Genetic analysis of Harbison’s Dun Skipper to inform population management and restoration on conserved lands in San Diego County

This report details the development and analysis of single nucleotide polymorphic loci to understand population genetic structure and diversity among local populations of the Harbison’s dun skipper, Euphyes vestris harbisoni, primarily in San Diego County, California, USA. We developed a set of 2984 SNPs. Local populations were clustered into two to three regional genetic clusters throughout the San Diego County study area: a southeast cluster, an admixed northeast cluster, and a cluster comprised of the two local populations sampled west of Interstate 15 in Lake Hodges and Elfin Forest. Increasing genetic isolation with geographic distance was significant among local populations. While effective population size estimates calculated for the 2016 cohorts in the Southeast and Lake Hodges clusters were both high (point estimates above 500), individual heterozygosity appeared to decline in both clusters over time, and notably so in the Lake Hodges cluster after 2016, suggesting that this cluster may have lost genetic diversity over time. The Southeast cluster appears to have the highest observed heterozygosity across all surveyed areas, but sample sizes in the Northeast cluster were low which may affect these estimates. Future collection efforts may benefit from additional sampling in the Northeast cluster to improve representation. The management plan for Harbison’s dun skipper encourages restoration and re-establishment efforts in unoccupied or recently extirpated sites, particularly in the central portion of the range. Re-establishment efforts could target individuals from large and annually stable local populations in the Southeast portion of the range for transplant, as these populations were also the most genetically diverse.