic -explains compensatory mechanisms like patch isolation and size -describes incidence functions that depict the prob. of occurrence of a species on patches to depend on island area -addition of local dynamics --also details idea that colonization/extinction depends on average pop. size -details different types of stochasticity and their effects on metapop. persistence}, author = {Hanski, Ilkka}, journal = {Biological Journal of the Linnean Society}, keywords = {dispersal,metapopulation,theoretical ecology}, pages = {17--38}, title = {{Single-species metapopulation dynamics: concepts, models and observations}}, volume = {42}, year = {1991} } @article{Ricard2011, abstract = {Meta-analyses of stock assessments can provide novel insight into marine population dynamics and the status of fished species, but the world's main stock assessment database (the Myers Stock-Recruitment Database) is now outdated. To facilitate new analyses, we developed a new database, the RAM Legacy Stock Assessment Database, for commercially exploited marine fishes and invertebrates. Time series of total biomass, spawner biomass, recruits, fishing mortality and catch/landings form the core of the database. Assessments were assembled from 21 national and international management agencies for a total of 331 stocks (295 fish stocks representing 46 families and 36 invertebrate stocks representing 12 families), including nine of the world's 10 largest fisheries. Stock assessments were available from 27 large marine ecosystems, the Caspian Sea and four High Seas regions, and include the Atlantic, Pacific, Indian, Arctic and Antarctic Oceans. Most assessments came from the USA, Europe, Canada, New Zealand and Australia. Assessed marine stocks represent a small proportion of harvested fish taxa (16{\%}), and an even smaller proportion of marine fish biodiversity (1{\%}), but provide high-quality data for intensively studied stocks. The database provides new insight into the status of exploited populations: 58{\%} of stocks with reference points (n = 214) were estimated to be below the biomass resulting in maximum sustainable yield (BMSY) and 30{\%} had exploitation levels above the exploitation rate resulting in maximum sustainable yield (UMSY). We anticipate that the database will facilitate new research in population dynamics and fishery management, and we encourage further data contributions from stock assessment scientists.}, annote = {-RAM legacy database is essentially an updated version of the Myers Stock-Recruitment Database -contains commercially exploited marine fish and inverts -the core of the database consists of time series of total biomass, spawner biomass, recruits, fishing mortality and catch or landings -pulls in data from many national and inter national groups {\_}{\_}{\_} -the original database, the Stock-Recruitment Database was developed by Myers and others in the mid 90's --containing good time series data of stock and recruitment, mortality rates, but biological reference points were pretty much absent --database was shown to advance fisheries in a number of ways 1) relate recruitment to spawning stick size 2) depensation in stock-recruitment relationships 3) discover patterns in annual reproductive rates 4) density dependence in juvenile mortality rates (see Myers 2001, Munto 2008) 5) develop Bayesian priors 6) examine collapse and recovery of exploited stocks (Hilborn 1997, Hutchings 2000, 2001) -database is now out of date, doesn't contain biological reference points RAM Legacy Stock Database, first stock assessment database to: 1) use formal relational database structure 2) more often updated 3) geographic locations, type of assessment model, original data for different stocks worldwide 4) includes biological reference points and stock-specific life history parameters {\_}{\_}{\_} Database core (output of population dynamics models, except total catch): -vert and invert populations with time series of spawning stock biomass, total biomass, recruits, total catch/landings, and fishing mortality -also BRPs, life history information -geographic and taxonomic information for each stock Structure: -PostgreSQL relationeel database system -several data quality tests were performed for each stock -each stock is assigned to taxonomic and ecosystem groups as well as linked to other databases {\_}{\_}{\_}{\_} Results: -331 stock assessments for 295 marine fish stocks and 36 invertebrate stocks -147 marine fish species and 16 invertebrate species -represents 16 percent of harvested fish species and 1 percent of all fish species -very number of stocks to include different variables -most time series data was on average over 30 years ({\~{}}1966-2007) -break data stock information by country and area -huge discrepancy by country fishery information -most stocks used catch-at-age/length models, virtual population analyses, and biomass dynamics models -mostly MSY reference points -show large number of overexploited stocks -show density kernel maps for exploration rate vs. biomass {\_}{\_}{\_}{\_} Discussion: -112 more stocks than previous database -hard to do large meta analyses with biased data in regards to geographic and taxonomic concerns -discuss need to use historical, thus baseline, data -58 percent of stocks were below B{\_}MSY -discuss currents states of specific countries --New Zealand appears to be doing well in management efforts -Pacific RFMOs appear to be doing better than the Atlantic {\_}{\_}{\_}{\_} Applications so far (see citations): -comparative analyses of fisheries status -mean trophic level as biodiversity indicator -relationship between catch and stock assessment data -relationship between life history traits and stocks propensity to collapse Caveats: -model estimates, not raw data -reference points can be iffy Future development: -updated stock information -freshwater and anadromous stocks -management action timelines }, author = {Ricard, Daniel and Minto, C{\'{o}}il{\'{i}}n and Jensen, Olaf P and Baum, Julia K}, doi = {10.1111/j.1467-2979.2011.00435.x}, journal = {Fish and Fisheries}, keywords = {extinction,fisheries,statistics}, title = {{Examining the knowledge base and status of commercially exploited marine species with the RAM Legacy Stock Assessment Database}}, year = {2011} } @article{Simpfendorfer1993, abstract = {At least eight species of sharks of the families Carcharhinidae and Sphyrnidae use Cleveland Bay in northern Australia as a communal nursery area. Carcharhinus dussumieri, C. fitzroyensis, C. limbatus and C. tilstoni use the bay as a seasonal primary nursery, with juveniles occurring in it for only a few months each year immediately after birth. Alternatively, Carcharhinus sorrah, Rhizoprionodon acutus and R. taylori use the bay as a year-round primary and secondary nursery, with juveniles remaining in it up to the size at maturity. Adult R. taylori also persist in the bay, a behavioural pattern possibly explained by their small maximum size. While present immediately after birth the type of utilisation pattern displayed by Sphyrna lewini could not be clarified in this study. Although diets of these species in the bay are similar, there is probably little direct competition for food due to the highly productive habitats in the bay supporting an abundance of food resources. The highest numbers of juveniles occur when prey species are the most abundant, and when temporal separation of some seasonally-occurring species of sharks in effect.}, annote = {{\textless}m:note{\textgreater}10.1007/BF00005200{\textless}/m:note{\textgreater}}, author = {Simpfendorfer, Colin A and Milward, Norman E}, issn = {0378-1909}, journal = {Environmental Biology of Fishes}, keywords = {nursery site,shark}, number = {4}, pages = {337--345}, publisher = {Springer Netherlands}, title = {{Utilisation of a tropical bay as a nursery area by sharks of the families Carcharhinidae and Sphyrnidae}}, url = {http://dx.doi.org/10.1007/BF00005200}, volume = {37}, year = {1993} } @article{Ward-Paige2012, abstract = {Many elasmobranchs have experienced strong population declines, which have been largely attributed to the direct and indirect effects of exploitation. Recently, however, live elasmobranchs are being increasingly valued for their role in marine ecosystems, dive tourism and intrinsic worth. Thus, management plans have been implemented to slow and ultimately reverse negative trends, including shark-specific (e.g. anti-finning laws) to ecosystem-based (e.g. no-take marine reserves) strategies. Yet it is unclear how successful these measures are, or will be, given the degree of depletion and slow recovery potential of most elasmobranchs. Here, current understanding of elasmobranch pop- ulation recoveries is reviewed. The potential and realized extent of population increases, including rates of increase, timelines and drivers are evaluated. Across 40 increasing populations, only 25{\%} were attributed to decreased anthropogenic mortality, while the majority was attributed to predation release. It is also shown that even low exploitation rates (2--6{\%} per year) can halt or reverse positive population trends in six populations currently managed under recovery plans. Management mea- sures that help restore elasmobranch populations include enforcement or near-zero fishing mortality, protection of critical habitats, monitoring and education. These measures are highlighted in a case study from the south-eastern U.S.A., where some evidence of recovery is seen in Pristis pectinata, Galeocerdo cuvier and Sphyrna lewini populations. It is concluded that recovery of elasmobranchs is certainly possible but requires time and a combination of strong and dedicated management actions to be successful.}, annote = {-REVIEW- lots of good citations for future reading -review paper that examines if elasmobranch recovery is possible and in what situations different management schemes can and have been successful -give a number of examples of populations that are increasing {\_}{\_}{\_}{\_} -examine 40 species that are showing population increasing from various databases --18 of which are sharks --most of these increases are seen in smaller elasmobranchs which argues their recoveries are more attributed to predator releases --25 percent of increases are attributed at least in part to management efforts -calculate rates of increase only after low point following with an assumption of exponential growth in order to compare between multiple populations and species -find that species with good management plans can only recovery with very low mortality rates, explain how even small increases in mortality can be detrimental -discuss conservation options for elasmobranchs --Restricting fishing mortality --Shark-finning prohibitions --Shark sanctuaries --Habitat restoration --Species-specific conservation (67 species listed as endangered)- doesn't seem to work well --Raising awareness and education {\_}{\_}{\_}{\_} -give positive effects of management in southeastern united states with increases in populations of P. pectinata, S. lewini and G. cuvier -}, author = {Ward-Paige, C A and Keith, D M and Worm, B and Lotze, H K}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Ward-Paige et al. - 2012 - Recovery potential and conservation options for elasmobranchs.pdf:pdf}, journal = {Journal of Fish Biology}, keywords = {fisheries,review,shark}, pages = {1844--1869}, title = {{Recovery potential and conservation options for elasmobranchs}}, volume = {80}, year = {2012} } @article{Lewison2004, abstract = {Hunting by humans played a major role in extirpating terrestrial megafauna on several continents and mega- faunal loss continues today in both terrestrial and marine ecosystems. Recent declines of large marine vertebrates that are of little or no commercial value, such as sea turtles, seabirds and marine mammals, have focused attention on the ecological impacts of incidental take, or bycatch, in global fisheries. In spite of the recognition of the problem of bycatch, few comprehen- sive assessments of its effects have been conducted. Many vulnerable species live in pelagic habitats, making surveys logistically complex and expensive. Bycatch data are sparse and our understanding of the demo- graphy of the affected populations is often rudimentary. These factors, combined with the large spatial scales that pelagic vertebrates and fishing fleets cover, make accurate and timely bycatch assessments difficult. Here, we review the current research that addresses these challenging questions in the face of uncertainty, analytical limitations and mounting conservation crises.}, annote = {Review paper-lots of good citations -paper examines research that has looked at the impact of fisheries on large non commercial species like sea turtles, seabirds and marine mammals -discuss difficulty of making accurate censuses and lack of knowledge of general demography of species affected {\_}{\_}{\_}{\_} -fisheries by catch is attributed to decline of loggerhead, leatherback, harbor porpoises, vaquita, striped dolphins, wandering albatross, and white-chinned petrel -discuss the common traits large megafauna often share: long lifespan, mature late, low reproductive output, and iteroparous reproduction (reproduce multiple times over long lifespan) -high rates of sub-adult and adult survival offset low fecundity -discuss elasticity analysis and how it can be used to predict sensitive age classes and stages -also show that these types of analysis can help fill in gaps in our knowledge about the demography of a species -discuss data limitations and uncertainty found in data collected and uncertainty that will always be present in dynamic marine systems }, author = {Lewison, Rebecca L and Crowder, Larry B and Read, Andrew J and Freeman, Sloan A}, journal = {TRENDS in Ecology and Evolution}, keywords = {demography,fisheries,megafauna,shark,turtle}, month = {nov}, number = {11}, pages = {598--604}, title = {{Understanding impacts of fisheries bycatch on marine megafauna}}, volume = {19}, year = {2004} } @article{Hisano2011, abstract = {Overfishing of sharks is a global concern, with increasing numbers of species threatened by overfishing. For many sharks, both catch rates and underwater visual surveys have been criticized as indices of abundance. In this context, estimation of population trends using individual demographic rates provides an important alternative means of assessing population status. However, such estimates involve uncertainties that must be appropriately characterized to credibly and effectively inform conservation efforts and management. Incorporating uncertainties into population assessment is especially important when key demographic rates are obtained via indirect methods, as is often the case for mortality rates of marine organisms subject to fishing. Here, focusing on two reef shark species on the Great Barrier Reef, Australia, we estimated natural and total mortality rates using several indirect methods, and determined the population growth rates resulting from each. We used bootstrapping to quantify the uncertainty associated with each estimate, and to evaluate the extent of agreement between estimates. Multiple models produced highly concordant natural and total mortality rates, and associated population growth rates, once the uncertainties associated with the individual estimates were taken into account. Consensus estimates of natural and total population growth across multiple models support the hypothesis that these species are declining rapidly due to fishing, in contrast to conclusions previously drawn from catch rate trends. Moreover, quantitative projections of abundance differences on fished versus unfished reefs, based on the population growth rate estimates, are comparable to those found in previous studies using underwater visual surveys. These findings appear to justify management actions to substantially reduce the fishing mortality of reef sharks. They also highlight the potential utility of rigorously characterizing uncertainty, and applying multiple assessment methods, to obtain robust estimates of population trends in species threatened by overfishing.}, annote = {-argue catch rates and visual surveys have been criticized so they want to use demographic rates to assess pop. status -want to incorporate uncertainty into mortality rates and such -estimate natural and fishing mortality using multiple methods-{\textgreater} then determined pop. growth rates -show the extent of the impact of fishing {\_}{\_}{\_}{\_}{\_}{\_} -a lot of sources and information from underwater visual surveys of sharks --alternative to this is using a population model --we would know most parameters except for that of mortality -=sometimes use catch-curve analysis?? -Study is to examine mortality and pop. growth rates for two species of reef sharks on the Great Barrier Reef {\_}{\_}{\_}{\_}{\_}{\_}{\_} used von Bertalanffy growth function for some of methods that required growth parameters Estimated mortality rates a number of ways: -Catch curves -Bevertin-Holt -Hoenig --this method using maximum age to estimate mortality rate, may work for our work ln(Z{\_}h) = a+b*ln(t{\_}max) --use method based on fish or cetaceans -More specifically methods are specific to natural mortality: Pauly- log equation relating mortality rate to VBGF parameters and environmental temperature Chen and Yuan Chen and Watanabe- relate age dependent mortality to longevity and length at time t ---may also be useful in our model Jensen They also needed to estimate growth rates -they implement Leslie matrices with annual rates of survival and fecundities -looked to see if different mortality methods differed significantly {\_}{\_}{\_}{\_} mortality rates ranged from 0.19 to 0.23 per year natural mortality ranged from 0.04 to 0.17 per year -populations are declining- so they looked at other parameters like maximum age to see what that would have to be to make the population viable -also looked at pop. growth rate when no fishing was present- potential there}, author = {HIsano, Mizue and Connolly, Sean R and Robbins, William D}, journal = {PLoSONE}, keywords = {population model,shark}, month = {sep}, title = {{Population Growth Rates of Reef Sharks with and without Fishing on the Great Barrier Reef: Robust Estimation with Multiple Models}}, year = {2011} } @article{Newman2007, abstract = {Mangrove and nearshore seagrass macrofaunal communities were concurrently sampled in two areas of contrasting primary productivity (North Sound: low; South Bimini: high) off Bimini, Bahamas. Over 200,000 individuals, comprising 175 spe- cies, were identified from catches of block nets, seines, and trawls between March 2000 and March 2003. The Index of Relative Importance (IRI), which is typically used for dietary analysis and combines percentage weight, abundance and occur- rence, was applied to catch data to enable easy spatial and temporal variations in community composition. Cluster-analysis revealed distinct mangrove and seagrass communities, with Morisita's index indicating a greater degree of spatial and tempo- ral homogeneity in the North Sound. Catch diversity and biomass were significantly greater in the mangroves than over seagrass in both locations, and highest off South Bimini. Low productivity, faunal diversity, and abundance in the North Sound were probably due to extreme abiotic variables. Juveniles of most species were present in mangroves and seagrass beds around Bimini, and therefore the protection of man- groves in the Bahamas should be an issue of immediate concern.