Vol.:(0123456789) 1 3 Conservation Genetics https://doi.org/10.1007/s10592-018-1125-0 RESEARCH ARTICLE Genetic source–sink dynamics among naturally structured and anthropogenically fragmented puma populations Kyle D. Gustafson 1,2  · Roderick B. Gagne 1  · T. Winston Vickers 3  · Seth P. D. Riley 4  · Christopher C. Wilmers 5  · Vernon C. Bleich 6  · Becky M. Pierce 7  · Marc Kenyon 8  · Tracy L. Drazenovich 9  · Jef A. Sikich 4  · Walter M. Boyce 3  · Holly B. Ernest 1 Received: 11 May 2018 / Accepted: 15 November 2018 © This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2018 Abstract 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 identifed 10 genetic populations throughout the states of California and Nevada, USA. Although some genetic populations had large efective 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). Specifcally, 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 fow, and tended to be genetic sinks. The strong population genetic structuring of pumas across California (F ST = 0.05–0.39) is vastly diferent than other genetic studies in less-urbanized states, including our analysis in Nevada, where pumas had few barriers to gene fow and weak population diferentiation. 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. Keywords Mountain lion · Cougar · Puma concolor · Population genetics · Genetic structure Introduction Fragmentation of wildlife habitat and resultant impacts to populations are increasing worldwide and urbanization is one of the primary contributors (Crooks et al. 2017; Fahrig 2003; Haddad et al. 2015; Newbold et al. 2016). Unlike Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10592-018-1125-0) contains supplementary material, which is available to authorized users. * Holly B. Ernest holly.ernest@uwyo.edu 1 Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY 82070, USA 2 Department of Biology & Environmental Health, Missouri Southern State University, Joplin, MO 64870, USA 3 Karen C. Drayer Wildlife Health Center, School of Veterinary Medicine, University of California, Davis, CA 95616, USA 4 National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA 91360, USA 5 Environmental Studies Department, University of California, Santa Cruz, CA 95064, USA 6 Department of Natural Resources and Environmental Science, University of Nevada Reno, Reno, NV 89557, USA 7 Bishop, CA 93515, USA 8 Division of Fish, Wildlife, & Parks, Wisconsin Department of Natural Resources, Wisconsin Rapids, WI 54494, USA 9 Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA