Biology subjects

Jason Munshi-South

Publications and source records attributed to Jason Munshi-South.

4 recordsLinked to original sources

bioRxiv2016

Global population divergence and admixture of the brown rat (Rattus norvegicus)

Once restricted to northern China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution due to the evolution of commensalism with humans. In contrast to black rats and the house mouse, which have tracked the regional and global development of human agricultural settlements, brown rats do not appear in the European historical record until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade and modern sea-faring. We inferred the global phylogeography of brown rats using 32k SNPs to reconstruct invasion routes from estimates of population divergence and admixture. Globally, we detected 13 evolutionary clusters within five expansion routes. One cluster arose following a southward expansion into Southeast Asia. Three additional clusters arose from two independent eastward expansions: one expansion from Russia to the Aleutian Archipelago, and a second to western North America. Rapid westward expansion resulted in the colonization of Europe from which subsequent colonization of Africa, the Americas, and Australasia occurred, and multiple evolutionary clusters were detected. An astonishing degree of fine-grained clustering found both between and within our sampling sites underscored the extent to which urban heterogeneity can shape the genetic structure of commensal rodents. Surprisingly, few individuals were recent migrants despite continual global transport, suggesting that recruitment into established populations is limited. Understanding the global population structure of R. norvegicus offers novel perspectives on the forces driving the spread of zoonotic disease, and yields greater capacity to develop targeted rat eradication programs.

Evolutionary Biology↗

bioRxiv2016

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

Urbanization significantly alters natural ecosystems and has accelerated globally as humans move into dense urban centers. Urban wildlife populations are often highly fragmented by an inhospitable matrix of human infrastructure. Isolated populations may adapt in response to novel urban pressures, but few studies have found evidence of selection in urban environments. We used multiple approaches to examine signatures of selection in transcriptomes from white-footed mice (Peromyscus leucopus) in New York City. We analyzed transcriptomes from 48 P. leucopus individuals from three urban and three rural populations for evidence of rapid local adaption in isolated urban habitats. We generated a dataset of 154,770 SNPs and analyzed patterns of genetic differentiation between urban and rural sites. We also used genome scans and genotype-by-environment (GEA) analyses to identify signatures of selection in a large subset of genes. Neutral demographic processes may create allele frequency patterns that are indistinguishable from positive selection. Thus, we accounted for demography by simulating a neutral SNP dataset under the inferred demographic history for the sampled P. leucopus populations to serve as a null model for outlier analysis. We then annotated outlier genes and further validated them by associating allele frequency differences with two urbanization variables: percent impervious surface and human population density. Many candidate genes were involved in metabolic functions, especially dietary specialization. A subset of these genes have well-established roles in metabolizing lipids and carbohydrates, including transport of cholesterol and desaturation of fatty acids. Our results reveal clear genetic differentiation between rural and urban sites that resulted from rapid local adaptation and drift in urbanizing habitats. The specific outlier loci that we identified suggest that populations of P. leucopus are using novel food resources in urban habitats and selection pressures are acting to change metabolic pathways. Our findings support the idea that cities represent novel ecosystems with a unique set of selective pressures.

Evolutionary Biology↗

bioRxiv2015

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

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 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 SNPs genotyped in 23 populations sampled along an urban-to-rural gradient. Both prehistoric climatic events and recent urbanization impacted these populations. Our modeling 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 New York City.

Evolutionary Biology↗

bioRxiv2015

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.

Evolutionary Biology↗