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Noninvasive genetic surveys, often conducted by collecting fecal samples, have become a popular tool for surveying wildlife, but have primarily been applied to species with large and conspicuous scat. Although many small mammals are threatened, endangered, or data deficient, noninvasive genetic surveys have rarely been applied due to the challenges of detecting their inconspicuous fecal pellets. As part of a broader study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), we developed a noninvasive genetic survey technique for the community of small mammals in their putative range. We designed bait stations to passively collect fecal samples from rodents, and developed a multiplex primer set that amplified unique fragment sizes for salt marsh harvest mice and four other sympatric species. We tested the primer set on positive controls and on fecal pellets collected from bait stations at two regularly monitored field sites known to have very different densities of salt marsh harvest mice. The multiplex amplified DNA from all five species, even when all five species were present in a single sample. A positive species identification was made for all field-collected samples, and 43% of these field-collected samples had multispecies detections. The combination of bait stations and genetic species identification proved to be an effective means of noninvasively surveying small mammals in potential salt marsh harvest mouse habitat. The sampling technique should be applicable to a wide variety of small mammals in other systems.

Preserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped > 500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (> 2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization.

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

The salt marsh harvest mouse (SMHM; Reithrodontomys raviventris) is a state and federally listed endangered species endemic to the coastal marshes of the San Francisco Estuary of California. Of two subspecies, the southern (R. r. raviventris) is most endangered and lacks reliable morphological field tools to distinguish from the sympatric western harvest mouse (WHM; R. megalotis). We trapped and collected genetic samples and morphological data from 204 harvest mice from 14 locations from across the range of the southern SMHM. Genetic species identification indicated these to be composed of 48 SMHM and 156 WHM, which we compared at ten morphological characters. Most continuous characters overlapped between species. Color characters were significantly differentiated and we identified a number of species-specific diagnostic pelage categories in both species. A random forest analysis indicated that ventral coloration of the abdomen and the ventral tail hair color were the most useful for differentiating between species. We used these two morphological characters to develop a decision tree which correctly classified 94% of harvest mice to species with 99% accuracy. These findings suggest that our decision tree can be used to reliably identify the species of most harvest mice in the range of the southern SMHM, with a small proportion (6% in our study) needing genetic confirmation. The decision tree should be tested on additional harvest mice that were not used in its development, particularly from novel locations across the range.

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 re-colonization 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 an increased mammalian fauna 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.

Movement ecology and dispersal capabilities inherently drive genetic structure across landscapes. Through understanding dispersal and gene flow of giant kangaroo rats (Dipodomys ingens), conservation efforts can be focused, and we can further understand how genetic structure persists in this highly endemic small mammal. Here, we genetically identify parent–offspring and sibship relationships among 239 giant kangaroo rats using 15 microsatellites in the northern part of the species range and describe the individual genetic-spatial variation using a Moran eigenvector map (MEM). We further employ two landscape genetic analyses (isolation by resistance [IBR] and least cost paths [LCPs]) and two individual-based genetic metrics (Dps and a codominant marker distance from GenAlEx) to determine landscape factors (precipitation, slope, vegetation community, and roads) that influence gene flow. We found 19 pairs of related individuals, of which 18 were less than 250 m apart, but one sibling pair was 5.52 km apart, suggesting greater dispersal capabilities than previously noted. We found hierarchal spatial genetic structure using a MEM, with 3–4 genetically similar regions and two genetically similar subregions. Finally, we found low correlative strength between landscape features and gene flow. IBR consistently outperformed LCPs, and there was evidence that regions with 250–350 mm of precipitation and slope ≤ 5° promoted connectivity. We recommend that managers focus on habitat protection rather than corridor maintenance, with the caveat that anthropogenic factors were minimally considered in this study.

From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species’ range, including 1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and 2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This keystone species underwent a ~97% range reduction over the past century, resulting in a current range that is highly fragmented, with 2 dominant northern and southern populations occurring 150 km apart. We sequenced >800 bp of mitochondrial DNA and genotyped 17 nuclear microsatellites in >275 D. ingens to assess the evolutionary relationship of these populations as well as the genetic structure within the northern metapopulation. A Bayesian Skyline Plot indicated that the species experienced a demographic expansion toward the end of the Pleistocene, with a recent population decline. Northern and southern D. ingens split 1857–13 443 years ago, prior to the massive conversion of the San Joaquin Valley to irrigated agriculture. We recommend that the northern and southern populations of D. ingens be re-classified as distinct population segments under the United States Endangered Species Act. We also observed population structure and asymmetrical migration within northern D. ingens where the Tumey Hills acted as a source contributing gene flow to all peripheral populations. This emphasized the importance of this location in the conservation of the metapopulation as a whole.

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.

