Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

Stephen E Harris; Jason Munshi-South; Craig Obergfell; Rachel O'Neill

doi:10.7287/peerj.preprints.13v2

Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area

Stephen E Harris¹, Jason Munshi-South ², Craig Obergfell³, Rachel O'Neill³

1 Program in Ecology, Evolutionary Biology, and Behavior, The Graduate Center, City University of New York, New York, NY, USA

2 Biological Sciences & Louis Calder Center, Fordham University, Armonk, NY, USA

3 Molecular & Cell Biology, University of Connecticut, Storrs, CT, USA

DOI: 10.7287/peerj.preprints.13v2

Published: 2013-08-21
Accepted: 2013-08-21

Subject Areas: Ecology, Evolutionary Studies, Genomics, Zoology
Keywords: rapid evolution, transcriptome, Peromyscus, urban ecology, directional selection, candidate gene, nonsynonymous substitution, divergent ecosystem, 454 next-generation sequencing, microevolution

Copyright: © 2013 Harris et al.
Licence: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Cite this article: Harris SE, Munshi-South J, Obergfell C, O'Neill R. 2013. Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area. PeerJ PrePrints 1:e13v2 https://doi.org/10.7287/peerj.preprints.13v2

Abstract

Urbanization is a major cause of ecological degradation around the world, and human settlement in large cities is accelerating. New York City (NYC) is one of the oldest and most urbanized cities in North America, but still maintains 20% vegetation cover and substantial populations of some native wildlife. The white-footed mouse, Peromyscus leucopus, is a common resident of NYC’s forest fragments and an emerging model system for examining the evolutionary consequences of urbanization. In this study, we developed transcriptomic resources for urban P. leucopus to examine evolutionary changes in protein-coding regions for an exemplar ‘urban adapter’. We used Roche 454 GS FLX+ high throughput sequencing to derive transcriptomes from multiple tissues from individuals across both urban and rural populations. From these data, we identified 31,015 SNPs and several candidate genes potentially experiencing positive selection in urban populations of P. leucopus. These candidate genes are involved in xenobiotic metabolism, innate immune response, demethylation activity, and other important biological phenomena in novel urban environments. This study is one of the first to report candidate genes exhibiting signatures of directional selection in divergent urban ecosystems.