Chromosome-level assembly of the gray fox (Urocyon cinereoargenteus) confirms the basal loss of PRDM9 in Canidae.

Reference genome assemblies have been created from multiple lineages within the Canidae family; however, despite its phylogenetic relevance as a basal genus within the clade, there is currently no reference genome for the gray fox (Urocyon cinereoargenteus). Here, we present a chromosome-level assembly for the gray fox (U. cinereoargenteus), which represents the most contiguous, non-domestic canid reference genome available to date, with 90% of the genome contained in just 34 scaffolds and a contig N50 and scaffold N50 of 59.4 and 72.9 Megabases, respectively. Repeat analyses identified an increased number of simple repeats relative to other canids. Based on mitochondrial DNA, our Vermont sample clusters with other gray fox samples from the northeastern United States and contains slightly lower levels of heterozygosity than gray foxes on the west coast of California. This new assembly lays the groundwork for future studies to describe past and present population dynamics, including the delineation of evolutionarily significant units of management relevance. Importantly, the phylogenetic position of Urocyon allows us to verify the loss of PRDM9 functionality in the basal canid lineage, confirming that pseudogenization occurred at least 10 million years ago.

Epizootiology and Pathology of Sarcoptic Mange in Two Species of Fox (Lycalopex spp.) in Human-Dominated Landscapes of Central Chile.

Sarcoptic mange caused by Sarcoptes scabiei can have catastrophic consequences for wildlife. We inspected 122 Andean foxes (Lycalopex culpaeus), collected by active (n=66) or passive (n=56) surveillance, and 28 South American gray foxes (Lycalopex griseus; all from passive surveillance) for mange in Chile (2015-19). In Andean foxes, gross lesions of mange were diagnosed in 24% of passively and 9% of actively collected foxes, although observed prevalences might be underestimated. Seroprevalence was 37 and 18%, respectively, indicating that some individuals recovered from infection or were developing the disease. No differences were found between age and sex groups. Comparing data from passive surveillance, occurrence of gross lesions was lower in gray foxes (5%). Body condition was significantly better in Andean foxes without lesions than in diseased foxes, which had significantly lower albumin concentrations than healthy individuals. Among the 12 foxes with gross lesions, four, six and two individuals were categorized as having type I, type II, and type III lesions, respectively, based on clinical severity. Histologic severity correlated with gross lesions and included irregular epidermal hyperplasia with hyperkeratosis, which was marked in type II and III infections. Conventional PCR targeting of the cox1 gene fragment revealed four nucleotide sequence types, showing 99-100% identity among them and between 99% and 100% identity with previously published sequences of S. scabiei. A significant association between the occurrence of mange in foxes and distance to the nearest house was found. We speculate that diseased foxes tended to approach human settlements, perhaps in search of food. Visual inspection of 211 rural dogs from the study area did not reveal gross mange lesions in any animal. Sarcoptic mange is enzootic in the Andean fox in the study area and should be considered in the management of the species.

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.

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.

High Prevalence of Antibodies against Canine Parvovirus and Canine Distemper Virus among Coyotes and Foxes from Pennsylvania: Implications for the Intersection of Companion Animals and Wildlife.

Canine distemper virus (CDV) and Canine parvovirus (CPV) can cause deadly infections in wildlife and companion animals. In this report, we screened serum from free-ranging eastern coyotes (Canis latrans; N = 268), red foxes (Vulpes vulpes; N = 63), and gray foxes (Urocyon cinereoargenteus; N = 16) from Pennsylvania, USA, for antibodies (Abs) to CDV and CPV. This comprehensive screening was achieved using a commercially available enzyme-linked immunosorbent assay (ELISA)-based colorimetric assay. Abs to CDV and CPV were detected in 25.4% and 45.5% of coyotes, 36.5% and 52.4% of red foxes, and 12.5% and 68.8% of gray foxes, respectively. Abs to both viruses were detected in 9.7% of coyotes, 19.1% of red foxes, and 12.5% of gray foxes. This study demonstrates significant wildlife exposure in a northeastern state to CDV and CPV. As wildlife species continue to urbanize, the probability of spillover between domestic animals and wildlife will increase. Ongoing surveillance of wildlife for CDV and CPV exposure is warranted. IMPORTANCECanine distemper virus (CDV) and Canine parvovirus (CPV) are significant health threats to domestic dogs (Canis familiaris) and wildlife. CDV and CPV have been identified in diverse vertebrates, including endangered wildlife species. Susceptibility to these viral pathogens varies significantly among geographic regions and between host species. High morbidity and mortality have been reported with infection by either virus in susceptible species, including dogs. As humans and companion animals encroach on wildlife habitat, and as wildlife becomes increasingly urbanized, the potential for transmission between species increases. This study assessed CPV and CDV Ab prevalence in wild canids (eastern coyotes, red foxes, and gray foxes) harvested in Pennsylvania between 2015 and 2020. High Ab prevalence was demonstrated for both viruses in each species. Ongoing monitoring of CPV and CDV in wildlife and increased efforts to vaccinate dogs and prevent spillover events are essential.

