California is home to both the native state-threatened Sierra Nevada red fox (Vulpes vulpes necator), which historically inhabited high elevations of the Sierra Nevada and Cascade mountains, and to multiple low-elevation red fox populations thought to be of exotic origin. During the past few decades the lowland populations have dramatically expanded their distribution, and possibly moved into the historic range of the native high-elevation fox. To determine whether the native red fox persists in its historic range in California, we compared mitochondrial cytochrome-b haplotypes of the only currently-known high-elevation population (n = 9 individuals) to samples from 3 modern lowland populations (n = 35) and historic (1911–1941) high-elevation (n = 22) and lowland (n = 7) populations. We found no significant population differentiation among the modern and historic high-elevation populations (average pairwise F ST = 0.06), but these populations differed substantially from all modern and historic lowland populations (average pairwise F ST = 0.52). Among lowland populations, the historic and modern Sacramento Valley populations were not significantly differentiated from one another (F ST = −0.06), but differed significantly from recently founded populations in the San Francisco Bay region and in southern California (average pairwise F ST = 0.42). Analysis of molecular variance indicated that 3 population groupings (mountain, Sacramento Valley, and other lowland regions) explained 45% of molecular variance (F CT = 0.45) whereas only 4.5% of the variance was partitioned among populations within these groupings (F SC = 0.08). These findings provide strong evidence that the native Sierra Nevada red fox has persisted in northern California. However, all nine samples from this population had the same haplotype, suggesting that several historic haplotypes may have become lost. Unidentified barriers have apparently prevented gene flow from the Sacramento Valley population to other eastern or southern populations in California. Future studies involving nuclear markers are needed to assess the origin of the Sierra Nevada red fox and to quantify levels of nuclear gene flow.
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