Though mule deer (Odocoileus hemionus) persist in robust populations throughout most of their North American distribution, habitat loss, unregulated hunting, and other factors have reduced their historical range in México. Two of the 6 putative subspecies inhabiting México’s deserts and Baja California peninsula are of conservation concern, occupying islands in the Pacific Ocean (Odocoileus hemionus cerrosensis on Cedros Island: endangered) and Sea of Cortés (Odocoileus hemionus sheldoni on Tiburón Island: threatened). Focusing on the desert southwest (n = 448), we sampled Tiburón (n = 22) and Cedros (n = 15) Island mule deer using contemporary samples and natural history museum specimens to complete a phylogeographic evaluation of the species complex, and assess the phylogeography of these insular subspecies. Both insular subspecies formed endemic haplotype lineages, consistent with island biogeographic theory. Bayesian skyline plots were consistent with Holocene demographic expansion. Cedros Island deer were genetically most similar to adjacent mainland Baja California deer, but exhibited a suite of unique haplotypes and reduced genetic variation. Tiburón Island deer haplotypes unexpectedly nested within a mainland lineage found in distant New Mexico, rather than the adjacent mainland Sonoran lineage. Such findings suggest the importance of postglacial climate fluctuations and biotic community turnover in the phylogeographic history of mule deer in the desert southwest. Our genetic data corroborates cultural, archaeological, and phenotypic evidence supporting Cedros and Tiburón deer endemicity and subspecies status. Reduced genetic variation, divergence from mainland populations, and demographic trends on both islands indicate that conservation, monitoring, and management are critical to ensure persistence of these endemic insular subspecies.

The critically endangered Amargosa vole (Microtus californicus scirpensis) is found only in rare marsh habitat near Tecopa, California in a plant community dominated by three-square bulrush (Schoenoplectus americanus). Since the earliest research on the Amargosa vole, the existing paradigm has been that these voles are obligatorily dependent on bulrush as their only food source and for the three-dimensional canopy and litter structure it provides for predator avoidance. However, no prior research has confirmed the diet of the Amargosa vole. In this study we characterized the Amargosa vole' nutritional needs, analyzed the quality of bulrush by forage analysis, and performed microhistological and metabarcoding analyses of vole feces to determine what foods were consumed in the wild. All bulrush plant tissues analyzed were low in fat (from 0.9% of dry matter in roots to 3.6% in seeds), high in neutral detergent fiber (from 5.9% in rhizomes to 33.6% in seeds), and low in protein (7.3-8.4%). These findings support the conclusion that bulrush alone is unlikely to support vole survival and reproduction. Fecal microhistology and DNA metabarcoding revealed relatively diverse diets including plants in 14 families, with rushes (Juncaceae), bulrushes (Cyperaceae), and grasses (Poaceae) being the most common diet items. On microhistology, all analyzed samples contained bulrush, sedges (Carex sp.), rushes (Juncus sp.), and beaked spikerush (Eleocharis rostrellata) even from marshes where non-bulrush plants were uncommon. There was evidence of insects at

Temperate terrestrial species in Europe were hypothesized to have been restricted to southern peninsular refugia (Iberia, Italy, Balkans) during the height of the last glacial period. However, recent analyses of fossil evidence indicate that some temperate species existed outside these areas during the last glacial maximum (LGM). Red foxes (Vulpes vulpes) in particular, could have been distributed across the southern half of the continent, potentially forming one continuous population. To investigate these hypotheses, we used 21 nuclear microsatellite loci and two fragments (768 bp) of mitochondrial DNA to characterize the population structure among a continent-wide sample of 288 European red foxes. We tested whether European red foxes clustered into discrete populations corresponding to the hypothetical peninsular refugia. Additionally, we sought to determine if distinct northern populations were formed after post-glacial recolonization. Our results indicated that only the foxes of Iberia appeared to have remained distinct over a considerable period of time (32–104 kya). Spanish red foxes formed their own genotypic cluster; all mtDNA haplotypes were endemic and closely related, and together both the mitochondrial and nuclear datasets indicated this population contributed little to postglacial recolonization of Northern Europe. In contrast, red foxes from Italy and the Balkans contributed significantly to, or were part of, a wider, admixed population stretching across mid-latitude Europe. In Northern Europe, we identified a Scandinavian population that had an ancestral relationship with red foxes to the south, and a more recent relationship with those to the east, in Russia. We also resolved two distinct populations on the islands of Ireland and Britain that had been separated from one another, and from those on the continent, since the late Pleistocene/mid Holocene (~4–24 kya

Global climate change induces species range shifts and population expansion to higher latitudes in response to rising temperatures. One consequence of climate-induced range shifts is an increased sympatry between related but previously isolated species, potentially resulting in interspecific interactions and hybridization. The Arctic is more rapidly affected by climate warming than any region on Earth and resident species may be prone to interspecific hybridization due to the immigration of new colonizing species. The red fox Vulpes vulpes expanded its range into the Arctic during the twentieth century and is now in sympatry with the native Arctic fox Vulpes lagopus in many places. In this context, an Arctic-like fox displaying an unusual reddish winter coat was observed in 2013 in Nunavut, Canada, a phenotype unknown by Inuit people to date. In this study, we assessed the biological origin of this specimen with a multigenic approach using markers located on mitochondrial DNA, sex (X and Y) chromosomes, and autosomes (microsatellites and the melanocortin 1 receptor (MC1R) gene; a gene involved in the color polymorphism in canids). Our comparative analyses with genetic material from Arctic and red foxes displaying “classic” phenotypes (N = 14 and 16, respectively) suggested a pure Arctic fox origin of the specimen. Specifically, this fox yielded mtDNA, X-linked, Y-linked, and MC1R alleles specific to Arctic fox. Bayesian genetic assignment based on 16 microsatellite loci assigned it to Arctic fox with high confidence (q = 99.7%). Thus, a recent hybrid origin for this specimen is excluded. This alternative winter coat color polymorphism in Arctic fox requires further analyses to determine its underlying genetic mechanism.

