http://datadryad.org:80 The Dryad digital repository captures, stores, indexes, preserves, and distributes digital data supporting scientific publications. 2017-07-08T07:42:13Z http://datadryad.org/resource/doi:10.5061/dryad.12546 Frogs (Anura) are one of the most diverse groups of vertebrates and comprise nearly 90% of living amphibian species. Their worldwide distribution and diverse biology make them well-suited for assessing fundamental questions in evolution, ecology, and conservation. However, despite their scientific importance, the evolutionary history and tempo of frog diversification remain poorly understood. By using a molecular dataset of unprecedented size, including 88-kb characters from 95 nuclear genes of 156 frog species, in conjunction with 20 fossil-based calibrations, our analyses result in the most strongly supported phylogeny of all major frog lineages and provide a timescale of frog evolution that suggests much younger divergence times than suggested by earlier studies. Unexpectedly, our divergence-time analyses show that three species-rich clades (Hyloidea, Microhylidae, and Natatanura), which together comprise ∼88% of extant anuran species, simultaneously underwent rapid diversification at the Cretaceous–Paleogene (K–Pg) boundary (KPB). Moreover, anuran families and subfamilies containing arboreal species originated near or after the KPB. These results suggest that the K–Pg mass extinction may have triggered explosive radiations of frogs by creating new ecological opportunities. This phylogeny also reveals relationships such as Microhylidae being sister to all other ranoid frogs and African continental lineages of Natatanura forming a clade that is sister to a clade of Eurasian, Indian, Melanesian, and Malagasy lineages. Biogeographical analyses suggest that the ancestral area of modern frogs was Africa, and their current distribution is largely associated with the breakup of Pangaea and subsequent Gondwanan fragmentation. 2017-07-07T18:28:45Z http://datadryad.org/resource/doi:10.5061/dryad.p3h3r As the value of a limited resource such as a territory increases, animals should invest more in the defence of that resource. Because reproductive success often depends on the quality of a breeding territory, reproductive success or failure may alter the perceived value of territory and affect an animal's investment in territorial defence. We used common loons (Gavia immer) to test the hypothesis that animals with recent breeding success would show stronger territorial defence than those with no recent breeding success. Surprisingly, successful loons responded less, not more, to a simulated intrusion. However, birds with success in the previous season also increased their territorial response as the breeding season progressed. In conjunction with past data showing that recently successful loons experience an increase in conspecific intrusions on their territories, we interpret our data to suggest that loons with recent success offset the cost of increased intrusions by adopting a more efficient strategy for territorial defence (e.g., limiting investment in resource defence until the time of the season when it is most critical). 2017-06-28T13:58:57Z http://datadryad.org/resource/doi:10.5061/dryad.07k21 Pathogens such as bacteria, fungi and malaria and related haemosporidians provoke negative effects on the fitness of their hosts. Animals have developed a range of defensive mechanisms to resist or eliminate these parasitic infections and their negative fitness costs. The uropygial gland secretion has been proposed to act as defensive barrier of skin and plumage in the fight against bacteria and fungi, and may prevent birds from acquiring haemosporidian infections. Thus, the secretion of uropygial glands of birds may favour survival of individuals. However, whether uropygial gland secretion influence survival remains unknown. Here we explore if the size of the uropygial gland and malaria infection influence survival of house martins Delichon urbica. We showed, for the first time, that the volume of the uropygial gland positively predicted survival prospects of malaria infected house martins. Malaria infected birds had the lowest probability of survival, with the effect of gland size on survival prospects depending on infection: Infected house martins with larger uropygial glands were better able to survive to the next breeding season, while infected birds with small uropygial glands were not. These results highlight the importance of uropygial gland secretion in the life history of wild birds. 2017-06-28T14:07:38Z http://datadryad.org/resource/doi:10.5061/dryad.nr654 Survivorship following major mass extinctions may be associated with a decrease in body size—a phenomenon called the Lilliput Effect. Body size is a strong predictor of many life history traits (LHTs), and is known to influence demography and intrinsic biological processes. Pronounced changes in organismal size throughout Earth history are therefore likely to be associated with concomitant genome-wide changes in evolutionary rates. Here, we report pronounced heterogeneity in rates of molecular evolution (varying up to ~20-fold) across a large-scale avian phylogenomic dataset, and show that nucleotide substitution rates are strongly correlated with body size and metabolic rate. We also identify potential body size reductions associated with the Cretaceous-Paleogene (K-Pg) transition, consistent with a Lilliput Effect in the wake of that mass extinction event. We posit that selection for reduced body size across the K-Pg extinction horizon may have resulted in transient increases in substitution rate along the deepest branches of the extant avian tree of life. This ‘hidden’ rate acceleration may result in both strict and relaxed molecular clocks over-estimating the age of the avian crown group through the relationship between life history and demographic parameters that scale with molecular substitution rate. If reductions in body size (and/or selection for related demographic parameters like short generation times) are a common property of lineages surviving mass extinctions, this phenomenon may help resolve persistent divergence time debates across the tree of life. Furthermore, our results suggest that selection for certain life history traits may be associated with deterministic molecular evolutionary outcomes. 2017-07-07T14:57:06Z http://datadryad.org/resource/doi:10.5061/dryad.c4g76 1. Contemporary global change, including the widespread mortality of foundation tree species, is altering ecosystems and plant communities at unprecedented rates. Plant-soil interactions drive myriad community dynamics, and we hypothesized such interactions may be an important driver of succession following the loss of foundation tree species. 2. We examined whether plant-soil biota interactions, in the context of a putatively important light gradient associated with foundation tree decline, mediate the expansion of Rhododendron maximum in southeastern US forests where Tsuga canadensis (eastern hemlock), a dominant foundation tree species, is in decline. Using an 11-month, controlled inoculation experiment paired with Illumina sequencing, we tested the following hypotheses: (1) Relative to conspecific (R. maximum-conditioned) soils, R. maximum seedlings have higher performance in soils conditioned by T. canadensis and lower performance in interspace soils (conditioned by neither T. canadensis nor R. maximum) due to variation in soil fungal biota, and (2) seedling performance is greater in high light versus low light environments (matching environments under infested versus uninfested T. canadensis crowns, respectively). 3. In partial support of the first hypothesis, we found that R. maximum seedling performance was highest in T. canadensis-conditioned and R. maximum-conditioned soils and lowest in interspace soils. Mechanistically, soils conditioned by T. canadensis and R. maximum had more ericoid and ectomycorrhizal fungi, less saprotrophic fungi, and were less species-rich than interspace soils, and variation in these community traits predicted substantial variation in R. maximum seedling biomass. However, in support of our second hypothesis, soil effects on plant performance were evident in high light only; in low light, soil inoculation did not affect plant performance and plants performed worse. 4. Synthesis. Our findings suggest interactions with soil biota act synergistically with altered abiotic environments to mediate species responses to widespread foundation tree mortality, providing evidence for a novel mechanism of plant response to large-scale disturbance. Examining plant-soil interactions in the context of relevant abiotic gradients can therefore enhance our understanding, predictions, and management of community development processes following forest disturbance. 2017-07-07T14:55:07Z http://datadryad.org/resource/doi:10.5061/dryad.8t2q2 1. Abiotic factors, biotic interactions and dispersal ability determine the spatial distribution of species. Theory predicts that abiotic constraints set range limits under harsh climatic conditions and biotic interactions set range limits under benign climatic conditions, whereas dispersal ability should limit both ends of the distribution. However, empirical studies exploring how these three components jointly affect species across environmental gradients are scarce. 2. Here we present a study that jointly examines these factors to investigate the constraints of the recruitment of Swiss stone pine (Pinus cembra) across and beyond its elevational range in the Swiss Alps. We investigated the natural recruitment of pines and additionally conducted seed transplant experiments to test how much abiotic factors (mean summer and winter temperatures, soil moisture), biotic interactions (understorey vegetation cover, canopy cover, seed predation) and / or seed deposition by the Spotted nutcracker (Nucifraga caryocatactes) affect pine establishment. 3. We found significant effects of biotic interactions and seed deposition by Spotted nutcrackers on the recruitment of Swiss stone pine at both the upper and lower elevational range, but could not detect significant effects of abiotic factors. Importantly, dispersal limitation rather than temperature and soil moisture restricted the recruitment of pines at the upper elevational range. 4. Synthesis. Our study highlights the importance of biotic interactions and dispersal ability in setting the upper range limits of species that have been regarded as mainly controlled by climate. This suggests that potential range shifts of plants in response to climate warming may strongly depend on seed dispersal and biotic interactions and not only on climatic factors. 