A few iconic examples have proven the value of facilitated gene flow for counteracting inbreeding depression and staving off extinction; yet, the practice is often not implemented for fear of causing outbreeding depression. Using genomic sequencing, climatic niche modeling, and demographic reconstruction, we sought to assess the risks and benefits of using translocations as a tool for recovery of endangered montane red fox (Vulpes vulpes) populations in the western United States. We demonstrated elevated inbreeding and homozygosity of deleterious alleles across all populations, but especially those isolated in the Cascade and Sierra Nevada ranges. Consequently, translocations would be expected to increase population growth by masking deleterious recessive alleles. Demographic reconstructions further indicated shallow divergences of less than a few thousand years among montane populations, suggesting low risk of outbreeding depression. These genomic-guided findings set the stage for future management, the documentation of which will provide a roadmap for recovery of other data-deficient taxa.

Carnivores play critical roles in ecosystems, yet many species are declining worldwide. The Sierra Nevada Red Fox (Vulpes vulpes necator; SNRF) is a rare and endangered subspecies of red fox limited to upper montane forests, subalpine, and alpine environments of California and Oregon, United States. Having experienced significant distribution contractions and population declines in the last century, the subspecies is listed as at-risk by relevant federal and state agencies. Updated information on its contemporary distribution and density is needed to guide and evaluate conservation and management actions. We combined 12 years (2009-2020) of detection and nondetection data collected throughout California and Oregon to model the potential distribution and density of SNRFs throughout their historical and contemporary ranges. We used an integrated species distribution and density modeling approach, which predicted SNRF density in sampled locations based on observed relationships between environmental covariates and detection frequencies, and then projected those predictions to unsampled locations based on the estimated correlations with environmental covariates. This approach provided predictions that serve as density estimates in sampled regions and projections in unsampled areas. Our model predicted a density of 1.06 (95% credible interval = 0.8-1.36) foxes per 100 km2 distributed throughout 22,926 km2 in three distinct regions of California and Oregon-Sierra Nevada, Lassen Peak, and Oregon Cascades. SNRFs were most likely to be found in areas with low minimum temperatures and high snow water equivalent. Our results provide a contemporary baseline to inform the development and evaluation of conservation and management actions, and guide future survey efforts.

As anthropogenic disturbances continue to drive habitat loss and range contractions, the maintenance of evolutionary processes will increasingly require targeting measures to the population level, even for common and widespread species. Doing so requires detailed knowledge of population genetic structure, both to identify populations of conservation need and value, as well as to evaluate suitability of potential donor populations. We conducted a range-wide analysis of the genetic structure of red foxes in the contiguous western U.S., including a federally endangered distinct population segment of the Sierra Nevada subspecies, with the objectives of contextualizing field observations of relative scarcity in the Pacific mountains and increasing abundance in the cold desert basins of the Intermountain West. Using 31 autosomal microsatellites, along with mitochondrial and Y-chromosome markers, we found that populations of the Pacific mountains were isolated from one another and genetically depauperate (e.g., estimated Ne range = 3-9). In contrast, red foxes in the Intermountain regions showed relatively high connectivity and genetic diversity. Although most Intermountain red foxes carried indigenous western matrilines (78%) and patrilines (85%), the presence of nonindigenous haplotypes at lower elevations indicated admixture with fur-farm foxes and possibly expanding midcontinent populations as well. Our findings suggest that some Pacific mountain populations could likely benefit from increased connectivity (i.e., genetic rescue) but that nonnative admixture makes expanding populations in the Intermountain basins a non-ideal source. However, our results also suggest contact between Pacific mountain and Intermountain basin populations is likely to increase regardless, warranting consideration of risks and benefits of proactive measures to mitigate against unwanted effects of Intermountain gene flow.