This README_Schlis-Elias_Malaney_Microtus_island_rule.txt file was generated on 2021-12-29 by Mariah Schlis-Elias GENERAL INFORMATION 1. Title of Dataset: Cranial size and shape variation of Microtus pennsylvanicus in the context of Island Rule 2. Authors Mariah C. Schlis-Elias and Jason L. Malaney 3. Dates of data collection: November 2017 to July 2019 4. Geographic location of data collection: Cranium specimens of Microtus pennsylvanicus were either borrowed from or visited and photographed by MCSE. Thirteen Islesboro island specimens used were photographed by Mark D. Omura at Harvard's Museum of Comparative Zoology. Specimens are located at eleven natural history collections, including the University of Kansas Biodiversity Institute, Museum of Southwestern Biology, University of Alaska Museum of the North, University of Michigan Museum of Zoology, National Museum of Natural History, Smithsonian Institution, University of Connecticut Biodiversity Research Collections, Cornell University Museum of Vertebrates, Harvard University Museum of Comparative Zoology, New York State Museum, UC Berkeley Museum of Vertebrate Zoology, and the American Museum of Natural History. Geometric morphometrics were used to address research questions. Landmark coordinates were collected by MCSE using the tps suite of software (Rohlf 2018). 5. Funding Sources: This research was supported by a Graduate Student Research Support Grant (2018) from Austin Peay State University and a Grant-in-Aid of Research (2019) from the American Society of Mammalogists. 6. Associated Publication Citation: Schlis-Elias, M. C. and Malaney, J. L. 2021. Island biogeography predicts skull gigantism and shape variation in meadow voles (Microtus pennsylvanicus) through ecological release and allometry. -- Oikos. DOI: 10.1111/oik.08777. SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: No restrictions on the data provided. 2. Was data derived from another source? yes A. If yes, list source(s): WorldClim Database (https://www.worldclim.org/) DATA & FILE OVERVIEW 1. File/Folder List: centroid-size-figure-materials (folder) - contains all data needed to generate Figure 3 from the associated Oikos publication north-Atlantic-mainland-vs-Maine-islands.csv (file) - contains data from North Atlantic mainland and island populations required to generate Figure 3 Pacific-mainland-vs-Pacific-islands.csv - contains data from Pacific mainland and island populations required to generate Figure 3 south-Atlantic-mainland-vs-south-Atlantic-islands.csv - contains data from South Atlantic mainland and island populations required to generate Figure 3 data-files (folder) - contains all data files needed to run statistical analyses used in the associated Oikos publication all-island-size-TRE-ER.csv (file) - contains average centroid size and island variable values for each island population (both Atlantic and Pacific) studied Atlantic-island-gps.csv - contains average latitude and longitude for each Atlantic island studied Atlantic-island-TRE-ER-variables.csv - contains average centroid size and island variable values for each Atlantic island population studied Atlantic-mainland-gps.csv - contains latitude and longitude of each Atlantic mainland specimen sampled Atlantic-mainland-TRE-variables.csv - contains specimen catalog numbers, centroid size, population ID, GPS coordinates, and bioclimatic variable values for all Atlantic mainland specimens dorsal-variables-Procrustes-order.csv - contains specimen catalog numbers, centroid sizes, population ID, and other information for all specimens in the order they were in following Procrustes superimposition mean-size-ecoregion-type.csv - contains the average centroid size, ecoregion, and population type of each population studied Pacific-mainland-gps.csv - contains latitude and longitude of each Pacific mainland specimen sampled Pacific-mainland-TRE-variables.csv - contains specimen catalog numbers, centroid size, population ID, GPS coordinates, and bioclimatic variable values for all Pacific mainland specimens ventral-variables-Procrustes-order.csv - contains specimen catalog numbers, centroid sizes, population ID, and other information for all specimens in the order they were in following Procrustes superimposition R-scripts (folder) - contains all R code needed to run statistical analyses and generate Figure 5 and supplemental figures used in the associated Oikos publication Atlantic-island-ER-path-model.R (file) - contains annotated R script that runs the ecological release path model; produces a path model figure centroid-size-figure.R - contains annotated R script for generating Figure 3 centroid-size-variation.R - contains annotated R script that runs all general centroid size analyses dorsal-pca-figure.R (file) - contains annotated R script for generating Figure 5a; this was produced using the gmShiny application dorsal-pca-figure.RData - RData file containing the data necessary to produce Figure 5a dorsal-raw-shape.R - contains annotated R script used to test for dorsal shape differences among populations dorsal-shape-size.R - contains annotated R script used to test for allometry (association between dorsal cranium shape and size) dorsal-symmetry-permutations.RData - RData file containing dorsal shape symmetry permutations used in R shape analysis scripts island-shape-size-TRE-ER.R - contains annotated R script that runs all shape/size models against island variables for dorsal and ventral data (island populations only) island-size-ER-models.R - contains annotated R script that runs all island size models against ecological release variables island-size-TRE-models.R - contains annotated R script that runs all island size models against thermoregulation and endurance variables mainland-size-TRE-models.R - contains annotated R script that runs all mainland size models against thermoregulation and endurance variables ventral-pca-figure.R - contains annotated R script for generating Figure 5b; this was produced using the gmShiny application ventral-pca-figure.RData - RData file containing the data necessary to produce Figure 5b ventral-raw-shape.R - contains annotated R script used to test for ventral shape differences among populations ventral-shape-size.R - contains annotated