}, author = {Newman, Steven P and Handy, Richard D and Gruber, Samuel H}, journal = {Bulletin of Marine Science}, keywords = {bimini,environmental stochasticity,shark}, number = {3}, pages = {529--553}, title = {{Spatial and Temporal Variations in Mangrove and Seagrass Faunal Communities at Bimini, Bahamas}}, volume = {80}, year = {2007} } @article{Jaramillo-Legorreta2007, annote = {-discuss three questions remaining related to vaquita conservation and offer answers for each of these questions -estimate only 150 vaquita remain in 2007 --they found this out through extrapolation of 567 animals in 1997 -use 50 animals as minimum number needed for any type of conservation to be possible --only two years left until the pop. size would reach this number -make estimates of how much money would need to be spent on surveys to simply identify a 10 percent per year decline in the population size -detected the 4 percent expected increase with annual surveys would take 25 years and 17 million dollars -going by decades 4 million would be spent and 51 years would be needed -find equal difficulties with by catch surveys in the three fishing villages -suggest the most important task is to remove entangling nets and buy out fishermen }, author = {Jaramillo-Legorreta, Armando and Rojas-Brancho, Lorenzo and Jr., Robert L Brownell and Read, Andrew J and Reeves, Randall R and Ralls, Katherine and Taylor, Barbara L}, journal = {Conservation Biology}, keywords = {extinction,review,vaquita}, number = {6}, pages = {1653--1655}, title = {{Saving the Vaquita: Immediate Action, Not More Data}}, volume = {21}, year = {2007} } @article{Mills1999, abstract = {Matrix population models have entered the mainstream of conservation biology, with analysis of proportional sensitivities (elasticity analysis) of demographic rates becoming important components of conservation decision making. We identify areas where management applications using elasticity analysis potentially conflict with the mathematical basis of the technique, and we use a hypothetical example and three real data sets (Prairie Chicken [Tympanuchus cupido], desert tortoise [Gopherus agassizii],and killer whale [Orcinus orca]) to evaluate the extent to which conservation recommendations based on elasticities might be misleading. First, changes in one demographic rate can change the qualitative ranking of the elasticity val- ues calculated from a population matrix, a result that dampens enthusiasm for ranking conservation actions based solely on which rates have the highest elasticity values. Second, although elasticities often provide accurate predictions of future changes in population growth rate under management perturbations that are large or that affect more than one rate concurrently, concordance frequently fails when different rates vary by different amounts. In particular, when vital rates change to their high or low values observed in nature, predictions offuture growth rate based on elasticities of a mean matrix can be misleading, even predicting population increase when the population growth rate actually declines following a perturbation. Elasticity measures will continue to be useful tools for applied ecologists, but they should be interpreted with consider- able care. We suggest that studies using analytical elasticity analysis explicitly consider the range of variation possible for different rates and that simulation methods are a useful tool to this end.}, annote = {-study looks at problems of elasticity analysis that can occur when trying to make conservation and management decisions -Two issues: --changes in one demographic rate can significantly alter the ranking of importance of different components of the transition matrix --when different rates vary by different amounts, predictions are often not accurate -suggest that elasticity analyses be examined in whole ranges of parameter values of interest {\_}{\_}{\_} -advocate for examining particular vital rates that underlie the different components of a given matrix element --use chain rule to determine contribution of given vital rate -use LTRE (life table response experiment) approach to overcome problems related to the range of variation that can occur in different rates --can create very different results in measurements like growth rate --suggest that to apply LTRE to nonlinear systems is best done through simulations -unequal ranges of variation also poise a problem in these types of models- can predict wildly different measures for lambda -find that if changes are in fact equal for different vital rates than the population can indeed endure large proportional changes in vital rates (this is not biologically likely)}, author = {Mills, L Scott and Doak, Daniel F and Wisdom, Michael J}, journal = {Conservation Biology}, keywords = {conservation,elasticity,matrices,population model}, number = {4}, pages = {815--829}, title = {{Reliability of Conservation Actions Based on Elasticity Analysis of Matrix Models}}, volume = {13}, year = {1999} } @article{Hilborn2012, abstract = {Abstract. This paper reviews the changes in quanti- tative marine fisheries management between 1985 and 2010. The two primary areas where quantitative methods have been employed are in the assessment of stock size and exploitation rates, and in the design and evaluation of harvest strategies. In 1985, some areas had well established assessment programs in place, and the assessment methods have been relatively stable over the 25 years in question. In other places, the evolution of methods has been much more dramatic, and where there were either no assessments performed or early virtual pop- ulation analysis (VPA) was done using mainly catch-at-age data, complex statistical models using maximum likelihood or Bayesian statistics are now common. Harvest strategies have generally evolved even more. In 1985, most harvest strategies were based on fixed exploitation rates from yield-per-recruit analyses. By 2010, most agencies had adopted harvest strate- gies that specifically reduced exploitation rates as abundance dropped below the biomass that will produce maximum sus- tainable yield. Simulation testing of these harvest strategies has become an integral part of their design, often using the uncertainty from the assessments to bound the robustness tri- als for the harvest strategy. Two major areas of new quantita- tive methods are (i) spatially explicit models that can be used for marine spatial planning, and (ii) in ecosystem models to evaluate ecosystem wide impacts of fishing. }, annote = {-review paper discusses the changes in fisheries management in regards to quantitative techniques from 1985-2010 (also look at Quinn 2003) -states that most methods are looking at stock size/exploitation rates and in evaluating harvest strategies **use this in shark paper -most strategies in 1985 focused on yield per recruit where as most now look a maximum sustainable yield -says future methods will include spatial modeling and whole ecosystem models {\_}{\_}{\_}{\_}{\_} -in 2010 many countries and organizations have developed a management structure i) annual data collection ii) assessment process using population dynamics to examine data collected iii) harvest rules from assessment process iv) monitoring of those rules -stock assessments either use statistical catch-at-age or -length (SCA/SCL) or virtual population analysis (VPA) --SCA is useful because it can utilize so many different types of data -discuss importance of evolving tag technologies -in 1985 reducing and controlling fishing primary focused on technical abilities where as quotas and shares are more prominent now {\_}{\_}{\_}{\_}{\_} -first example is the US salmon, pollock, and ocean perch fisheries --salmon management focuses on constant number of fish spawning as opposed to harvest rates like other fisheries --little has changed in methods used, just improving how uncertainty is quantified -Bering Sea polluck is largest US fishery TAC- actual hard total allowable catches {\_}{\_}{\_}{\_}{\_} -Pacific halibut --monitored by IPHS since 1923 -now use SCA models for assessments {\_}{\_}{\_}{\_} -Northern cod in Canada -aimed at keeping a harvest rate at 20{\%} -total collapse and moratorium in 1992- no sign of recovery till mid 2000's {\_}{\_}{\_}{\_} -New Zealand hoki and rock lobster -use analysis methods only to evaluate robustness of decision making {\_}{\_}{\_} -North sea ground fish -assessment methods have changed little but management system has changed considerably --used to try and simply hold stocks at constant level but this still led to a decline{\{}{\ldots}{\}}now have quotas {\_}{\_}{\_}{\_}{\_} -Australian fisheries -in 1985 there was very little data collected and few management techniques-changed a lot since then -school and gummy sharks are an important fishery --use same harvest strategy for sharks as they do other fish (SCA) {\_}{\_}{\_}{\_}{\_} -Bluefin tuna (Thunnus thynnus)- focusing on southern bluefin fishery by Japan and Australia --multi country agreement on catch limits for different countries but has no formal harvest strategies in place -the Atlantic bluefin tuna was listed as threatened for extinction by CITES in 2010 --ICCAT simply set limits for each country based on VPA in 1985 --a new VPA model is now used with the FMSY strategy employed {\_}{\_}{\_}{\_}{\_}{\_} -Chilean jack mackerel --huge fishery but still has no formal harvest strategy in place {\_}{\_}{\_}{\_}{\_} -Antarctic fisheries -largest fishery is Krill with a formal harvest strategy of maintaining 75{\%} of original population level -also discusses sub antarctic fisheries like the Patagonian tooth fish {\_}{\_}{\_}{\_} -discusses how a shift of who is producing new fishery techniques- used to be N. Atlantic but is down dominated by Pacific Canada and the United States -says VPA methods only work if good catch data is available and exploration rates are high -a lot of development in harvest strategies has occurred recently too {\_}{\_}{\_}{\_}}, author = {Hilborn, Ray}, journal = {Natural Resource Modeling}, keywords = {fisheries,review,shark}, month = {feb}, number = {1}, pages = {122--144}, title = {{The Evolution of Quantitative Marine Fisheries Management 1985-2010}}, volume = {25}, year = {2012} } @article{Senko2013, abstract = {Marine megafauna such as seabirds, marine mammals and sea turtles are subject to high mortality from incidental capture or bycatch in fisheries. Recent research suggests that fishing effort is increasing worldwide, highlighting the need to evalu- ate strategies intended to reduce marine megafauna bycatch. Here, we use three focal species (i.e. leatherback turtle $\backslash$emph{\{}Dermochelys coriacea{\}}, black-footed albatross $\backslash$emph{\{}Phoebastria nigripes{\}} and vaquita porpoise $\backslash$emph{\{}Phocoena sinus{\}}) as case studies to compare management outcomes of four bycatch mitigation measures: time--area closures, individual bycatch limits, gear modifications and buy-outs. Time--area closures were used for leatherbacks and vaquitas with limited effectiveness, although timing, size and enforcement influenced their efficacy. Individual bycatch limits were employed for leatherbacks in one fishery, sometimes simulta- neously with gear modifications and closures. Gear modifications consistently reduced bycatch of leatherbacks and black-footed albatross and showed strong promise for vaquitas. True buy-outs were only used for vaquitas and were costly, most fishers were unwilling to be bought out, and it is unclear if they reduced bycatch. Our review suggests that gear modifications were the most widely used and generally most promising technique for these species, although management outcomes of each strategy depended largely on the species--fishery interaction, fishery characteristics and socioeconomic context. Based on lessons learned from our case studies, we outline when and where a particular approach may be most effective, provide recommendations for improving each strategy and highlight priorities for future research.}, author = {Senko, Jesse and White, Easton R and Heppell, Selina S and Gerber, Leah R}, doi = {10.1111/acv.12051}, journal = {Animal Conservation}, keywords = {extinction,reserve,review}, number = {1}, title = {{Comparing bycatch mitigation strategies for vulnerable marine megafauna}}, volume = {1}, year = {2014} } @article{Krause2009, abstract = {Abstract Network analysis has a long history in the mathematical and social sciences and the aim of this introduction is to provide a brief overview of the potential that it holds for the study of animal behaviour. One of the most attractive features of the network paradigm is that it provides a single conceptual framework with which we can study the social organisation of animals at all levels (individual, dyad, group, population) and for all types of interaction (aggressive, cooperative, sexual etc.). Graphical tools allow a visual inspection of networks which often helps inspire ideas for testable hypotheses. Network analysis itself provides a multitude of novel statistical tools that can be used to characterise social patterns in animal populations. Among the important insights that networks have facilitated is that indirect social connections matter. Interactions between individuals generate a social environ- ment at the population level which in turn selects for behavioural strategies at the individual level. A social network is often a perfect means by which to represent heterogeneous relationships in a population. Probing the biological drivers for these heterogeneities, often as a function of time, forms the basis of many of the current uses of network analysis in the behavioural sciences. This special issue on social networks brings together a diverse group of practitioners whose study systems range from social insects over reptiles to birds, cetaceans, ungulates and primates in order to illustrate the wide-ranging applications of network analysis.}, annote = {REVIEW -review paper documents tools of network analysis and how it can be useful in animal behavioral studies {\_}{\_}{\_} -network analysis allows researchers to study individual behaviors and how that influences populations as a whole and how it affects the fitness of the individual -this paper focuses more on how animals as 'nodes' interact with each other via 'edges' -discusses game theory relevance as behaviors of individuals affect population consequences which in turn affects fitness of individuals displaying behaviors (Maynard Smith 1982) --early game theory models allowed individuals to mix and interact freely, where as in animal populations there is a more structured social organization that forms -give plenty of interesting examples of applications: --spider monkeys where adult females were identified as the core of the social structure --baboons vary in social organization depending on season --cluster analysis to identify groups in populations --looking for evidence of "unshared consensus decisions" in bottle nose dolphins --information transfer or disease transmission --even examples of studies that are now able to make solid predications -often there are differences in how network analysis is applied to vertebrate vs. invertebrate systems }, author = {Krause, Jens and Lusseau, David and James, Richard}, journal = {Behav. Ecol. Sociobiol.}, keywords = {movement,network analysis,shark}, pages = {967--973}, title = {{Animal social networks: an introduction}}, volume = {63}, year = {2009} } @article{Kinney2009, abstract = {Abstract Concern over declining shark populations has led to an intense interest in their conservation and management. Due to the difficulties involved in managing adult sharks, focus has been placed on young juvenile and neonate age classes that inhabit discrete inshore nursery areas. However, past confusion over what qualifies as a nursery habitat has led to the identification of vast coastal areas as nurseries, making conservation unfeasible. With the establishment of more discerning criteria for nursery area identification such concerns have been somewhat alleviated, but while effort has been put into defining, identifying, mapping, and in some cases protecting nursery areas, little attention has been paid to the practical value of nurseries for the recovery of exploited shark pop- ulations. Often neonate and young juveniles are considered the most critical age classes in terms of population stability/recovery, but evidence is mount- ing that suggests life stages outside the nursery may be more important in this regard. While nursery area protection should remain a component in shark management strategies it will be critical to link early life stage conservation with management strategies that encompass older individuals residing outside nurseries if effective management is to be achieved.