DNA fingerprinting of Southern Mule Deer (Odocoileus hemionus fuliginatus) in North San Diego County, California (2018-19)

Abstract

Throughout the western United States, efforts are underway to better understand and preserve migration and movement corridors for mule deer and other big game and to minimize the impacts of development and other land-use change on populations. San Diego County is home to a unique non-migratory subspecies of mule deer, the Southern mule deer ( Odocoileus hemionus fuliginatus ; herein referred to as “mule deer”). Because it is the only large herbivorous mammal in San Diego, connectivity among mule deer groups is an important indicator of functional connectivity throughout San Diego County urban preserves and has therefore been monitored within central and eastern San Diego County using DNA fingerprinting since 2005. To continue this effort and to assess genetic connectivity in north San Diego County (herein “North County”), we genotyped scat samples from preserves in the area and tissue samples from Marine Corps Base Camp Pendleton (MCBCP). We used non-invasive capture/recapture analyses and pedigree analyses for assessing short-term movement and population clustering analyses to assess gene flow in North County. Additionally, we performed similar analyses on the combined San Diego County dataset, which was composed of the North County dataset collected for this study and a previously collected dataset from central and eastern San Diego County. Using recapture data, we found multiple instances of mule deer crossing roads in urban North County preserves, with several of these events occurring in areas where there are underpasses and culverts known to be used by mule deer. Corroborating previous studies in the region and statewide, pedigree and population structure analyses support the presence of two genetic clusters for mule deer in San Diego County—the “Coastal” and “Inland/Mountain” clusters. Low estimates of effective population size, especially in the Coastal cluster, suggest that to further understand potential vulnerabilities of mule deer in this region, it is important to continue to monitor connectivity, in particular, at the boundary between these two clusters.