TEMPORAL AND SPATIAL PATTERNS IN CANINE DISTEMPER VIRUS CASES IN WILDLIFE DIAGNOSED AT THE SOUTHEASTERN COOPERATIVE WILDLIFE DISEASE STUDY, 1975-2019.

Canine distemper is a high-impact disease of many mammal species and has caused substantial carnivore population declines. Analysis was conducted on passive surveillance data of canine distemper (CDV)-positive wild mammal cases submitted to the Southeastern Cooperative Wildlife Disease Study, Athens, Georgia, US, between January 1975 and December 2019. Overall, 964 cases from 17 states were CDV positive, including 646 raccoons (Procyon lotor), 254 gray foxes (Urocyon cinereoargenteus), 33 striped skunks (Mephitis mephitis), 18 coyotes (Canis latrans), four red foxes (Vulpes vulpes), three gray wolves (Canis lupus), three American black bears (Ursus americanus), two American mink (Mustela vison), and one long-tailed weasel (Mustela frenata). Raccoon and gray fox case data from the state of Georgia (n=441) were selected for further analysis. Autoregressive integrated moving average models were developed predicting raccoon and gray fox case numbers. The best-performing model for gray foxes used numbers of gray fox CDV cases from the previous 2 mo and of raccoon cases in the present month to predict the numbers of gray fox cases in the present month. The best-performing model for raccoon prediction used numbers of raccoon CDV cases from the previous month and of gray fox cases in the present month and previous 2 mo to predict numbers of raccoon cases in the present month. Temporal trends existed in CDV cases for both species, with cases more likely to occur during the breeding season. Spatial clustering of cases was more likely to occur in areas of medium to high human population density; fewer cases occurred in both the most densely populated and sparsely populated areas. This pattern was most prominent for raccoons, which may correspond to high transmission rates in suburban areas, where raccoon population densities are probably highest, possibly because of a combination of suitable habitat and supplemental resources.

Mesocarnivore landscape use along a gradient of urban, rural, and forest cover.

Mesocarnivores fill a vital role in ecosystems through effects on community health and structure. Anthropogenic-altered landscapes can benefit some species and adversely affect others. For some carnivores, prey availability increases with urbanization, but landscape use can be complicated by interactions among carnivores as well as differing human tolerance of some species. We used camera traps to survey along a gradient of urban, rural, and forest cover to quantify how carnivore landscape use varies among guild members and determine if a species was a human exploiter, adapter, or avoider. Our study was conducted in and around Corvallis, Oregon from April 2018 to February 2019 (11,914 trap nights) using 47 camera trap locations on a gradient from urban to rural. Our focal species were bobcat (Lynx rufus), coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), opossum (Didelphis virginiana), raccoon (Procyon lotor), and striped skunk (Mephitis mephitis). Raccoon and opossum were human exploiters with low use of forest cover and positive association with urban and rural developed areas likely due to human-derived resources as well as some refugia from larger predators. Coyote and gray fox were human adapters with high use of natural habitats while the effects of urbanization ranged from weak to indiscernible. Bobcat and striped skunk appeared to be human avoiders with negative relationship with urban cover and higher landscape use of forest cover. We conducted a diel temporal activity analysis and found mostly nocturnal activity within the guild, but more diurnal activity by larger-bodied predators compared to the smaller species. Although these species coexist as a community in human-dominated landscapes throughout much of North America, the effects of urbanization were not equal across species. Our results, especially for gray fox and striped skunk, are counter to research in other regions, suggesting that mesopredator use of urbanized landscapes can vary depending on the environmental conditions of the study area and management actions are likely to be most effective when decisions are based on locally derived data.

Concurrent Infection of Skunk Adenovirus-1, Listeria monocytogenes, and a Regionally Specific Clade of Canine Distemper Virus in One Gray Fox (Urocyon cinereoargenteus) and Concurrent Listeriosis and Canine Distemper in a Second Gray Fox.