}, annote = {-notice a lot of effort going to early age classes and nursery sites in regards to management efforts -want to establish criteria for what constitutes an actual nursery site -link importance of older age classes as well in conservation efforts {\_}{\_}{\_}{\_} -want to examine the importance of nursery sites in recovery and management efforts -review only focuses on species that utilize nursery sites and authors point this out -points out Gallucci 2006 found that survival of juveniles near maturity was proportionally more important than any other age class, Simpfendorfer 1999 also found this{\{}{\ldots}{\}}..this size of juveniles would not be protected in a nursery area -Cortes 1999, Heppell 1999, and Simpfendorfer 1999 all found neonate survival to have little influence on population growth rate -points out issues with stage-based modeling approaches -explain australian shark fishery that protected nursery sites but still had a population crash -Simpfendorfer 1999 showed another fishery that fished only young age classes could be sustainable -Prince 2005 found same results as Simpfendorfer 1999 --this type of fishery is called a gauntlet-style fishery --relates to the stock-recruitment curve (relationship between number of recruits and number of breeders) --Simpfendorfer also points out that nursery sites need to be evaluated individually if this type of fishing is to be used because of different nursery sites producing different growth rates --Application to N. brevirostris-- -Frisk et al. 2005 found that juveniles approaching maturity had the highest elasticity values -Dibattista et al. 2007 found a maximum residency time in nurseries to be 4 years -evidence that nursery site protection alone would not protect these larger juveniles -find similar older juvenile results in other animals: loggerhead turtles, C. plumbs, C. caretta, other turtle species {\_}{\_}{\_}{\_}{\_} **Management efforts simply need to be species and population specific}, author = {Kinney, Michael John and Simpfendorfer, Colin A}, journal = {Conservation Letters}, keywords = {nursery site,shark}, pages = {53--60}, title = {{Reassessing the value of nursery areas to shark conservation and management}}, volume = {2}, year = {2009} } @article{Jensen1996, abstract = {Abstract: The Beverton and Holt invariants are three special relations among life history parameters: Mxm = C1, M/K = C2, and L(xm)/Linf = C3, where M is the instantaneous natural mortality rate per individual, xm is age at maturity, K is the von Bertalanffy growth coefficient, L(xm) is length at maturity, Linf is asymptotic length, and C1, C2, and C3 are constants. In this study the Beverton and Holt invariants were obtained from maximization of the fecundity function that optimizes the trade-off between survival and fecundity; this approach applies conventional fishery models and provides estimates of the constants C1, C2, and C3. These estimates can be compared with the estimates obtained by regression of 1/M on xm, M on K, and L(xm) on Linf across species and across populations within species. The values of the constants obtained from regression across species agree closely with the theoretical values of the constants. In fishery assessments, natural mortality is often approximated using growth parameters, and the analyses reported here indicate that the relations are not just statistical relations, but rather result from fundamental ecological relations among the parameters.}, annote = {-Jensen is studying the Beverton and Holt relationships between mortality and age at maturity, growth constant, length at maturity, and the asymptotic length -wanted to maximize the fecundity function while looking at balance between survival and fecundity -shows that relationships between all these variables are of actual ecological significance and not just statistical significance {\_}{\_}{\_} -find useful relationships between variables that maximize certain quantities like fecundity -finds relationships between mortality and age at maturity and between mortality and K (growth rate of fish)}, author = {Jensen, A L}, journal = {Canadian Journal of Fisheries and Aquatic Sciences}, keywords = {growth,mortality,shark}, pages = {820--822}, title = {{Beverton and Holt life history invariants result from optimal trade-off of reproduction and survival}}, volume = {53}, year = {1996} } @article{Sundelof2006, abstract = {The most commonly used birth function in two-sex demographic models is the harmonic mean birth function. This function treats all individuals of one sex as identical, i.e., stage specific fecundity is not taken into account. In the analysis presented here, the harmonic mean birth function is developed to incorporate size and sex specific fecundities. This structured birth function is compared with the harmonic mean birth function using both a hypothetical population and data for populations of the limpet Patella vulgata. A general expression to calculate the threshold value where the unstructured and the structured birth functions coincide is also provided. Using the structured birth function resulted in changes in population dynamics, growth rate, proportion of males and reproductive output. In conclusion, the choice of birth function is important due to its effects on the deterministic population characteristics, which in turn may have consequences for the managements of endangered or vulnerable species.}, annote = {-analyze use of different birth functions in stage-structured, two sex models -compare to actual data of the limpet (Patella vulgate) -need to use their style of modeling if their is size-dependent fecundity!!! {\_}{\_}{\_} -constructed model where two different classes of males and females were constructed. All four of which had different fecundity outputs -choice of birth function does change the dynamics in the model significantly -structured birth functions performs better than the unstructured one --elasticity changes dramatically-{\textgreater} affects management strategies }, author = {Sundel{\"{o}}f, Andreas and {\AA}berg, Per}, journal = {Ecological Modelling}, keywords = {birth,demography,sea lions,two-sex}, pages = {787--795}, title = {{Birth Functions in stage structured two-sex models}}, volume = {193}, year = {2006} } @article{PeacockSmith1997, abstract = {Abstract Habitat fragmentation is becoming increasing- ly common, yet, the effect of habitat spatial structure on population dynamics remains undetermined for most species. Populations of a single species found in frag- mented and nonfragmented habitat present a rare oppor- tunity to examine the effect of habitat spatial structure on population dynamics. This study investigates the impact of highly fragmented habitat on dispersal patterns, mat- ing behavior, and genetic variation in a pika (Ochotona princeps) population with a mainland-island spatial structure. Juvenile dispersal patterns in fragmented habi- tat revealed that individuals tended to disperse to neigh- boring habitat patches. However, within-patch band- sharing scores from multilocus DNA fingerprints did not differ from what would be expected if individuals were assorting randomly among habitat patches each year. Multiple, short-distance dispersal targets for juveniles and occasional long-distance dispersal events suggest that habitat fragmentation on this scale has not resulted in restricted dispersal and a genetically subdivided popu- lation. Although pikas tended to mate with the closest available partner, DNA fingerprinting band-sharing scores between mated pairs were consistent with a ran- dom mating hypothesis. Random mating in this popula- tion appears to be an incidental effect of dispersal in a fragmented habitat. This pattern is distinct from that found in nonfragmented habitat (large talus patches) where mating was non-random and consistent with mat- ing between individuals of intermediate relatedness. DNA fingerprinting data revealed within-species varia- tion in the mating habits of the pika directly attributable to habitat spatial structure.}, annote = {-studying how fragmentation affects dispersal, mating behavior, and genetic variation -from the genetics she believes that the pikas are actually assertive random mating -therefore there is no restricted dispersal and no subdivision in the pop. -15 juveniles and i adult dispersed during study (max distance for juvenile was a 1000m) *-all high peak dispersers settled on high peak -one pika settled on patch after investigated 4 prior -continually hits on the point that dispersal in fragmented habitat has made a pattern of random mating. (Can't this just be gene flow and now animal flow??) -believes that high peak is a mainland because of dispersal and population genetic data, also with extinction of the South (Why has the south only now gone extinct?) -believes spatial structure there is different mate selection within species(found through DNA fingerprinting) **Also says that movements between smaller islands and from smaller islands to high peak make no difference in the persistence of a mainland-island metapopulation -she does say these types of movement patterns are an important part to occupancy rates and the genetic variation -may be lots of gene flow but this would imply its a small population at pipet tarn}, author = {Peacock, Mary M and Smith, Andrew T}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Peacock, Smith - 1997 - The effect of habitat fragmentation on dispersal patterns, mating behavior, and genetic variation in a pika (emp.pdf:pdf}, journal = {Oecologia}, keywords = {bodie,dispersal,genetics,pika}, pages = {524--533}, title = {{The effect of habitat fragmentation on dispersal patterns, mating behavior, and genetic variation in a pika ($\backslash$emph{\{}Ochotona princeps{\}}) metapopulation}}, volume = {112}, year = {1997} } @article{Rojas-Bracho2006, annote = {-vaquita is most endangered marine small cetacean- 1997 survey says there are 567 left -primary mortality is caused by gill nets for fish and shrimp -reserve started in 2005 for vaquitas specifically {\_}{\_}{\_} -very small range in northern golf of mexico near colorado river delta, few sightings outside this area -believe that species has always been rare with extreme loss of genetic diversity -with rarity they are hard to find and study in general Life history: -live to 20 years, mature between 3 and 6 yeas, seasonal breeders (early March) -feed on variety of species (ethic teleosts and squids) {\_}{\_}FISHERIES{\_}{\_} -from 1930's to 70's gill net fishing for totoaba killed a lot of vaquita but this fishery was closed in 1975 --experimental fishery in 1990s revealed upwards of 59 vaquitas may have been killed per year -many still get caught in nets of shrimp, sharks, rays, mackerel, chano, and totoaba (give number for 1985 to 1992) at least 128 killed -capture occurs in trawl, drift and gill nets -only good study done on vaquita by catch was D'Agrosa, Lennert-Cody and Vidal 2000 --at least 39 killed per year between 1993 and 1995 -Table 3 lists catch of all fisheries from 1987 to 2004 in mexico** -they are not sure if trawling has direct or indirect effects on vaquitas but acknowledge it must have negative effects on sea floor communities -Rojas-Brancho and Taylor (1999) concluded that by catch is fisheries is biggest threat to vaquita -even after the reserve was designated and gill net size modifications occurred a number of vaquitas were still taken in fisheries -in 1997 a committee was formed and set a goal of simply observing an increasing trend in the population, even this simple goal has turned out to be difficult --set a number of also goals and concerns including gear modifications (very little work has actually seen done on this issue) and closures and social economics (little has been done) -reserve has fallen short of goals and compensation of loss of wealth in areas still has done materialized after 11 years --162 vessels fish in reserve each year --much of the vaquita distribution (40{\%}) is also outside of this reserve -Program for Protection of Vaquita was established in 2005- 1 million dollars assigned for implementation- many fallbacks still to this plan, even if well executed -have discussed other gear modifications like pingers (argued not to work for this population) -social-economic concerns have still not been addressed and both government and fishermen find the reserve to be of "environmental imperialism" }, author = {Rojas-Brancho, Lorenzo and Reeves, Randall R and Jaramillo-Legorreta, Armando}, journal = {Mammal Review}, keywords = {review,vaquita}, number = {3}, pages = {179--216}, title = {{Conservation of the vaquita $\backslash$emph{\{}Phocoena sinus{\}}}}, volume = {36}, year = {2006} } @article{Guttridge2010, abstract = {Group behaviours are widespread among fish but comparatively little is known about the interactions between free-ranging individuals and how these might change across different spatio-temporal scales. This is largely due to the difficulty of observing wild fish groups directly underwater over long enough time periods to quantify group structure and individual associations. Here we describe the use of a novel technology, an animal-borne acoustic proximity receiver that records close-spatial associations between free-ranging fish by detection of acoustic signals emitted from transmitters on other individuals. Validation trials, held within enclosures in the natural environment, on juvenile lemon sharks Negaprion brevirostris fitted with external receivers and transmitters, showed receivers logged interactions between individuals regularly when sharks were within 4 m (,4 body lengths) of each other, but rarely when at 10 m distance. A field trial lasting 17 days with 5 juvenile lemon sharks implanted with proximity receivers showed one receiver successfully recorded association data, demonstrating this shark associated with 9 other juvenile lemon sharks on 128 occasions. This study describes the use of acoustic underwater proximity receivers to quantify interactions among wild sharks, setting the scene for new advances in understanding the social behaviours of marine animals.}, annote = {-describe study on wild juvenile lemons fitted with transmitters for whenever they come in contact with one another -this study mainly discusses how these research techniques can actually be used in studies {\_}{\_}{\_}{\_} -use pen trials to determine what length of proximity to another shark can be considered an actual social interaction in the wild -compared these interactions to SUR locations to determine location of sharks -only a small chunk of the data could actually be used but showed where and when sharks may be aggregated and for durations of the interactions }, author = {Guttridge, Tristan L and Gruber, Samuel H and Krause, Jens and Sims, David W}, journal = {PLoSONE}, keywords = {bimini,movement,shark}, month = {feb}, number = {2}, pages = {1--8}, title = {{Novel Acoustic Technology for Studying Free-Ranging Shark Social Behavior by Recording Individuals' Interactions}}, volume = {5}, year = {2010} } @article{Dennis2001, abstract = {A defining hypothesis of theoretical ecology during the past century has been that population fluctuations might largely be explained by relatively low-dimensional, nonlinear ecological interactions, provided such interactions could be correctly identified and modeled. The realization in recent decades that such nonlinear interactions might result in chaos and other exotic dynamic behaviors has been exciting but tantalizing, in that attributing the fluctuations of a particular real population to the complex dynamics of a particular mathematical model has proved to be an elusive goal. We experimentally tested a model-predicted sequence of transitions (bifurcations) in the dynamic behavior of a population from stable equilibria to quasiperiodic and periodic cycles to chaos to three-cycles using cultures of the flour beetle Tribolium. The predictions arose from a system of difference equations (the LPA model) describing the nonlinear life-stage interactions, predominantly cannibalism. We built a stochastic version of the model incorporating demographic variability and obtained conditional least-squares estimates for the model parameters. We generated 2000 ``bootstrapped data sets'' with a time-series bootstrap technique, and for each set we reestimated the model parameters. The resulting 2000 bootstrapped parameter vectors were used to obtain confidence intervals for the model parameters and estimated distributions of the Liapunov exponents for the deterministic portion (the skeleton) of the model as well as for the full stochastic model. Frequency distributions of estimated dynamic behaviors of the skeleton at each experimental treatment were produced. For one treatment, over 83{\%} of the bootstrapped parameter estimates corresponded to chaotic attractors, and the remainder of the estimates yielded high-period cycles. The low-dimensional skeleton accounted for at least 90{\%} of the variability in the population abundances and accurately described the responses of populations to experimental demographic manipulations, including treatments for which the predicted dynamic behavior was chaos. Demographic stochasticity described the remaining noise quite well. We conclude that the fluctuations of experimental flour beetle populations are explained largely by known nonlinear forces involving cannibalistic-stage interactions. Claims of dynamic behavior such as periodic cycles or chaos must be accompanied by a consideration of the reliability of the estimated parameters and a realization that the population fluctuations are a blend of deterministic forces and stochastic events }, author = {Dennis, Brian and Desharnais, Robert A and Cushing, J M and Henson, Shandelle M and Costantino, R F}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Dennis et al. - 2001 - Estimating chaos and complex dynamics in an insect population.pdf:pdf}, journal = {Ecological Monographs}, keywords = {Tribolium,cannibalism,chaos,demography,population model}, number = {2}, pages = {277--303}, title = {{Estimating chaos and complex dynamics in an insect population}}, volume = {71}, year = {2001} } @article{White1967, annote = {REVIEW -discusses role of world views in the ecological crisis --in particular the Judeo-Christian viewpoint 1) human modification/destruction of nature 2) significance of world views 3) technology and alienation argument 4) Christian-culpability for the environmental crisis 5) the anthropocentrism argument}, author = {{Lynn White}, Jr.