Genetic source–sink dynamics among naturally structured and anthropogenically fragmented puma populations


Fragmentation of wildlife populations is increasing on a global scale and understanding current population genetic structure, genetic diversity, and genetic connectivity is key to informing wildlife management and conservation. We genotyped 992 pumas (Puma concolor) at 42 previously developed microsatellite loci and identified 10 genetic populations throughout the states of California and Nevada, USA. Although some genetic populations had large effective population sizes, others were small and inbred. Genetic diversity was extremely variable (heterozygosity, uHe = 0.33–0.53), with some populations nearly as low as an endangered subspecies, the Florida Panther (P. c. coryi, uHe = 0.24). Specifically, pumas in the Sierra Nevada were genetically diverse and formed the largest genetic source population in the region. In contrast, coastal and southern populations surrounded by urbanization had low genetic diversity, fragmented gene flow, and tended to be genetic sinks. The strong population genetic structuring of pumas across California (FST = 0.05–0.39) is vastly different than other genetic studies in less-urbanized states, including our analysis in Nevada, where pumas had few barriers to gene flow and weak population differentiation. Our results have far-reaching conservation and management implications for pumas and indicate large-scale fragmentation in one of North America’s most biodiverse and rapidly-urbanizing regions.

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Data availability

Through agreements with non-profit organizations, private landowners, and Native American Tribes, exact GPS locations of puma samples are not to be publicly shared. Thus, puma GPS locations are referenced to the nearest town or city. Sampling locations and microsatellite genotypes are available on Dryad:


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We thank S. Cunningham, C. Lackey, Q. Martins, S. Torres, D. Clifford, J. Rudd, B. Gonzales, M. Miller, P. Swift, J. Ostergard, J. Davis, P. Partridge, C. Wylie, D. Tichenor, B. Milsap, T. Collinsworth, P. Houghtaling, Y. Shakeri, C. Fust, S. McCain, V. Yovovich, Y. Wang, J. Smith, M. Allen, J. Bauer, C. Bell, R. Botta, E. Boydston, K. Brennan, M. Brinkman, P. Bryant, K. Crooks, K. Davis, D. Dawn, M. Elbroch, J. Ewanyk, D. Garcelon, R. Fisher, K. Krause, D. Krucki, K. Logan, L. Lyren, B. Martin, J. Messin, B. Millsap, M. Puzzo, T. Ryan, D. Sforza, L. Sweanor, P. Taylor, C. Wallace, S. Weldy, C. Wiley, S. Winston, E. York, numerous CDFW volunteers and interns, and pathologists from the CAHFS lab for sample collection and handling. We thank L. Dalbeck, J. Well, C. Penedo, N. Pederson, and M. Buchalski for genetics assistance. We thank G. Lee, M. Plancarte, L. Hull, and L. Stockbridge for technical and administrative assistance. This is Professional Paper 119 from the Eastern Sierra Center for Applied Population Ecology.


For funding, we thank the California State Parks Department, California Department of Fish and Wildlife, the U.S. Fish and Wildlife Service Wildlife and Sport Fish Restoration Program, The Nature Conservancy, The Foothill East Transportation Corridor Agency, San Diego County Association of Governments, The National Science Foundation (#0963022 and #1255913), Natural Communities Coalition of Orange County, The San Diego Foundation, The Anza Borrego Foundation, The McBeth Foundation, Felidae Fund, the Gordon and Betty Moore Foundation, Midpeninsula Regional Open Space District, the Eastern Sierra Center for Applied Population Ecology, and the Institute for Wildlife Studies.

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Correspondence to Holly B. Ernest.

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The authors declare that they have no conflict of interest.

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Permission to carry out fieldwork and necessary permits were obtained from CDFW, California Department of Parks and Recreation, The Nature Conservancy, United States (U.S.) Fish and Wildlife Service, U.S. Forest Service, U.S. Bureau of Land Management, U.S. Navy/Marine Corps, Orange County Parks Department, San Diego County Parks Department, Riverside County Parks Department, San Diego State University, University of California—Riverside, Audubon Starr Ranch, Vista Irrigation District, Rancho Mission Viejo/San Juan Company, Sweetwater Authority, California Department of Transportation, the City of San Diego Water Department and Parks Department, and the Irvine Ranch Conservancy.

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Gustafson, K.D., Gagne, R.B., Vickers, T.W. et al. Genetic source–sink dynamics among naturally structured and anthropogenically fragmented puma populations. Conserv Genet 20, 215–227 (2019).

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  • Mountain lion
  • Cougar
  • Puma concolor
  • Population genetics
  • Genetic structure