Missing History of a Modern Domesticate: Historical Demographics and Genetic Diversity in Farm-bred Red Fox Populations.

The first record of captive bred red foxes (Vulpes vulpes) dates to 1896, when a breeding enterprise emerged in the provinces of Atlantic Canada. Because its domestication happened during recent history, the red fox offers a unique opportunity to examine the genetic diversity of an emerging domesticated species in the context of documented historical and economic influences. In particular, the historical record suggests that North American and Eurasian farm-bred populations likely experienced different demographic trajectories. Here, we focus on the likely impacts of founder effects and genetic drift given historical trends in fox farming on North American and Eurasian farms. A total of 15 mitochondrial haplotypes were identified in 369 foxes from 10 farm populations that we genotyped (n=161) or that were previously published. All haplotypes are endemic to North America. Although most haplotypes were consistent with eastern Canadian ancestry, a small number of foxes carried haplotypes typically found in Alaska and other regions of western North America. The presence of these haplotypes supports historical reports of wild foxes outside of Atlantic Canada being introduced into the breeding stock. These putative Alaskan and Western haplotypes were more frequently identified in Eurasian farms compared to North American farms, consistent with historical documentation suggesting that Eurasian economic and breeding practices were likely to maintain low-frequency haplotypes more effectively than in North America. Contextualizing inter- versus intra-farm genetic diversity alongside the historical record is critical to understanding of the origins of this emerging domesticate and the relationships between wild and farm-bred fox populations.

The history of Coast Salish "woolly dogs" revealed by ancient genomics and Indigenous Knowledge.

Ancestral Coast Salish societies in the Pacific Northwest kept long-haired "woolly dogs" that were bred and cared for over millennia. However, the dog wool-weaving tradition declined during the 19th century, and the population was lost. In this study, we analyzed genomic and isotopic data from a preserved woolly dog pelt from "Mutton," collected in 1859. Mutton is the only known example of an Indigenous North American dog with dominant precolonial ancestry postdating the onset of settler colonialism. We identified candidate genetic variants potentially linked with their distinct woolly phenotype. We integrated these data with interviews from Coast Salish Elders, Knowledge Keepers, and weavers about shared traditional knowledge and memories surrounding woolly dogs, their importance within Coast Salish societies, and how colonial policies led directly to their disappearance.

Genomic analysis of wolves from Pakistan clarifies boundaries among three divergent wolf lineages.

Among the three main divergent lineages of gray wolf (Canis lupus), the Holarctic lineage is the most widespread and best-studied, particularly in North America and Europe. Less is known about Tibetan (also called Himalayan) and Indian wolf lineages in southern Asia, especially in areas surrounding Pakistan where all three lineages are thought to meet. Given the endangered status of the Indian wolf in neighboring India and unclear southwestern boundary of the Tibetan wolf range, we conducted mitochondrial and genome-wide sequencing of wolves from Pakistan and Kyrgyzstan. Sequences of the mitochondrial D-loop region of 81 wolves from Pakistan indicated contact zones between Holarctic and Indian lineages across the northern and western mountains of Pakistan. Reduced-representation genome sequencing of 8 wolves indicated an east-to-west cline of Indian to Holarctic ancestry, consistent with a contact zone between these two lineages in Pakistan. The western boundary of the Tibetan lineage corresponded to the Ladakh region of India's Himalayas with a narrow zone of admixture spanning this boundary from the Karakoram Mountains of northern Pakistan into Ladakh, India. Our results highlight the conservation significance of Pakistan's wolf populations, especially the remaining populations in Sindh and Southern Punjab that represent the highly endangered Indian lineage.

Deer dietary responses to wildfire: Optimal foraging, individual specialization, or opportunism?

