Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus ) in New York City

Abstract

How urbanization shapes population genomic diversity and evolution of urban wildlife is largely unexplored. We investigated the impact of urbanization on white-footed mice, Peromyscus leucopus, in the New York City (NYC) metropolitan area using coalescent-based simulations to infer demographic history from the site-frequency spectrum. We assigned individuals to evolutionary clusters and then inferred recent divergence times, population size changes and migration using genome-wide single nucleotide polymorphisms genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modelling indicates that post-glacial sea-level rise led to isolation of mainland and Long Island populations. These models also indicate that several urban parks represent recently isolated P. leucopus populations, and the estimated divergence times for these populations are consistent with the history of urbanization in NYC.

Signatures of positive selection and local adaptation to urbanization in white‐footed mice (Peromyscus leucopus)

“…While balancing selection has been found to maintain variation in immune loci in fragmented urban population of bobcats ( Lynx rufus ) (Serieys et al 2015), it is difficult to distinguish whether demography or selection drives Tajima’s D values in many cases (MacManes & Eisen 2014). We have estimated the complex demographic history for P. leucopus populations in NYC (Harris et al 2016), suggesting Tajima’s D may not be the best tool for identifying selection in this system. Outlier tests are more robust to demography and we explicitly accounted for the specific demographic history of P. leucopus in the null models used during analysis of our genome scan methods.…”

“…The window within each contig with the highest CLR score is considered the likely location of a selective sweep. Similar to the method used for BayeScan, statistical significance was established from a null distribution generated by running SweeD on SNP datasets simulated under the inferred demographic history for P. leucopus populations (Harris et al 2016). SweeD does not inherently identify outlier regions.…”

“…Munshi-South (2012) found barriers to dispersal between isolated NYC parks, with migrants only moving through significantly vegetated corridors throughout the city. There is also substantial genetic structure between NYC parks as measured by microsatellites (Munshi-South & Kharchenko 2010), genome-wide SNPs (Munshi-South et al 2016) and demographic modeling (Harris et al 2016). We have also previously identified signatures of selection in urban populations of NYC white-footed mice (Harris et al 2013), though we used smaller datasets and more limited approaches than presented here.…”

“…However, neutral demographic processes such as population bottlenecks can produce signatures of genetic variation similar to those produced by selection (Oleksyk et al 2010; Li et al 2012). We accounted for this possibility by incorporating a simulated neutral SNP dataset from an inferred demographic history (Harris et al 2016) directly into our null model for identifying outliers (Excoffier et al 2009; Gutenkunst et al 2009; Li et al 2012; Vitti et al 2013; Lotterhos & Whitlock 2015). …”

Urban driven phenotypic changes: empirical observations and theoretical implications for eco-evolutionary feedback

“…An example of a direct impact on human health is that of white-footed mice in the New York metropolitan area. Studies by Munshi-South et al [14,[77][78][79] and Harris et al [80]. show signals of directional selection in urban ecosystems for these mice which are the critical hosts for black-legged ticks (Ixodes scapularis) that carry the Lyme disease bacterium Borrelia burgdorferi, leading to spikes of human exposure to this organism.…”