}, journal = {Science}, keywords = {extinction,review}, number = {3767}, pages = {1203--1207}, title = {{The Historical Roots of Our Ecologic Crisis}}, volume = {155}, year = {1967} } @phdthesis{Franks2007, address = {Philadelphia, Pennsylvania}, author = {Franks, Bryan R}, keywords = {bimini,demography,juvenile,spatial}, school = {Drexel University}, title = {{The spatial ecology and resource selection of juvenile lemon sharks ($\backslash$emph{\{}Negaprion brevirostris{\}}) in their primary nursery areas}}, type = {Ph.D. diss.}, year = {2007} } @article{Jacoby2011, abstract = {There are widespread records of grouping behaviour in both adult and juvenile sharks and rays (Class Chondrichthyes, Subclass Elasmobranchii). Yet despite burgeoning descriptions of these events, many of the proximate and ultimate causes of group living in these top predators remain elusive. Given the documented negative anthropogenic effects on many shark populations globally, there is an increasing need to understand how behaviourally mediated grouping influences population distributions and abundance, and the role this plays in exacerbating vulnerability to fishing mortality. Here, we analyse group living in elasmobranchs: we describe our current understanding of the patterns, mechanisms and functions of both aggrega- tion (where grouping is not driven by social mechanisms) and social grouping (where grouping is influenced by social interaction) and discuss some of the current methods used to study social behaviour in this taxa. In particular, social preferences in elasmobranchs have received relatively little attention. We propose that the study of shark aggregations may benefit from a more fine-scale analytical approach offered by detailed exploration of social interactions using social network analysis. Better understanding of the frequency and longevity of social relations, in conjunction with current long-term data on habitat use and site philopatry, will likely serve for a more informed approach to coastal and pelagic elasmobranch conservation initiatives.}, annote = {REVIEW -paper examines literature on group living in elasmobranchs, differences between aggregations and social grouping, and current methods -want to use network theory to acquire a deeper understanding of social interactions -knowledge of aggression and schooling behavior is important for population estimates and management strategies {\_}{\_}{\_} -many costs and benefits of social groups that can have implications on fitness in animals -review looks to compare what is known in teleost fishes compared to elasmobranchs and future work that needs to be done {\_}{\_}{\_} -point out that aggregation behavior has been much more frequently studied than social grouping, though aggregation could be an important prerequisite to social grouping (i.e. in S. lewini) -aggregations have been attribute to environmental factors, geographic locations, time of year, high prey abundance -still a lack of behavioral or social reasons for such aggregation behaviors -discussing Guttridge 2011, first real study on social structures of wild shark populations -discussing Klimley's work on S. lewini in detail -there has been a number of studies in the teleost literature to examine the reason for social behavior: anti predatory functions, reduced energetic demand, information transfer, decision making {\_}{\_}{\_}{\_} -discuss applications of network analysis to social behaviors in sharks on the basis that different animals in the group differ in the abilities to affect group behavior through varying dyadic interactions -discuss different graphical procedures and statistical tests on the nxn association matrix that is generated to produce said graphs -can examine if an individual's phenotypic properties affects its role in the group (although see Croft 2011 for potential statistical problems) {\_}{\_}{\_}{\_} -schooling behavior has the obvious cost to the exposure of overfishing pressures -need to account for these behavioral mechanisms when examining fishing pressures on different species and populations of sharks -grouping behaviors also have impact on ecotourism activities }, author = {Jacoby, David M P and Croft, Darren P and Sims, David W}, journal = {Fish and Fisheries}, keywords = {behavior,network analysis,review,shark}, title = {{Social behaviour in sharks and rays: analysis, patterns and implications for conservation}}, volume = {doi: 10.11}, year = {2011} } @article{Thorson1973, annote = {{\textless}m:note{\textgreater}see paper for more detailed analysis {\textless}/m:note{\textgreater}}, author = {Thorson, Thomas B and Cowan, C Michael and Watson, Donald E}, journal = {Physiological Zoology}, keywords = {osmoregulation,shark}, month = {jan}, number = {1}, pages = {29--42}, title = {{Body Fluid Solutes of Juveniles and Adults of the Euryhaline Bull Shark $\backslash$textit{\{}Carcharhinus leucas{\}} from Freshwater and Saltwater Environments}}, volume = {46}, year = {1973} } @incollection{HazenCrowder2012, annote = {{\textless}m:note{\textgreater}-begin with a brief introduction to all the sub-disciplines of fisheries ecology{\textless}m:linebreak/{\textgreater} {\textless}/m:note{\textgreater}}, author = {Hazen, Elliot Lee and Crowder, Larry B}, chapter = {Fisheries }, edition = {1}, editor = {Hastings, Alan and Gross, Louis J}, keywords = {fisheries,theoretical}, pages = {280--287}, publisher = {University of California Press}, title = {{Encyclopedia of Theoretical Ecology}}, volume = {4}, year = {2012} } @article{Fujiwara2001, abstract = {Northern right whales (Eubalaena glacialis) were formerly abun- dant in the northwestern Atlantic, but by 1900 they had been hunted to near extinction. After the end of commercial whaling the population was thought to be recovering slowly; however, evidence indicates that it has been declining since about 1990 (ref. 1). There are now fewer than 300 individuals, and the species may already be functionally extinct2,3 owing to demographic stochasticity or the dif{\{}$\backslash$textregistered{\}}culty of females locating mates in the vast Atlantic Ocean (Allee effect4). Using a data set containing over 10,000 sightings of photographically identi{\{}$\backslash$textregistered{\}}ed individuals we estimated trends in right whale demographic parameters since 1980. Here we construct, using these estimates, matrix population models allowing us to analyse the causes of right whale imperil- ment. Mortality has increased, especially among mother whales, causing declines in population growth rate, life expectancy and the mean lifetime number of reproductive events between the period 1980$\backslash$pm1995. Increased mortality of mother whales can explain the declining population size, suggesting that the popula- tion is not doomed to extinction as a result of the Allee effect. An analysis of extinction time shows that demographic stochasticity has only a small effect, but preventing the deaths of only two female right whales per year would increase the population growth rate to replacement level.}, annote = {-use photographic records of Northern right whales to assess population recovery and find that the population is still declining opposing what was previously thought -use matrix population models to examine cause of declines -find population growth when demographic parameters are independent of time but a decline when these parameters actually change and are a function of time between 1980 and 1995 -find that a decline in the survivability of mothers caused most of decline seen in time period --still not sure what has caused the drip in survival of mothers -also calculate a probability distribution of times to extinction and find a mean time to extinction to be 208 years -find that simply preventing two female deaths per year would allow population growth rate to be above 1 }, author = {Fujiwara, Masami and Caswell, Hal}, journal = {NatureFujiwara, M., {\&} Caswell, H. (2001). Demography of the endangered North Atlantic right whale. Nature, 414, 537–541.}, keywords = {demography,extinction,megafauna}, month = {nov}, pages = {537--541}, title = {{Demography of the endangered North Atlantic right whale}}, volume = {414}, year = {2001} } @article{Baum2003, abstract = {Overexploitation threatens the future of many large vertebrates. In the ocean, tunas and sea turtles are current conservation concerns because of this intense pressure. The status of most shark species, in contrast, remains uncertain. Using the largest data set in the Northwest Atlantic, we show rapid large declines in large coastal and oceanic shark populations. Scalloped hammerhead, white, and thresher sharks are each estimated to have declined by over 75{\%} in the past 15 years. Closed-area models highlight priority areas for shark conservation, and the need to consider effort reallocation and site selection if marine reserves are to benefit multiple threatened species.}, annote = {-use NW Atlantic data set to show large declines in both coastal and pelagic shark populations -in particular scalloped hammerhead, white, and thresher sharks have all declined by at least 75 percent in the past 15 years -use closed-area models to highlight certain areas as priority for shark conservation {\_}{\_}{\_}{\_}{\_} -use longline (swordfish and tuna) data logbooks from 1986 to 2000 -8 species recorded in total for shark -issues occur with missing values or zeros in the logbooks, develop technique using generalized linear models to overcome this problem --assumes that if positive number of sharks is recorded then it is in fact approx. correct -life history traits show expected pattern as to which shark species would have larger declines -suggest many of these species are at risk for extirpation {\_}{\_}{\_}{\_} -use models to assess success marine reserves would have -show that merely displacing fishing to somewhere else can also have negative effects -then show which areas would protect which species and to what degree -need to place these reserves carefully for them to work }, author = {Baum, Julia K and Myers, Ransom A and Kehler, Daniel G and Worm, Boris and Harley, Shelton J and Doherty, Penny A}, journal = {Science}, keywords = {fisheries,population model,shark}, month = {jan}, pages = {389--392}, title = {{Collapse and conservation of shark populations in the Northwest Atlantic}}, volume = {299}, year = {2003} } @article{Mora2009, abstract = {Ongoing declines in production of the world's fisheries may have serious ecological and socioeconomic consequences. As a result, a number of international efforts have sought to improve management and prevent overexploitation, while helping to maintain biodiversity and a sustainable food supply. Although these initiatives have received broad acceptance, the extent to which corrective measures have been implemented and are effective remains largely unknown. We used a survey approach, validated with empirical data, and enquiries to over 13,000 fisheries experts (of which 1,188 responded) to assess the current effectiveness of fisheries management regimes worldwide; for each of those regimes, we also calculated the probable sustainability of reported catches to determine how management affects fisheries sustainability. Our survey shows that 7{\%} of all coastal states undergo rigorous scientific assessment for the generation of management policies, 1.4{\%} also have a participatory and transparent processes to convert scientific recommendations into policy, and 0.95{\%} also provide for robust mechanisms to ensure the compliance with regulations; none is also free of the effects of excess fishing capacity, subsidies, or access to foreign fishing. A comparison of fisheries management attributes with the sustainability of reported fisheries catches indicated that the conversion of scientific advice into policy, through a participatory and transparent process, is at the core of achieving fisheries sustainability, regardless of other attributes of the fisheries. Our results illustrate the great vulnerability of the world's fisheries and the urgent need to meet well-identified guidelines for sustainable management; they also provide a baseline against which future changes can be quantified.}, annote = {-evaluate effectiveness of implemented management schemes --use survey and empirical data -show that core of management is the ability to convert scientific understanding into policy {\_}{\_}{\_}{\_} -found that 97 percent of the world's 209 EEZs have someone who has a relevant scientific background for making fisheries recommendations -only 7 percent of these use holistic models as basis for recommendations -find that a majority of places feel pressure to use risky management schemes (91 percent) -upwards of 83 percent of EEZs face corruption or bribery -wealthy countries have capability to include scientific measures typically -still contend that one of the toughest issues is implementation and regulation of given strategies --17 percent have proper enforcement of policies -*find that scientific robustness did not influence the sustainability of fisheries, instead socioeconomic costs and different pressures may prevent the science from being enacted properly --give example of Mediterranean Bluefin Tuna}, author = {Mora, Camilo and Myers, Ransom A and Coll, Marta and Libralato, Simone and Pitcher, Tony J and Sumaila, Rashid U and Zeller, Dirk and Watson, Reg and Gaston, Kevin J and Worm, Boris}, doi = {10.1371/journal.pbio.1000131}, journal = {PLoS Biol}, keywords = {fisheries}, number = {6}, pages = {e1000131}, title = {{Management Effectiveness of the World's Marine Fisheries}}, volume = {7}, year = {2009} } @article{Benton1995, annote = {-Are investigating to see if biology of red deer to see if relaxing the assumption of short-term variation in environment does not affect mortality/fecundity -21 years of population data in Scotland -Growth rates were estimated using "Tuljapurkar's small noise approximation" What is this? -Enviromental stochastic causes only slight reduction in predicted growth rate, ----these do not affect the deer's fitness -life histories favored by selection are affected by environmental variance }, author = {Benton, T G and Grant, A and Clutton-Brock, T H}, journal = {Evolutionary Ecology}, keywords = {environmental stochasticity,ungulate}, pages = {559--574}, title = {{Does environmental stochasticity matter? Analysis of red deer life-histories on Rum}}, volume = {9}, year = {1995} } @article{Moilanen1998, abstract = {-use incidence function model which includes spatial dynamics -is able to predict patch occupancy consistent with Bodie -show South is relatively unstable {\_}{\_}{\_}{\_} -Incident function model has been used in butterfly population studies (Hanski 1994) --takes into account many metapopulation features: --spatial structure is explicit --colonization of patches is distance dependent --large patches send out more migrants --extinction probability depends on patch size --effect of immigration on extinction risk --all model needs is patch occupancy data -estimate model parameters based on the idea that patch occupancy is a quasi-stationary state -accounts for rescue effect -incidence function model is the Levins model but it includes variation in patch sizes and colonization as function of distance {\_}{\_}{\_}{\_} -were able to see the expected differences in patch occupancy in the north, middle, and south -also ran the three networks separately to get a better of picture of what was going on -also looked at probability that South would go extinct in 19 years --found regional stochasticty drove this **found that removing mainland patch did make the north more unstable, north was still more persistent than the south -middle network is very unstable -colonization potential was used to rank the patches in order of decreasing importance- removing the four most important patches made the entire metapopulation unstable!! COOL! -found that they did not need any environmental change to cause the decline in pikas!!