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.

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.

Occurrence of Ancylostoma Caninum from a Gray Fox Urocyon Cinereoargenteus in Southeastern Mexico.

The hookworm Ancylostoma caninum is a common nematode of wild and domestic canids worldwide. In Mexico, there are few records of helminths in wild canids, especially in the southeastern region. The aim of the present study was to examine the helminths from a gray fox Urocyon cinereoargenteus in southeastern Mexico. A road-killed female gray fox found in Merida, Yucatan, Mexico, was examined for helminths. Only nematodes were found in the intestine of the gray fox and identified using morphological studies and molecular analysis of 28S rRNA gene fragments. The characteristics exhibited by the nematode specimens were in accordance with descriptions of A. caninum: e. g. oral opening with a pair of prominent chitinous plates bearing three pairs of ventral teeth, lateral rays with a common trunk, dorsal ray divided into two branches with each branch terminating in three digitations. BLAST analysis of the 28S sequence showed similarity and coverage values of 99.8 % and 100 %, respectively, with a sequence of A. caninum from the domestic dog Canis familiaris in Australia. The genetic distance between the Australian specimen and the Yucatan specimen of A. caninum was 0.1 %, that is, they were only different in a single nucleotide. The gray fox examined in this study was found close to a rural community where A. caninum has been recorded from domestic dogs, which could be the source of infection. Our study increases the distribution of this nematode parasitizing the gray fox in Mexico and provides the first nucleotide sequence of A. caninum from the gray fox.

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.

Endozoochorous dispersal of forest seeds by carnivorous mammals in Sierra Fría, Aguascalientes, Mexico.

Some carnivorous mammals ingest fruit and disperse seeds of forest plant species capable of colonizing disturbed areas in ecosystems. The objective of the present study was to evaluate the dissemination of Arctostaphylos pungens and Juniperus deppeana seeds by the gray fox (Urocyon cinereoargenteus), coyote (Canis latrans), and other carnivores in the Protected Natural Area Sierra Fría, in Aguascalientes, Mexico. Scat collection was undertaken via transects using the direct search method, while the seasonal phenology of A. pungens and J. deppeana was evaluated by recording flower and fruit abundance on both the plant and the surrounding forest floor ground. Seed viability was assessed by optical densitometry via X-ray and a germination test. It was found that the gray fox, coyote, ringtail (Bassariscus astutus), and bobcat (Lynx rufus) disseminated seeds of A. pungens (212 ± 48.9 seeds/scat) and J. deppeana (23.6 ± 4.9 seeds/scat), since a large proportion of the collected scat of these species contained seeds (28/30 = 93.33%, 12/43 = 27.9%, 6/12 = 50% and 7/25 = 28% respectively). The gray fox, coyote, ringtail, and bobcat presented an average of seed dispersion of both plant species of 185.4 ± 228.7, 4.0 ± 20.0, 12.1 ± 30.4, and 0.8 ± 1.5 per scat; the seed proportions in the gray fox, coyote, ringtail, and bobcat were 89.6/10.4%, 82.3/17.7%, 90.4/9.6%, and 38.1/61.9% for A. pungens and J. deppeana, respectively. The phenology indicated a finding related to the greater abundance of ripe fruit in autumn and winter (p < .01). This coincided with the greater abundance of seeds found in scats during these seasons. Endozoochory and diploendozoochory enhanced the viability and germination of the seeds (p > .05), except in those of A. pungens dispersed by coyote. These results suggest that carnivores, particularly the gray fox, the coyote, and the bobcat, play an important role in forest seed dissemination, and thus forest regeneration, by making both a quantitative and qualitative contribution to the dispersal of the two pioneer species under study.

Dental Pathology of the Grey Fox (Urocyon cinereoargenteus).

Museum specimens from 637 grey foxes (Urocyon cinereoargenteus) were examined macroscopically according to predefined criteria. Of the 637 specimens, 569 were included for further examination. The study population included more males (n = 261, 45.9%) than females (n = 196, 34.4%) and animals of unknown sex (n = 112, 19.7%). Additionally, 481 (84.5%) adults, 67 (11.8%) young adults and 21 (3.7%) individuals of unknown age comprised the study population, with juveniles and neonates excluded. The number of teeth present for examination was 23,066 (96.5%) with 624 (2.6%) absent artefactually, 15 (0.06%) absent congenitally and 193 (0.8%) lost ante mortem through acquired tooth loss. No persistent deciduous teeth or temporomandibular joint osteoarthritis were found in any of the specimens. Ten supernumerary teeth from nine (1.6%) specimens were encountered. Teeth with extra roots were found in 61 individuals (10.7%), with 0.4% of all teeth affected. Of the alveoli examined, 1,529 (6.4%) displayed bony changes suggestive of periodontitis, with 276 (48.7%) of individuals affected. Significantly more adults were affected by bony changes associated with stage 3 periodontitis than young adults. All specimens displaying stage 4 periodontitis were adults. Fractures affected 446 (78.4%) of the specimens examined and 3,554 (15.4%) of teeth present. Almost half (n = 10,856, 47.1%) of the teeth available for examination and most specimens (n = 487, 85.6%) displayed some degree of attrition or abrasion. Two individuals (0.4%) exhibited periapical lesions. Traumatic skull injuries affected 56 (9.8%) specimens. Characterizing the dental pathology in the grey fox provides key insight into the ecology of the species and factors contributing to fitness.