2017-07-07T14:48:55Z http://datadryad.org/resource/doi:10.5061/dryad.kq30q 1. Establishing a horizontally transmitted mutualism is a critical step for many organisms, particularly when an individual can engage with only one partner over its lifetime. Ant foundresses shed their wings before they start to lay eggs, which makes host choice particularly critical for plant-ants that exclusively colonize myrmecophytes. 2. Volatile organic compounds (VOCs) can indicate the identity and physiological condition of an individual and frequently serve as signals or cues that facilitate partner choice. Thus, we hypothesised that obligate plant-ants use VOCs to determine the quality of potential host plants. 3. Indeed, winged females of the plant-ant, Pseudomyrmex ferrugineus, used plant odours to identify high-quality acacia hosts among different species and among individuals of the same species. The VOC blend of a branch was related to reward production and, interestingly, the least attractive blend contained the highest number of compounds. 4. Whereas only seven different VOCs could be detected in the blend of the high-reward host species, the low-reward host emitted 13 different compounds, among which (S)-(-)-limonene and β-linalool were the dominant ones. Complementing the odour of the high-reward host with (S)-(-)-limonene, β-linalool or α-terpinene reduced its attractiveness. Strikingly, these compounds inhibited bacterial pathogens of the host plant. 5. Synthesis. Plant-ants can utilise host plant odours that contain resistance-related VOCs to judge on host quality, likely because of negative crosstalk between direct resistance to disease and investment in ant-mediated defence. VOCs can serve as cues that provide reliable information for partner choice, particularly when their emission results from a physiological process that causally relates to the quality of an individual as a mutualist. 2017-07-07T14:43:42Z http://datadryad.org/resource/doi:10.5061/dryad.kn21m Incorporating an understanding of animal behaviour into conservation programmes can influence conservation outcomes. Exotic predators can have devastating impacts on native prey species and thwart reintroduction efforts, in part due to prey naïveté caused by an absence of co-evolution between predators and prey. Attempts have been made to improve the anti-predator behaviours of reintroduced native prey by conducting laboratory-based predator recognition training but results have been varied and have rarely led to improved survival in reintroduction programmes. We investigated whether in situ predator exposure could improve anti-predator responses of a predator-naïve mammal by exposing prey populations to low densities of introduced predators under controlled conditions. We reintroduced 352 burrowing bettongs to a 26-km2 fenced exclosure at the Arid Recovery Reserve in South Australia and exposed them to feral cats (density 0.03–0.15 cats/km2) over an 18-month period. At the same time, we translocated a different group of bettongs into an exclosure free of introduced predators, as a control. We compared three behaviours (flight initiation distances, trap docility and behaviour at feeding trays) of cat-exposed and control bettongs before the translocations, then at 6, 12 and 18 months post-translocation. Cat-exposed bettongs displayed changes in behaviour that suggested increased wariness, relative to control bettongs. At 18 months post-reintroduction, cat-exposed bettongs had greater flight initiation distances and approached feed trays more slowly than control bettongs. Cat-exposed bettongs also increased their trap docility over time. Synthesis and applications. Translocation is recommended as a conservation tool for many threatened species yet success rates are generally low. We demonstrate that controlled levels of in situ predator exposure can increase wariness in the behaviour of naïve prey. Our findings provide support for the hypothesis that in situ predator exposure could be used as a method to improve the anti-predator responses of predator-naïve threatened species populations. 2017-07-07T14:35:38Z http://datadryad.org/resource/doi:10.5061/dryad.46fr1 1. Flowering plants exhibit striking interspecific and intraspecific variation in flower number, which strongly influences the reproductive success of animal-pollinated plants. However, the reproductive consequences of producing a single flower are poorly understood. 2. Here, we test if plants producing a single flower have a reproductive disadvantage compared to plants producing multiple flowers by combining field investigation of five deceptive orchids and a survey of published literature. Pollen limitation was estimated by comparing fruit production between hand pollination and open pollination. Flowering frequency was monitored over years to assess the potential advantage of producing a single flower. 3. Both single- and multiple-flowered species suffered strong pollen limitation. However, single-flowered species had significantly lower fruit set and produced fewer seeds per individual, though they had a significantly higher pollen removal than species with multiple flowers. A phylogenetically independent contrast (PIC) of 28 species representing four out of the five subfamilies of Orchidaceae revealed that fruit set was significantly positively associated with flower number. Both pollen removal and fruit set had a positive relationship with flower number within the multiple-flowered species. 4. Synthesis Current data and PIC support the hypothesis that producing a single flower has reproductive disadvantages. Single-flowered species may compensate for low female success through high flowering frequency over years. This study provides insight into costs and benefits of producing a single flower in deceptive orchids. 2017-07-07T14:35:14Z http://datadryad.org/resource/doi:10.5061/dryad.474mm Understanding mutation rates can greatly extend the utility of population and conservation genetic analyses. Herein we present an estimate of genome-wide microsatellite mutation rate in Atlantic sturgeon (Acipenser oxyrinchus) based on parent-offspring transmission patterns. We screened 307 individuals for parentage and mutation-rate analysis applying 43 variable markers. Out of 13,228 allele transfers, 11 mutations were detected, producing a mutation rate of 8.3x10-4 per locus per generation (95%CI: 1.48x10-3, 4.15x10-4). Single-step mutations predominated and there were trends toward mutations in loci with greater polymorphism and allele length. Two of the detected mutations were most probably cluster mutations, being identified in 12 and 28 sibs, respectively. Finally, we observed evidences of polyploidy based on the sporadic presence of 3 or 4 alleles per locus in the genotyped individuals, supporting previous reports of incomplete diploidization in Atlantic sturgeon. 2017-06-30T14:10:53Z http://datadryad.org/resource/doi:10.5061/dryad.2t208 A three-dimensional cell-based mechanical model of coronary artery tunica media is proposed. The model is composed of spherical cells forming a hexagonal close-packed lattice. Tissue anisotropy is taken into account by varying interaction forces with the direction of intercellular connection. Several cell-centre interaction potentials for repulsion and attraction are considered, including the Hertz contact model and its neo-Hookean extension, the Johnson–Kendall–Roberts model of adhesive contact, and a wormlike chain model. The model is validated against data from in vitro uni-axial tension tests performed on dissected strips of tunica media. The wormlike chain potential in combination with the neo-Hookean Hertz contact model produces stress–stretch curves which represent the experimental data very well. 2017-07-07T14:15:40Z http://datadryad.org/resource/doi:10.5061/dryad.5t0g4 Flying animals ranging in size from fruit flies to hummingbirds are nimble fliers with remarkable rotational manoeuvrability. The degrees of manoeuvrability among these animals, however, are noticeably diverse and do not simply follow scaling rules of flight dynamics or muscle power capacity. As all manoeuvres emerge from the complex interactions of neural, physiological and biomechanical processes of an animal's flight control system, these processes give rise to multiple limiting factors that dictate the maximal manoeuvrability attainable by an animal. Here using functional models of an animal's flight control system, we investigate the effects of three such limiting factors, including neural and biomechanical (from limited flapping frequency) delays and muscle mechanical power, for two insect species and two hummingbird species, undergoing roll, pitch and yaw rotations. The results show that for animals with similar degree of manoeuvrability, for example, fruit flies and hummingbirds, the underlying limiting factors are different, as the manoeuvrability of fruit flies is only limited by neural delays and that of hummingbirds could be limited by all three factors. In addition, the manoeuvrability also appears to be the highest about the roll axis as it requires the least muscle mechanical power and can tolerate the largest neural delays. 2017-07-07T14:09:05Z http://datadryad.org/resource/doi:10.5061/dryad.6d159 Objective: To systematically search for research about the effectiveness of mandatory reporting of child maltreatment and to synthesize qualitative research that explores mandated reporters’ (MRs) experiences with reporting. Design: As no studies assessing the effectiveness of mandatory reporting were retrieved from our systematic search, we conducted a meta-synthesis of retrieved qualitative research. Searches in Medline (OVID), Embase, PsycINFO, CINAHL, Sociological Abstracts, ERIC, Criminal Justice Abstracts, and Cochrane Library yielded over 6000 citations, which were deduplicated and then screened by two independent reviewers. English-language, primary qualitative studies that investigated MRs’ experiences with reporting of child maltreatment were included. Critical appraisal involved a modified checklist from the Critical Appraisal Skills Programme (CASP) and qualitative meta-synthesis was used to combine results from the primary studies. Setting: All healthcare and social-service settings implicated by mandatory reporting laws were included. Included studies crossed nine high-income countries (United States, Australia, Sweden, Taiwan, Canada, Norway, Finland, Israel and Cyprus) and three middle-income countries (South Africa, Brazil, and El Salvador). Participants: The studies represent the views of 1088 MRs. Outcomes: Factors that influence MRs’ decision to report and MRs’ views towards and experiences with mandatory reporting of child maltreatment. Results: Forty-four articles reporting 42 studies were included. Findings indicate that MRs struggle to identify and respond to less overt forms of child maltreatment. While some articles (14%) described positive experiences MRs had with the reporting process, negative experiences were reported in 73% of articles and included accounts of harm to therapeutic relationships and child death following removal from their family of origin. Conclusions: The findings of this meta-synthesis suggest that there are many potentially harmful experiences associated with mandatory reporting and that research on the effectiveness of this process is urgently needed. 