Increasing impacts of wildfire on arid regions of the world fuelled by climate change highlight the need to better understand how natural communities respond to fire. We took advantage of a large (1660-km2 ) wildfire that erupted in northern California during an in-progress study of black-tailed deer (Odocoileus hemionus columbianus) to investigate deer use of and diets within burned and unburned habitats before and after the fire. We compared deer diet breadth to predictions of optimal foraging theory, the niche variation hypothesis, and opportunistic (i.e., generalist) foraging expectations under the assumption that overall availability and diversity of forage in burned areas declined immediately after the fire and increased as the plant community recovered in the next 3 years after the fire. We used faecal pellet counts to document space use and metabarcoding to study diet during pre-fire, post-fire, and recovery periods. Pellet counts supported predictions that deer increased use of unburned sites and reduced use of burn sites after the fire and began to return to burned sites in subsequent sampling years. Diet diversity did not differ significantly between control and burn sites before the fire, but was lower in burn than control sites post-fire (p < .001), when and where diet was dominated by oak (Quercus spp). In contrast, during subsequent years, diet diversity was higher (including more herbaceous plants) in burn than control sites (p < .05). In contrast to predictions of optimal foraging and niche variation hypotheses, individual deer foraged as generalists for which changes in dietary niche breadth paralleled fire-induced changes in diversity of the plant community.

Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages?

Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.

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.

Genomic analyses of gray fox lineages suggest ancient divergence and secondary contact in the southern Great Plains.

The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that eastern and western lineages met in the southern Great Plains (i.e. Texas and Oklahoma), where they maintained high differentiation. Admixture was generally low, with the majority of admixed individuals carrying <10% ancestry from the other lineage. Divergence times confirmed a mid-Pleistocene split, similar to the mitochondrial estimates. Taken together, findings suggest gray fox lineages represent an ancient divergence event, far older than most intraspecific divergences in North American carnivores. Low admixture may reflect a relatively recent time since secondary contact (e.g. post-Pleistocene) or, alternatively, ecological or reproductive barriers between lineages. Though further research is needed to disentangle these factors, our genomic investigation suggests species-level divergence exists between eastern and western gray fox lineages.

Evolutionary legacy of the extirpated red wolf clings to life in gulf-coast canids.

Before Europeans colonized North America, a uniquely American wolf roamed the eastern forests of southern Canada to Florida and west to the Great Plains. Known today as "red wolf" (Canis rufus) in the south and "eastern wolf" (Canis lycaon) in the north, evidence suggests that these indigenous forest wolves shared a common evolutionary history until only a few centuries ago when they were extirpated from the intervening majority of their historical range. While the eastern wolf persists today primarily as a small population in Algonquin Provincial Park, Canada, the red wolf was ostensibly driven from its last stronghold in gulf-coastal Louisiana and Texas by 1980. The last-known red wolves were taken captive for propagation and reintroduction. Today, the red wolf exists as ~250 descendants of 12 founders and are distributed among 42 captive breeding facilities and one reintroduced population in coastal North Carolina. As red and eastern wolves declined in the 20th century, coyotes expanded from the west into the eastern forests, replacing them. Along with human persecution, coyote hybridization has been blamed for the late 20th century demise of the red wolf. However, rather than helping to drive the red wolf to extinction, coyote hybridization may have instead helped to preserve it. In this issue of Molecular Ecology, vonHoldt and colleagues provide the most comprehensive description yet of the substantial quantity and distribution of red wolf ancestry sequestered in southeastern coyote populations. They find the highest frequency of red wolf genes in coyotes from the gulf-coastal sites where the last known wild red wolves occurred, but also present evidence for a high prevalence of red wolf genes in coyotes throughout the southeastern expansion zone. Given the significant reduction in genetic diversity in extant red wolves owing to their late 20th century population bottleneck, this coyote-sequestered reservoir of red wolf genes could prove an important resource for red wolf conservation.

Population Genetics of California Gray Foxes Clarify Origins of the Island Fox.

