In principle, genetic augmentations can rescue inbred populations from extinction vortices. In practice, genetic rescue is seldom used as a management tool due to uncertainty about risks and long-term benefits. We analyzed 34 whole genome sequences of North American red foxes to support planning for genetic augmentation of a small, isolated population of Sierra Nevada red foxes (Vulpes vulpes necator) in the vicinity of Lassen National Park, California. We found high levels of recent inbreeding in the Lassen population and elevated homozygosity of putative deleterious alleles, supporting inbreeding as a plausible factor influencing viability. We then evaluated the genomic suitability of candidate source populations by comparing the demographic histories and levels of deleterious variation across multiple North American red fox populations. Montane populations share a long-term history and became isolated from each other relatively recently, suggesting low risk of outbreeding depression. Different intensities of anthropogenic declines, however, have created tradeoffs in the potential and realized load of novel deleterious alleles that source populations may contribute to the Lassen population. Such tradeoffs may be particularly influential in genetic rescue of extremely small populations and thus bear careful consideration in source selection for the Lassen Sierra Nevada red fox.

Hybridization has a large impact on the generation and maintenance of biodiversity. However, genetic integrity among distinct lineages and populations has the potential to be eroded through admixture, thus directly influencing evolutionary trajectories and management policies. Mule deer (Odocoileus hemionus) are an important and intensively managed game species in California. We examined the genomic evidence for six putative mule deer subspecies resident to California using low coverage (~1.1X) whole genome resequencing data. We also used whole mitogenomes to evaluate the evolutionary relationships between mule deer in California and white-tailed deer (Odocoileus virginanus). Principal component and admixture analyses based on ~215,644 SNPs recovered varying levels of differentiation among putative subspecies. Our results primarily supported the presence of Columbia black-tailed, Rocky Mountain, Southern, and California mule deer lineages with pronounced admixture in regions of sympatry. Our mitogenome phylogenetic estimate suggested close affiliation of Rocky Mountain mule deer in northeastern California with white-tailed deer, similar to previous studies of those two lineages in other regions of North America. Our findings offer insights into the geographic scale of genetic structure and admixture among mule deer subspecies in California, which provides a foundation for future research on adaptative introgression and aid in management decisions.

Since 2020, the California Department of Fish and Wildlife (CDFW) Law Enforcement Division’s Wildlife Forensic Laboratory (WFL) has utilized genetic methods to detect individual black bears (Ursus americanus) involved in human-wildlife conflict incidents resulting in property damage and public safety concerns in the Tahoe Basin. The collection of DNA samples from home and vehicle invasions has provided a novel and unique opportunity to non-invasively track black bears through their genetic profiles in near real time. Samples are analyzed using forensically validated methods to ensure accuracy of results and to provide statistical significance when an individual profile is detected multiple times. Turn-around time from raw sample to DNA profile ranges from 4 to 12 hours depending on the sample type, and the profiles generated enable historic and near real time geographic tracking of bears without the use of a radio tracking collar. The combination of field and genetic investigation has given insight into the behavioral patterns that are passed down generationally from sow to cub(s) and the need for active management practices.

Since 2016, the Wildlife Forensic Laboratory (WFL) of the California Department of Fish and Wildlife’s (CDFW) Law Enforcement Division has used a variety of genetic methods to non-invasively detect and monitor gray wolves (C. l. lupus) in California. Over 1500 potential gray wolf samples have been collected and analyzed since inception, detecting a total of 88 different wolves. These methods allow CDFW to genetically detect 1) successful matings, 2) mortalities, 3) migration, and 4) relatedness to known wolves and packs both within and outside of California. In investigations of illegal take or depredation on livestock, the WFL can compare collected evidence with the genetic profiles of known wolves to confirm identity or distinguish from other canid species (i.e. coyotes, domestic dogs, hybrids). Collaborative efforts with outside agencies have yielded nearly 400 gray wolf reference samples from the Northern Rocky Mountain ecosystem, Great Lakes region, Alaska, and parts of Canada, which have been used to construct a genetic database for statistical analyses of individual identification and kinship. Using this information, the pedigree of our California gray wolf packs has been reconstructed through six generations, which traces back to the parents of OR7, the first wolf to enter California since the 1800s.