2017-07-07T13:59:12Z http://datadryad.org/resource/doi:10.5061/dryad.c5961 Early experiences can have enduring impacts on brain and behavior, but the strength of these effects can be influenced by genetic variation. In principle, polymorphic CpGs (polyCpGs) may contribute to gene-by-environment interactions (GxE) by altering DNA methylation. In this study, we investigate the influence of polyCpGs on the development of vasopressin receptor 1a abundance in the retrosplenial cortex (RSC-V1aR) of prairie voles (Microtus ochrogaster). Two alternative alleles (HI/LO) predict RSC avpr1a expression, V1aR abundance and sexual fidelity in adulthood; these alleles differ in the frequency of CpG sites and in methylation at a putative intron enhancer. We hypothesized that the elevated CpG abundance in LO alleles would make homozygous LO/LO voles more sensitive to developmental perturbations. We found that genotype differences in RSC-V1aR abundance emerged early in ontogeny and were accompanied by differences in methylation of the putative enhancer. As predicted, postnatal treatment with an oxytocin receptor antagonist (OTA) reduced RSC-V1aR abundance in LO/LO adults but not their HI/HI siblings. Similarly, methylation inhibition by zebularine increased RSC-V1aR in LO/LO adults, but not in HI/HI siblings. These data demonstrate a gene-by-environment interaction in RSC-V1aR. Surprisingly, however, neither OTA nor zebularine altered adult methylation of the intronic enhancer, suggesting that differences in sensitivity could not be explained by CpG density at the enhancer alone. Methylated DNA immunoprecipiation-sequencing (MeDIP-seq) revealed additional differentially methylated regions between HI/HI and LO/LO voles. Future research should examine the role of these regions and other regulatory elements in the ontogeny of RSC-V1aR and its developmentally induced changes. 2017-07-05T15:45:59Z http://datadryad.org/resource/doi:10.5061/dryad.11j13 Geography and habitat availability may be key drivers underlying spatial patterns of larval supply and recruitment success of nearshore marine fishes, but they are poorly understood. We assessed spatial recruitment patterns of nearshore young-of-the-year Pacific rockfishes Sebastes spp. in kelp forest and eelgrass meadow habitats from 2004 to 2014 on the west coast of Vancouver Island, British Columbia. Our sites varied in habitat area, wave exposure, sea surface temperature, and distance from the open coast. We observed recruitment of several species of rockfish, including black rockfish S. melanops, bocaccio rockfish S. paucispinis, and a complex of copper, quillback, and brown rockfishes (S. caurinus, S. maliger, and S. auriculatus; CQB). For black rockfish, the species recruiting in highest abundances, we found that although the environmental variables that predicted recruitment were temporally variable, in some years recruitment was higher at sites with colder sea surface temperature, higher tidal velocity, higher fetch, and higher salinity. In contrast, CQB rockfish recruitment was consistently higher at sites with higher fetch but lower tidal velocity, and this relationship was stable through time. Interactions among environmental variables and habitat area explained the counterintuitive observation of higher recruitment in smaller eelgrass meadows but larger kelp forests. Moreover, sites in or on the boundary of a rockfish conservation area experienced the lowest recruitment during an exceptionally strong black rockfish recruitment event in 2006. These results suggest that temporal variability in the ability of environmental variables to predict the spatial distribution of young-of-the-year rockfishes should be considered in models of population connectivity. 2017-07-07T12:54:06Z http://datadryad.org/resource/doi:10.5061/dryad.606ks Studying herbal products derived from local and traditional knowledge and their value chains is one of the main challenges in ethnopharmacology. The majority of these products have a long history of use, but non-harmonized trade and differences in regulatory policies between countries impact their value chains and lead to concerns over product efficacy, safety and quality. Veronica officinalis L. (common speedwell), a member of Plantaginaceae family, has a long history of use in European traditional medicine, mainly in central eastern Europe and the Balkans. However, no specified control tests are available either to establish the quality of derived herbal products or for the discrimination of its most common substitute, V. chamaedrys L. (germander speedwell). In this study, we use DNA metabarcoding and high performance liquid chromatography coupled with mass spectrometry (HPLC-MS) to authenticate sixteen V. officinalis herbal products and compare the potential of the two approaches to detect substitution, adulteration and the use of unreported constituents. HPLC-MS showed high resolution in detecting phytochemical target compounds, but did not enable detection of specific plant species in the products. DNA metabarcoding detected V. officinalis in only 15% of the products, whereas it detected V. chamaedrys in 62% of the products. The results confirm that DNA metabarcoding can be used to test for the presence of Veronica species, and detect substitution and/or admixture of other Veronica species, as well as simultaneously detect all other species present. Our results confirm that none of the herbal products contained exactly the species listed on the label, and all included substitutes, contaminants or fillers. This study highlights the need for authentication of raw herbals along the value chain of these products. An integrative methodology can assess both the quality of herbal products in terms of target compound concentrations and species composition, as well as admixture and substitution with other chemical compounds and plants. 2017-07-06T20:02:57Z http://datadryad.org/resource/doi:10.5061/dryad.7d1sn Aim: Habitat specialization can constrain patterns of dispersal and drive allopatric speciation in organisms with limited dispersal ability. Herein, we tested biogeographic patterns and dispersal in a salamander with surface-dwelling larvae and obligate cave-dwelling adults. Location: Ozark Plateau, eastern North America. Methods: A population-level phylogeny of grotto salamanders (Eurycea spelaea complex) was reconstructed using mitochondrial (mtDNA) and multi-locus nuclear DNA (nucDNA), primarily derived from anchored hybrid enrichment (AHE). We tested patterns of molecular variance among populations and associations between genetic distance and geographic features. Results: Divergence time estimates suggest rapid formation of three major lineages in the Middle Miocene. Contemporary gene flow among divergent lineages appears negligible, and mtDNA suggests that most populations are isolated. There is a significant association between phylogenetic distance and palaeodrainages, contemporary drainages and sub-plateaus of the Ozarks, as all features explain a proportion of genetic variation. However, the combined effects of palaeodrainages and sub-plateaus explain the greatest proportion of genetic variation. Main conclusions: The geological and hydrological history of the Ozark Plateau has influenced lineage diversification in the grotto salamander, leading to genetic isolation among populations. Limited gene flow and strong phylogeographic structure in this complex may result from the restriction of highly specialized adults to caves. 2017-07-06T19:17:26Z http://datadryad.org/resource/doi:10.5061/dryad.vv53d The spread of cancer cells from primary tumors to regional lymph nodes is often associated with reduced survival. One prevailing model to explain this association posits that fatal, distant metastases are seeded by lymph node metastases. This view provides a mechanistic basis for the TNM staging system and is the rationale for surgical resection of tumor-draining lymph nodes. Here we examine the evolutionary relationship between primary tumor, lymph node, and distant metastases in human colorectal cancer. Studying 213 archival biopsy samples from 17 patients, we used somatic variants in hypermutable DNA regions to reconstruct high-confidence phylogenetic trees. We found that in 65% of cases, lymphatic and distant metastases arose from independent subclones in the primary tumor, whereas in 35% of cases they shared common subclonal origin. Therefore, two different lineage relationships between lymphatic and distant metastases exist in colorectal cancer. 2017-07-06T19:06:03Z http://datadryad.org/resource/doi:10.5061/dryad.t6j7f Coastal habitats including saltmarshes and mangrove forests can accumulate and store significant blue carbon stocks, which may persist for millennia. Despite this implied stability, the distribution and structure of intertidal-supratidal wetlands is known to respond to changes imposed by geomorphic evolution, climatic, sea level and anthropogenic influences. In this study, we reconstruct environmental histories and biogeochemical conditions in four wetlands of similar contemporary vegetation in SE Australia. The objective is to assess the importance of historic factors to contemporary organic carbon (C) stocks and accumulation rates. Results from the four cores – two collected from marine influenced saltmarshes (WAP-M and POR-M) and two from fluvial influenced saltmarshes (WAP-F and POR-F) – highlight different environmental histories and preservation conditions. High C stocks are associated with the presence of a mangrove phase below the contemporary saltmarsh sediments in the POR-M and POR-F cores. 