Distribution, fine-scale subdivision, and population size of San Joaquin kit foxes in the Ciervo-Panoche Natural Area, California

Tammy R Wilbert,Jesús E Maldonado,Deborah A Smith Woollett,Michael F Westphal,Alice Whitelaw,Katherine Ralls

doi:10.1007/s10592-018-1122-3

Abstract

The endangered San Joaquin kit fox (SJKF; Vulpes macrotis mutica) is strongly linked ecologically to xeric areas with high abundance of kangaroo rats. Endemic to the San Joaquin Desert of central California, the elusive nature of SJKF, coupled with steady habitat loss and lack of comprehensive surveys, has precluded efforts to quantify the species’ population size and distribution, especially in the central and northern parts of its range. Because the Ciervo-Panoche Natural Area contains the largest area of high-quality habitat in this central/northern region, we conducted systematic transect surveys for SJKF scats with professionally trained dog-handler teams throughout the area during 2009–2011. We collected almost 600 scats over 473 km of transects, documenting the freshness and location of each scat. Using molecular methods, we identified 93 SJKF individuals (56 males and 37 females) from 332 samples. Half of the individuals carried a mtDNA haplotype with a 16 bp deletion that had not been previously detected in other areas surveyed. Four individuals were recaptured in 2010 and five in 2011, including one female that was captured every year. We documented a unique mtDNA haplotype and more individuals across a wider area of the Ciervo-Panoche Natural Area than expected. Population analyses revealed two distinct subpopulations, with low connectivity between foxes in the Panoche Valley that are separated by hills with unsuitable habitat from those on the adjacent valley floor next to a major Interstate highway (I-5). While individuals detected within 6 km of each other were closely related, overall relatedness within each subpopulation approached zero. Genetic population models indicated a conservative population estimate of 90 kit foxes in total, with 60–90 individuals in the Panoche Valley and 17–27 individuals in the I-5 area. These results will help to inform management of the SJKF and identify areas that may be important to maintaining connectivity between populations.

Highlights

Informed management decisions require reliable data about the distribution and abundance of an endangered species
We investigated the likelihood of the number of genetic clusters (K) from 1 to 8 with 10 independent replicates, admixture ancestry and correlated allele frequency models, and Markov chain Monte Carlo resampling for 400,000 generations following a burn-in of 100,000
Because we found two or more scats for many individuals and there are no programs that can incorporate more than one geographic location per individual for this type of analysis, we chose one Global Positioning System (GPS) point for each individual that was located in the middle of its sample distribution

Summary

Introduction

Informed management decisions require reliable data about the distribution and abundance of an endangered species. In 1998, a recovery plan identified three geographically-distinct core populations whose enhanced protection and management was critical to a sound conservation strategy: the Carrizo Plain, western Kern County (including Elk Hills, Buena Vista Valley, and Lokern Natural Area), and the Ciervo-Panoche Natural Area (CPNA; U.S Fish and Wildlife Service 1998; Phillips 2013). Both the Carrizo Plain and western Kern County are located in the southwest end of the range and are known to have high SJKF densities. Little is known about SJKF in the CPNA, the area contains large portions of habitat with moderate and high suitability for SJKF and is thought to have a substantial fox population (Cypher et al 2013)

Methods

Results

Conclusion