R script used to test for allometry (association between ventral cranium shape and size) ventral-symmetry-permutations.RData - RData file containing ventral shape symmetry permutations used in R shape analysis scripts shape-coordinate-tps-files (folder) - contains all specimen shape coordiantes in tps file format dorsal-mean-shape-coords.tps (file) - tps file containing the average dorsal shape coordinates of each population (these are already Procrustes-aligned) dorsal-raw-landmark-coords.tps - tps file containing all specimens' raw dorsal landmark coordinates (not yet aligned by Procrustes superimposition) dorsal-symmetric-shape-component-coords.tps - tps file containing the dorsal symmetric shape coordinates (already Procrustes-aligned) for each specimen ventral-mean-shape-coords.tps - tps file containing the average ventral shape coordinates of each population (these are already Procrustes-aligned) ventral-raw-landmark-coords.tps - tps file containing all specimens' raw ventral landmark coordinates (not yet aligned by Procrustes superimposition) ventral-symmetric-shape-component-coords.tps - tps file containing the dorsal symmetric shape coordinates (already Procrustes-aligned) for each specimen METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: Specimen information was obtained from the VertNet and Arctos museum databases. Landmark coordinates were obtained using tpsDig from 2-dimensional photographs of the crania examined. All analyses were carried out in RStudio using R v4.1.1. 2. Instrument- or software-specific information needed to interpret the data: R packages required to run included R script abind v1.4-5 forcats v0.5.1 geomorph v4.0.1 rrpp v1.1.0 ggplot2 v3.3.5 ggthemes v4.2.4 lavaan v0.6-9 Morpho v2.9 vegan v2.5-7 3. Describe any quality-assurance procedures performed on the data: Error assessment was conducted on landmark digitization and specimen orientation according to methods described by Fruciano (2016). Digitization and orientation error each accounted for < 1% of shape variation in the data. 4. People involved with sample collection, processing, analysis and/or submission: MCSE collected and processed most data and ran all analyses. JLM obtained bioclimatic data. DATA-SPECIFIC INFORMATION Data abbreviations listed in alphabetical order (applies to all csv files included in upload) agescore = age score assigned to each speicmen by MCSE using a rubric established by Snyder (1954) area = island area (in kilometers squared); measured using the polygon tool in Google Earth Pro catalognumber = unique catalog number of each specimen used (includes the 2-4 letter institution code, followed by the specimen number after an underscore); can be used to reference specimen data on VertNet or Arctos databases county = county (or equivalent division of land) that a specimen was collected in dsize = unmodified dorsal centroid size (represents either a population average or measurement from an individual specimen depending on file) ecoregion = ecoregion that an individual specimen or population belongs to (either Atlantic for specimens/populations sampled from the east coast of North America or Pacific for those sampled from the west coast of North America) ER = Ecological Release hypothesis (involves the variables island area, isolation, number of mammalian predators, and number of reptilian predators) ID = unique number assigned to populations for R script using the "mean-size-ecoregion-type.csv" file; required for proper pairing of multiple data sources imageID = unique name for the specific photo (jpeg file) used to represent a specimen and collect data from it iso = island isolation; measured as the shortest, uninterrupted distance between an island's coast and the nearest mainland coast; measured using the ruler tool in Google Earth Pro lat = decimal degrees latitude (represents either a population average or measurement from an individual specimen depending on file) lnarea = natural logarithm-transformed island area lndsize = natural logarithm-transformed dorsal centroid size (represents either a population average or measurement from an individual specimen depending on file) lnvsize = natural logarithm-transformed ventral centroid size (represents either a population average or measurement from an individual specimen depending on file) lon = decimal degrees longitude (represents either a population average or measurement from an individual specimen depending on file) mam = number of mammalian predator species inhabiting an island pairs = population assignment of each specimen for analyses using a more paired structure North Atlantic islands were paired with North Atlantic mainland individuals (represented by MainlandA1) South Atlantic islands were paired with South Atlantic mainland individuals (represented by MainlandA2) PCNM1 = eigenvalues from the first component of a Principal Component of Neighbourhood Matrix analysis conducted on GPS coordinates of specimens (represents either a population average or measurement from an individual specimen depending on file) population = island or mainland population that specimen belongs to (or average data represents) rep = number of reptilian predator species inhabiting an island scientificname = scientific name of a specimen (as determined by specimen collectors or collections staff, not the authors) seas = temperature seasonality; this variable was bio4 pulled from the WorldClim dataset for each georeferenced specimen divided by 100 sex = biological sex of a specimen (as determined by specimen collectors, not the authors) stateprovince = state (if collected in the United States) or province (if collected in Canada) that a specimen was collected in temp = minimum temperature of the coldest month; this variable was bio6 pulled from the WorldClim dataset for each georeferenced specimen divided by 10 TRE = Thermoregulation and Endurance hypothesis (involves the variables latitude, PCNM1, temperature seasonality, and minimum temperature of the coldest month) type = classifies population type (either mainland or island) vsize = unmodified ventral centroid size (represents either a population average or measurement from an individual specimen depending on file) year = year that a specimen was collected