13C NMR analyses show this historic mangrove root C to be remarkably stable in its molecular composition despite its age, consistent with its position in deep sediments. WAP-M and WAP-F cores did not contain mangrove root C, however, significant preservation of char C (up to 46% of C in some depths) in WAP-F reveals the importance of historic catchment processes to this site. Together, these results highlight the importance of integrating historic ecosystem and catchment factors into attempts to upscale C accounting to broader spatial scales. 2017-07-06T17:47:57Z http://datadryad.org/resource/doi:10.5061/dryad.j3t86 Toxic pollutants such as crude oil have direct negative effects for a wide array of marine life. While mortality from acute exposure to oil is obvious, sub-lethal consequences of exposure to petroleum derivatives for growth and reproduction are less evident and sub-lethal effects in fish populations are obscured by natural environmental variation, fishing, and measurement error. We use fisheries independent surveys in the Gulf of Alaska to examine the consequences of the 1989 Exxon Valdez oil spill (EVOS) for demersal fish. We delineate areas across a range of exposure to EVOS and use spatio-temporal models to quantify the abundance of 53 species-groups over 31 years. We compare multiple community metrics for demersal fish in EVOS and Control areas. We find that areas more exposed to EVOS have more negative trends in total groundfish biomass than non-EVOS areas, and that this change is driven primarily by reductions in the abundance of the apex predator guild. We show no signature of increased variability or increased levels of synchrony within EVOS areas. Our analysis supports mild consequences of EVOS for groundfish communities, but suggests that long time-series and assessments of changes at the community level may reveal sub-lethal effects in marine communities. 2017-07-06T17:38:53Z http://datadryad.org/resource/doi:10.5061/dryad.g14k2 1. Metabarcoding of environmental samples has many challenges and limitations that require carefully considered laboratory and analysis pipelines to ensure reliable results. We explore how decisions regarding study design, laboratory work and bioinformatic processing affect the final results, and provide guidelines for reliable study of environmental samples. 2. We evaluate the performance of four primer sets targeting COI and 16S regions characterising arthropod diversity in bat faecal samples, and investigate how metabarcoding results are affected by parameters including: i) number of PCR replicates per sample, ii) sequencing depth, iii) PCR replicate processing strategy (i.e. either additively, by combining the sequences obtained from the PCR replicates, or restrictively, by only retaining sequences that occur in multiple PCR replicates for each sample), iv) minimum copy number for sequences to be retained, v) chimera removal, and vi) similarity thresholds for OTU clustering. Lastly, we measure within- and between-taxa dissimilarities when using sequences from public databases to determine the most appropriate thresholds for OTU clustering and taxonomy assignment. 3. Our results show that the use of multiple primer sets reduces taxonomic biases and increases taxonomic coverage. Taxonomic profiles resulting from each primer set are principally affected by how many PCR replicates are carried out per sample and how sequences are filtered across them, the sequence copy number threshold and the OTU clustering threshold. We also report considerable diversity differences between PCR replicates from each sample. Sequencing depth increases the dissimilarity between PCR replicates unless the bioinformatic strategies to remove allegedly artefactual sequences are adjusted according to the number of analysed sequences. Finally, we show that the appropriate identity thresholds for OTU clustering and taxonomy assignment differ between target markers. 4. Metabarcoding of complex environmental samples ideally requires i) investigation of whether more than one primer sets targeting the same taxonomic group is needed to offset the effect of primer biases, ii) more than one PCR replicate per sample, iii) bioinformatic processing approaches of sequences that balance diversity detection with removal of artificial sequences, and iv) empirical selection of OTU clustering and taxonomy assignment thresholds tailored to each genetic marker and the obtained taxa. 2017-07-06T16:28:12Z http://datadryad.org/resource/doi:10.5061/dryad.sc682 1. We have developed a reliable technique for extracting DNA from single microscopic fungal thalli, including efficient cell disruption and transfer of cell content for subsequent polymerase chain reaction (PCR). The technique was primarily developed for members of the ascomycete order Laboulbeniales, which are minute fungi with tough cell walls that are exceedingly difficult to disrupt with standard extraction techniques. 2. Our method makes routine amplification of DNA from single thalli possible, even from small species or poorly developed individuals. DNA release is accomplished in an entirely mechanical manner using an arbor press fitted with custom-made components. This approach has eliminated additional treatment such as laborious freeze-thaw cycles, enzymes, or lysing agents. 3. The overall PCR success rate of 89% is comparable to or better than alternative protocols that make use of substantially larger amounts of fungal tissue. From 97% of the successful PCRs a total of 156 sequences from four gene regions were produced. 4. Being able to restrict DNA extractions to a single thallus is critical to all genetic studies requiring data at the level of individual, e.g., population genetics. Since all researchers working with minute uncultivable organisms in many respects face the same problems (effective handling of the material, small quantities of DNA etc.), the methodology described here has a potential to be widely applicable. Necessary custom-made components can be manufactured at fairly low cost by any precision-tool workshop using our detail drawings. 2017-07-06T16:19:07Z http://datadryad.org/resource/doi:10.5061/dryad.qt5bd Warming of the Arctic has resulted in earlier snowmelt and green-up of plants in spring, potentially disrupting the synchrony between plant phenology and breeding phenology in herbivores. A negative relationship between offspring survival in West-Greenland caribou and the timing of vegetation emergence was the first finding of such a mismatch in Arctic mammals. However, other studies indicate that the energy for foetal growth and early lactation is predominantly drawn from stored energy reserves typical of ‘capital’ breeders, suggesting that conditions well before spring influence calf production more than the timing of spring onset. Here we use 20 years of observations of marked Svalbard reindeer to evaluate determinants of annual recruitment, as measured by the presence of a calf at foot in mid-summer. Spring temperatures and the Enhanced Vegetation Index were used as proxies for spring onset, while data on body mass and pregnancy rates in late winter allowed us to determine maternal condition and the reproductive status before spring. Pregnancy rate, offspring survival and annual recruitment were all strongly correlated with average late winter adult female body mass (r = 0.87; r = 0.83; r = 0.92, respectively). Contrary to the findings in West Greenland, neither early calf survival nor annual recruitment were correlated with the two measures of annual variation in spring phenology (r= – 0.07, p = 0.8 and r = – 0.15, p = 0.6, respectively). We also revisit the Greenland data and reveal that the pattern of covariance between early and late measures of fecundity, as well as between early measures of fecundity and offspring survival, correspond with the results from Svalbard. Our results emphasize that conditions affecting maternal body mass during winter explain close to all the variation in recruitment, questioning the importance of the role of a mismatch between plant phenology and calving date. 2016-11-30T19:14:57Z http://datadryad.org/resource/doi:10.5061/dryad.8j5s7 Hypothenemus eruditus is regarded as the world’s most common bark beetle, collected from numerous host plants on all forested continents. Previous taxonomic treatments remark that the species is morphologically variable and difficult to identify, but to date, no study has analyzed molecular data to investigate possible cryptic or seemingly cryptic (pseudo-cryptic) diversity in this species. We sequenced 216 specimens matching or closely resembling the currently accepted description of H. eruditus for a mitochondrial (COI) and a nuclear marker (28S), and scored six morphological characters. We also compared the morphology of H. eruditus syntypes and type material of 26 synonymized species with the sequenced material. The sequenced material grouped in 21 operational taxonomic units (OTUs) supported by both molecular and morphological data, 17 of which were part of an apparent H. eruditus species complex. Another nine cryptic OTUs, distinguishable only by molecular data, were also included in the complex. Only one of the OTUs revealed a morphological match with the H. eruditus syntypes. The 26 synonymized species were split into 14 tentative morphs, 11 of which did not match the H. eruditus syntypes. We argue that many of our sequenced OTUs deserve species status, and that many species synonymized under H. eruditus should be resurrected. 