}, annote = {have environmental noise for all models nut see table two they remove the mainland and find the north is less stable but is still better of than the south -find that four really important patches are present (3 in north, one in south) -look at patch occupanyc- dont deal with local dynamics on individual patches I like the wording for simulations, "Dynamis in the entire patch network were simulated, but the proportion of occupied patches was recorded seperately for the different parts of the network... -- THey ran the simulations again, but seperated the parts of the metapopulation They require regional stochasticity for the south to go extinct Cicular reasoning by compairing observed turnover vs predicated turnover}, author = {Moilanen, Atte and Smith, Andrew T and Hanski, Ilkka}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Moilanen, Smith, Hanski - 1998 - Long-Term Dynamics in a Metapopulation of the American Pika.pdf:pdf}, journal = {The American Naturalist}, keywords = {metapopulation,pika}, month = {oct}, number = {4}, title = {{Long-Term Dynamics in a Metapopulation of the American Pika}}, volume = {152}, year = {1998} } @article{Hoenig1990, annote = {-discuss ideas as to sharks being k selected species unlike most teleosts -answer how to affects conservation and management -use leslie matrix to address questions of population increase and to estimate parameters {\_}{\_}{\_}{\_}{\_} -discuss a lot about why animals may have evolved given k selected traits -discuss aspects of important life-history traits -even reference Carey 1971 discussing elevated body temps of some shark species -very little work done on estimates of prey consumed by shark pops -Gruber 1988 discusses restricted movement of juvenile lemons -say max age of 21 for lemon sharks based on Brown and Gruber 1988 -discuss estimated natural mortality of shark species -discuss r/K selection theory in depth -discuss work by MacArthur, Lotka, and Volterra --here talk about logistic growth model in depth {\_}{\_}{\_}{\_} -use a set of leslie matrices with 26 age classes to examine adult mortality -set mortality rate for all 1+ age classes to be 15 percent and for it to range between 39-60 {\%} for newborns}, author = {Hoenig, John M and Gruber, Samuel H}, journal = {NOAA Technical Report}, keywords = {bimini,demography,shark}, pages = {1--16}, title = {{Life-History Patterns in the Elasmobranchs: Implications for Fisheries Managment}}, volume = {90}, year = {1990} } @article{SmithWeston1990, annote = {-paper discusses in detail Ochotona princeps natural history and different subspecies -seperation of O. collaris in the north and O. princeps in the South is most likely due to the Wisconsinan glaciation -pikas used to be grassland habituates and did not become talus dwelling till 7500 years ago -warming caused pika habitats to become split on to only suitable mountain tops -2 molts per year -in both sexes the rectal canal and urogenital canal are only separated by a septum that ends 2-3mm from the single "pseudocloacal" opening -American pikas of both sexes have procaine gland complex in lower cheek used for "cheek rubbing" typically during the active season -two types of feces: "hard brown round pellet and soft black shiny string" -many lagomorphs reinvest caecal pellets immediately (coprophagy) while pikas may do this but may also store them for later -do not hibernate -has high body temp around 40.1 degrees -gestation of 30 days with two litters per year -less than 10 percent of weaned animals can be attributed to the second litter -average litter size is between 2.34 and 3.68 (high elevation around 3-3.1) -have ability to reabsorb young or entire litters -can reach adult size within 3 months of birth -at 3-4 weeks of age weening occurs -show age can be calculated accurately following von Bertalanffy growth curve -mortality of 37 to 46 percent is standard throughout their range -max age of 7, age specific mortality greatest at year 1,5,6,7 -territory size is 55 percent of home range size -at Bodie hay piles are 21.8 meters apart -predators may include Coyote (Canis latrans), long tail weasels (Mustela frenata), shorttail weasels (Mustela erminea), pine matens (Mates americana) -typically active for 30 percent of daylight hours --seen doing surveillance, haying/feeding, vocalizing, territory establishment/maintenance -short (warn of predators and ward off conspecifics) and long calls -appears that only 25 percent of juveniles may try and disperse (Smith 87, Brandt 85, Tapper 73) -Genetics --68 chromosomes}, author = {Smith, Andrew T and Weston, Marla L}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Smith, Weston - 1990 - emph{\{}Ochotona princeps{\}}.pdf:pdf}, journal = {Mammalian Species}, keywords = {pika}, pages = {392--397}, title = {{$\backslash$emph{\{}Ochotona princeps{\}}}}, volume = {352}, year = {1990} } @article{Maunder2004, abstract = {The primary indices of abundance for many of the world's most valuable species (e.g. tunas) and vulnerable species (e.g. sharks) are based on catch and effort data collected from commercial and recreational fishers. These indices can, however, be misleading because changes over time in catch rates can occur because of factors other than changes in abundance. Catch-effort standardization is used to attempt to remove the impact of these factors. This paper reviews the current state of the art in the methods for standardizing catch and effort data. It outlines the major estimation approaches being applied, the methods for dealing with zero observations, how to identify and select appropriate explanatory variables, and how standardized catch rate data can be used when conducting stock assessments.}, annote = {REVIEW -paper reviews work on how to standardize catch data and how to remove potential conflicting factors {\_}{\_}{\_} -have general relationship C=qEN -C (catch), q (fraction of abundance that is captured by one unit of effort), E (fishing effort), N (density) -with this you cannot simply use raw catch or CPUE numbers because factors change in time and space -Beverton and Holt (1957) originally looked at stock assessments but could not deal with time or location very easily -now it is more common to fit statistical models to catch data sets {\_}{\_}{\_} "GLMs are defined by a statistical distribution of some response variable (like catch rate) and how some linear combination of different explanatory variables relate to an expected value of the response variable" -can incorporate nonlinearity by the link function, interaction terms, and transforming explanatory variables Steps: 1) choose response variable 2) select appropriate sampling distribution for the response variable 3) choose link function for appropriate distribution 4) select set of explanatory variables (one must be "year" of course) Generalized additive models- characterized as an extension to GLMs but has a non-parametric aspect Generalized linear mixed models extend GLM by letting some parameters in the linear predictor to be treated as random variables instead {\_}{\_}{\_}{\_} Number of issues arise when estimated abundance -dealing with zero catches (can happen for many reasons and all have different solutions) --the delta approach deals with this problem explicitly -a number of distributions can handle zero values -however, if processes that lead to zero catches are not the same as non-zero catches, an inflated zero catch model is needed (simply a peace wise description of a given distribution)- versions exist of this for the Poisson and negative binomial Delta approaches: -essentially models probability of getting a zero catch in the first place and then the catch rate given the catch is in fact non zero (two combined sub models) --can utilize a number of distributions: log normal, gamma, Poisson, negative binomial {\_}{\_}{\_}{\_}{\_} -include explanatory variables only if they may impact catch ability --avoid including variables that are collinear (relate to each other in some way) -then using Akaike information criterion the best model can be selected AIC= -2 ln (l) + 2p l=likelihood function p=number of parameters n= number of observations -typically you also need to apply additional criteria (i.e. only if model reduces deviance- R{\^{}}2 is increased- by some given percentage)- this overcomes errors that occur with huge data sets -also have to identify significant interactions relationships between variables and there biological interpretations or hypotheses they generate {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} Additional notes: -model catch with poisson and use fishing effort as an offset or as an explanatory variable -avoid raising covariates to higher powers if you can help it -GAMS offer nonparametric approach -Use NB when data is dispersed -included other species in model may remove time trends in catch rate -because there are so many data points, AIC and BIC may select more complicated models-{\textgreater} should also look out adding variables affects deviance to reduce by a pre-defned percentage }, author = {Maunder, Mark N. and Punt, Andr{\'{e}} E.}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Maunder, Punt - 2004 - Standardizing catch and effort data a review of recent approaches.pdf:pdf}, journal = {Fisheries Research}, keywords = {fisheries,population model,review,shark}, pages = {141--159}, title = {{Standardizing catch and effort data: a review of recent approaches}}, volume = {70}, year = {2004} } @article{Knip2012, abstract = {Mortality plays a crucial role in the dynamics of all shark populations. However, our understanding of mor- tality and the factors that affect survival in wild populations remains limited, particularly for adult sharks. Long-term acoustic monitoring data were used to estimate mortality rates for juvenile pigeye (Carcharhi- nus amboinensis) and adult spottail (Carcharhinus sorrah) sharks within the same coastal area. {\{}{\ldots}{\}}{\{}{\ldots}{\}}{\{}{\ldots}{\}}.., despite the difference in species life stages. All monitored individuals were similar in body size, however, suggesting that size may play a greater role than age in the mortality rates for some shark species. High survivorship indicates that this coastal area provides a low mortality environment for both juvenile C. amboinensis and adult C. sorrah. Low mortality for these species is likely a reflection of low predation risk and sufficient prey resources. This, coupled with marine protected areas, may provide juvenile C. amboinensis and adult C. sorrah with similar opportunities and levels of protection. }, annote = {-used acoustic monitoring to estimate mortality rates for juvenile pigeye (larger species) and adult spottail (smaller shark) -find mortality rates to be low and little difference in mortality between species--this would seem to indicate that size and not age has a greater effect on mortality rates -attribute low rates to the coastal area in which the species live {\_}{\_}{\_}{\_} -discusses all the paper that have directly measured juvenile/neonate mortality rates {\_}{\_}{\_}{\_} -same study site Knip has discussed in other papers at Cleveland Bay, a series of acoustic receivers were positioned around study site in MPAs -could calculate natural, fishing, and total mortalities -also used six indirect methods to estimate lifetime mortality -use procedure from Kaplan-Meier survival estimates to figure out mortality rates in study -found rates of 0.11-0.13 for C. amboinensis and 0.08 for C. sorrah {\_}{\_}{\_}{\_} -results suggest MPA may do a good job at maintaining low mortality rates -interesting that size and not age may have greater effect on mortality rates -cites lemon sharks as having mortality rate between 0.35 and 0.75 from (Manire and Gruber 1993, Gruber et al. 2001, and de Freitas et al. 2009) -their juvenile death rates were more on par with juvenile bull sharks -field studies suggest mortality rates much lower than those estimated by indirect methods -majority of total mortality was in fact fishing mortality (70{\%})}, author = {Knip, Danielle M and Heupel, Michelle R and Simpfendorfer, Colin A}, journal = {Fisheries Research}, keywords = {mortality,shark}, pages = {184--189}, title = {{Mortality rates for two shark species occupying a shared coastal environment}}, volume = {125-126}, year = {2012} } @article{Hernandez-Matias2013, abstract = {Population viability analysis (PVA) has become a basic tool of current conservation practice. However, if not accounted for properly, the uncertainties inherent to PVA predictions can decrease the reliability of this type of analysis. In the present study, we performed a PVA of the whole western European population (France, Portugal, and Spain) of the endangered Bonelli's Eagle ($\backslash$emph{\{}Aquila fasciata{\}}), in which we thoroughly explored the consequences of uncertainty in population processes and parameters on PVA predictions. First, we estimated key vital rates (survival, fertility, recruitment, and dispersal rates) using monitoring, ringing, and bibliographic data from the period 1990--2009 from 12 populations found throughout the studied geographic range. Second, we evaluated the uncertainty about model structure (i.e., the assumed processes that govern individual fates and population dynamics) by comparing the observed growth rates of the studied populations with model predictions for the same period. Third, using the model structures suggested in the previous step, we assessed the viability of both the local populations and the overall population. Finally, we analyzed the effects of model and parameter uncertainty on PVA predictions. Our results strongly support the idea that all local populations in western Europe belong to a single, spatially structured population operating as a source-- sink system, whereby the populations in the south of the Iberian Peninsula act as sources and, thanks to dispersal, sustain all other local populations, which would otherwise decline. Predictions regarding population dynamics varied considerably, and models assuming more constrained dispersal predicted more pessimistic population trends than models assuming greater dispersal. Model predictions accounting for parameter uncertainty revealed a marked increase in the risk of population declines over the next 50 years. Sensitivity analyses indicated that adult and pre-adult survival are the chief vital rates regulating these populations, and thus, the conservation efforts aimed at improving these survival rates should be strengthened in order to guarantee the long-term viability of the European populations of this endangered species. Overall, the study provides a framework for the implementation of multi-site PVAs and highlights the importance of dispersal processes in shaping the population dynamics of long-lived birds distributed across heterogeneous landscapes.}, annote = {-study combines a number of techniques to conduct a PVA analysis on eagle populations in western Europe Methods This study examines a Bonelli's Eagle metapopulation in Eastern Europe. A number of sites have been well studied of the past twenty years (1990-2005). They utilize a number of techniques that are extremely relevant to our pika metapopulation work (ex. using specific dispersal kernels to allow eagles to disperse according to distance, birds only disperse once; they are also territorial). Have a five stage model with fledglings, juveniles, immature, subadult and adult (construct model based on age like my shark model). Parameter estimates are made from past studies and beta distributions were used to simulate survivals while a stretched beta distribution was used for productivities. Each site in model had a maximum number of possible breeding pairs (similar to pika model). Use a total of six different models that include various elements: closed or connected population, density dependence, shape of natal dispersal kernel, and the ability for birds to be able to disperse more than once. Population growth rate was used as a pattern to evaluate model success. The model ranking was determined by comparing the negative log likelihoods of each model. The study also identified conservation targets by changing vital rates and comparing patterns of sensitivity and elasticity. Results Means and standard errors were calculated for each parameter. The natal dispersal kernel was best fit with the exponential model (lambda=9.75 x 10{\^{}}-3). Their best model could explain 79 percent of the observed variance. The different populations were shown to be at high risk or no risk for quasi-extinction over the next 50 years. As expected, adult survival and pre-adult survival vital rates were the most important in terms of conservation targets. Overall, the population acted as a source-sink system. Discussion }, author = {Hern{\'{a}}ndez-Mart$\backslash$'ias, Antonio and Real, Joan and Mole{\'{o}}n, Marcos and Palma, Luis and S{\'{a}}nchez-Zapata, Jose Antonio and Pradel, Roger and Carrete, Martina and Gil-S{\'{a}}nchez, Jose Mar$\backslash$'ia and Beja, Pedro and Balbont$\backslash$'in, Javier and Vincent-Martin, Nicolas and Ravayrol, Alain and Ben$\backslash$'itez, Jose Ram{\'{o}}n and Arroyo, Bernardo and Fern{\'{a}}ndez, Carmelo and Ferreiro, Ernesto and Garc$\backslash$'ia, Javier}, doi = {http://dx.doi.org/10.1890/12-1248.1}, journal = {Ecological Monographs}, keywords = {PVA,dispersal,extinction,inverse modelling,metapopulation}, number = {2}, pages = {239--261}, title = {{From local monitoring to a broad-scale viability assessment: a case study for the Bonelli's Eagle in western Europe}}, volume = {83}, year = {2013} } @article{Hughes2011, abstract = {Conservation of marine resources is critical to the wellbeing of human communities. Coastal artisanal fishing communities are particularly reliant on marine resources for food and for their livelihoods. Management actions aimed at marine conservation may lead to unanticipated changes in human behavior that influence the ability of conservation programs to achieve their goals. We examine how marine conservation strategies may impact labor decisions that influence both the ecosystem and human livelihoods using simulation modeling. We consider two conservation strategies in the model: direct action through fisheries regulation enforcement, and indirect action through land conservation. Our results indicate that both strategies can increase the abundance of fish, and thus contribute to the maintenance of marine resources. However, our results also show that marine fisheries enforcement may negatively impact the livelihoods of human communities. Land conservation, on the other hand, potentially enhances the livelihood of the human populations. Thus, depending on management objectives, indirect or a combination of direct and indirect conservation strategies may be effective at achieving conservation and sustainability goals. These results highlight the importance of accounting for changes in human behavior resulting from management actions in conservation and management.