The red foxes (Vulpes vulpes) indigenous to the mountains of the western United States are high-elevation specialists that could face range reduction due to climatic warming, as well as potential encroachment, loss of adaptive alleles, and displacement by introduced nonnative red foxes. We investigated the genetic integrity of the native Rocky Mountain red fox (V. v. macroura) in Colorado through analysis of the composition, distribution, and patterns of gene flow between native and nonnative red fox populations along an elevational gradient. The study area spanned the high plains around Denver in the east to the alpine zone of the Rocky Mountains adjacent to Gunnison and Crested Butte in the west. We used microsatellites and mitochondrial DNA (mtDNA) from Colorado foxes, along with previously published reference data from other native western and nonnative populations, to evaluate the distribution of native versus nonnative ancestry and its relationship to elevation, distance, and landscape type. Nonnative red fox ancestry predominated in Denver and low-lying areas, whereas native ancestry was most prevalent at high elevations. The genetic integrity of foxes at higher elevations (i.e., within the historical native range) was greater in terms of mtDNA than nuclear DNA, consistent with higher male-mediated gene flow. Nonnative admixture was most pronounced in human-altered landscapes. Our findings provide baseline data necessary to monitor future trends of these Rocky Mountain red fox populations and highlight the potential for similar threats to affect genetic integrity of endangered montane red fox subspecies along the Pacific Crest.

The Sacramento Valley red fox Vulpes vulpes patwin of California is a newly named subspecies recently found to be distinct both from other native red foxes and nearby introduced populations. The Sacramento Valley red fox experienced a historical demographic bottleneck resulting in a critically small genetic effective population size, causing concern over its current status and management requirements, yet little is known about its contemporary abundance, demographic trajectory, or habitat use. The hot, arid Sacramento Valley contrasts starkly in climate and physiography with the boreal habitats of other indigenous red foxes in western North America, indicating the need to obtain information specifically on the habitat requirements of this subspecies. A 3-y effort to locate reproductive den sites throughout the Sacramento Valley resulted in 42 independent dens, which we used to obtain preliminary information on habitat use and to develop a distribution model for this subspecies, and 28 Sacramento Valley red foxes killed by vehicles, which we used as independent data to test the models. Foxes were present significantly more than expected in grasslands and less than expected in wetlands and flooded agriculture and also tended to occur in proximity to human development, potentially as refuges from coyotes Canis latrans. We used Maxent to build predictive models. The best model, which incorporated vegetation/land-use classes and proximity to human development, identified 24% of the study area as predicted-presence habitat, which contained 76% of the den sites used to construct the model and 89% of independent locations used to test the model. Our model greatly narrowed the area over which foxes are predicted to occur and will facilitate future surveys to assess occupancy and ultimately abundance and population trends.

Fur-animal farms can affect the genetic constitution of wild conspecifics through escape and subsequent interbreeding. We studied this problem in red foxes (Vulpes vulpes) on the Canadian island of Newfoundland, where a large commercial fox farm (the only large farm on the island) has operated adjacent to the native wild red fox population for >30 years. To test for gene flow from these fur-farm foxes into the wild population, we compared mitochondrial DNA (mtDNA) sequences and nuclear microsatellite genotypes (21 loci) of 93 individuals from the fox farm to those of 79 modern wild foxes sampled from across the island. For reference, we also included 12 historical museum specimens of wild eastern Canadian red fox, all of which were sampled before the introduction of fur farming in the region. Many mtDNA haplotypes were shared among contemporary farmed and wild foxes and the historical eastern Canadian samples, as expected based on the eastern Canadian origin of fur-farming. However, only the fur farm additionally contained haplotypes originating from other parts of North America. More significantly, microsatellite markers, which reflect contemporary gene flow, indicated strong differentiation (F ST ≥ 0.14, P

Questions concerning the effects on other wildlife species by coyotes (Canis latrans) in recently colonized areas, including the southeastern United States, continue to receive attention in the literature. Coyote abundance estimates, achieved via genetic sampling of feces, can be useful in answering such questions. However, rapid degradation of fecal DNA in humid subtropical climates, like that of the southeastern United States, may limit the efficacy of the technique. To evaluate this hypothesis, we collected and analyzed 434 suspected coyote scats from February 2010 to April 2012 on 2 sites in central Georgia, USA. We quantified seasonal and comprehensive genotyping success, and the effect of sampling effort on precision of closed population abundance estimates. We successfully species-typed 316 (73%) scats, 219 (69%) of which belonged to coyotes. Of those, 136 (62%) yielded multilocus genotypes. The seasonal probability of genotyping a scat ranged from 0.53 to 0.71. Scats collected during spring were more likely to yield consensus genotypes, but the overall effect of season on genotyping success was minimal. The median CV for model-averaged Nˆ (i.e., coyote abundance) using the complete data set was relatively precise (

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is an endangered species endemic to the San Francisco Bay region of California, USA, where habitat loss and fragmentation over the past century have reduced the mouse’s distribution to

Author(s): Smith, Katherine R.; Riley, Melissa K.; Barthman–Thompson, Laureen; Statham, Mark J.; Estrella, Sarah; Kelt, Douglas | Abstract: [Abstracts are not presented for essays. -The SFEWS Editors.]

