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The population genetics of urban and rural amphibians in North America

Citation

Schmidt, Chloé; Garroway, Colin (2021), The population genetics of urban and rural amphibians in North America, Dryad, Dataset, https://doi.org/10.5061/dryad.qv9s4mwf0

Abstract

Human land transformation is one of the leading causes of vertebrate population declines. These declines are thought to be partly due to decreased connectivity and habitat loss reducing animal population sizes in disturbed habitats. With time, this can lead to declines in effective population size and genetic diversity which restricts the ability of wildlife to efficiently cope with environmental change through genetic adaptation. However, it is not well understood whether these effects generally hold across taxa. We address this question by repurposing and synthesizing raw microsatellite data from online repositories for 19 amphibian species sampled at 554 georeferenced sites in North America. For each site, we estimated gene diversity, allelic richness, effective population size, and population differentiation. Using binary urban-rural census designations, and continuous measures of human population density, the Human Footprint Index, and impervious surface cover, we tested for generalizable effects of human land use on amphibian genetic diversity. We found minimal evidence, either positive or negative, for relationships between genetic metrics and urbanization in our repurposed data. Together with previous work on focal species that also found varying effects of urbanization on genetic composition, it seems likely that the consequences of urbanization are not easily generalizable within or across amphibian species. Questions about the genetic consequences of urbanization for amphibians should be addressed on a case-by-case basis. This contrasts with general negative effects of urbanization in mammals and consistent, but species-specific, positive and negative effects in birds.

Usage Notes

Data & code accompanying Schmidt & Garroway (2021) The population genetics of urban and rural amphibians in North America

Data:
amph_data.csv
Columns:
- pop: unique site identifier
- species: formatted as Genus_species
- author: author of original data source (see Table S2 for full list of references)
- order: taxonomic order; Anura/Caudata
- lon, lat: longitude & latitude coordinates in decimal degrees, WGS84
- num_individuals: number of individuals sampled
- gene_diversity: Nei's gene diversity
- allelic_richness: rarefied allelic richness (min. 5 individuals)
- global_fst: population-specific FST
- Ne: effective population size estimate
- Ne_upper, Ne_lower: upper and lower bounds of effective population size
- num_loci: number of loci sampled
- urban: 1 = urban sample site; 0 = non-urban sample site
- road_1_km; road_5_km; road_10_km; road_15_km: road lengths within 1, 5, 10, 15 km buffers around sites
- pd_1_km; pd_5_km; pd_10_km; pd_15_km: mean human population density within 1, 5, 10, 15 km buffers around sites
- hfi_1_km; hfi_5_km; hfi_10_km; hfi_15_km: mean Human Footprint Index within 1, 5, 10, 15 km buffers around sites
- imp_30m; imp_1_km; imp_5_km; imp_10_km; imp_15_km: mean % impervious surface cover within 30m and 1, 5, 10, 15 km buffers around sites

Code: https://github.com/chloewsch/amphibianopolis/