SYMP 1-4 - Putting wildlife conservation genomics into practice in California: genomic approaches to species reintroduction, recovery, and management

Effective wildlife management requires understanding of the ecological interactions determining geographic distribution, as well as evolutionary forces that shape genomic variation. Here we advocate for a paradigm shift in wildlife management to recognize the importance of whole genome sequence data as a complement to traditional metrics of distribution and abundance. We present three case studies integrating ecological and whole genome data for wildlife management in California, including population assessment, translocation, and species reintroduction. Characterizing population units and their interactions remains a critical need within wildlife conservation and management. In a multidisciplinary statewide assessment of bobcats (Lynx rufus) spatially explicit capture-recapture modeling, informed by radio telemetry data, are providing distribution and density estimates across distinct ecoregions. Simultaneously, whole genome sequences provide increased power to resolve fine-scale population structure, heterozygosity, and evidence for local adaption. This study represents the most extensive investigation of small wild cats yet undertaken. Human-driven habitat fragmentation has reduced gene flow within natural metapopulations of bighorn sheep (Ovis canadensis), but the threats inbreeding depression and genetic load pose have not been adequately investigated. Nor have the risks of translocating individuals from large, genetically diverse populations to facilitate genetic rescue, as such individuals may harbor high levels of deleterious recessive alleles. To characterize the effects of intense inbreeding and complete isolation, we sequenced whole genomes from a 45-year-old population of bighorn sheep introduced to southern California. Runs of homozygosity and the frequency of strongly deleterious alleles will be used to quantify the extent of inbreeding and genetic load. Population genetic simulation will be used to evaluate extinction risk associated with translocating migrants from moderate-sized versus large source populations with higher genetic load. This study will guide future bighorn sheep translocations for genetic rescue throughout North America. Recovery of endangered species often requires re-establishing populations in unoccupied range. A multi-institutional collaboration is currently underway to reintroduce Sonoran pronghorn (Antilocapra americana sonoriensis) to southern California. Feasibility assessment includes both habitat suitability modeling and whole genome sequencing of potential founders from two captive populations in Arizona. Heterozygosity, runs of homozygosity, and deleterious allele frequencies will establish a genomic baseline for stochastic, individual-based simulations to quantify population viability under various reintroduction scenarios. This will be followed by genetic monitoring that can establish pedigrees to track individual fitness and close inbreeding. This project is the first reintroduction action founded on whole genome data, beginning with source stock selection through long-term genetic monitoring.