2017-07-06T15:27:20Z http://datadryad.org/resource/doi:10.5061/dryad.868mr Despite more than a century of interest, body-mass estimation in the fossil record remains contentious, particularly when estimating the body mass of taxa outside the size scope of living animals. One estimation approach uses humeral and femoral (stylopodial) circumferences collected from extant (living) terrestrial vertebrates to infer the body masses of extinct tetrapods through scaling models. When applied to very large extinct taxa, extant-based scaling approaches incur obvious methodological extrapolations leading some to suggest that they may overestimate the body masses of large terrestrial vertebrates. Here, I test the implicit assumption of such assertions: that a quadratic model provides a better fit to the combined humeral and femoral circumferences-to-body mass relationship. I then examine the extrapolation potential of these models through a series of subsetting exercises in which lower body-mass sets are used to estimate larger sets. Model fitting recovered greater support for the original linear model, and a nonsignificant second-degree term indicates that the quadratic relationship is statistically linear. Nevertheless, some statistical support was obtained for the quadratic model, and application of the quadratic model to a series of dinosaurs provides lower mass estimates at larger sizes that are more consistent with recent estimates using a minimum convex-hull (MCH) approach. Given this consistency, a quadratic model may be preferred at this time. Still, caution is advised; extrapolations of quadratic functions are unpredictable compared with linear functions. Further research testing the MCH approach (e.g., the use of a universal upscaling factor) may shed light on the linear versus quadratic nature of the relationship between the combined femoral and humeral circumferences and body mass. 2017-03-21T13:25:16Z http://datadryad.org/resource/doi:10.5061/dryad.r00n0 Group size is a fundamental component of sociality, and has important consequences for an individual's fitness as well as the collective and cooperative behaviours of the group as a whole. This review focuses on how the costs and benefits of group living vary in female primates as a function of group size, with a particular emphasis on how competition within and between groups affects an individual's energetic balance. Because the repercussions of chronic energetic stress can lower an animal's fitness, identifying the predictors of energetic stress has important implications for understanding variation in survivorship and reproductive success within and between populations. Notably, we extend previous literature on this topic by discussing three physiological measures of energetic balance—glucocorticoids, c-peptides and thyroid hormones. Because these hormones can provide clear signals of metabolic states and processes, they present an important complement to field studies of spatial and temporal changes in food availability. We anticipate that their further application will play a crucial role in elucidating the adaptive significance of group size in different social and ecological contexts. 2017-07-06T15:13:01Z http://datadryad.org/resource/doi:10.5061/dryad.54df2 Clade E, or the Hesperis-clade is one of the major Brassicaceae (Crucifereae) clades comprising some 48 genera and 351 species classified into seven tribes and is predominantly distributed across arid and montane regions of Asia. Several taxa have socio-economic significance, being important ornamental but also weedy and invasive species. From the comparative genomic perspective, the clade is noteworthy as it harbors species with the largest crucifer genomes but low numbers of chromosomes (n = 5 - 7). By applying comparative cytogenetic analysis and whole-chloroplast phylogenetics, we constructed the first partial and complete cytogenetic maps for selected representatives of Clade E tribes and investigated their relationships in a family-wide context. The Hesperis-clade is a well-supported monophyletic lineage comprising seven tribes: Anchonieae, Buniadeae, Chorisporeae, Dontostemoneae, Euclidieae, Hesperideae, and Shehbazieae. The clade diverged from other Brassicaceae crown-group clades during the Oligocene, followed by subsequent Miocene tribal diversifications in central/south-western Asia. The inferred Ancestral Karyotype of Clade E (CEK, n = 7) originated from an older n = 8 genome, which was also the purported progenitor of tribe Arabideae (KAA genome). In most taxa of Clade E, the seven linkage groups of CEK either remained conserved (Chorisporeae) or were reshuffled by chromosomal translocations (Euclidieae). In c. 50% of Anchonieae and Hesperideae species, the CEK genome has undergone descending dysploidy toward n = 6 (5). This genomic data elucidates early genome evolution in Brassicaceae, and paves the way for future whole-genome sequencing and assembly efforts in this, as yet genomically neglected group of crucifer plants. 2017-07-06T15:05:40Z http://datadryad.org/resource/doi:10.5061/dryad.19sq4 The depth distribution of reef-building corals exposes their photosynthetic symbionts of the genus Symbiodinium to extreme gradients in the intensity and spectral quality of the ambient light environment. Characterizing the mechanisms used by the coral holobiont to respond to the low intensity and reduced spectral composition of the light environment in deeper reefs (greater than 20 m) is fundamental to our understanding of the functioning and structure of reefs across depth gradients. Here, we demonstrate that host pigments, specifically photoconvertible red fluorescent proteins (pcRFPs), can promote coral adaptation/acclimatization to deeper-water light environments by transforming the prevalent blue light into orange-red light, which can penetrate deeper within zooxanthellae-containing tissues; this facilitates a more homogeneous distribution of photons across symbiont communities. The ecological importance of pcRFPs in deeper reefs is supported by the increasing proportion of red fluorescent corals with depth (measured down to 45 m) and increased survival of colour morphs with strong expression of pcRFPs in long-term light manipulation experiments. In addition to screening by host pigments from high light intensities in shallow water, the spectral transformation observed in deeper-water corals highlights the importance of GFP-like protein expression as an ecological mechanism to support the functioning of the coral–Symbiodinium association across steep environmental gradients. 2017-06-23T15:49:09Z http://datadryad.org/resource/doi:10.5061/dryad.f36mq Diapause is an important escape mechanism from seasonal stress in many insects. A certain minimum amount of time in diapause is generally needed in order for it to terminate. The mechanisms of time-keeping in diapause are poorly understood, but it can be hypothesized that a well-developed neural system is required. However, since neural tissue is metabolically costly to maintain there might exist conflicting selective pressures on overall brain development during diapause, on one hand to save energy and on the other hand to provide reliable information processing during diapause. We performed the first ever investigation of neural development during diapause and non-diapause (direct) development in pupae of the butterfly Pieris napi from a population whose diapause duration is known. The brain grew in size similarly in pupae of both pathways up to three days after pupation, when development in the diapause brain was arrested. While development in the brain of direct pupae continued steadily after this point, no further development occurred during diapause until temperatures increased far after diapause termination. Interestingly, sensory structures related to vision were remarkably well developed in pupae from both pathways, in contrast to neuropils related to olfaction, which only developed in direct pupae. The results suggest that a well-developed visual system might be important for normal diapause development. 2017-06-07T13:09:45Z http://datadryad.org/resource/doi:10.5061/dryad.179h5 Recent experiments indicate that male preferential harassment of high-quality females reduces the variance in female fitness, thereby weakening natural selection through females and hampering adaptation and purging. We propose that this phenomenon, which results from a combination of male choice and male-induced harm, should be mediated by the physical environment in which intersexual interactions occur. Using Drosophila melanogaster, we examined intersexual interactions in small and simple (standard fly vials) versus slightly more realistic (small cages with spatial structure) environments. We show that in these more realistic environments, sexual interactions are less frequent, are no longer biased towards high-quality females, and that overall male harm is reduced. Next, we examine the selective advantage of high- over low-quality females while manipulating the opportunity for male choice. Male choice weakens the viability advantage of high-quality females in the simple environment, consistent with previous work, but strengthens selection on females in the more realistic environment. Laboratory studies in simple environments have strongly shaped our understanding of sexual conflict but may provide biased insight. Our results suggest that the physical environment plays a key role in the evolutionary consequences of sexual interactions and ultimately the alignment of natural and sexual selection. 2017-06-01T05:36:39Z http://datadryad.org/resource/doi:10.5061/dryad.mp818 Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, inter-specific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of eight species, we evaluated the relative performances of concatenation and coalescent methods to resolve phylogenetic relationships. Specifically, we focused on assessing the robustness of both approaches to variations in the parameter used to estimate sequence orthology (clustering threshold). Concatenation analyses suffered from strong systematic bias, as revealed by the high statistical support for multiple alternative topologies depending on clustering threshold values. By contrast, topologies produced by two coalescent-based methods (NJst, SVDquartets) were robust to variations in the clustering threshold. Reticulate evolution may partly explain incongruences between NJst, SVDquartets and concatenated trees. Integration of morphometric and coalescent-based phylogenetic results revealed (1) extensive morphological divergence associated with recent splits between geographically close or sympatric sister species, and (2) morphological convergence in geographically disjunct species. These patterns are particularly true for floral traits related to pollinator specialisation, including nectar spur length, tube width and corolla colour, suggesting pollinator-driven diversification. Given its relatively simple and inexpensive implementation, GBS is a promising technique for the phylogenetic and systematic study of recent radiations, but care must be taken to evaluate the robustness of results to variation of data assembly parameters. 