Genetic factors in the decline of small populations are extremely difficult to study in nature. We leveraged a natural experiment to investigate evidence of inbreeding depression and genetic rescue in a remnant population of subalpine-specialized Sierra Nevada red foxes (Vulpes vulpes necator) using noninvasive genetic monitoring during 2010–2017. Only 7 individuals were detected in the first 2 years. These individuals assigned genetically to the historical population and exhibited genetic hallmarks of inbreeding and no evidence of reproduction. Two years into the study, we detected 2 first-generation immigrant males from a recently expanding population of red foxes in the Great Basin Desert. Through annual resampling of individuals (634 red fox DNA samples, 41 individuals) and molecular reconstruction of pedigrees, we documented 1–3 litters/year for 5 years, all descended directly or indirectly from matings involving immigrant foxes. The observed heterozygosity and allelic richness of the population nearly doubled in 2 years. Abundance increased, indicative of a rapidly expanding population. Throughout the study, adult survival was high. Restoration of gene flow apparently improved the demographic trajectory of this population in the short term. Whether these benefits continue in the longer term could depend on numerous factors, such as maintenance of any locally adapted alleles. This study highlights the value of noninvasive genetic monitoring to assess rapidly shifting conditions in small populations. Uncertainties about the longer-term trajectory of this population underscore the need to continue monitoring and to research potential for both negative and positive aspects of continued genetic infusion.

The red wolf (Canis rufus) of the eastern US was driven to near‐extinction by colonial‐era persecution and habitat conversion, which facilitated coyote (C. latrans) range expansion and widespread hybridization with red wolves. The observation of some grey wolf (C. lupus) ancestry within red wolves sparked controversy over whether it was historically a subspecies of grey wolf with its predominant “coyote‐like” ancestry obtained from post‐colonial coyote hybridization (2‐species hypothesis) versus a distinct species closely related to the coyote that hybridized with grey wolf (3‐species hypothesis). We analysed mitogenomes sourced from before the 20th century bottleneck and coyote invasion, along with hundreds of modern amplicons, which led us to reject the 2‐species model and to investigate a broader phylogeographic 3‐species model suggested by the fossil record. Our findings broadly support this model, in which red wolves ranged the width of the American continent prior to arrival of the grey wolf to the mid‐continent 60–80 ka; red wolves subsequently disappeared from the mid‐continent, relegated to California and the eastern forests, which ushered in emergence of the coyote in their place (50–30 ka); by the early Holocene (12–10 ka), coyotes had expanded into California, where they admixed with and phenotypically replaced western red wolves in a process analogous to the 20th century coyote invasion of the eastern forests. Findings indicate that the red wolf pre‐dated not only European colonization but human, and possibly coyote, presence in North America. These findings highlight the urgency of expanding conservation efforts for the red wolf.

No abstract

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.

The complex topography, climate, and geological history of Western North America have shaped contemporary patterns of biodiversity and species distributions in the region. Pacific martens (Martes caurina) are distributed along the northern Pacific Coast of North America with disjunct populations found throughout the Northwestern Forested Mountains and Marine West Coast Forest ecoregions of the West Coast. Martes in this region have been classified into subspecies; however, the subspecific designation has been extensively debated. In this study, we use genomic data to delineate conservation units of Pacific marten in the Sierra-Cascade-Coastal montane belt in the western United States. We analyzed the mitochondrial genome for 94 individuals to evaluate the spatial distribution and divergence times of major lineages. We further genotyped 401 individuals at 13 microsatellite loci to investigate major patterns of population structure. Both nuclear and mitochondrial DNA suggest substantial genetic substructure concordant with historical subspecies designations. Our results revealed that the region contains 2 distinct mitochondrial lineages: a Cascades/Sierra lineage that diverged from the Cascades/coastal lineage 2.23 (1.48–3.14 mya), consistent with orogeny of the Cascade Mountain chain. Interestingly, Pacific Martes share phylogeographic patterns similar with other sympatric taxa, suggesting that the complex geological history has shaped the biota of this region. The information is critical for conservation and management efforts, and further investigation of adaptive diversity is warranted following appropriate revision of conservation management designations.

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.

Island spotted skunks (Spilogale gracilis amphiala) are a rare subspecies endemic to the California Channel Islands, currently extant on Santa Cruz and Santa Rosa islands. How and when skunks arrived on the islands is unknown, hindering decision-making about their taxonomic status and conservation priority. We investigated these questions by sequencing the complete mitochondrial genomes of 55 skunks from the two islands and mainland (California and Arizona) and examining phylogenetic patterns and estimations of isolation times among populations. Island spotted skunks grouped in a single monophyletic clade distinct from mainland spotted skunks. A haplotype network analysis had the most recent common ancestral haplotype sampled from an individual on Santa Rosa, suggesting both islands were colonized by a single matriline. Additionally, no haplotypes were shared between skunk populations on the two islands. These patterns imply that both island populations were derived from a common ancestral population shortly after establishment and have remained isolated from each other ever since. Together with divergence estimates from three methods, this topology is consistent with colonization of the super-island, Santarosae, by a single ancestral population of spotted skunks in the early Holocene, followed by divergence as the sea level rose and split Santarosae into Santa Cruz and Santa Rosa islands 9,400–9,700 years ago. Such a scenario of colonization could be explained either by rafting or one-time transport by Native Americans. Given their distinct evolutionary history, high levels of endemism, and current population status, island spotted skunks may warrant management as distinct evolutionarily significant units.

red fox, state-threatened, Vulpes vulpes necator _________________________________________________________________________ The Sierra Nevada red fox (Vulpes vulpes necator; SNRF) is a subspecies of red fox native to the upper montane, subalpine, and alpine zones of the Sierra Nevada and Cascades in California and Oregon (Grinnell et al. 1937;Perrine et al. 2010;Sacks et al. 2010). Declines in the distribution and abundance of SNRF populations led to the designation of the subspecies as state-threatened in California in 1980 (Gould 1980. More recently, the remnant population in the Sierra Nevada was proposed for federal listing as an endangered Distinct Population Segment (USFWS 2020). Lack of certainty as to the distribution of remnant SNRF populations has hindered conservation efforts and population recovery. Using noninvasive survey techniques, we documented the southernmost SNRF detections in recent decades, greatly expanding the known contemporary range of this state-threatened subspecies (Perrine et al. 2010;Hatfield et al. 2020).Although the subspecies existed historically as far south as the Mt. Whitney region (Grinnell et al. 1937), the verified contemporary distribution of SNRF in the Sierra Nevada is far more restricted.