Author(s): Smith, Katherine R.; Riley, Melissa K.; Barthman–Thompson, Laureen; Woo, Isa; Statham, Mark J.; Estrella, Sarah; Kelt, Douglas A. | Abstract: The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) is an endangered species, endemic to the San Francisco Estuary. Despite being protected for almost half a century and being included in a large number of recovery, restoration, and management plans, significant data gaps hinder conservation and management of the species, a challenge further complicated by developing threats such as climate change. In this review, we present the current state of knowledge; highlight research gaps on habitat requirements and distribution, taxonomic status and genetic structure, physiology, reproduction and demographics, population dynamics, and behavior and community interactions; and present an overview of threats to the species. Our review indicates that substantial data gaps exist; although some aspects of SMHM ecology, such as habitat use, have been addressed extensively, others, such as the effects of environmental contamination, are largely unaddressed. We suggest that conservation and restoration-planning processes consider experimental approaches within restoration designs to address these deficiencies. Continued investment in basic and applied SMHM ecology to collect baseline and long-term data will also be beneficial. Additionally, further coordination among managers and researchers can facilitate more effective responses to uncertainties and emerging threats, especially climate change, which threatens the SMHM and its habitat throughout its range.

Understanding the response of boreal species to past climate warming can help to predict future responses to climate change. In the Northern Hemisphere, the distribution and abundance of northern populations have been influenced by previous glaciations. In this study, we investigated the population history of the Fennoscandian red fox (Vulpes vulpes), which is a generalist carnivore currently undergoing range expansion in the tundra ecosystem. By analysing a 696 bp sequence of the mitochondrial DNA (N = 259) and two Y chromosome-specific microsatellite loci (N = 120), we specifically investigated where the red fox survived the Last Glacial Maximum and how Fennoscandia was recolonized. There was high genetic continuity across most of Fennoscandia, and we identified at least two recolonization pathways: one from continental Europe and one from the northeast (Siberia). Mitochondrial haplotype diversity displayed a significant decline with increasing latitude, consistent with expectations of unidirectional colonization. Each region displayed signatures of recent demographic and/or range expansions. For Finland, an additional recolonization route was suggested from the mismatch distribution analysis and identification of novel haplotypes. We concluded that, as with many boreal generalist species, the Fennoscandian red fox originates from multiple refugia, suggesting that it has benefited from diverse evolutionary histories, potentially enhancing its tolerance to different habitat conditions.

Red foxes were absent or rare in the southeastern United States until the late 1800s. Their origins potentially include natural population increase/expansion, translocations from Europe, and, eventually, 20th century fur farming. Previous studies have found no European haplotypes in North America, but few samples were sourced from the Atlantic coastal plain, closer to the source of putative introductions. Through analysis of mitochondrial DNA in 584 red foxes from this region, we identified indigenous haplotypes in ≥ 35% of foxes, 1 of 2 European haplotypes in 17% of foxes and fur farm haplotypes in ≥ 13% of foxes; another 35% of foxes had haplotypes potentially indigenous or native. In contrast, only 3 of 135 (2%) male foxes carried a single European Y chromosome haplotype. Most European and fur farm haplotypes were found near the densely human-populated coastal plain and Hudson River lowlands; most red foxes of the Appalachians and Piedmont had native eastern haplotypes. Our findings suggest that the more remote, upland populations primarily reflect indigenous red fox matrilines, whereas urban-associated populations in and around the mid-Atlantic coastal plain and Hudson lowlands reflect an admixture of native and nonnative maternal sources. Autosomal markers are needed to further elucidate the extent of European and fur farm introgression in the Appalachians and further west.

Population expansions of boreal species are among the most substantial ecological consequences of climate change, potentially transforming both structure and processes of northern ecosystems. Despite their importance, little is known about expansion dynamics of boreal species. Red foxes (Vulpes vulpes) are forecasted to become a keystone species in northern Europe, a process stemming from population expansions that began in the 19th century. To identify the relative roles of geographic and demographic factors and the sources of northern European red fox population expansion, we genotyped 21 microsatellite loci in modern and historical (1835-1941) Fennoscandian red foxes. Using Bayesian clustering and Bayesian inference of migration rates, we identified high connectivity and asymmetric migration rates across the region, consistent with source-sink dynamics, whereby more recently colonized sampling regions received immigrants from multiple sources. There were no clear clines in allele frequency or genetic diversity as would be expected from a unidirectional range expansion from south to north. Instead, migration inferences, demographic models and comparison to historical red fox genotypes suggested that the population expansion of the red fox is a consequence of dispersal from multiple sources, as well as in situ demographic growth. Together, these findings provide a rare glimpse into the anatomy of a boreal range expansion and enable informed predictions about future changes in boreal communities.

Western North America contains a mosaic of indigenous and introduced red fox (Vulpes vulpes) populations. Historically, native red foxes occurred in subalpine zones of the Cascade, Rocky, and Sierra Nevada mountain ranges, and in the desert-like Sacramento Valley of California. The origins of red foxes observed in the Intermountain West since the early 1900s are unclear, potentially representing native population relicts from the last ice age, dispersers from adjacent mountain populations, or early fur-farm escapees. These foxes carry a native 696-bp mitochondrial haplotype (A-19), which was also the most basal and widespread among western populations and thus equally consistent with ancient and contemporary origins. Here, to increase resolution, we sequenced an additional 3,308 bp (totaling 4,004bp) of the mitochondrial genome corresponding to A-19 and related haplotypes (O-24 and D-19) from historical and modern samples collected throughout western North America. The expanded sequences revealed previous...

