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 genome-wide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genome-wide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genome-wide variation was estimated as a proxy for evolutionary potential using more than 10,000 SNP markers generated by ddRAD-Seq. We found that genome-wide 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 genome-wide 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 genome-wide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.

城市化会引发广泛的生境破碎化，并通过瓶颈效应与遗传漂变降低种群的现存遗传变异。全基因组遗传变异的丧失，最终可能会削弱处于快速变化环境中的动物种群的进化潜力。本研究以纽约都会区沿城市化梯度采样的23个白足鼠（Peromyscus leucopus）种群为对象，对其全基因组遗传变异展开分析。研究利用ddRAD-Seq技术获得的逾10000个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记，将全基因组变异作为进化潜力的替代指标进行估算。结果显示，全基因组遗传变异与以不透水面覆盖率衡量的城市化水平呈负相关，且与人类人口密度的相关性相对较弱。同时本研究证实，城市化会加剧城市种群间的全基因组遗传分化。这些种群未表现出距离隔离模式，但基于不透水面的阻力隔离模型能够显著解释遗传分化的分布格局。环境隔离建模结果同样表明，与郊区或乡村种群相比，城市种群的等位基因频率与全球等位基因频率的偏差程度显著更高。本研究首次沿城乡梯度分析了全基因组单核苷酸多态性变异的丧失情况，并量化了城市化作为种群基因组格局驱动因子的作用。