A hierarchical modeling approach to predict the distribution and density of Sierra Nevada Red Fox (Vulpes vulpes necator)

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.

Contrasting genetic trajectories of endangered and expanding red fox populations in the western U.S

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.

The Red Fox Y-Chromosome in Comparative Context

While the number of mammalian genome assemblies has proliferated, Y-chromosome assemblies have lagged behind. This discrepancy is caused by biological features of the Y-chromosome, such as its high repeat content, that present challenges to assembly with short-read, next-generation sequencing technologies. Partial Y-chromosome assemblies have been developed for the cat (Feliscatus), dog (Canislupusfamiliaris), and grey wolf (Canislupuslupus), providing the opportunity to examine the red fox (Vulpesvulpes) Y-chromosome in the context of closely related species. Here we present a data-driven approach to identifying Y-chromosome sequence among the scaffolds that comprise the short-read assembled red fox genome. First, scaffolds containing genes found on the Y-chromosomes of cats, dogs, and wolves were identified. Next, analysis of the resequenced genomes of 15 male and 15 female foxes revealed scaffolds containing male-specific k-mers and patterns of inter-sex copy number variation consistent with the heterogametic chromosome. Analyzing variation across these two metrics revealed 171 scaffolds containing 3.37 Mbp of putative Y-chromosome sequence. The gene content of these scaffolds is consistent overall with that of the Y-chromosome in other carnivore species, though the red fox Y-chromosome carries more copies of BCORY2 and UBE1Y than has been reported in related species and fewer copies of SRY than in other canids. The assignment of these scaffolds to the Y-chromosome serves to further characterize the content of the red fox draft genome while providing resources for future analyses of canid Y-chromosome evolution.

Predicting the Potential Distribution of the Sierra Nevada Red Fox in the Oregon Cascades

The Sierra Nevada red fox Vulpes vulpes necator is a native subspecies associated with subalpine regions in the Sierra Nevada and Cascade mountain ranges of California and Oregon. In the past century, the Sierra Nevada red fox experienced a major range contraction and decline in California. However, the number, size, and connectivity of populations extant in Oregon remain unclear. This knowledge gap impedes efficient monitoring and hinders development of a cohesive conservation strategy for the subspecies. The historical range is large and includes rugged terrain with low accessibility; therefore, a predictive model is needed to facilitate more comprehensive and systematic surveys in the future. We initiated a multiagency collaborative effort to survey portions of the range in the Oregon Cascades during 2011–2016 (verified genetic and photographic detections) and to assemble existing sighting reports dating back to 1985 (unverified), which we used to create Maxent models to predict the potential distribution of Sierra Nevada red fox within Oregon. To identify optimal levels of model complexity, we compared cross-validation accuracy of models that varied in levels of protection against overfitting (regularization). The highest-performing models utilized intermediate regularization, and included minimum January temperature and land-cover type. Regardless of regularization or data set (verified detections, all putative detections), all models agreed in predictions of a high-probability region covering approximately 3,470 km2 or 6% of the Cascade region, corresponding to the high-elevation portion of the crest. With the exception of a gap between Mount Hood and Mt. Jefferson, this core area of predicted presence was continuous along the north–south extent of the crest, suggesting a capacity for high connectivity among observed clusters of occurrence. Use of modeled potential distributions in future survey design will improve efficiency of field data collection, facilitating more precise evaluations of the distribution, abundance, and genetic integrity and connectivity of Sierra Nevada red fox in Oregon.