Detecting the Endangered San Joaquin Kit Fox (Vulpes macrotis mutica) and Other Canine Species in Kern County, CA: Applying a Non-Invasive PCR-Based Method to Four Case Study Sites

The endangered San Joaquin kit fox (SJKF) (Vulpes macrotis mutica), which is endemic to the San Joaquin Valley in California, has lost most of its natural habitat due to urban sprawl and change in land use over time. Many studies have been conducted to restore and protect the remaining habitat, involving presence/absence surveys prior to urban development using camera monitoring, tracking dogs, tracking plates, spotlighting, and trapping. While these traditional methods work well, they can be invasive, expensive, labor-intensive, and require permits to perform. In our study, we used a non-invasive method based on DNA extraction from scat collected in the environment, followed by a diagnostic Polymerase Chain Reaction (PCR)-based approach on mitochondrial DNA fragments and investigated the presence of the SJKF on four case study sites that shared a high SJKF habitat suitability index but are under the threat of development. We found that the diagnostic PCR was able to accurately differentiate between different canids present at the sites, in a time- and cost-effective manner. Including this non-invasive method in the Department of Fish and Wildlife’s standardized recommendations for survey methods would help to improve future environmental assessments for SJKF populations in the Central Valley of California.