Genetic population structure of Peninsular bighorn sheep (Ovis canadensis nelsoni) indicates substantial gene flow across US–Mexico border

•We examined the population genetics of Peninsular bighorn sheep.•Three distinct genetic populations were identified in the US-Mexico border region.•Substantial genetic diversity was observed at both nuclear and mitochondrial loci.•Assignment tests indicate inter-population dispersal among both sexes.•Low genetic differentiation suggests gene flow across the international border. Within the United States (US), Peninsular bighorn sheep (Ovis canadensis nelsoni, PBS) are listed as federally endangered. Despite known metapopulation structure, little is known regarding functional connectivity across the international border with Mexico. Increasing threats to connectivity associated with highway expansion, renewable energy development, and completion of the US–Mexico border fence, led us to conduct a study of genetic variation and spatial structure. Blood and fecal samples were collected (n=224) on both sides of the border from 1992 to 2013. Genetic data was obtained for 25 microsatellite loci and 515 base pairs of the mitochondrial DNA control region. Microsatellite diversity (observed heterozygosity=0.56; allelic richness=4.1; inbreeding coefficient=0.01) was substantial despite past demographic declines. STRUCTURE analysis indicated the presence of three genetic populations, one of which spanned the international border. This pattern of genetic structure was supported by analysis of molecular variance for both microsatellites and mitochondrial DNA (P