2017-07-06T14:32:06Z http://datadryad.org/resource/doi:10.5061/dryad.2h6nf The effect of viewing distance on the perception of visual texture is well known: spatial frequencies higher than the resolution limit of an observer's visual system will be summed and perceived as a single combined colour. In animal defensive colour patterns, distance-dependent pattern blending may allow aposematic patterns, salient at close range, to match the background to distant observers. Indeed, recent research has indicated that reducing the distance from which a salient signal can be detected can increase survival over camouflage or conspicuous aposematism alone. We investigated whether the spatial frequency of conspicuous and cryptically coloured stripes affects the rate of avian predation. Our results are consistent with pattern blending acting to camouflage salient aposematic signals effectively at a distance. Experiments into the relative rate of avian predation on edible model caterpillars found that increasing spatial frequency (thinner stripes) increased survival. Similarly, visual modelling of avian predators showed that pattern blending increased the similarity between caterpillar and background. These results show how a colour pattern can be tuned to reveal or conceal different information at different distances, and produce tangible survival benefits. 2017-06-02T13:52:29Z http://datadryad.org/resource/doi:10.5061/dryad.6s48n In waterjet and laser milling, material is removed from a solid surface in a succession of layers to create a new shape, in a depth-controlled manner. The inverse problem consists of defining the control parameters, in particular, the two-dimensional beam path, to arrive at a prescribed freeform surface. Waterjet milling (WJM) and pulsed laser ablation (PLA) are studied in this paper, since a generic nonlinear material removal model is appropriate for both of these processes. The inverse problem is usually solved for this kind of process by simply controlling dwell time in proportion to the required depth of milling at a sequence of pixels on the surface. However, this approach is only valid when shallow surfaces are etched, since it does not take into account either the footprint of the beam or its overlapping on successive passes. A discrete adjoint algorithm is proposed in this paper to improve the solution. Nonlinear effects and non-straight passes are included in the optimization, while the calculation of the Jacobian matrix does not require large computation times. Several tests are performed to validate the proposed method and the results show that tracking error is reduced typically by a factor of two in comparison to the pixel-by-pixel approach and the classical raster path strategy with straight passes. The tracking error can be as low as 2–5% and 1–2% for WJM and PLA, respectively, depending on the complexity of the target surface. 2017-06-22T18:54:11Z http://datadryad.org/resource/doi:10.5061/dryad.2m353 Open ocean surface CO2 levels are projected to reach approximately 800 µatm, and ocean pH to decrease by approximately 0.3 units by the year 2100 due to anthropogenic CO2 emissions and the subsequent process of ocean acidification (OA). When exposed to these CO2/pH values, several fish species display abnormal behaviour in laboratory tests, an effect proposed to be linked to altered neuronal GABAA­ receptor function. Juvenile blacksmith (Chromis punctipinnis) are social fish that regularly experience CO2/pH fluctuations through kelp forest diurnal primary production and upwelling events, so we hypothesized that they might be resilient to OA. Blacksmiths were exposed to control conditions (pH ∼ 7.92; pCO2 ∼ 540 µatm), constant acidification (pH ∼ 7.71; pCO2 ∼ 921 µatm) and oscillating acidification (pH ∼ 7.91, pCO2 ∼ 560 µatm (day), pH ∼ 7.70, pCO2 ∼ 955 µatm (night)), and caught and tested in two seasons of the year when the ocean temperature was different: winter (16.5 ± 0.1°C) and summer (23.1 ± 0.1°C). Neither constant nor oscillating CO2-induced acidification affected blacksmith individual light/dark preference, inter-individual distance in a shoal or the shoal's response to a novel object, suggesting that blacksmiths are tolerant to projected future OA conditions. However, blacksmiths tested during the winter demonstrated significantly higher dark preference in the individual light/dark preference test, thus confirming season and/or water temperature as relevant factors to consider in behavioural tests. 2017-06-09T13:42:16Z http://datadryad.org/resource/doi:10.5061/dryad.m6909 Chromium oxide coatings prepared by radiofrequency reactive magnetron sputtering on stainless steel substrates were exposed to Ringer's physiological solution and tested for their electrochemical corrosion stability using an open circuit potential measurement, potentiodynamic polarization, electrochemical impedance spectroscopy and Mott–Schottky analysis. The coatings were found to be predominantly Cr2O3, based on the observation of the dominance of A1gA1g and Eg symmetric modes in our Raman spectroscopic investigation and the Eu vibrational modes in our Fourier transform infrared spectroscopic measurements on the coatings. We investigated for the presence of chromium ions in Ringer's solution after all of the above electrochemical tests using atomic absorption spectroscopy, without finding a trace of chromium ions at the ppm level for coatings tested under open circuit and at the lower potentials implants are likely to experience in the human body. The coatings were further exposed to Ringer's solution for one month and tested for adhesion strength changes, and we found that they retained substantial adhesion to the substrates. We expect this finding to be significant for future orthopaedic implants where chromium ion release is still a major challenge. 2017-06-16T16:18:42Z http://datadryad.org/resource/doi:10.5061/dryad.770sn Burying beetles (Nicrophorus vespilloides) bear distinctive and variable orange-black patterning on their elytra and produce an anal exudate from their abdomen when threatened. During breeding, the anal exudates contribute to the antimicrobial defence of the breeding resource. We investigated whether the anal exudates also provide a responsive chemical defence, which is advertised to potential avian predators by the beetle’s orange and black elytral markings. We found that that the orange-black elytral markings of the burying beetle are highly conspicuous for avian predators against range of backgrounds, by using computer simulations. Using bioassays with wood ants, we also showed that the burying beetle’s anal exudates are aversive to potential predators. From these results, and other evidence in the literature, we conclude that the evidence for aposematism in the burying beetle is as strong as the evidence for many other classically aposematic species, such as defended Hymenopterans, ladybirds or poisonous frogs. Nevertheless, we also report unexpectedly high levels of individual variation in coloration and chemical defences, as well as sex differences. We suggest that this variation might be due partly to conflicting selection pressures, particularly on the dual function of the exudates, and partly to nutritional differences in the developmental environment. The ecology of the burying beetles (Nicrophorus spp.) differs markedly from better-studied aposematic insects. This genus thus offers new potential for understanding the evolution of aposematism in general. 2017-07-06T14:08:04Z http://datadryad.org/resource/doi:10.5061/dryad.7b2p6 The ability to tolerate infection is a key component of host defence and offers potential novel therapeutic approaches for infectious diseases. To yield successful targets for therapeutic intervention, it is important that the analytical tools employed to measure disease tolerance are able to capture distinct host responses to infection. Here, we show that commonly used methods that estimate tolerance as a linear relationship should be complemented with more flexible, nonlinear estimates of this relationship which may reveal variation in distinct components such as host vigour, sensitivity to increases in pathogen loads, and the severity of the infection. To illustrate this, we measured the survival of Drosophila melanogaster carrying either a functional or non-functional regulator of the JAK-STAT immune pathway (G9a) when challenged with a range of concentrations of Drosophila C virus (DCV). While classical linear model analyses indicated that G9a affected tolerance only in females, a more powerful nonlinear logistic model showed that G9a mediates viral tolerance to different extents in both sexes. This analysis also revealed that G9a acts by changing the sensitivity to increasing pathogen burdens, but does not reduce the ultimate severity of disease. These results indicate that fitting nonlinear models to host health–pathogen burden relationships may offer better and more detailed estimates of disease tolerance. 2017-06-01T14:33:54Z http://datadryad.org/resource/doi:10.5061/dryad.vr666 Maternal reproductive investment can critically influence offspring phenotype, and thus these maternal effects are expected to be under strong natural selection. Knowledge on the extent of heritable variation in the physiological mechanisms underlying maternal effects is however limited. In birds, resource allocation to eggs is a key mechanism for mothers to affect their offspring and different components of the egg may or may not be independently adjusted. We studied the heritability of egg components and their genetic and phenotypic covariation in great tits (Parus major), using captive-bred full siblings of wild origin. Egg mass, testosterone (T) and androstenedione (A4) hormone concentrations showed moderate heritability, in agreement with earlier findings. Interestingly, yolk triiodothyronine hormone (T3), but not its precursor, thyroxine hormone (T4), concentration was heritable. An immune factor, albumen lysozyme, showed moderate heritability, but yolk immunoglobulins (IgY) did not. The genetic correlation estimates were moderate but statistically nonsignificant; a trend for a positive genetic correlation was found between A4 and egg mass, T and lysozyme and IgY and lysozyme, respectively. Interestingly, phenotypic correlations were found only between A4 and T, and T4 and T3, respectively. Given that these egg components are associated with fitness-related traits in the offspring (and mother), and that we show that some components are heritable, it opens the possibility that natural selection may shape the rate and direction of phenotypic change via egg composition. 2017-07-06T06:30:07Z http://datadryad.org/resource/doi:10.5061/dryad.gm061 Many parasites infect multiple sympatric host species, and there is a general assumption that parasite transmission between co-occurring host species is commonplace. Such between-species transmission could be key to parasite persistence within a disease reservoir and is consequently an emerging focus for disease control. However, while a growing body of theory indicates the potential importance of between-species transmission for parasite persistence, conclusive empirical evidence from natural communities is lacking, and the assumption that between-species transmission is inevitable may therefore be wrong. We investigated the occurrence of between-species transmission in a well-studied multihost parasite system. We identified the flea-borne Bartonella parasites infecting sympatric populations of Apodemus sylvaticus (wood mice) and Myodes glareolus (bank voles) in the UK and confirmed that several Bartonella species infect both rodent species. However, counter to previous knowledge, genetic characterization of these parasites revealed covert host specificity, where each host species is associated with a distinct assemblage of genetic variants, indicating that between-species transmission is rare. Limited between-species transmission could result from rare encounters between one host species and the parasites infecting another and/or host–parasite incompatibility. We investigated the occurrence of such encounter and compatibility barriers by identifying the flea species associated with each rodent host, and the Bartonella variants carried by individual fleas. We found that the majority of fleas were host-generalists but the assemblage of Bartonella variants in fleas tended to reflect the assemblage of Bartonella variants in the host species they were collected from, thus providing evidence of encounter barriers mediated by limited between-species flea transfer. However, we also found several fleas that were carrying variants never found in the host species from which they were collected, indicating some degree of host–pathogen incompatibility when barriers to encounter are overcome. Overall, these findings challenge our default perceptions of multihost parasite persistence, as they show that despite considerable overlaps in host species ecology, separate populations of the same parasite species may circulate and persist independently in different sympatric host species. This questions our fundamental understanding of endemic transmission dynamics and the control of infection within natural reservoir communities. 2016-07-16T14:44:11Z http://datadryad.org/resource/doi:10.5061/dryad.d3m1j Pathogen emergence can drive major changes in host population demography, with implications for population dynamics and sensitivity to environmental fluctuations. The amphibian disease chytridiomycosis, caused by infection with the fungal pathogen Batrachochytrium dendrobatidis (Bd), is implicated in the severe decline of over 200 amphibian species. In species that have declined but not become extinct, Bd persists and can cause substantial ongoing mortality. High rates of mortality associated with Bd may drive major changes in host demography, but this process is poorly understood. Here, we compared population age structure of Bd-infected populations, Bd-free populations and museum specimens collected prior to Bd emergence for the endangered Australian frog, Litoria verreauxii alpina (alpine tree frog). We then used population simulations to investigate how pathogen-associated demographic shifts affect the ability of populations to persist in stochastic environments. We found that Bd-infected populations have a severely truncated age structure associated with very high rates of annual adult mortality. Near-complete annual adult turnover in Bd-infected populations means that individuals breed once, compared with Bd-free populations where adults may breed across multiple years. Our simulations showed that truncated age structure erodes the capacity of populations to withstand periodic recruitment failure; a common challenge for species reproducing in uncertain environments. We document previously undescribed demographic shifts associated with a globally emerging pathogen and demonstrate how these shifts alter host ecology. Truncation of age structure associated with Bd effectively reduces host niche width and can help explain the contraction of L. v. alpina to perennial waterbodies where the risk of drought-induced recruitment failure is low. Reduced capacity to tolerate other sources of mortality may explain variation in decline severity among other chytridiomycosis-challenged species and highlights the potential to mitigate disease impacts through minimizing other sources of mortality. 2016-07-16T14:42:41Z http://datadryad.org/resource/doi:10.5061/dryad.77rn2 Introduced entomophilous non-native plants usually become well integrated into the diet of generalist pollinators. This integration can affect the entire recipient plant–pollinator network. Effects vary from facilitative to competitive, and understanding the factors that govern such variability is one of the fundamental goals in invasion ecology. Species traits determine the linking patterns between plant and pollinator species. Therefore, trait similarity among plants or among pollinators might modulate how they affect each other. We conducted a flower removal experiment to investigate the effects of the non-native entomophilous legume Hedysarum coronarium on the pollination patterns of a Mediterranean shrubland plant–pollinator network. Specifically, we explored whether effects were influenced by similarity with the resident plant species in flower morphology (papilionate vs. non-papilionate), and whether effects on the pollinator community were influenced by similarity in functional group with its main visitor species (bees vs. non-bees). In addition, we explored whether Hedysarum had an effect on the identity of interactions. For this purpose, we calculated the interaction rewiring, that is the number of plant–pollinator interactions that were gained or lost after invasion. Hedysarum was well integrated into the diet of 15 generalist pollinators having the honeybee as its main visitor species. Such integration did not affect visitation rates, normalized degree (i.e. proportion of pollinators they are visited by) nor niche overlap (i.e. proportion of plant species they share pollinators with) of plants, irrespective of their flower morphology. Only the proportion of honeybee visits to resident plants decreased with invasion. On the other hand, Hedysarum reduced visitation rates and niche overlap of pollinators, mainly those of bee species. Finally, we observed that changes in the foraging behaviour of the honeybee were positively associated with the interaction rewiring involving the rest (92 taxa) of pollinators. In conclusion, pollinators show a plastic use of floral resources, responding to the presence of non-native plants. When the non-native attracts highly competitive pollinators such as the honeybee, plasticity is especially significant in pollinators that are functionally close to that competitive pollinator. The result is an interaction rewiring, probably due to pollinators avoiding competition with the honeybee. Though this plasticity might not quantitatively affect the pollination of plants, consequences on their reproduction and the functioning of the network can derive from the interaction rewiring. 2016-07-15T14:44:10Z http://datadryad.org/resource/doi:10.5061/dryad.s4f13 The classification of melanoma into four histological subtypes has been questioned regarding its clinical validity in providing relevant information for treatment for metastatic tumors. Specific genetic alterations are associated with particular clinical and histopathological features, suggesting that these could be helpful in refining existing melanoma classification schemes. We analyzed BRAF V600E mutated melanomas to explore the Reflectance confocal microscopy (RCM) utility as a screening aid in the evaluation of the most appropriate patients for genetic testing. Thus, 32 melanomas were assessed regarding their BRAF V600E mutational status. Experts blinded to dermoscopic images and V600E immunohistochemistry results evaluated RCM images regarding previously described melanoma features. BRAF positive melanomas were related to younger age (p=0.035), invasive melanomas (p=0.03) and to the presence of hiporreflective cells (p=0.02), epidermal nests (p=0.02), dermal-epidermal junction nests (p=0.05), edged papillae (p=0.05), and bright dots (p=0.05), and to absence of junctional thickening due to isolated cells (p=0.01) and meshwork (p=0.02). This study can not characterize other mutations in the BRAF, because the immunohistochemistry is specific to the type V600E. The findings should encourage the genetic evaluation of BRAF mutation. This study highlights the potential of RCM as a supplementary tool in the screening of BRAF-mutated melanomas. 2017-07-05T17:36:27Z http://datadryad.org/resource/doi:10.5061/dryad.5mh53 Foodborne disease poses a serious threat to public health. In the UK, half a million cases are linked to known pathogens and more than half of all outbreaks are associated with catering establishments. The UK Food Standards Agency (FSA) has initiated the UK Food Hygiene Rating Scheme in which commercial food establishments are inspected and scored with the results made public. In this study we investigate the prevalence of food risk increasing behaviours among chefs, catering students and the public. Given the incentive for respondents to misreport when asked about illegal or illicit behaviours we employed a Randomised Response Technique designed to elicit more accurate prevalence rates of such behaviours. We found 14% of the public not always hand-washing immediately after handling raw meat, poultry or fish; 32% of chefs and catering students had worked within 48 hours of suffering from diarrhoea or vomiting. 22% of the public admitted having served meat "on the turn" and 33% of chefs and catering students admitted working in kitchens where such meat was served; 12% of the public and 16% of chefs and catering students admitted having served chicken at a barbeque when not totally sure it was fully cooked. Chefs in fine-dining establishment were less likely to wash their hands after handling meat and fish and those who worked in award winning restaurants were more likely to have returned to work within 48 hours of suffering from diarrhoea and vomiting. We found no correlation between the price of a meal in an establishment, nor its Food Hygiene Rating Score, and the likelihood of any of the food malpractices occurring. 