Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area
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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.
Cite this as
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 PeerJ PrePrints 1:e13v2 https://doi.org/10.7287/peerj.preprints.13v2note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
Author comment
This is a preprint of the final version of a manuscript that has been accepted at PLOS One.
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Competing Interests
The authors declare that there are no competing interests regarding this manuscript.
Author Contributions
Stephen E Harris conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper.
Jason Munshi-South conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper.
Craig Obergfell performed the experiments, contributed reagents/materials/analysis tools.
Rachel O'Neill conceived and designed the experiments, contributed reagents/materials/analysis tools, wrote the paper.
Animal Ethics
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
All animal procedures were approved by the Institutional Animal Care and Use Committee at Brooklyn College, CUNY (Protocol No. 247), and adhered to the Guidelines of the American Society of Mammalogists for the Use of Wild Mammals in Research (Sikes & Gannon 2011).
Field Study Permissions
The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):
New York State Department of Environmental Conservation (License to Collect or Possess Wildlife No. 1603)
New York City Department of Parks and Recreation
Grant Disclosures
The following grant information was disclosed by the authors:
National Science Foundation DEB 0817259
National Institute of General Medical Sciences / National Institutes of Health 1R15GM099055-01A1
DNA Deposition
The following information was supplied regarding the deposition of DNA sequences:
GenBank Sequence Read Archive (SRA) Accession Number SRP020005
Data Deposition
The following information was supplied regarding the deposition of related data:
Datasets associated with this preprint will be available on Data Dryad at http://dx.doi.org/10.5061/dryad.r8ns3
Funding
This work was funded by grants from the National Science Foundation (DEB 0817259) and National Institute of General Medical Sciences / National Institutes of Health (1R15GM099055-01A1) to JM-S, and a National Science Foundation Graduate Research Fellowship to SEH. The Center for Applied Genetics and Technology at UCONN provided funding for RO and CO. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