Recent evidence from across the southeastern United States indicating high predation rates by coyotes (Canis latrans) on white-tailed deer (Odocoileus virginianus) fawns has led some managers to implement coyote control. Although some evidence suggests coyote control can improve recruitment, success appears to be site dependent. Therefore, we designed an experiment to assess feasibility of coyote control as a management action to increase recruitment on B.F. Grant and Cedar Creek Wildlife Management Areas (WMA) in central Georgia, USA. We estimated annual coyote abundance during 2010–2012 using a noninvasive mark–recapture design and fawn recruitment using infrared-triggered camera surveys. During March–June 2011 and March–April 2012, trappers removed coyotes from both sites. Estimates of coyote abundance on B.F. Grant WMA after trapping were 81% (2011) and 24% (2012) lower than during preremoval. Coyote abundance estimates were similar among years on Cedar Creek WMA. Fawn recruitment on B.F. Grant WMA averaged 0.65 fawns/adult female prior to removal and 1.01 fawns/adult female during the 2 years following the removals. Fawn recruitment on Cedar Creek WMA did not differ among years during the study, and was similar to that prior to coyote arrival. The differential coyote impacts and variable effectiveness of trapping we observed on nearby sites suggest coyote control may not achieve management objectives in some areas. Furthermore, transient behavior and the potential for coyotes to adapt to control efforts likely reduce efficacy of this management action. However, we observed an increase in recruitment on B.F. Grant WMA during one year, and others have seen similar responses. Therefore if lowered fawn recruitment is hindering achievement of management objectives, we recommend managers who opt to control coyotes continuously monitor recruitment to determine whether a response occurs. © 2015 The Wildlife Society.

The red fox (Vulpes vulpes) expanded its distribution over large parts of the Canadian Arctic during the twentieth century and is now considered a threat to the arctic fox (Vulpes lagopus). Some authors have proposed that the European red fox, introduced in Eastern North America during the eighteenth century, may have spread and caused the species’ expansion in the Arctic. Assessing the biological origin of red foxes in the Nearctic is critical to determine whether their presence constitutes a case of an invading exotic species. We analyzed genetic material obtained from four red foxes at Herschel Island (Yukon) and Bylot Island (Nunavut), at the northern expanding front of the species. Samples from Bylot provide the northernmost genetic information on red fox obtained worldwide. We identified mitochondrial DNA haplotypes in red foxes from both Arctic locations that were phylogenetically divergent from those in Eurasia, but shared with neighboring indigenous North American populations. Thus, our results indicate that the twentieth century expansion of red foxes in the Canadian Arctic involved nearby populations potentially benefiting from habitat changes, rather than an exotic species invading new habitats.

The red fox (Vulpes vulpes) occurs on multiple continents in diverse habitats, making it an informative system for evolutionary genomic research. However, its phylogeography remains unclear. Previously, mitochondrial DNA and small numbers of nuclear loci provided discordant views. Both markers indicated deep divergence (~ 0.5 million years [MY]) between Eurasian and southern North American populations but differed in the apparent continental affinity of Alaskan red foxes, implying some degree of gene exchange during secondary contact (~0.1 MY). We assayed >173000 nuclear genomic sites in 52 red foxes, along with 2 Rueppell's foxes (Vulpes rueppellii) and a gray wolf (Canis lupus) using the Illumina CanineHD BeadChip. We obtained 5107 single nucleotide polymorphisms (SNPs) in the foxes. Consistent with the Afro-Eurasian origins of red foxes, genetic diversity was higher in Eurasian than North American samples. Phylogenetic trees indicated that Alaskan and southern North American red foxes formed a monophyletic group nested within the Eurasian clade. However, admixture models suggested Alaskan red foxes contained up to 40% Eurasian ancestry. We hypothesize that North American red foxes either hybridized with Eurasian foxes in Beringia at the start of the last glaciation or merged with a Beringian population after the last glaciation. Future work is needed to test between these scenarios and assess speciation.

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum.We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe.

The present study examined the contemporary genetic composition of the Eurasian badger, Meles meles, in Ireland, Britain and Western Europe, using six nuclear microsatellite loci and a 215-bp fragment of the mitochondrial DNA control region. Significant population structure was evident within Europe (global multilocus microsatellite FST = 0.205, P < 0.001; global mitochondrial control region ΦST = 0.399, P < 0.001). Microsatellite-based cluster analyses detected one population in Ireland, whereas badgers from Britain could be subdivided into several populations. Excluding the island populations of Ireland and Britain, badgers from Western Europe showed further structuring, with evidence of discrete Scandinavian, Central European, and Spanish populations. Mitochondrial DNA cluster analysis grouped the Irish population with Scandinavia and Spain, whereas the majority of British haplotypes grouped with those from Central Europe. The findings of the present study suggest that British and Irish badger populations colonized from different refugial areas, or that there were different waves of colonization from the source population. There are indications for the presence of an Atlantic fringe element, which has been seen in other Irish species. We discuss the results in light of the controversy about natural versus human-mediated introductions

The Sierra Nevada red fox (Vulpes vulpes necator) occurred historically throughout the high elevations of California's Sierra Nevada and southern Cascade Mountains. Before this study, the only known remaining population in California consisted of ≤ 20 individuals restricted to the Lassen Peak region in the southern Cascades. In August 2010, we photographed a red fox in the Sonora Pass area of the Sierra Nevada, > 100 km from the Lassen Peak region. To determine if multiple individuals were present and were indigenous, we set up additional camera stations, collected genetic samples (saliva, scat, hair, and a carcass), and conducted a comparative genetic analysis between these individuals and historical and modern reference samples. Photo-detections identified at least three individuals based on pelage characteristics. Genetic analyses identified two females and one male, whose microsatellite profiles suggested they were closely related. A genetic assignment analysis indicated that all three indivi...