}, annote = {-use simulations to determine if direct and indirect methods of conservation help or hinder both conservation efforts and the livelihoods of local human communities -find that land conservation can help marine fish and help locals -shows importance of modeling human aspects in decisions-making {\_}{\_}{\_} -discuss concerns in implementing conservation strategies that rely solely on the biology of a species -study side at Loreto Bay, Mexico- 80 percent of employment here is in fishing or tourism --focus on fishing and scuba diving and how it relates to the leopard grouper {\_}{\_}{\_} -increasing tourism draws locals away from fishing- has same effect as limiting fishing through management schemes }, author = {Hughes, Zachary D and Fenichel, Eli P and Gerber, Leah R}, doi = {10.1371/journal.pone.0023722}, journal = {PLoSONE}, keywords = {fisheries,megafauna,mexico,reserve}, number = {8}, pages = {e23722}, title = {{The Potential Impact of Labor Choices on the Efficacy of Marine Conservation Strategies}}, volume = {6}, year = {2011} } @techreport{WWF2010, annote = {-project tested industrial and artisanal versions of the RS-INP trawling prototype developed by the National Fisheries Institute of Mexico -showed effectiveness in GoC, operational and economic merits, and possibilities for widespread adoption {\_}{\_}{\_} -found that on the industrial side, the prototype reduced by catch:shrimp ration by 20-50 percent without reducing target catch rates -artisanal trawl prototype failed to produce any significant results in northern Gulf --however, the prototype did have a higher size selectivity of shrimp- more valuable}, author = {Aguilar-Ram{\'{i}}rez, Daniel and Rodr{\'{i}}quez-Valencia, Jos{\'{e}} Alejandro}, institution = {World Wildlife Fund}, keywords = {by catch,mexico,review,vaquita}, title = {{Reducing Bycatch with Better Technology in the Gulf of California Shrimp Fishery}}, type = {Technical and Financial Report}, year = {2010} } @article{Morzaria-Luna2012, abstract = {Background: Minimizing fishery bycatch threats might involve trade-offs between maintaining viable populations and economic benefits. Understanding these trade-offs can help managers reconcile conflicting goals. An example is a set of bycatch reduction measures for the Critically Endangered vaquita porpoise (Phocoena sinus), in the Northern Gulf of California, Mexico. The vaquita is an endemic species threatened with extinction by artisanal net bycatch within its limited range; in this area fisheries are the chief source of economic productivity. Methodology/Principal Findings: We analyze trade-offs between conservation of the vaquita and fisheries, using an end- to-end Atlantis ecosystem model for the Northern Gulf of California. Atlantis is a spatially-explicit model intended as a strategic tool to test alternative management strategies. We simulated increasingly restrictive fisheries regulations contained in the vaquita conservation plan: implementing progressively larger spatial management areas that exclude gillnets, shrimp driftnets and introduce a fishing gear that has no vaquita bycatch. We found that only the most extensive spatial management scenarios recovered the vaquita population above the threshold necessary to downlist the species from Critically Endangered. The scenario that excludes existing net gear from the 2008 area of vaquita distribution led to moderate decrease in net present value (US 42 million) relative to the best-performing scenario and a two-fold increase in the abundance of adult vaquita over the course of 30 years. Conclusions/Significance: Extended spatial management resulted in the highest recovery of the vaquita population. The economic cost of proposed management actions was unequally divided between fishing fleets; the loss of value from finfish gillnet fisheries was never recovered. Our analysis shows that managers will have to confront difficult trade-offs between management scenarios for vaquita conservation.}, annote = {-use an ecosystem base modeling approach (Atlantis) to evaluate ecological and socio-economic tradeoffs in vaquita conservation and artisnal fisheries -find that only the most extensive spatial management plan will improve the vaquita population to a high enough level -loss of US 42 million for this type of vaquita recovery over the course of 30 years {\_}{\_}{\_}{\_} -discuss rent out, switchouts and buyouts of fishermen in area -compare five different management plans over 30 years from 2008-2038 {\_}{\_}{\_}{\_} -find very different results for both vaquita pop size and fishery profits in the different management scenarios -find primary area management scheme to be best compromise between conservation and fisheries --however, costs are benefits are different amongst different fisheries }, author = {Morzaria-Luna, Hem Nalini and Ainsworth, Cameron H and Kaplan, Issac C and Levin, Phillip S and Fulton, Elizabeth A}, journal = {PLoSONE}, keywords = {fisheries,megafauna,vaquita}, number = {8}, pages = {1--11}, title = {{Exploring Trade-Offs between Fisheries and Conservation of the Vaquita Porpoise ($\backslash$emph{\{}Phocoena sinus{\}}) Using an Atlantis Ecosystem Model}}, volume = {7}, year = {2012} } @article{Bascompte2005, abstract = {The stability of ecological communities largely depends on the strength of interactions between predators and their prey. Here we show that these interaction strengths are structured nonran- domly in a large Caribbean marine food web. Specifically, the cooccurrence of strong interactions on two consecutive levels of food chains occurs less frequently than expected by chance. Even when they occur, these strongly interacting chains are accompa- nied by strong omnivory more often than expected by chance. By using a food web model, we show that these interaction strength combinations reduce the likelihood of trophic cascades after the overfishing of top predators. However, fishing selectively removes predators that are overrepresented in strongly interacting chains. Hence, the potential for strong community-wide effects remains a threat.}, annote = {-examine effects of the interaction strength of a predator-prey food web in the Caribbean -show that interactions are in fact non random- helps reduce risk of trophic cascades -however fishing selectively still has strong effects on the whole community {\_}{\_}{\_}{\_} -construct large food web from Caribbean ecosystem of 3,313 total interactions -define interaction strength of each of the interactions with a simple formula -they produced random replicates of the food web to determine if the interactions were truly non-random -use three types of functional responses in model}, author = {Bascompte, Jordi and Meli{\'{a}}n, Carlos J and Sala, Enric}, journal = {PNAS}, keywords = {fisheries,predation}, month = {apr}, number = {15}, pages = {5443--5447}, title = {{Interaction strength combinations and the overfishing of a marine food web}}, volume = {102}, year = {2005} } @article{Pikitch2005, abstract = {ABSTRACT: A 5 yr spring and summer survey (July 2000 to May 2004) of the elasmobranch fauna of Glover's Reef Marine Reserve, Belize, documents the use of this oceanic atoll by at least 12 elasmobranch species, including early life-stages of nurse sharks Ginglymostoma cirratum, Caribbean reef sharks Carcharhinus perezi, lemon sharks Negaprion brevirostris, and southern stingrays Dasyatis americana. Elasmobranch abundance was sampled in 3 atoll macrohabitats (deep lagoon, ocean reef, shallow lagoon) using standardized longlines. Total elasmobranch abundance did not change from year to year, but was significantly higher inside the lagoon than on the ocean reef outside the atoll. G. cirratum dominated both shallow and deep lagoon catches, with smaller individuals more prevalent in the shallow lagoon. C. perezi of all size classes dominated the ocean reef catches, but small juveniles of this species were also common in the deep lagoon. This species rarely utilized the shallow lagoon. A wide range of sizes of C. perezi and G. cirratum occupy Glover's Reef in spring and summer, with males maturing at 150 to 170 cm and 185 to 200 cm total length, respectively. The sex ratios of these species did not deviate from unity. A large juvenile Gal{\{}{\'{a}}{\}}pagos shark, C. galapagensis, was collected on the ocean reef, extending the range of this species into the Western Caribbean. Opportunistic surveys of fish markets on the Belize mainland revealed that inshore areas are utilized by early life-stages of sharks from the families Carcharhinidae (C. limbatus, N. brevirostris, Rhizoprionodon porosus) and Sphyrnidae (Sphyrna tiburo, S. lewini, S. mokarran).}, annote = {-surveys conducted over a couple of years at Glover's reef, Belize -very much structured by habitat (depth and reef type) -most catches were nurse sharks -12 total elasmobranch species caught -a number of juveniles from species use the reef -found it to be a possible nursery similar to florida and the bahamas -more and intensive and informed conservation is needed in the area}, author = {Pikitch, Ellen K and Chapman, Demian D and Babcock, Elizabeth A and Shivji, Mahmood S}, journal = {Marine Ecology Progress Series}, keywords = {habitat,population model,reserve,shark}, pages = {187--197}, title = {{Habitat use and demographic population structure of elasmobranchs at a Caribbean atoll (Glover's Reef, Belize)}}, volume = {302}, year = {2005} } @article{Lewison2011, abstract = {Minimizing fisheries bycatch, the incidental capture of non-target species, is a global environmental challenge. In many regions, bycatch of imperiled species is one of a number of issues that threatens species viability and impedes the development of sustainable fisheries. Effectively addressing bycatch of species of conservation concern and improving fisheries sustainability require cross-sectoral integration of information on the biological, socioeconomic, and political contexts of each fishery. Several gaps present simultaneous challenges, including: limited engagement with fisher communities, a lack of data, a need for more robust analyses of available data, and a need for coordinated governance from local to global scales. Here we present a framework to address fisheries bycatch that builds on established methods in community collaboration and engagement, field-based interviews, quantitative bycatch analyses, and ocean policy governance. Although these individual approaches to reduce bycatch are well established, there has yet to be a comprehensive application of an integrated approach. We review these essential approaches and present a broadly applicable model for their integration.}, annote = {Review -discuss current challenges of fisheries by catch management and create framework to integrate methods from different areas to solve this problem -show examples of community involvement, missing data, quantitative by catch research, role of governance, and an integrated framework {\_}{\_}{\_} -mostly focuses on examples from sea turtle and marine mammal literature -a lot of discussion regarding small scale fisheries management *important point of having international bodies on regulating by catch is that different countries regard different species or taxa as by catch of commercially important -continue to stress the need to integrate community, data collection, quantitative research and governance in management efforts}, author = {Lewison, R L and Soykan, C U and Cox, T and Peckham, H and Pilcher, N and LeBoeuf, N and McDonald, S and Moore, J and Safina, C and Crowder, L B}, journal = {Bulletin of Marine Science}, keywords = {fisheries,megafauna,turtle}, number = {2}, pages = {1--16}, title = {{Ingredients for Addressing the Challenges of Fisheries Bycatch}}, volume = {87}, year = {2011} } @article{Gutierrez2011, author = {Guti{\'{e}}rrez, Nicol{\'{a}}s L and Hilborn, Ray and Defeo, Omar}, journal = {Nature}, keywords = {fisheries}, pages = {386--389}, title = {{Leadership, social capital and incentive promote successful fisheries}}, volume = {470}, year = {2011} } @article{Morrissey1993, author = {Morrissey, John F and Gruber, Samuel H}, journal = {Copeia}, keywords = {bimini,habitat,nursery site,shark}, pages = {425--434}, title = {{Habitat selection of juvenile lemon shark $\backslash$emph{\{}Negaprion brevirostris{\}}}}, volume = {2}, year = {1993} } @article{Pauly1998, abstract = {The mean trophic level of the species drops reported in Food and Agricultural Organization global fisheries statistics declined from 1950 to 1994. This reflects a gradual transition in landings from ling-lived, high trophic level, piscivourous bottom fish toward short-lived, low trophic level invertebrates and planktivorous pelagic fish. This effects also found to be occurring in inland fisheries, is most pronounced in the Northern Hemisphere. Fishing down food webs (that is, at lower trophic levels) leaves at first to increasing catches, then to a phase transition associated with stagnating or declining catches, These results indicate the present exploitation patterns are unsustainable. }, annote = {-study examined data from FAO on global fisheries statistics from 1950 to 1994 -find that the mean number of species in each trophic level has been decreasing --indicates a switch from large long-lived species to low trophic level short-lived species "Fishing down food webs" {\_}{\_}{\_} -use two datasets: one generated from 60 studies on trophic levels of 220 species or groups of fish and global statistics of fisheries landings from FAO from 1950 to 1994 -in all areas observed decreases in mean trophic levels were found -discuss importance of a species in ecosystem and how their removal can cause major ecosystem problems--cascading effects--}, author = {Pauly, Daniel and Christensen, Villy and Dalsgaard, Johanne and Froese, Rainer and Jr., Francisco Torres}, journal = {Science}, keywords = {fisheries,megafauna,shark}, month = {feb}, number = {5352}, pages = {860--863}, title = {{Fishing Down Marine Food Webs}}, volume = {279}, year = {1998} } @article{Pauly2013, annote = {-Article is a comment and debate between Daniel Pauly and Hilborn {\&} Branch regarding the use of fish catch data to assess fisheries health Pauly's argument for use of catch data -most data (outside of developed fisheries nations) are just estimates of weight of fish caught -need to simply collect more data (fishing effort, economic value of catches, fishing costs) to compliment fish biomass caught -FAO data suggests most catches are dramatically underreported Counterpoints -amount of fish caught does not always reflect amount of fish present argue that using catch data makes public feel that fisheries management is what is failing -argue we must conduct proper scientific stock assessments -changes in taxonomy may also make predictions less accurate -argue that MPA's overlook success of many fisheries management schemes}, author = {Pauly, Daniel and Hilborn, Ray and Branch, Trevor A}, journal = {Nature}, keywords = {fisheries}, number = {7437}, pages = {303--306}, title = {{Does catch reflect abundance?}}, volume = {494}, year = {2013} } @article{Gedamke2007, abstract = {Abstract.---Leslie matrices and life tables are demographic models commonly used to evaluate the ability of specific elasmobranch life history strategies to sustain given levels and patterns of fishing pressure. These models are generally density independent and provide an instantaneous rate of population growth for a specified set of life history traits that correspond to a specific population size. Many investigators are using these models to compute rates of population growth that they claim are estimates of the maximum population growth rate (rintrinsic); they then use these estimates to compute purported estimates of maximum sustainable fishing mortality. However, neither a Leslie matrix nor a life table can be used to estimate rintrinsic without additional information, except in the special case where a severely depleted population is modeled. Only in a severely depleted population will competition for resources be at a minimum and both density-dependent compensation and the rate of population growth be at a maximum (i.e., at rintrinsic). The fundamental problem is to determine the life history parameters that would occur if the population were extremely depleted because extensive observations on extremely depleted populations are rare. In the absence of such data, rintrinsic can only be estimated from these types of density-independent models by extrapolating observed population growth rates toward zero population size. We illustrate the problems in, and describe methods for, estimating rintrinsic and present information on two species of elasmobranch: barndoor skate Dipturus laevis and lemon shark Negaprion brevirostris.}, annote = {-state that other studies have used leslie matrices and life tables incorrectly or interpret them incorrectly -specifically interested in r{\_}intrinsic and what it would mean if estimated -want to incorporate density dependent factors to make models more accurate -apply this to lemon sharks and the ban door skate {\_}{\_}{\_}{\_}{\_}{\_}{\_} -use classic Caswell matrix description Discuss a review of several topics: -r calculation and interpretation -use of leslie matrix -give description of how to estimate different parameters -how to rank species -advances in methodology {\_}{\_}{\_}{\_}{\_} -Apply to lemon sharks using empirical data for first year survival -State that lemon sharks have 12 pups every two years?? Where do they get this number? -are able to estimate range r{\_}intrinsic using bounded parameters {\_}{\_}{\_}{\_}{\_} -Also apply these models to the barn door skate because it is on the brink of extinction (they now know the empirical growth rate after fishing was stopped 15 years ago) -these are born at a large size so mortalities can be assumed equal over age classes {\_}{\_}{\_}{\_}{\_} }, author = {Gedamke, Todd and Hoenig, John M and Musick, John A and DuPaul, William D and Gruber, Samuel H}, journal = {North American Journal of Fisheries Management}, keywords = {bimini,demography,shark}, pages = {605--618}, title = {{Using Demographic Models to Determine Intrinsic Rate of Increase and Sustainable Fishing for Elasmobranchs: Pitfalls, Advances, and Applications}}, volume = {27}, year = {2007} } @article{MacArthur, author = {MacArthur, R H and Wilson, E O}, journal = {Princeton University Press, N.J.