One free-ranging Gray fox (Urocyon cinereoargenteus) underwent autopsy following neurologic disease, with findings including morbilliviral inclusions and associated lesions in numerous tissues, adenoviral intranuclear inclusions in bronchial epithelial cells, and septic pleuropneumonia, hepatitis, splenitis, and meningoencephalitis. Molecular diagnostics on fresh lung identified a strain within a distinct clade of canine distemper that is currently unique to wildlife in New England, as well as the emerging multi-host viral pathogen skunk adenovirus-1. Bacterial culture of fresh liver resulted in a pure growth of Listeria monocytogenes, with whole genome sequencing indicating that the isolate had a vast array of antimicrobial resistance and virulence-associated genes. One year later, a second fox was euthanized for inappropriate behavior in a residential area, and diagnostic workup revealed canine distemper and septic L. monocytogenes, with the former closely related to the distemper virus found in the previous fox and the latter divergent from the L. monocytogenes from the previous fox.

Purging of Strongly Deleterious Mutations Explains Long-Term Persistence and Absence of Inbreeding Depression in Island Foxes.

The recovery and persistence of rare and endangered species are often threatened by genetic factors, such as the accumulation of deleterious mutations, loss of adaptive potential, and inbreeding depression [1]. Island foxes (Urocyon littoralis), the dwarfed descendants of mainland gray foxes (Urocyon cinereoargenteus), have inhabited California's Channel Islands for >9,000 years [2-4]. Previous genomic analyses revealed that island foxes have exceptionally low levels of diversity and elevated levels of putatively deleterious variation [5]. Nonetheless, all six populations have persisted for thousands of generations, and several populations rebounded rapidly after recent severe bottlenecks [6, 7]. Here, we combine morphological and genomic data with population-genetic simulations to determine the mechanism underlying the enigmatic persistence of these foxes. First, through analysis of genomes from 1929 to 2009, we show that island foxes have remained at small population sizes with low diversity for many generations. Second, we present morphological data indicating an absence of inbreeding depression in island foxes, confirming that they are not afflicted with congenital defects common to other small and inbred populations. Lastly, our population-genetic simulations suggest that long-term small population size results in a reduced burden of strongly deleterious recessive alleles, providing a mechanism for the absence of inbreeding depression in island foxes. Importantly, the island fox illustrates a scenario in which genetic restoration through human-assisted gene flow could be a counterproductive or even harmful conservation strategy. Our study sheds light on the puzzle of island fox persistence, a unique success story that provides a model for the preservation of small populations.

Gray fox (Urocyon cinereoargenteus) parasite diversity in central Mexico.

Mexico has a long history of parasitological studies in communities of vertebrates. However, the mega diversity of the country makes fauna inventories an ongoing priority. Presently, there is little published on the parasite fauna of gray foxes (Urocyon cinereoargenteus Schereber, 1775) and this study provides new records of parasites for gray foxes in central Mexico. It is a continuation of a series of previous parasitological studies conducted with this carnivore in Mexico from 2003 to the present. A total of 24 foxes in the Parque Nacional El Cimatario (PANEC) were trapped, anaesthetized, and parasites recovered. The species found were Dirofilaria immitis, Ctenocephalides canis, C. felis, Euhoplopsillus glacialis affinis (first report for gray foxes in Mexico) Pulex simulants, and Ixodes sp. Three additional gray fox carcasses were necropsied and the parasites collected were adult nematodes Physaloptera praeputialis and Toxocara canis. The intensive study of the gray fox population selected for the 2013-2015 recent period allowed for a two-fold increase in the number of parasite species recorded for this carnivore since 2003 (nine to 18 parasite species), mainly recording parasitic arthropods, Dirofilaria immitis filariae and adult nematodes. The parasite species recorded are generalists that can survive in anthropic environments; which is characteristic of the present ecological scenario in central Mexico. The close proximity of the PANEC to the city of Santiago de Queretaro suggests possible parasite transmission between the foxes and domestic and feral dogs. Furthermore, packs of feral dogs in the PANEC might have altered habitat use by foxes, with possible impacts on transmission.