Red foxes (Vulpes vulpes) are native to boreal and western montane portions of North America but their origins are unknown in many lowland areas of the United States. Red foxes were historically absent from much of the East Coast at the time of European settlement and did not become common until the mid-1800s. Some early naturalists described an apparent southward expansion of native foxes that coincided with anthropogenic habitat changes in the region. Alternatively, red foxes introduced from Europe during Colonial times may have become established in the east and subsequently expanded their range westward. The red fox also was absent historically from most lowland areas of the western United States. Extant populations of red foxes in those areas are considered to have arisen from intentional introductions from the east (and by extension are putatively European), escapes or releases from fur farms, or range expansions by native populations. To test these hypotheses we compared mitochondrial DNA sequences (cytochrome b and D-loop) from 110 individuals from 6 recently established populations to 327 native (primarily historical) individuals from Eurasia, Alaska, Canada, the northeastern United States, and montane areas in the western contiguous United States, and to 38 individuals from fur farms. We found no Eurasian haplotypes in North America, but found native haplotypes in recently established populations in the southeastern United States and in parts of the western United States. Red foxes from the southeastern United States were closely related to native populations in eastern Canada and the northeastern United States, suggesting that they originated from natural range expansions, not from translocation of European lineages, as was widely believed prior to this study. Similarly, recently established populations in the Great Basin and in western Oregon originated primarily from native populations in western montane regions, but also contained a few nonnative North American haplotypes. In contrast, populations in western Washington and southern California contained nonnative, highly admixed stock that clearly resulted from intracontinental translocations. Several common haplotypes in these populations originated in regions where fur-farm stocks originated. Although European red foxes translocated to the eastern United States during Colonial times may have contributed genetically to extant populations in that region, our findings suggest that most of the matrilineal ancestry of eastern red foxes originated in North America.

The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In this study we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mtDNA, cytochrome b and D-loop, from 24 Novosibirsk foxes (8 foxes from each population) and compared them with corresponding sequences of native red foxes from Europe, Asia, Alaska and Western Canada, Eastern Canada, and the Western Mountains of the USA. We identified seven cytochrome b - D-loop haplotypes in Novosibirsk populations, four of which were previously observed in Eastern North America. The three remaining haplotypes differed by one or two base change from the most common haplotype in Eastern Canada. Φ(ST) analysis showed significant differentiation between Novosibirsk populations and red fox populations from all geographic regions except Eastern Canada. No haplotypes of Eurasian origin were identified in the Novosibirsk populations. These results are consistent with historical records indicating that the original breeding stock of farm-bred foxes originated from Prince Edward Island, Canada. Mitochondrial DNA data together with historical records indicate two stages in the selection of domesticated foxes: the first includes captive breeding for ~50 years with unconscious selection for behaviour; the second corresponds to over 50 further years of intensive selection for tame behaviour.

The salt marsh harvest mouse (SMHM, Reithrodontomys raviventris) only exists in a patchwork of salt marshes scattered throughout the San Francisco, San Pablo, and Suisun Bays of California. The species has declined significantly from its historical distribution due to habitat loss and fragmentation and is categorized as an endangered species under the US Endangered Species Act and by the IUCN. We identified ten microsatellite loci that amplify in the SMHM and the western harvest mouse [western harvest mouse (WHM); R. megalotis], a sympatric congener. Screening in 30 SMHM identified eight polymorphic loci, with an average of 4.6 alleles per locus, an observed heterozygosity of 0.45, and an expected heterozygosity of 0.55. Four of these loci and an additional one amplified in the WHM, of which two were polymorphic and three enabled species differentiation. We amplified all markers in two multiplexes, which will provide important tools for the conservation and monitoring of this flagship endangered species.

Reintroduction of terrestrial vertebrates with the goal of ecosystem restoration typically establishes small and isolated populations that may experience reduced genetic variability due to founder effects and genetic drift. Understanding the genetic structure of these populations and maintaining adequate genetic diversity is important for long-term restoration success. We quantified genetic variability at six microsatellite loci for a reintroduced population of Cervus elaphus (elk) restored to the tallgrass prairie ecosystem of northeastern Kansas. Allelic richness, observed and expected heterozygosity were intermediate to levels reported in other North American elk populations. Current levels of genetic variability in restored North American elk populations were not well explained by founding population size, number of founding populations, or number of years since the last translocation. Simulation results suggest that the retention of genetic variability in isolated populations is strongly influenced by mating system while also being impacted by temporal variability in population size and population growth rate. Our results have implications for understanding how translocation strategies and post-reintroduction management may influence genetic variability in restored populations.