}, keywords = {biogeography}, title = {{The Theory of Island Biogeography}}, year = {1967} } @article{Kroon2000, abstract = {Abstract. Elasticity is a perturbation measurein matrixprojectionmodels that quan- tifies the proportionalchange in population growth rate as a function of a proportional changein a demographictransition(growth,survival,reproduction,etc.). Elasticitiesthus indicatethe relative "importance"of life cycle transitionsfor populationgrowthandmain- tenance.Inthispaper,we discusstheapplicationsof elasticityanalysis,andits extension, loop analysis, in life history studies and conservation.Elasticity can be interpretedas the relativecontributionof a demographicparameterto populationgrowthrate.Loop analysis reveals the underlyingpathway structureof the life cycle graph. The different kinds of results of the two analyses in studies of life histories are emphasized.Because elasticities quantifythe relative importanceof life cycle transitionsto populationgrowth rate, it is generally inferredthat managementshould focus on the transitionswith the largest elas- ticities. Suchpredictionsbasedon elasticities seemrobust,butwe do identifythreesituations where problems may arise. The mathematicalproperties and biological constraintsthat underlie these pitfalls are explained. Examples illustrate the additional informationthat needs to be takeninto accountfor a sensible use of elasticities in populationmanagement. We conclude by indicatingtopics that are in need of researc}, annote = {- paper is a review on how elasticities are used and the limitations of using them "Elasticity is a perturbation measure in matrix projection models that quantifies the proportional change in population growth rate as a function of a proportional change in demographic transition" -these can then be used to assess the relative importance and contribution of different life history transitions to population growth rate -using only the greatest elasticity to focus management efforts towards is not always the best idea {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -often important to determine how many age classes or stages are needed as it changes the value of elasticities --use a log linear analysis or use of algorithms designed to minimize error Basic analysis -continued multiplication of transition matrix will will allow population growth rate to converge and equals the dominant eigenvalue of the matrix -left eigenvector= stable reproductive distribution -right eigenvector = stable state distribution -a life cycle graph is simply a set of difference equations and can be solved using a z-transform - a z-transform explains the relative contribution of each life history path to the growth rate -elasticities= compare relative effects in lambda -sensitivities= quantify absolute effects on lambda -second derivatives of population growth rate measure the effects of changes in elasticity to other matrix elements {\_}{\_}{\_} examples: -in long lived species like trees self loops make up 97.5 percent of loop elasticity -these high levels of elasticities may not be good places to help a population but can show where it is most vulnerable -low growth rates in a population would have a better analysis through loop analysis instead of standard elasticity analysis }, author = {de Kroon, Hans and van Groenendael, Jan and Ehrl{\'{e}}n, Johan}, journal = {Ecology}, keywords = {leslie matrix,matrixes,population model}, number = {3}, pages = {607--618}, publisher = {Ecology}, title = {{Elasticities: A Review of Methods and Model Limitations}}, volume = {81}, year = {2000} } @article{Cortes2007, abstract = {Increasing knowledge of the life history of numerous species of chondrichthyans has spawned a rather large body of literature on demographic models in the past two decades. These life tables or matrix population models typically aim at estimating the pro- ductivity of a given species or population and characterizing its vulnerability to exploitation.}, annote = {-discusses use and abuse of demographic modeling of sharks over the past 20 years -says two big assumptions of modeling attempts are time invariance and density independence -discussing how only Gruber 2001 and Heupel/Simpfendorfer 2002 are the only two papers that directly measure mortality -says Chen/Watanabe 1989 and Siegfried 2006 offer best age specific mortality curves -terminal year in population should consist of 1{\%} of population (Hoenig 1983) -need density mechanisms to have compensatory responses and to examine time lags in those responses -a modified demographic model is found by Au and Smith (1997) which incorporates density dependence in juvenile survival -explains how models need to output qualitative results as to what management measures should be taken -still need more knowledge on what age classes are important and which if any you could harvest from 'Expanding demographic models to estimate quantities such as the steepness of the stock-recruitment curve, lifetime reproductive rate, and the inflection point of population growth curves can be of direct practical use in age-structured stock assessment models, particularly when density-dependent considerations are taken into account."}, author = {Cort{\'{e}}s, Enric}, journal = {Marine Freshwater Research}, keywords = {demography,shark}, pages = {4--6}, title = {{Chondrichthyan demographic modeling: an essay on its use, abuse and future}}, volume = {58}, year = {2007} } @article{Baum2009, abstract = {1. Top-down control can be an important determinant of ecosystem structure and function, but in oceanic ecosystems, where cascading effects of predator depletions, recoveries, and invasions could be significant, such effects had rarely been demonstrated until recently. 2. Here we synthesize the evidence for oceanic top-down control that has emerged over the last decade, focusing on large, high trophic-level predators inhabiting continental shelves, seas, and the open ocean. 3. In these ecosystems,where controlled manipulations are largely infeasible,`pseudo-experimental' analyses of predator--prey interactions that treat independent predator populations as `replicates', and temporal or spatial contrasts in predator populations and climate as `treatments', are increasingly employed to help disentangle predator effects from environmental variation and noise. 4. Substantial reductions in marine mammals, sharks, and piscivorous fishes have led to meso- predator and invertebrate predator increases. Conversely, abundant oceanic predators have suppressed prey abundances. Predation has also inhibited recovery of depleted species, sometimes through predator--prey role reversals. Trophic cascades have been initiated by oceanic predators linking to neritic food webs, but seem inconsistent in the pelagic realm with effects often attenuating at plankton. 5. Top-down control is not uniformly strong in the ocean, and appears contingent on the intensity and nature of perturbations to predator abundances. Predator diversity may dampen cascading effects except where nonselective fisheries deplete entire predator functional groups. In other cases, simultaneous exploitation of predator and prey can inhibit prey responses. Explicit consideration of anthropogenic modifications to oceanic foodwebs should help inform predictions about trophic control. 6. Synthesis and applications. Oceanic top-down control can have important socio-economic, con- servation, and management implications as mesopredators and invertebrates assume dominance, and recovery of overexploited predators is impaired. Continued research aimed at integrating across trophic levels is needed to understand and forecast the ecosystem effects of changing oceanic predator abundances, the relative strength of top-down and bottom-up control, and interactions with intensifying anthropogenic stressors such as climate change.}, annote = {REVIEW -paper examines recent research studying top-down control, trophic cascades, and predator-prey dynamics in the ocean -explain use of pseudo-experiments for analyzing these relationships -give applications for what this means for socio-economic and conservation implications {\_}{\_}{\_} -show that there is plenty of research on trophic cascades and documented cases but much less is known regarding direct evidence for top-down control in oceanic ecosystems --this could be because there is no top-down effect, it just cannot be easily measured, or simply has not been studied very often {\_}{\_}{\_} -give a number of examples of recent studies showing hints of top-down control-still hard to interpret some studies because of a small sample size or badly crossed study design -very little work has been done to combine predator abundance treatments with abiotic variables in a fully crossed study -give examples of the mesopredator and benthic macro-invertebrates releases and declines in lower trophic levels below the mesopredators (ex. cow nose rays, lobster after cod collapse) -bring up interesting examples of how top-down effects have also been attributed to the removal of invasive species, recovering of predators, and seasonal convergences of predators -discuss the multiple cascades that were probably brought upon by both top-down effects and climatic changes -discuss importance of diversity in predators but point out the indiscminancy of modern fishing gear -major implications in conservation and management as importance of predator-prey relationships and trophic cascades may try more dynamics than previously thought {\_}{\_}{\_}{\_} -state that future research should focus on identifying priors useful for management decisions Future Questions: -what thresholds determine if cascades will occur? -importance of non-consumption effects of predators? -how to cascading effects propagate through a whole ecosystem? -interactions between top-down, bottom-up, and anthropogenic stresses?}, author = {Baum, Julia K and Worm, Boris}, journal = {Journal of Animal Ecology}, keywords = {fisheries,predation,shark}, pages = {699--714}, title = {{Cascading top-down effects of changing oceanic predator abundances}}, volume = {78}, year = {2009} } @article{Hazon2003, abstract = {Since the landmark contributions of Homer Smith and co-workers in the 1930s there has been a considerable advance in our knowledge regarding the osmoregulatory strategy of elasmobranch fish. Smith recognised that urea was retained in the body fluids as part of the `osmoregulatory ballast' of elasmobranch fish so that body fluid osmolality is raised to a level that is iso- or slightly hyper-osmotic to that of the surrounding medium. From studies at that time he also postulated that many marine dwelling elasmobranchs were not capable of adaptation to dilute environments. However, more recent investigations have demonstrated that, at least in some species, this may not be the case. Gradual acclimation of marine dwelling elasmobranchs to varying environmental salinities under laboratory conditions has demonstrated that these fish do have the capacity to acclimate to changes in salinity through independent regulation of Naq , Cly and urea levels. This suggests that many of the presumed stenohaline marine elasmobranchs could in fact be described as partially euryhaline. The contributions of Thomas Thorson in the 1970s demonstrated the osmoregulatory strategy of a fully euryhaline elasmobranch, the bull shark, Carcharhinus leucas, and more recent investigations have examined the mechanisms behind this strategy in the euryhaline elasmobranch, Dasyatis sabina. Both partially euryhaline and fully euryhaline species utilise the same physiological processes to control urea, Naq and Cly levels within the body fluids. The role of the gills, kidney, liver, rectal gland and drinking process is discussed in relation to the endocrine control of urea, Naq and Cly levels as elasmobranchs acclimate to different environmental salinities.}, annote = {REVIEW PAPER -first studies appeared in 30's by Homer Smith where he found the importance of urea in osmoregulation of elasmobranchs -Thorson in the 70's studied the bull shark in depth, and other recent studies have examined Dasyatis sabina -now know that euryhaline and fully euryhaline animals use same mechanisms in controlling urea, Na, and Cl -role of gills, kidneys, liver, rectal gland, and the drinking process are all very important {\_}{\_}{\_}{\_}{\_}{\_}{\_} -must know that plasma osmolarity is hyper-osmotic in freshwater and hypo in saltwater for elasmobranchs -all elasmobranchs -excluding freshwater- are ureotelic ----this means they make and excrete urea as end product of nitrogen metabolism (ornithine cycle) -normally urea could damage proteins and enzymes but sharks are able to overcome this by the presence of methyl amines ( a type of organic osmolytes) -one paper found there is optimal balance of 2:1 for urea:methylamines -the vast majority of methyl amines are specifically TMAO (trimethylamine oxide)- stored in muscle tissues {\_}{\_} Gills: }, author = {Hazon, Neil and Wells, Alan and Pillans, Richard D and Good, Jonathan P and Anderson, W Gary and Franklin, Craig E}, journal = {Comparative Biochemistry and Physiology Part B}, keywords = {osmoregulation,review,shark}, pages = {685--700}, title = {{Urea based osmoregulation and endocrine control in elasmobranch fish with special reference to euryhalinity}}, volume = {136}, year = {2003} } @article{McKaneNewman2005, author = {McKane, Alan J and Newman, Timothy J}, journal = {Physical Review Letters}, keywords = {demography,physics,population model,statistics}, number = {218102}, title = {{Predator-prey cycles from resonant amplification of demographic stochasticity}}, volume = {94}, year = {2005} } @article{Heupel2008, abstract = {ABSTRACT: The space utilization and distribution of young ({\textless}2 yr old) bull sharks Carcharhinus leu- cas within a 27 km stretch of the Caloosahatchee River estuary in Southwest Florida was examined using an array of acoustic monitors to define influences of environmental variables. A total of 56 young sharks from 3 cohorts (2003, 2004, 2005) were fitted with acoustic tags and monitored for up to 460 d. Sharks did not remain within the estuary continuously, but on average approximately one- third were present at any one time from each cohort. Salinity and freshwater inflow showed greatest influence on shark distribution, with temperature appearing to play a limited role. Although individ- uals occurred in salinities from 0.1 to 34, electivity analysis indicated that they generally avoided areas with salinity {\textless}7 and had an affinity for areas with salinities from 7 to at least 20. There were significant relationships between the mean location of a cohort within the estuary and salinity, with sharks occurring further up river when the river was more saline. These relationships were more pronounced for the youngest sharks, and strength of the relationship decreased with age. Since bull sharks are euryhaline, these results suggest that they may select environmental conditions via move- ment, possibly to reduce energetic costs associated with osmoregulation.}, annote = {-looked at young bull sharks in an estuary in Southwest Florida with acoustic monitors -56 sharks for 2003, 2004, 2005 were tagged and monitored for up to 460 days -salinity and freshwater inflow explained the greatest cause of shark distribution --surprisingly temp. has little effect -animals tried to avoid salinities less than 7 even though they were found at up to 34. 7 to 20 is the optimal range -these relationships decreased with age of the shark -sharks are choosing environmental conditions through movement {\_}{\_}{\_}{\_}{\_}{\_}{\_} -say reason for study is most research on osmoregulation has occurred in lab settings -it is known these animals can in fact often regulate over a full range of salinities but this may not reflect what is actually happening in nature "Euryhaline and marine elasmobranchs are typically ureotelic, hyperosmotic regulators, meaning that they retain elevated osmotic pressure relative to their environment, usually via retention of urea and trimethylamine oxide" {\_}{\_}{\_}{\_}{\_}{\_}{\_} -river system varies wildly in salinity and freshwater flows because of man made damns and regulation -used series of acoustic receivers -use a algorithm to determine where shark actually was in the river for each 30 minute period -used electively analysis to determine if sharks actually showed preference for salinity (may use in bimini work) {\_}{\_}{\_}{\_}{\_}{\_}{\_}{\_} -for all three cohorts there was a significant relationship between location of shark versus salinity and temperature -also show that as they aged the influence of water flow had less effects on their movements {\_}{\_}{\_} -showed that these young sharks use nurseries for at least 18 months like the lemons -contrary to past research they found that juveniles are using these nursery sites because of environmental reasons (not for food or avoidance of predators) }, author = {Heupel, Michelle R and Simpfendorfer, Colin A}, journal = {Aquatic Biology}, keywords = {demography,osmoregulation,shark}, month = {feb}, pages = {277--289}, title = {{Movement and distribution of young bull sharks $\backslash$textit{\{}Carcharhinus leucas{\}} in a variable estuarine environment}}, volume = {1}, year = {2008} } @article{Jacoby2012, abstract = {1. Determininghowanimalsmovewithintheirenvironmentisafundamentalknowledgethatcon- tributes to effective management and conservation. Continuous `round-the-clock' animal move- ment data are frequently gathered using biotelemetry technology, providing discrete data packages on the presence--absence of animals at known locations through time. Current analyses of such data do not generally account for the interconnectivity of locations as animals move between them and consequently do not integrate graphically or statistically a temporal component to spatial changes. 