The San Joaquin kit fox (Vulpes macrotis mutica) was once ubiquitous throughout California's San Joaquin Valley and its surrounds. However, most of its habitat has been lost to irrigated agriculture, urban development, and oil fields. The remaining foxes are concentrated in six areas, although there are several small pockets of foxes throughout the Valley. To help conserve kit foxes, we sought an ecological understanding of the level of genetic variation remaining in these locations and the extent of gene flow among them. We collected tissue from 317 kit foxes from 8 sites and estimated genetic variability in and gene flow among sites using data from 8 polymorphic, microsatellite markers. We found no differences in both observed and expected heterozygosity between locations using Bonferonni corrected paired t-tests. We found differences in mean number of alleles per locus, even after we used Monte Carlo simulations to adjust for sample size differences. Population subdivision was low among sites (F st ¼ 0.043), yet a matrix of pairwise F st values was correlated with a matrix of pairwise geographic distances. An assignment test classified only 45% of the individuals to the site where they were captured. Overall, these data suggest that kit fox dispersal between locations may still maintain genetic variation throughout most of the areas we sampled.

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