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Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide

DR Trumbo, PE Salerno, KA Logan, M Alldredge, RB Gagne, CP Kozakiewicz, S Kraberger, N Fountain-Jones, ME Craft, S Carver, HB Ernest, K Crooks, S VandeWoude, WC Funk
doi: https://doi.org/10.1101/679720
DR Trumbo
1Department of Biology, Colorado State University, Fort Collins, CO 80523 USA
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  • For correspondence: dtrumbo@colostate.edu
PE Salerno
1Department of Biology, Colorado State University, Fort Collins, CO 80523 USA
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KA Logan
2Colorado Parks and Wildlife, Montrose, CO 81401 USA
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M Alldredge
3Colorado Parks and Wildlife, Fort Collins, CO 80526 USA
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RB Gagne
4Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 USA
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CP Kozakiewicz
5Department of Biological Sciences, University of Tasmania, Hobart, TAS 7005 Australia
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S Kraberger
4Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 USA
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N Fountain-Jones
6Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108 USA
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ME Craft
6Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN 55108 USA
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S Carver
5Department of Biological Sciences, University of Tasmania, Hobart, TAS 7005 Australia
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HB Ernest
7Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070 USA
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K Crooks
8Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523 USA
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S VandeWoude
4Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 USA
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WC Funk
1Department of Biology, Colorado State University, Fort Collins, CO 80523 USA
9Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO 80523 USA
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Abstract

Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 134 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more overall population substructure in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.

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Posted June 22, 2019.
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Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide
DR Trumbo, PE Salerno, KA Logan, M Alldredge, RB Gagne, CP Kozakiewicz, S Kraberger, N Fountain-Jones, ME Craft, S Carver, HB Ernest, K Crooks, S VandeWoude, WC Funk
bioRxiv 679720; doi: https://doi.org/10.1101/679720
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Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide
DR Trumbo, PE Salerno, KA Logan, M Alldredge, RB Gagne, CP Kozakiewicz, S Kraberger, N Fountain-Jones, ME Craft, S Carver, HB Ernest, K Crooks, S VandeWoude, WC Funk
bioRxiv 679720; doi: https://doi.org/10.1101/679720

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