2. Here, we describe the novel application of network analyses to electronic tag data whereby nodes represent locations and edges of the movements of individuals. We demonstrate some of the descriptive and quantitative approaches for determining how an animal's movement interconnects home range habitats. Telemetry data from arrays of recorders provide movement data of individ- ual animals, and as examples of the method proposed, we examine the movements of two distinct shark species, the small-spotted catshark (Scyliorhinus canicula) and the Caribbean reef shark (Carcharhinus perezi). In doing so, we consider both local and global network properties from an animal movement perspective and simulate the effects of node disruption as a proxy for habitat disturbance. 3. Comparative visual representations of two catshark movement networks suggest, for example, potential differences in space use. Multiple regression quadratic assignment procedure shows that habitat is a significant predictor of movement behaviour. 4. Null modelling of C. perezi movement data, corrected for the spatial restriction of static nodes, demonstrated a significant, non-random distribution of directed movements among sites. Additionally, the connectivity of this animal's movement network is significantly reduced through targeted disruption of a site of high centrality but not through disruption of a randomly selected site. 5. Network theory is a well-established theoretical framework and its integration into the fast developing field of animal movement and telemetry might improve significantly how we interpret animal space use from electronically recorded data. This technique has potentially wide application in animal behaviour but may also inform the management of habitat harbouring threatened or endangered species via the simulation, modelling and intuitive visualisation of animal movement interactions.}, annote = {Sims 2010 does a more thorough review of movement data and analysis -feel current analyses of network data in animals simply focus on where and when animals may be at a particular location -they want to develop network analysis in this type of data to examine home ranges, habitat preferences, distribution of movement between sites -use small-spotted catshark and caribbean reef shark as examples {\_}{\_}{\_}{\_}{\_} -discuss history and importance of understanding animal movements -use technology such as radiotelemetry, acoustic receivers, archival tags, satellite tags, and GPS tags to understand movement, density of individuals and home ranges -define space utilization though a method called kernel utilization distribution (show core areas in a sense) -they feel a lot more data and analyses can be constructed on these large data sets --want to look more closely at location connectivity using graph theory {\_}{\_}{\_}{\_}{\_} -examine a number of measurements using their data: --centrality- looking at relative importance of node by its level of connectedness, can also see if certain nodes are more important for entrance or exits --betweenness- "number of paths that pass through a particular node from one node to another" by the shortest length possible (example would be a water hole for migratory elephants) --degree distribution- simply degree at which animals may distribute throughout different habitat locations --average path length- simply looks at how often an animal my move between locations on average (this is important for comparing specific individuals, and age classes or both --edge density- looks at number of actual edges present in a population instead of the suspected value equal to 1. This shows how animals may or may not be using space randomly -use a Matlab program called SOCPROG and a non matlab program UCINET -these programs create a interaction matrix for analysis --matrix usually total count of movements between two nodes or proportional movements -typically they filter data by looking at movements of animals from one site to another in set time or seasonal filters can be used {\_}{\_}{\_}{\_}{\_} -can read specifics of how they analyzed certain measurements with environmental variables and generating random movement data to compare there data to {\_}{\_}{\_}{\_}{\_} -found differences between male and female catsharks in habitat use and residency times --appeared that habit type is strong factor in female catshark movement -reef sharks showed different space and home ranges during different times of this year -found movements to be non random by comparing to randomly produced network dataset -also looked to see effect of removing nodes to simulate habitat degradation and showed hoe it does in fact reduce connectedness of the network {\_}{\_}{\_}{\_}{\_} -reef shark aged and movement appeared to be more orientated on the coastal shelf -"null modeling" (generating random movement data set to compare to) showed reef sharks are not in fact moving randomly }, author = {Jacoby, David M P and Brooks, Edward J and Croft, Darren P and Sims, David W}, journal = {Methods in Ecology and Evolution}, keywords = {demography,movement,network analysis,shark}, title = {{Developing a deeper understanding of animal movements and spatial dynamics through novel application of network analyses}}, year = {2012} } @article{Feldheim2002, abstract = {Surprisingly little is known about the reproductive behaviour and breeding biology of most shark species, especially in natural populations. Here, we characterize reproductive patterns and use of a natal nursery at Bimini, Bahamas by lemon sharks, Negaprion brevirostris. We systematically and exhaustively sampled young lemon sharks at Bimini annually from 1995 to 2000 and opportunistically sampled adults over the same period. Out of the 897 young sharks sampled, 119 could be assigned to five sampled mothers using microsatellite genotyping. Reproductive females showed strong philopatry to the nursery, returning to Bimini every two years to give birth. Each of these females may rely entirely on the Bimini nursery for recruitment. The protection of known nursery grounds should therefore figure prominently in conservation efforts for large coastal shark species. The reconstruction of paternal genotypes indicates that litters are sired by multiple males, and females mate with different males nearly every breeding cycle. The ubiquitous polyandry reported here raises the possibility that genetic incompatibility and post-copulatory paternity- biasing mechanisms may operate in viviparous sharks.}, annote = {{\textless}m:note{\textgreater}jfdjlafskd{\textless}/m:note{\textgreater}}, author = {Feldheim, Kevin A and Gruber, Samuel H and Ashley, Mary V}, journal = {Proceedings of the Royal Society}, keywords = {genetics,juvenile,shark}, pages = {1655--1661}, title = {{The breeding biology of lemon sharks at a tropical nursery lagoon}}, volume = {269}, year = {2002} } @article{Kneebone2012a, author = {Kneebone, J and Chisholm, J and Skomal, Gb}, doi = {10.3354/meps09989}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Kneebone, Chisholm, Skomal - 2012 - Seasonal residency, habitat use, and site fidelity of juvenile sand tiger sharks Carcharias taurus i.pdf:pdf}, issn = {0171-8630}, journal = {Marine Ecology Progress Series}, keywords = {acoustic telemetry,habitat use,nursery,of the publisher,permitted without written consent,resale or republication not,residency,sand tiger,site fidelity}, month = {dec}, pages = {165--181}, title = {{Seasonal residency, habitat use, and site fidelity of juvenile sand tiger sharks Carcharias taurus in a Massachusetts estuary}}, url = {http://www.int-res.com/abstracts/meps/v471/p165-181/}, volume = {471}, year = {2012} } @article{Bond2012a, abstract = {Carcharhinid sharks can make up a large fraction of the top predators inhabiting tropical marine ecosystems and have declined in many regions due to intense fishing pressure. There is some support for the hypothesis that carcharhinid species that complete their life-cycle within coral reef ecosystems, hereafter referred to as "reef sharks", are more abundant inside no-take marine reserves due to a reduction in fishing pressure (i.e., they benefit from marine reserves). Key predictions of this hypothesis are that (a) individual reef sharks exhibit high site-fidelity to these protected areas and (b) their relative abundance will generally be higher in these areas compared to fished reefs. To test this hypothesis for the first time in Caribbean coral reef ecosystems we combined acoustic monitoring and baited remote underwater video (BRUV) surveys to measure reef shark site-fidelity and relative abundance, respectively. We focused on the Caribbean reef shark (Carcharhinus perezi), the most common reef shark in the Western Atlantic, at Glover's Reef Marine Reserve (GRMR), Belize. Acoustically tagged sharks (N = 34) were detected throughout the year at this location and exhibited strong site-fidelity. Shark presence or absence on 200 BRUVs deployed at GRMR and three other sites (another reserve site and two fished reefs) showed that the factor "marine reserve" had a significant positive effect on reef shark presence. We rejected environmental factors or site-environment interactions as predominant drivers of this pattern. These results are consistent with the hypothesis that marine reserves can benefit reef shark populations and we suggest new hypotheses to determine the underlying mechanism(s) involved: reduced fishing mortality or enhanced prey availability.}, author = {Bond, Mark E and Babcock, Elizabeth a and Pikitch, Ellen K and Abercrombie, Debra L and Lamb, Norlan F and Chapman, Demian D}, doi = {10.1371/journal.pone.0032983}, file = {:Users/eastonwhite/Library/Application Support/Mendeley Desktop/Downloaded/Bond et al. - 2012 - Reef sharks exhibit site-fidelity and higher relative abundance in marine reserves on the Mesoamerican Barrier Reef.pdf:pdf}, issn = {1932-6203}, journal = {PloS one}, keywords = {Animals,Belize,Conservation of Natural Resources,Coral Reefs,Ecosystem,Population Dynamics,Sharks}, month = {jan}, number = {3}, pages = {e32983}, pmid = {22412965}, title = {{Reef sharks exhibit site-fidelity and higher relative abundance in marine reserves on the Mesoamerican Barrier Reef}}, url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3297616{\&}tool=pmcentrez{\&}rendertype=abstract}, volume = {7}, year = {2012} } @article{Wielgus2008, annote = {-use a technique that always estimation of demographic and growth rates from stage-specific data (done by quadratic programming- at ape of inverse method) - always someone to constrain what possible demographic values may be {\_}{\_}{\_} -looked at seven sites in the gulf of mexico and counted population status for {\~{}}14 years of different ages during breeding season when most of the sea lions are on land -also examined to see if El Nini/Nina had a major effect of the population through their models -are able to estimate all the parameters we know of for a single sex based stochastic model -also used elasticity and sensitivity analyses -also looked at how you could drive a declining population to be increasing **use equation that would be helpful in my work -adult survival had highest elasticities for almost every colony (2.4 to 10.6x more important than next highest) {\_}{\_}{\_}{\_}{\_} -advise efforts to focus on adult sea lions in gulf- directly related to fishing activities -found no effect on populations from el nino/la nina *lots of good sources }, author = {Wielgus, Jeffrey and Gonzalez-Suarez, Manuela and Aurioles-Gamboa, David and Gerber, Leah R}, journal = {Ecological Applications}, keywords = {demography,sea lions}, month = {jul}, number = {5}, pages = {1287--1296}, title = {{A Noninvasive Demographic Assessment of Sea Lions Based on Stage-Specific Abundances}}, volume = {18}, year = {2008} } @article{Dennis1991, abstract = {Abstract. Survivalorextinctionofanendangeredspeciesisinherentlystochastic.We develop statisticalmethodsforestimatingquantitiesrelatedto growthratesand extinction probabilitiesfromtimeseriesdata on theabundance ofa singlepopulation.The statistical methodsare based on a stochasticmodel ofexponentialgrowtharisingfromthebiological theoryof age- or stage-structurepdopulations. The model incorporatesthe so-called en- vironmentaltypeofstochasticfluctuationsand yieldsa lognormalprobabilitydistribution of population abundance. Calculation of maximum likelihood estimatesof the two un- known parametersin this model reduces to performinga simple linear regression.We describetechniquesforrigorouslytestingand evaluatingwhetherthemodel fitsa given data set.Variousgrowth-and extinction-relateqduantitiesarefunctionsofthetwoparam- eters,includingthecontinuousrateofincrease,thefiniterateofincrease,thegeometric finiterateofincrease,theprobabilityofreachinga lowerthresholdpopulationsize,the mean,median,and mostlikelytimeofattainingthethresholda,nd theprojectedpopulation size. Maximum likelihoodestimatesand minimumvarianceunbiasedestimatesofthese quantitiesare describedin detail. We provideexample analysesofdata on theWhoopingCrane (Grusamericana), grizzly bear (Ursus arctos horribilis)in Yellowstone, Kirtland's Warbler (Dendroica kirtlandii), California Condor (Gymnogypscalifornianus),Puerto Rican Parrot (Amazona vittata), Palila (Loxioidesballeui),andLaysanFinch(Telespyzacantans).Themodelresultsindicate a favorableoutlookfortheWhoopingCrane,butlong-termunfavorableprospectsforthe Yellowstonegrizzlybearpopulationand forKirtland'sWarbler.ResultsfortheCalifornia Condor, in a retrospectiveanalysis, indicate a virtual emergencyexisted in 1980. The analysessuggestthatthePuertoRican Parrotfaceslittleriskofextinctionfromordinary environmentalfluctuations,provided intensivemanagementeffortscontinue.However, the model does not account forthe possibilityof freakcatastrophicevents (hurricanes, fires,etc.), which are likelythe most severe source of riskto the Puerto Rican Parrot,as shownbytherecentdecimationofthispopulationbyHurricaneHugo. Model parameter estimatesforthe Palila and the Laysan Finch have wide uncertaintydue to the extreme fluctuationsin the population sizes of these species. In general,the model fitsthe example data sets well. We conclude thatthe model, and the associated statisticalmethods,can be usefulforinvestigatingvarious scientificand managementquestions concerningspecies preservation.}, annote = {-paper to develop statistical techniques for estimated qualities based on growth or extinction probabilities -works for stochastic model in which exponential growth arises in age structured biological systems {\_}{\_}{\_}{\_} -diffusion process (Wiener-drift) does a good job at projecting extinction probabilities -in this paper they define extinction to simply be some preset value that a population may or may not cross -quasi extinction- defined in the way extinction is defined in this paper -estimate $\mu$and $\sigma$from time series of population data -time to extinction (T) has a continuous probability distribution with a formula describing the CDF (function) --from the derivative of the Gaussian with respect to t (also known as the inverse Gaussian distribution) ---can also use this inverse Gaussian distribution to find time to upper threshold of a given population -estimate $\mu$and $\sigma${\^{}}2 through the product of transition probability density functions which is the likelihood function L($\mu$, $\sigma${\^{}}2) = p{\_}N(n{\_}1,$\tau${\_}1 | n{\_}0)*p{\_}N(n{\_}2,$\tau${\_}2 | n{\_}1){\{}{\ldots}{\}}{\{}{\ldots}{\}}.*p{\_}N(n{\_}q,$\tau${\_}q | n{\_}{\{}q-1{\}}) -can estimate $\mu$and $\sigma${\^{}}2 either through the desired ML (maximum likelihood approach) or through a linear regression approach y{\_}i = [log(frac{\{}n{\_}i{\}}{\{}n{\_}{\{}i-1{\}}{\}}]/sqrt{\{}$\tau${\_}i{\}}, i=1,{\{}{\ldots}{\}}{\{}{\ldots}{\}},q $\mu$hat is the slope parameter estimate $\sigma${\^{}}2 tilda is unbiased estimate of the error plot y1,y2,{\{}{\ldots}{\}}.yq against $\backslash$sqrt{\{}$\backslash$tau{\_}1{\}}{\{}{\ldots}{\}}..$\backslash$sqrt{\{}$\backslash$tau{\_}q{\}} {\_}{\_}{\_}{\_} -generate distributions and confidence intervals for when a population may decrease to a certain threshold **-can also find the mode of this distribution which corresponds to the inflection point of the curve (mode represents most likely time to extinction) {\_}{\_}{\_}{\_}Examples of implementation{\_}{\_}{\_}{\_}{\_} -Whooping crane census from 1938 to 1991 (maybe longer) -find overall exponential trend as population was so low at beginning {\_}{\_}{\_}{\_}{\_} -discuss how model assumes that observational estimates in the field are pretty good (model has trouble accounting for this even when extra variance terms are added) -point out lack of density dependence --could model diffusion process to include density-dependent feedback -four types of stochasticity: demographic, environmental, catastrophic, and genetic}, author = {Dennis, Brian and Munholland, Patricia L and Scott, J Michael}, journal = {Ecological Monographs}, keywords = {extinction,growth,sea lions}, month = {jun}, number = {2}, pages = {115--143}, title = {{Estimation of Growth and Extinction Parameters for Endangered Species}}, volume = {61}, year = {1991} }