2017-07-05T17:16:29Z http://datadryad.org/resource/doi:10.5061/dryad.19r5g Macroevolutionary developmental biology employs fossilized ontogenetic data and phylogenetic comparative methods to probe the evolution of development at ancient nodes. Despite the prevalence of ecologically differentiated larval forms in marine invertebrates, it has been frequently presumed that the ancestors of arthropods were direct developers, and that metamorphosis may not have evolved until the Ordovician or later. Using fossils and new dated phylogenies, I infer that metamorphosis was likely ancestral for crown arthropods, contradicting this assumption. Based on a published morphological dataset encompassing 217 exceptionally preserved fossil and 96 extant taxa, fossils were directly incorporated into both the topology and age estimates, as in “tip dating” analyses. Using data from post-embryonic fossils representing 25 species throughout stem and crown arthropod lineages (as well as most of the 96 extant taxa), characters for metamorphosis were assigned based on inferred ecological changes in development (e.g., changes in habitat and adaptive landscape). Under all phylogenetic hypotheses, metamorphosis was supported as most likely ancestral to both ecdysozoans and euarthropods. Care must be taken to account for potential drastic post-embryonic morphological changes in evolutionary analyses. Many stem group euarthrpods may have had ecologically differentiated larval stages that did not preserve in the fossil record. Moreover, a complex life cycle and planktonic ecology may have evolved in the Ediacaran or earlier, and may have typified the pre-Cambrian explosion “wormworld” prior to the origin of crown group euarthropods. 2017-07-05T16:46:02Z http://datadryad.org/resource/doi:10.5061/dryad.8gg2p The oceans are deteriorating at a fast pace. Conservation measures, such as Marine Protected Areas, are being implemented to relieve areas from local stressors and allow populations to restore to natural levels. Successful networks of MPAs operate if the space among MPAs is smaller than the dispersal capacity of the species under protection. We studied connectivity patterns across populations in a series of MPAs in the common yellowhead Jawfish, Opistognathus aurifrons. Using the power of genome-wide variation, we estimated that the maximum effective dispersal is 8.3 km. We found that MPAs exchange migrants likely via intermediate unprotected habitats through stepping stone dispersal. At scales >50 km such connectivity is decreased, particularly across the Mona Passage. The MPA network studied would be unable to maintain connectivity of these small benthic fishes if habitat in between them is extirpated. Our study highlights the power of SNPs to derive effective dispersal distance and the ability of SNPs to make inferences from single individuals. Given that overall reef fish diversity is driven by species with life histories similar to that of the yellowhead jawfish, managers face a challenge to develop strategies that allow connectivity and avoid isolation of populations and their possible extinction. 2017-07-05T16:23:59Z http://datadryad.org/resource/doi:10.5061/dryad.3v9h5 Early initiation of antiretroviral therapy (ART) reduces the risk of drug-sensitive HIV transmission but may increase the transmission of drug-resistant HIV. We used a mathematical model to estimate the long-term population-level benefits of ART and determine the scenarios under which earlier ART (treatment at 1 year post-infection, on average) could decrease simultaneously both total and drug-resistant HIV incidence (new infections). We constructed an infection-age-structured mathematical model that tracked the transmission rates over the course of infection and modelled the patients' life expectancy as a function of ART initiation timing. We fitted this model to the annual AIDS incidence and death data directly, and to resistance data and demographic data indirectly among men who have sex with men (MSM) in San Francisco. Using counterfactual scenarios, we assessed the impact on total and drug-resistant HIV incidence of ART initiation timing, frequency of acquired drug resistance, and second-line drug effectiveness (defined as the combination of resistance monitoring, biomedical drug efficacy and adherence). Earlier ART initiation could decrease the number of both total and drug-resistant HIV incidence when second-line drug effectiveness is sufficiently high (greater than 80%), but increase the proportion of new infections that are drug resistant. Thus, resistance may paradoxically appear to be increasing while actually decreasing. 2017-05-31T14:34:25Z http://datadryad.org/resource/doi:10.5061/dryad.s8k68 Background: Predation is ubiquitous in nature. One form of predation is cannibalism, which is affected by many factors such as size structure and resource density. However, cannibalism may also be influenced by abiotic factors such as seasonal time constraints. Since time constraints are greater at high latitudes, cannibalism could be stronger at such latitudes, but we know next to nothing about latitudinal variation in cannibalism. In this study we examined cannibalism and activity in larvae of the damselfly Lestes sponsa, along a latitudinal gradient across Europe. We did this by performing a laboratory study where we raised larvae from the eggs stage and manipulated temperature and photoperiod. Results: We found that the more seasonally time-constrained populations in northern latitudes and individuals subjected to greater seasonal time constraints exhibited a higher level of cannibalism. We also found that activity was higher at north latitude conditions, and thus correlated with cannibalism, suggesting that this behaviour mediates higher levels of cannibalism in time-constrained animals. Conclusions: Our results go counter to the classical latitude-predation pattern which predicts higher predation at lower latitudes, since we found that predation was stronger at higher latitudes. The differences in cannibalism might have implications for population dynamic along the latitudinal gradients, but further experiments are needed to explore this. 2017-07-05T14:21:54Z http://datadryad.org/resource/doi:10.5061/dryad.45qj3 Hoverflies are found across the globe, with approximately 6000 species described worldwide. Many hoverflies are being used in agriculture and some are emerging as model species for laboratory experiments. As such it is valuable to know more about their activity. Like many other dipteran flies, Eristalis hoverflies have been suggested to be strongly diurnal, but this is based on qualitative visualization by human observers. To quantify how hoverfly activity depends on internal and external factors, we here utilize a locomotor activity monitoring system. We show that Eristalis hoverflies are active during the entire light period when exposed to a 12 h light:12 h dark cycle, with a lower activity if exposed to light during the night. We show that the hoverflies’ locomotor activity is stable over their lifetime and that it does not depend on the diet provided. Surprisingly, we find no difference in activity between males and females, but the activity is significantly affected by the sex of an accompanying conspecific. Finally, we show that female hoverflies are more resilient to starvation than males. In summary, Eristalis hoverflies are resilient to a range of internal and external factors, supporting their use in long-term laboratory experiments. 2017-07-04T05:46:56Z http://datadryad.org/resource/doi:10.5061/dryad.b0846 Divergent natural selection regimes can contribute to adaptive population divergence, but can be sensitive to human-mediated environmental change. Nutrient loading of aquatic ecosystems, for example, might modify selection pressures by altering the abundance and distribution of resources and the prevalence and infectivity of parasites. Here, we used a mesocosm experiment to test for interactive effects of nutrient loading and parasitism on host condition and feeding ecology. Specifically, we investigated whether the common fish parasite Gyrodactylus sp. differentially affected recently diverged lake and stream ecotypes of three-spined stickleback (Gasterosteus aculeatus). We found that the stream ecotype had a higher resistance to Gyrodactylus sp. infections than the lake ecotype, and that both ecotypes experienced a cost of parasitism, indicated by negative relationships between parasite load and both stomach fullness and body condition. Overall, our results suggest that in the early stages of adaptive population divergence of hosts, parasites can affect host resistance, body condition, and diet. 2016-06-28T22:19:40Z http://datadryad.org/resource/doi:10.5061/dryad.rk398 With over half of earth’s terrestrial biota living beneath forest canopies, our ability to accurately capture organism-climate relationships in forested ecosystems is imperative for predicting species’ vulnerability to future climate change. Assessing the vulnerability of forest dependent species, however, hinges on quantifying microclimates that exist below the forest canopy and might be influenced by varying levels of disturbance in human-modified landscapes. The goal of our study was to examine the multi-scaled predictors of subcanopy microclimate variability across a heterogeneous landscape in Midwestern USA during winter, and to further evaluate whether a widely available interpolated climate model accurately captures this variability. By deploying a network of temperature sensors along a fragmentation gradient, we found that forests in more fragmented landscapes experienced colder minimum and average daily temperatures throughout the winter than forests in less fragmented landscapes. We found that greater tree densities and higher elevations led to warmer microclimates while increasing distances from urban centers led to colder microclimates. The negative effect of forest edge on minimum temperatures was lessened by the effect of increasing basal area, highlighting the importance of local- and landscape-scale features on microclimate heterogeneity. Temperature discrepancies between subcanopy microclimates and climate interpolations were influenced by many of the same features, and could be of a similar magnitude as those predicted by future climate change scenarios. Using a biological threshold based on metabolic and demographic constraints for winter birds, we found that the variability in microclimates along our forest fragmentation gradient (50 km) was comparable to the magnitude captured by weather stations across a latitudinal gradient spanning more than 650 km. Our results suggest that biophysical properties of landscapes can alter spatial gradients of microclimates and should be considered when assessing species’ vulnerabilities to future climate change. 2016-07-22T15:42:12Z