Data from: Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.VCF of SNP genotypes for 191 white-footed miceVCF (variant call format 4.0) file of SNP genotypes for 191 white-footed mice generated using ddRAD-Seq. SNPs and VCF file were generated using Stacks version 1.21. Sequences were not reference-aligned, so SNPs appear in an arbitrary order.wfm191vcf.zipGENEPOP file of SNP genotypes for 191 white-footed miceGENEPOP file of SNP genotypes for 191 white-footed mice generated using ddRAD-Seq. SNPs and GENEPOP file were generated using Stacks version 1.21. Sequences were not reference-aligned, so SNPs appear in an arbitrary order. File is compressed in a ZIP archive for ease of downloading.wfm191genepop.zipAllele counts for white-footed mouse populations for use in BEDASSLEThis text file includes allele counts for SNPs generated for white-footed mouse populations. This file can be used as input in the BEDASSLE R package. The number of columns are the number of biallelic SNP loci and the number of rows are the number of populations. Each value represents the number of times allele '1' is observed in each population. The choice of which allele is allele '1' is arbitrary but consistent across the populations.wfm_bedassle_alleles.txtSample sizes for white-footed mouse populations for use in the BEDASSLE R package.This text file includes sample sizes for white-footed mouse populations for use in the BEDASSLE R package. This file is a companion to the text file included the SNP allele counts. The number of rows is equal to the number of populations, and the number of columns is equal to the number of biallelic SNP loci sampled for this study. Each value represents the number of chromosomes successfully genotyped at each locus in each population.wfm_bedassle_samples.tx