Abundancia relativa de la zorra gris Urocyon cinereoargenteus(Carnívora: Canidae) en la zona centro de Veracruz, México / Relative abundance of the gray foxUrocyon cinereoargenteus(Carnívora: Canidae) in Veracruz central area, Mexico

ResumenLa zorra gris (Urocyon cinereoargenteus Schreber) es un cánido de tamaño mediano que se distribuye ampliamente en México. La mayoría de los estudios sobre esta especie se han enfocado en el uso de hábitat, el ámbito hogareño, la dieta, la competencia con otros carnívoros y su distribución en diferentes paisajes tanto urbanos como rurales. Se tiene conocimiento de su presencia en fragmentos de bosque mesófilo de montaña y cafetales de sombra en el centro de Veracruz, aunque no se ha comparado su abundancia con otras coberturas vegetales como los cultivos presentes en la región. En este estudio describimos las variaciones de la abundancia mensual de zorra gris a través del registro de excretas en transectos de 500 m en cañaverales, cafetales de sombra y fragmentos de bosque mesófilo de montaña entre octubre del 2008 y mayo del 2009. Reportamos el índice de abundancia relativa para cada cobertura y cada mes, y evaluamos la relación de cuatro variables del paisaje (porcentaje de sombra, densidad de caminos, densidad de población humana y entremezcla de hábitats) en áreas de influencia de 450 ha alrededor de los sitios de muestreo. La comparación de la abundancia entre coberturas, mostró abundancias menores en los fragmentos de bosque mesófilo y mayores en los cafetales de sombra y cañaverales. No se encontró diferencia significativa a través de los meses (P= 0.476). Se plantea que la abundancia mayor en los cultivos puede estar asociada a las plagas de roedores y a la presencia de árboles frutales que ofrecen alimento a la zorra gris. De las variables del paisaje evaluadas solo la densidad de caminos de impacto medio y la densidad de población se correlacionaron positivamente con la abundancia de zorra gris, lo que demuestra que puede cohabitar con el humano sobre todo en zonas rurales. Se destaca la capacidad de la zorra gris para aprovechar los paisajes heterogéneos.

AbstractThe gray fox, Urocyon cinereoargenteus, is a medium-size canid widely distributed in México. Most studies on this species focus on habitat use, home range, diet, intraguild competence, and lanscape distribution between urban and rural sites. In central Veracruz, gray foxes are present in fragments of cloud forest and in shaded coffee plantations; nevertheless, its abundance has not yet been compared among other vegetation types found in the area, such as sugarcane plantations. In this study we described gray foxes abundance variations using 500 m transects, among sugarcane plantations, shaded coffee plantations, and cloud forest fragments throughout eight months, by scat counting in three sites of each cover type. We reported the relative abundance index for each cover type and each month, and evaluated its relationship with four landscape features: (a) shade percent, (b) trail density, (c) human population density, and (d) habitat juxtaposition, in influence areas of 450 ha around sampling sites. Abundance comparison among cover types showed lower abundances in cloud forest fragments and higher abundances in coffee and sugarcane plantations. No significant differences were found throughout months (p = 0.476). We proposed that higher abundances in plantations may be related to the presence of rodent plagues and fruit trees which offer food resources to gray foxes. The evaluation of landscape features showed that only medium-impact trail density and human population density were positively correlated with gray fox abundance; fact that demonstrates that this canid can coexist with humans in rural sites. We highlight the gray fox capacity to take advantage of heterogeneous landscapes.

Isotopic investigation of niche partitioning among native carnivores and the non-native coyote (Canis latrans).

We employed stable carbon (δ(13)C) and nitrogen (δ(15)N) isotopes within a hypothetico-deductive framework to explore potential resource partitioning among terrestrial mammalian carnivores. Isotope values were acquired using guard hair samples from bobcat (Lynx rufus), coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), and red fox (Vulpes vulpes) in the Adirondack Park, NY, USA. Enrichment along the δ(13)C axis was expected to reflect the use of human sources of food (reflecting a corn subsidy), and by extension tolerance for human-modified environments, whereas enrichment along the δ(15)N axis was expected to reflect a higher level of carnivory (i.e. amount of animal-based protein in the diet) - two mechanisms by which these now sympatric species may achieve a dynamic coexistence. Although bobcats were the only obligate carnivore, all four species shared a similar δ(15)N space. In contrast, bobcat had a lower and distinct δ(13)C signature compared to foxes, consistent with the a priori expectation of bobcats being the species least tolerant of human activities. Isotope signatures for coyotes, which colonized the region in the 1920s, overlapped all three native carnivores, bobcats the least, gray fox the most, indicating their potential competitive influence on this suite of native carnivores.