The SAN joaquin kit FOX (sjkf vulpes macrotis mutica) is a federally endangered species with a CVP priority level of very high

The sjkf is identified in the recovery plan as an umbrella species representing habitat requirements of multiple species impacted by the CVP through loss of grassland and salt-desert shrub habitats to agricultural irrigation. Extant populations of sjkf are distributed among an urban population (BAKERSFIELD), 3 primary core populations (western kern taft, carrizo, panoche), and approximately a dozen smaller satellite populations for which connectivity is unknown (figure 1). A significant threat to the largest of these populations, that in BAKERSFIELD, is sarcoptic mange caused by the mite sarcoptes scabiei. This mange epizootic also threatens adjacent populations. A better understanding of the epidemiology of this disease, including density-dependence and transmission from other mammals, along with early detection surveys will help in preventing its spread to other regions of the range. In BAKERSFIELD, camera trapping has been used over the past 7 years to monitor both mange prevalence and kit FOX abundance, which is effective in this urban setting but infeasible to be applied range-wide. The current study, however, provides an opportunity to develop and validate other noninvasive tools that are more practical to apply widely and over longer periods of time. As part of the broader efforts to control and assess population level effects of the mange epizootic (see concurrent proposal by cypher ET AL.), we propose to develop an efficient noninvasive method to survey for and monitor mange prevalence, sjkf abundance, and sjkf diet as a potential long-term correlate of transmission risk. The study will entail two components: (I) development of a sufficiently sensitive and highly specific assay for S. Scabiei DNA in sjkf scats, and (II) a pilot study to test application of this tool in conjunction with noninvasive fecal DNA-based estimation of sjkf abundance and diet. I. For the first component (assay development), we will assess the efficacy of two approaches to detection of the 16S mitochondrial locus of S. Scabiei: real-time PCR and amplicon shotgun sequencing. Although real-time PCR is known to be highly sensitive, amplicon shotgun sequencing could be similarly so and would have the added advantage of allowing for simultaneous sequencing of prey DNA (as proposed here), as well as microbiomes or other pathogens through metabarcoding (matching specific sequences or barcodes to a barcode database). The assay will be tested both on synthetic DNA with known concentrations of mite DNA combined with fecal DNA and on scats from foxes known mange infestation status. Sensitivity and specificity will be quantified, enabling field surveys for early detection of mange in any population. II. For the pilot study, noninvasive field-sampling for sjkf scats will be used to estimate prevalence of mange, abundance of sjkf based on spatially explicit capture recapture analysis, and sjkf diet through metabarcoding. These metrics will be compared to those estimated concurrently and independently using direct, conventional methods. This research builds on, leverages, and complements ongoing and concurrent proposed research by cypher ET AL. And ongoing research by sacks ET AL. On the effects of mange on genetic status and population connectivity. Results will inform the mpva, including guidance toward assessment of locations for translocations and reintroductions and identification of strategic land acquisition targets that would maximize preservation and protection from mange. By providing a feasible method of estimating sjkf abundance as well as mange risk throughout the range, this project will contribute directly to recovery task 4.80 in the SJV upland species RP - conduct a spatially-explicit metapopulation viability analysis on SAN joaquin kit foxes.