Most native red foxes (Vulpes vulpes) in the western contiguous United States appear to be climatically restricted to colder regions in the major mountain ranges and, in some areas, have suffered precipitous declines in abundance that may be linked to warming trends. However, another population of unknown origin has occurred in arid habitats in the Sacramento Valley of California well out- side this narrow bioclimatic niche since at least 1880. If native, this population would be ecologically distinct among indigenous North American red foxes. We used mitochondrial and microsatellite markers from historical and modern samples (modes: 1910-1930 and 2000-2008, respectively) obtained throughout the western United States to determine the origins of the Sacramento Valley red fox, and assess the historical and modern connectivity and genetic effective population sizes of Sacramento Val- ley and montane red foxes. We found clear and consistent evidence supporting the indigenous origin of the Sacra- mento Valley population, including the phylogenetic positioning of the dominant, endemic mtDNA clade and microsatellite clustering of the Sacramento Valley popu- lation with the nearest montane population. Based on both mitochondrial and microsatellite AMOVAs, connectivity among Western populations of red foxes declined sub- stantially between historical and modern time periods. Estimates based on temporal losses in gene diversity for both marker types suggest that both the Sierra Nevada (including the Southern Cascades population) and the Sacramento Valley populations have small genetic effec- tive population sizes. Significant heterozygote excesses also indicate the occurrence of recent bottlenecks in these populations. Both substitutions distinguishing the 2 ende- mic Sacramento Valley haplotypes from the dominant montane haplotype were in the coding region and nonsynonymous, consistent with adaptive differences. These findings along with previously reported body size distinctions between Sacramento Valley and montane red foxes argue for distinct subspecific status for the Sacra- mento Valley red fox, for which we propose the designa- tion V. v. patwin n. subsp. The small genetic effective population size estimates for the Sierra Nevada red fox and Sacramento Valley red fox are cause for concern, as is the possibility of genetic introgression into the latter popula- tion from an adjacent, recently established nonnative

Climate change during the late Quaternary has been implicated as the cause of both massive range shifts and extinction events. We combined molecular marker data and previously published fossil data to reconstruct the late Quaternary history of a grassland-dependent species, the black-footed ferret (Mustela nigripes), and to determine whether populations from Pleistocene refugia in the Columbia Basin, eastern Beringia, and Great Plains persisted into the Holocene and Recent eras. Using DNA extracted from 97 museum specimens of extirpated populations, we amplified 309 bp of the mtDNA control region, and 8 microsatellite markers from the nuclear genome. Overall haplotype diversity from 309 base pairs (bp) of mitochondrial DNA (mtDNA) control region was low (5 haplotypes, nucleotide diversity = 0.001 ± 0.001 SD) and was contained within a single phylogenetic clade. The star phylogeny and unimodal mismatch distribution indicated that a rapid range expansion from a single Pleistocene refugium occurred....

Pleistocene aridification in central North America caused many temperate forest-associated vertebrates to split into eastern and western lineages. Such divisions can be cryptic when Holocene expansions have closed the gaps between once-disjunct ranges or when local morphological variation obscures deeper regional divergences. We investigated such cryptic divergence in the gray fox (Urocyon cinereoargenteus), the most basal extant canid in the world. We also investigated the phylogeography of this species and its diminutive relative, the island fox (U. littoralis), in California. The California Floristic Province was a significant source of Pleistocene diversification for a wide range of taxa and, we hypothesized, for the gray fox as well. Alternatively, gray foxes in California potentially reflected a recent Holocene expansion from further south. We sequenced mitochondrial DNA from 169 gray foxes from the southeastern and southwestern United States and 11 island foxes from three of the Channel Islands. We estimated a 1.3% sequence divergence in the cytochrome b gene between eastern and western foxes and used coalescent simulations to date the divergence to approximately 500,000 years before present (YBP), which is comparable to that between recognized sister species within the Canidae. Gray fox samples collected from throughout California exhibited high haplotype diversity, phylogeographic structure, and genetic signatures of a late-Holocene population decline. Bayesian skyline analysis also indicated an earlier population increase dating to the early Wisconsin glaciation (~70,000 YBP) and a root height extending back to the previous interglacial (~100,000 YBP). Together these findings support California’s role as a long-term Pleistocene refugium for western Urocyon. Lastly, based both on our results and re-interpretation of those of another study, we conclude that island foxes of the Channel Islands trace their origins to at least 3 distinct female founders from the mainland rather than to a single matriline, as previously suggested.

Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva.

Quaternary climatic fluctuations have had profound effects on the phylogeographic structure of many species. Classically, species were thought to have become isolated in peninsular refugia, but there is limited evidence that large, non-polar species survived outside traditional refugial areas. We examined the phylogeographic structure of the red fox (Vulpes vulpes), a species that shows high ecological adaptability in the western Palaearctic region. We compared mitochondrial DNA sequences (cytochrome b and control region) from 399 modern and 31 ancient individuals from across Europe. Our objective was to test whether red foxes colonised the British Isles from mainland Europe in the late Pleistocene, or whether there is evidence that they persisted in the region through the Last Glacial Maximum. We found red foxes to show a high degree of phylogeographic structuring across Europe and, consistent with palaeontological and ancient DNA evidence, confirmed via phylogenetic indicators that red foxes were persistent in areas outside peninsular refugia during the last ice age. Bayesian analyses and tests of neutrality indicated population expansion. We conclude that there is evidence that red foxes from the British Isles derived from central European populations that became isolated after the closure of the landbridge with Europe., Highlights ► Red foxes show a high degree of phylogeographic structuring across Europe. ► Foxes were persistent in areas outside peninsular refugia during the last ice age. ► British foxes originated in central Europe, becoming isolated after 8200 BP.