We used mitochondrial sequences and nuclear microsatellites to investigate population structure of gray foxes (Urocyon cinereoargenteus) and the evolutionary origins of the endemic island fox (Urocyon littoralis), which first appeared in the northern Channel Islands <13,000 years ago and in the southern Channel Islands <6000 years ago. It is unclear whether island foxes evolved directly from mainland gray foxes transported to the islands one or more times or from a now-extinct mainland population, already diverged from the gray fox. Our 345 mitochondrial sequences, combined with previous data, confirmed island foxes to be monophyletic, tracing to a most recent common ancestor approximately 85,000 years ago. Our rooted nuclear DNA tree additionally indicated genome-wide monophyly of island foxes relative to western gray foxes, although we detected admixture in northern island foxes from adjacent mainland gray foxes, consistent with some historical gene flow. Southern California gray foxes also bore a genetic signature of admixture and connectivity to a desert population, consistent with partial replacement by a late-Holocene range expansion. Using our outgroup analysis to root previous nuclear sequence-based trees indicated reciprocal monophyly of northern versus southern island foxes. Results were most consistent with island fox origins through multiple introductions from a now-extirpated mainland population.

Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding.

The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non-native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.

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.

Natural and human-driven selection of a single non-coding body size variant in ancient and modern canids.

Domestic dogs (Canis lupus familiaris) are the most variable-sized mammalian species on Earth, displaying a 40-fold size difference between breeds.1 Although dogs of variable size are found in the archeological record,2-4 the most dramatic shifts in body size are the result of selection over the last two centuries, as dog breeders selected and propagated phenotypic extremes within closed breeding populations.5 Analyses of over 200 domestic breeds have identified approximately 20 body size genes regulating insulin processing, fatty acid metabolism, TGFß signaling, and skeletal formation.6-10 Of these, insulin-like growth factor 1 (IGF1) predominates, controlling approximately 15% of body size variation between breeds.8 The identification of a functional mutation associated with IGF1 has thus far proven elusive.6,10,11 Here, to identify and elucidate the role of an ancestral IGF1 allele in the propagation of modern canids, we analyzed 1,431 genome sequences from 13 species, including both ancient and modern canids, thus allowing us to define the evolutionary history of both ancestral and derived alleles at this locus. We identified a single variant in an antisense long non-coding RNA (IGF1-AS) that interacts with the IGF1 gene, creating a duplex. While the derived mutation predominates in both modern gray wolves and large domestic breeds, the ancestral allele, which predisposes to small size, was common in small-sized breeds and smaller wild canids. Our analyses demonstrate that this major regulator of canid body size nearly vanished in Pleistocene wolves, before its recent resurgence resulting from human-imposed selection for small-sized breed dogs.

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe.

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

Ancient divergence of Indian and Tibetan wolves revealed by recombination-aware phylogenomics.

The grey wolf (Canis lupus) expanded its range across Holarctic regions during the late Pleistocene. Consequently, most grey wolves share recent (<100,000 years ago) maternal origins corresponding to a widespread Holarctic clade. However, two deeply divergent (200,000-700,000 years ago) mitochondrial clades are restricted, respectively, to the Indian subcontinent and the Tibetan Plateau, where remaining wolves are endangered. No genome-wide analysis had previously included wolves corresponding to the mitochondrial Indian clade or attempted to parse gene flow and phylogeny. We sequenced four Indian and two Tibetan wolves and included 31 additional canid genomes to resolve the phylogenomic history of grey wolves. Genomic analyses revealed Indian and Tibetan wolves to be distinct from each other and from broadly distributed wolf populations corresponding to the mitochondrial Holarctic clade. Despite gene flow, which was reflected disproportionately in high-recombination regions of the genome, analyses revealed Indian and Tibetan wolves to be basal to Holarctic grey wolves, in agreement with the mitochondrial phylogeny. In contrast to mitochondrial DNA, however, genomic findings suggest the possibility that the Indian wolf could be basal to the Tibetan wolf, a discordance potentially reflecting selection on the mitochondrial genome. Together, these findings imply that southern regions of Asia have been important centers for grey wolf evolution and that Indian and Tibetan wolves represent evolutionary significant units (ESUs). Further study is needed to assess whether these ESUs warrant recognition as distinct species. This question is especially urgent regarding the Indian wolf, which represents one of the world's most endangered wolf populations.

Pleistocene origins, western ghost lineages, and the emerging phylogeographic history of the red wolf and coyote.

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.

Sequencing Red Fox Y Chromosome Fragments to Develop Phylogenetically Informative SNP Markers and Glimpse Male-Specific Trans-Pacific Phylogeography.

