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Genetic Adaptation in New York City Rats

View ORCID ProfileArbel Harpak, View ORCID ProfileNandita Garud, View ORCID ProfileNoah A. Rosenberg, View ORCID ProfileDmitri A. Petrov, View ORCID ProfileMatthew Combs, View ORCID ProfilePleuni S. Pennings, View ORCID ProfileJason Munshi-South
doi: https://doi.org/10.1101/2020.02.07.938969
Arbel Harpak
1Department of Biological Sciences, Columbia University, New York, NY
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  • For correspondence: ah3586@columbia.edu jmunshisouth@fordham.edu
Nandita Garud
2Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA
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Noah A. Rosenberg
3Department of Biology, Stanford University, Stanford, CA
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Dmitri A. Petrov
3Department of Biology, Stanford University, Stanford, CA
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Matthew Combs
4Department of Biological Sciences, Fordham University, Armonk, NY
5Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, NY
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Pleuni S. Pennings
6Department of Biology, San Francisco State University, San Francisco, CA
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Jason Munshi-South
4Department of Biological Sciences, Fordham University, Armonk, NY
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  • For correspondence: ah3586@columbia.edu jmunshisouth@fordham.edu
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Abstract

Brown rats (Rattus norvegicus) thrive in urban environments by navigating the anthropocentric environment and taking advantage of human resources and by-products. From the human perspective, rats are a chronic problem that causes billions of dollars in damage to agriculture, health and infrastructure. Did genetic adaptation play a role in the spread of rats in cities? To approach this question, we collected whole-genome samples from 29 brown rats from New York City (NYC) and scanned for genetic signatures of adaptation. We applied multiple methods, testing for (i) high-frequency, extended haplotypes that could indicate selective sweeps and (ii) loci of extreme genetic divergence between the NYC sample and a sample from the presumed ancestral range of brown rats in rural north east China. We found candidate selective sweeps near or inside genes associated with metabolism, diet, organ morphogenesis and locomotory behavior. The divergence between NYC and rural Chinese rats at putative sweep loci suggests that many sweeps began after the split from the ancestral population. Together, our results suggest several hypotheses for a genetic component behind the adaptation of rats in response to human activity.

Footnotes

  • ↵* P.S.P. and J.M.-S. jointly supervised this work

  • https://arbelharpak.com/data/

Copyright 
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 February 08, 2020.
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Genetic Adaptation in New York City Rats
Arbel Harpak, Nandita Garud, Noah A. Rosenberg, Dmitri A. Petrov, Matthew Combs, Pleuni S. Pennings, Jason Munshi-South
bioRxiv 2020.02.07.938969; doi: https://doi.org/10.1101/2020.02.07.938969
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Genetic Adaptation in New York City Rats
Arbel Harpak, Nandita Garud, Noah A. Rosenberg, Dmitri A. Petrov, Matthew Combs, Pleuni S. Pennings, Jason Munshi-South
bioRxiv 2020.02.07.938969; doi: https://doi.org/10.1101/2020.02.07.938969

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