The foxes at Novosibirsk, Russia, are the only population of domesticated foxes in the world. These domesticated foxes originated from farm-bred silver foxes (Vulpes vulpes), whose genetic source is unknown. In this study we examined the origin of the domesticated strain of foxes and two other farm-bred fox populations (aggressive and unselected) maintained in Novosibirsk. To identify the phylogenetic origin of these populations we sequenced two regions of mtDNA, cytochrome b and D-loop, from 24 Novosibirsk foxes (8 foxes from each population) and compared them with corresponding sequences of native red foxes from Europe, Asia, Alaska and Western Canada, Eastern Canada, and the Western Mountains of the USA. We identified seven cytochrome b - D-loop haplotypes in Novosibirsk populations, four of which were previously observed in Eastern North America. The three remaining haplotypes differed by one or two base change from the most common haplotype in Eastern Canada. Φ(ST) analysis showed significant differentiation between Novosibirsk populations and red fox populations from all geographic regions except Eastern Canada. No haplotypes of Eurasian origin were identified in the Novosibirsk populations. These results are consistent with historical records indicating that the original breeding stock of farm-bred foxes originated from Prince Edward Island, Canada. Mitochondrial DNA data together with historical records indicate two stages in the selection of domesticated foxes: the first includes captive breeding for ~50 years with unconscious selection for behaviour; the second corresponds to over 50 further years of intensive selection for tame behaviour.

Introduced species can threaten native taxa in multiple ways, including competition and hybridization, which can reduce fitness, alter ecological niches or swamp native genomes. Encroachment and hybridization by introduced species also provide opportunities to study the dynamics of invasiveness and hybridization during early stages following contact. We used 33 microsatellites, 51 single nucleotide polymorphisms and a mtDNA marker to characterize the extent and spatial pattern of encroachment and hybridization between a native, endemic subspecies of red fox (Vulpes vulpes patwin) and an introduced red fox population composed of highly admixed, phylogenetically divergent stock, resulting from a century of domestication. Both nuclear and mtDNA markers indicated that hybridization was primarily restricted to a narrow zone where the two populations came into contact. Although a few introgressed genotypes were detected in the interior of the native range, we found no immigrant foxes or F(1) or F(2) hybrids there, suggesting native foxes excluded introduced individuals. We speculate that the observed interbreeding at the periphery was facilitated by low densities. In total, 98% of mtDNA haplotypes in the native range were native and 96% of the nuclear ancestry was estimated to be native. Although the introduced range had expanded fivefold over the past four decades, native and non-native haplotypes from museum samples collected in and near the native range three decades earlier showed a similar geographic distribution as today, suggesting that the native range and hybrid zone were relatively stable. We hypothesize that the monogamous mating system of red foxes and other wild canids may enhance their resistance to hybridization because of greater fitness consequences associated with mate discrimination.

Fossil, archaeological, and morphometric data suggest that indigenous red foxes in North America were derived from vicariance in two disjunct refugia during the last glaciation: one in Beringia and one in the contiguous USA. To test this hypothesis, we conducted a phylogeographical analysis of the North American red fox within its presettlement range. We sequenced portions of the mitochondrial cytochrome b (354 bp) gene and D-loop (342 bp) from 220 historical red fox specimens. Phylogenetic analysis of the cytochrome b gene produced two clades that diverged c. 400,000 years before present (bp): a Holarctic and a Nearctic clade. D-loop analyses of the Nearctic clade indicated three distinct subclades (or = 99% Bayesian posterior probability); two that were more recently derived (rho estimate c. 20,000 bp) and were restricted to the southwestern mountains and the eastern portion of North America, and one that was older (rho estimate c. 45,000 bp) and more widespread in North America. Populations that migrated north from the southern refugium following deglaciation were derived from the colonization of North America during or prior to the Illinoian glaciation (300,000-130,000 bp), whereas populations that migrated south from the northern refugium represent a more recent colonization event during the Wisconsin glaciation (100,000-10,000 bp). Our findings indicate that Nearctic clade red foxes are phylogenetically distinct from their Holarctic counterparts, and reflect long-term isolation in two disjunct forest refugia during the Pleistocene. The montane lineage, which includes endangered populations, may be ecologically and evolutionarily distinct.

SNPs are fast becoming the marker of choice in population genetics studies of model organisms. However, a lack of efficient means to assay sufficient numbers of SNPs in non-model organisms has prevented their widespread use for conservation-related applications. We established a SNP genotyping assay (including development of new SNP markers) for detection of genetic variation in coding and non-coding parts of the fox genome, using a 96-locus multiplex format. Coding SNPs were associated with Agouti and Mc1r coat-color alleles, phylogenetically basal mitochondrial mutations, sex markers, B-chromosome proto-oncogenes, and serotonin-receptor genes. Non-coding SNPs (n = 51) included 27 newly described microsatellite-linked SNPs. A panel of red foxes (n = 96) was used to characterize minor allele frequencies and Hardy–Weinberg equilibrium. Genotyping accuracy was 99% for 72 SNPs relative to sequenced and known-phenotype animals.