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

Stephen E. Harris, View ORCID ProfileJason Munshi-South
doi: https://doi.org/10.1101/038141
Stephen E. Harris
1The Graduate Center, City University of New York (CUNY), New York, NY 10016 USA
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  • For correspondence: harris.stephen.e@gmail.com
Jason Munshi-South
2Louis Calder Center—Biological Field Station, Fordham University, 31 Whippoorwill Road Armonk, NY 10504 USA
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ABSTRACT

Urbanization significantly alters natural ecosystems and has accelerated globally. Urban wildlife populations are often highly fragmented by human infrastructure, and isolated populations may adapt in response to local urban pressures. However, relatively few studies have identified genomic signatures of adaptation in urban animals. We used a landscape genomics approach to examine signatures of selection in urban populations of white-footed mice (Peromyscus leucopus) in New York City. We analyzed 154,770 SNPs identified from transcriptome data from 48 P. leucopus individuals from three urban and three rural populations, and used outlier tests to identify evidence of urban adaptation. We accounted for demography by simulating a neutral SNP dataset under an inferred demographic history as a null model for outlier analysis. We also tested whether candidate genes were associated with environmental variables related to urbanization. In total, we detected 381 outlier loci and after stringent filtering, identified and annotated 19 candidate loci. Many of the candidate genes were involved in metabolic processes, and have well-established roles in metabolizing lipids and carbohydrates. Our results indicate that white-footed mice in NYC are adapting at the biomolecular level to local selective pressures in urban habitats. Annotation of outlier loci suggest selection is acting on metabolic pathways in urban populations, likely related to novel diets in cities that differ from diets in less disturbed areas.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted September 26, 2017.
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Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)
Stephen E. Harris, Jason Munshi-South
bioRxiv 038141; doi: https://doi.org/10.1101/038141
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Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus)
Stephen E. Harris, Jason Munshi-South
bioRxiv 038141; doi: https://doi.org/10.1101/038141

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