The red fox (Vulpes vulpes) has a wide global distribution with many ecotypes and has been bred in captivity for various traits, making it a useful evolutionary model system. The Y chromosome represents one of the most informative markers of phylogeography, yet it has not been well-studied in the red fox due to a lack of the necessary genomic resources. We used a target capture approach to sequence a portion of the red fox Y chromosome in a geographically diverse red fox sample, along with other canid species, to develop single nucleotide polymorphism (SNP) markers, 13 of which we validated for use in subsequent studies. Phylogenetic analyses of the Y chromosome sequences, including calibration to outgroups, confirmed previous estimates of the timing of two intercontinental exchanges of red foxes, the initial colonization of North America from Eurasia approximately half a million years ago and a subsequent continental exchange before the last Pleistocene glaciation (~100,000 years ago). However, in contrast to mtDNA, which showed unidirectional transfer from Eurasia to North America prior to the last glaciation, the Y chromosome appears to have been transferred from North America to Eurasia during this period. Additional sampling is needed to confirm this pattern and to further clarify red fox Y chromosome phylogeography.

Whole mitochondrial genome of long-clawed mole vole (Prometheomys schaposchnikowi) from Turkey, with its phylogenetic relationships.

The mitogenome of Prometheomys schaposchnikowi was characterized for the first time as a circular DNA molecule (16.284 bp), containing 37 coding and 2 non-coding regions. In the mitogenome, ND6 and 8 tRNA genes were encoded on the light chain, while 12 PCGs, 14 tRNAs, 2 rRNAs, D-loop and OL were encoded on the heavy chain. The most common initiation codon in PCGs was ATG. As in many mammals, incomplete stop codons in P. schaposchnikowi were in the COX3, ND1 and ND4. Phylogenetic relationships were revealed using Bayesian method and the 13 PCGs. Seven genera (Arvicola, Dicrostonyx, Lasiopodomys, Myodes, Ondatra, Proedromys and Prometheomys) formed a monophyletic group, while Eothenomys, Microtus and Neodon were paraphyletic. P. schaposchnikowi constituted the most basal group within Arvicolinae. Divergence time estimation suggested that P. schaposchnikowi diversified during the Miocene (16.28 Mya). Further molecular studies are needed to test the distinctiveness and diversity of the genus Prometheomys.

Pliocene-Early Pleistocene Geological Events Structure Pacific Martens (Martes caurina).

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.

Using Ancestry-Informative SNPs to Quantify Introgression of European Alleles into North American Red Foxes.

A recent study demonstrated that British red foxes introduced to the mid-Atlantic coastal plain (ACP) of the eastern United States during the late 18th century successfully interbred with indigenous American red foxes despite half a million year's divergence. However, a large disparity in frequency of European mitochondria (27%) versus Y chromosomes (1%) left unclear the magnitude of genetic exchange. We sought to quantify genomic introgression using 35 autosomal and 5 X-chromosome ancestry-informative markers (AIMs) in conjunction with diagnostic Y chromosome single nucleotide polymorphism (Y-SNP) markers to characterize the modern state of red foxes in the eastern United States and to gain insight into the potential role of reproductive barriers. European admixture was highest in the ACP and apparently restricted to the central eastern United States. We estimated only slightly (and nonsignificantly) European ancestry in autosomal than X-chromosome markers. European ancestry from autosomal and X-chromosome markers (36.4%) was higher than the corresponding mitochondrial (mt) DNA estimate (26.4%) in the ACP. Only 1 of 124 males (<1%) in the ACP had European Y chromosomes, which was similar to the neighboring regions, in which 2 of 99 (2%) males carried a European Y chromosome (the same haplotype). Although we could not rule out drift as the cause of low European Y-chromosome frequency, results were also consistent with F1 male infertility. In the future, more extensive genomic sequencing will enable a more thorough investigation of possible barrier genes on the X chromosome as well as throughout the genome.

Noninvasive Sampling Reveals Short-Term Genetic Rescue in an Insular Red Fox Population.

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.