Genetic structure of California's elk: a legacy of extirpations, reintroductions, population expansions, and admixture

California, USA, is home to 3 subspecies of North American elk (Cervus canadensis): Roosevelt (C. c. roosevelti), Rocky Mountain (C. c. nelsoni), and tule (C. c. nannodes). Effective management requires a baseline understanding of each subspecies' range, admixture zones, and geographic patterns of genetic diversity. To address these questions, we genotyped 1,271 individual elk from California (n = 1,204) and reference populations of Rocky Mountain and Roosevelt elk from Nevada (n = 32) and Oregon (n = 35), USA. Using 19 polymorphic microsatellite loci, we detected admixture between Roosevelt and Rocky Mountain elk at a contact zone in northern California, and between Roosevelt and tule elk in north‐coastal California and central‐coastal California. We identified a genetically distinct population of Roosevelt elk in northwestern California, likely reflecting the remnant population that survived a large demographic decline from overhunting during the 1800s. Tule elk exhibited lower levels of heterozygosity (0.44 ± 0.03 [SD]) and allelic richness (2.9 ± 0.2) than Rocky Mountain (0.58 ± 0.05, 4.9 ± 0.4, respectively) and Roosevelt (0.50 ± 0.06, 4.4 ± 0.6, respectively) elk. Among tule elk populations, heterozygosity varied, with the lowest heterozygosity (0.23 ± 0.05) corresponding to the oldest enclosed herd used over the past century as a source of translocations. Among tule elk populations, genetic structure revealed several cases of successful and unsuccessful reintroduction or augmentation attempts. Results provide an essential baseline for future monitoring and decisions about harvest management, translocations to preserve genetic diversity, and landscape‐level conservation planning to maintain, enhance, or obstruct connectivity of elk populations. Genome‐wide sequencing and analyses are needed to quantify inbreeding absolutely and assess genetic load and the age of admixture where subspecies currently exchange genes. California is home to 3 subspecies of North American elk. To obtain a baseline understanding of each subspecies' range, admixture zones, and geographic patterns of genetic diversity, we genotyped 1,271 individual elk from the western United States at 19 microsatellite loci. Findings provide an essential baseline to inform future monitoring and decisions about harvest management, translocations to preserve genetic diversity, and landscape‐level conservation planning to maintain, enhance, or obstruct connectivity of elk populations.