UC Davis

ABSTRACT California is the only state or province that contains 3 unique subspecies of North American elk (Cervus canadensis): Roosevelt (C. c. roosevelti), Rocky Mountain (C. c. nelsoni), and tule (C. c. nannodes) elk. Where populations overlap, subspecies can interbreed, creating zones of hybridization. Effective management of these subspecies requires a baseline understanding of each subspecies’ range, identification of hybridization zones, and the ability to monitor and track changes in the genetic diversity and integrity of the subspecies over time. It is also important to monitor the magnitude of actual gene flow resulting from translocations and range expansion. One of the primary goals stated in California’s 2018 Elk Conservation and Management Plan was ensuring long-term persistence of all 3 subspecies (California Department of Fish and Wildlife [CDFW] 2018). To aid in these goals we conducted the most comprehensive genetic assessment of California’s elk to date. During this collaborative study, we created updated range maps for all 3 subspecies, mapped hybridization, characterized the heterozygosity and effective population sizes of subspecies and individual Elk Management Units (EMUs), and analyzed spatial population structure. Tissue, hair, and fecal samples were used for DNA extraction and genotyping of 19 polymorphic microsatellite loci. We obtained genotypes for 1,271 individual elk from California, Nevada, and Oregon. We detected hybridization between Roosevelt and Rocky Mountain elk at a natural contact zone in northern California and identified 2 introduced Rocky Mountain elk populations with little or no introgression from Roosevelt elk. An admixture analysis also revealed the existence of a genetically distinct population of Roosevelt elk in Humboldt County potentially reflecting a remnant population that survived a large decline from overhunting during the 1800s. We detected hybridization between Roosevelt and tule elk in Mendocino County and between tule and either Rocky Mountain or Roosevelt elk in San Luis Obispo County. Tule elk exhibited lower levels of heterozygosity and allelic richness than Rocky Mountain and Roosevelt elk. The Tupman and East Park Reservoir tule elk populations exhibited the lowest levels of heterozygosity and allelic richness. This study provides information that is essential for understanding the genetic landscape of elk in California, and will inform decisions about harvest management, translocations, and landscape-level conservation planning to maintain and enhance connectivity of elk populations where desired. Our study should be followed up with more intensive genomic analyses of inbreeding and admixture, but nevertheless provides a strong foundation for future genetic monitoring and informed management practices.