DOI: 10.5061/dryad.d48f9
title: Data from: Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

description: 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.
description: 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.txt