Dynamic occupancy modelling reveals a hierarchy of competition among fishers, grey foxes and ringtails.

Determining how species coexist is critical for understanding functional diversity, niche partitioning and interspecific interactions. Identifying the direct and indirect interactions among sympatric carnivores that enable their coexistence is particularly important to elucidate because they are integral for maintaining ecosystem function. We studied the effects of removing nine fishers (Pekania pennanti) on their population dynamics and used this perturbation to elucidate the interspecific interactions among fishers, grey foxes (Urocyon cinereoargenteus) and ringtails (Bassariscus astutus). Grey foxes (family: Canidae) are likely to compete with fishers due to their similar body sizes and dietary overlap, and ringtails (family: Procyonidae), like fishers, are semi-arboreal species of conservation concern. We used spatial capture-recapture to investigate fisher population numbers and dynamic occupancy models that incorporated interspecific interactions to investigate the effects members of these species had on the colonization and persistence of each other's site occupancy. The fisher population showed no change in density for up to 3 years following the removals of fishers for translocations. In contrast, fisher site occupancy decreased in the years immediately following the translocations. During this same time period, site occupancy by grey foxes increased and remained elevated through the end of the study. We found a complicated hierarchy among fishers, foxes and ringtails. Fishers affected grey fox site persistence negatively but had a positive effect on their colonization. Foxes had a positive effect on ringtail site colonization. Thus, fishers were the dominant small carnivore where present and negatively affected foxes directly and ringtails indirectly. Coexistence among the small carnivores we studied appears to reflect dynamic spatial partitioning. Conservation and management efforts should investigate how intraguild interactions may influence the recolonization of carnivores to previously occupied landscapes.

Ecological Potential for Rabies Virus Transmission via Scavenging of Dead Bats by Mesocarnivores.

Multiple species of bats are reservoirs of rabies virus in the Americas and are occasionally the source of spillover infections into mesocarnivore species. Although rabies transmission generally is assumed to occur via bite, laboratory studies have demonstrated the potential for rabies transmission via ingestion of rabid animals. We investigated the ecological potential for this mode of transmission by assessing mesocarnivore scavenging behavior of dead bats in suburban habitats of Flagstaff, Arizona, US. In autumn 2013, summer 2014, and autumn 2015, we placed 104 rabies-negative bat carcasses either near buildings, in wildland areas, or in residential yards and then monitored them with trail cameras for 5 d. Overall, 52 (50%) bat carcasses were scavenged, with 39 (75%) of those scavenged by striped skunks ( Mephitis mephitis ). Within our study area, striped skunks had a higher ecological potential to contract rabies via ingestion of bat carcasses compared to other mesocarnivore species, due both to a greater number of encounters and a higher probability of ingestion per encounter (91%), and they were significantly more likely to approach bat carcasses in yards than in wildland areas. Raccoons ( Procyon lotor ) and gray foxes ( Urocyon cinereoargenteus ) had fewer encounters (nine and 13, respectively) and lower probability of ingesting bats (33% and 8%, respectively).

High Trypanosoma cruzi infection prevalence associated with minimal cardiac pathology among wild carnivores in central Texas.

Infection with the zoonotic vector-borne protozoal parasite Trypanosoma cruzi causes Chagas disease in humans and dogs throughout the Americas. Despite the recognized importance of various wildlife species for perpetuating Trypanosoma cruzi in nature, relatively little is known about the development of cardiac disease in infected wildlife. Using a cross-sectional study design, we collected cardiac tissue and blood from hunter-donated wildlife carcasses- including raccoon (Procyon lotor), coyote (Canis latrans), gray fox (Urocyon cinereoargenteus), and bobcat (Lynx rufus) - from central Texas, a region with established populations of infected triatomine vectors and increasing diagnoses of Chagas disease in domestic dogs. Based on PCR analysis, we found that 2 bobcats (14.3%), 12 coyotes (14.3%), 8 foxes (13.8%), and 49 raccoons (70.0%) were positive for T. cruzi in at least one sample (right ventricle, apex, and/or blood clot). Although a histologic survey of right ventricles showed that 21.1% of 19 PCR-positive hearts were characterized by mild lymphoplasmocytic infiltration, no other lesions and no amastigotes were observed in any histologic section. DNA sequencing of the TcSC5D gene revealed that raccoons were infected with T. cruzi strain TcIV, and a single racoon harbored a TcI/TcIV mixed infection. Relative to other wildlife species tested here, our data suggest that raccoons may be important reservoirs of TcIV in Texas and a source of infection for indigenous triatomine bugs. The overall high level of infection in this wildlife community likely reflects high levels of vector contact, including ingestion of bugs. Although the relationship between the sylvatic cycle of T. cruzi transmission and human disease risk in the United States has yet to be defined, our data suggest that hunters and wildlife professionals should take precautions to avoid direct contact with potentially infected wildlife tissues.

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.