DOI: 10.5061/dryad.qv9s4mwf0
title: The population genetics of urban and rural amphibians in North America

description: 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.
description: Data & code accompanying Schmidt & Garroway
 (2021) The population genetics of urban and rural amphibians in North
 America <strong>Data:</strong><br>
 amph_data.csv<br> Columns:<br> - pop: unique site
 identifier<br> - species: formatted as Genus_species<br> -
 author: author of original data source (see Table S2 for full list of
 references)<br> - order: taxonomic order; Anura/Caudata<br> -
 lon, lat: longitude & latitude coordinates in decimal degrees,
 WGS84<br> - num_individuals: number of individuals sampled<br>
 - gene_diversity: Nei's gene diversity<br> - allelic_richness:
 rarefied allelic richness (min. 5 individuals)<br> - global_fst:
 population-specific FST<br> - Ne: effective population size
 estimate<br> - Ne_upper, Ne_lower: upper and lower bounds of
 effective population size<br> - num_loci: number of loci
 sampled<br> - urban: 1 = urban sample site; 0 = non-urban sample
 site<br> - road_1_km; road_5_km; road_10_km; road_15_km: road
 lengths within 1, 5, 10, 15 km buffers around sites<br> - 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<br> - 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<br> - 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 <strong>Code:</strong>
 https://github.com/chloewsch/amphibianopolis/