Genetic Tracking of a Rabid Coyote (Canis latrans) Detected beyond a Rabies Enzootic Area in West Virginia, US

Wildlife translocation and cross-species transmission can impede control and elimination of emerging zoonotic diseases. Tracking the geographic origin of both host and virus (i.e., translocation versus local infection) may help determine the most effective response when high-risk cases of emerging pathogens are identified in wildlife. In May 2022, a coyote (Canis latrans) infected with the raccoon (Procyon lotor) rabies virus variant (RRV) was collected in Lewis County, West Virginia, US, an area free from RRV. We applied host population genomics and RRV phylogenetic analyses to determine the most likely geographic origin of the rabid coyote. Coyote genomic analyses included animals from multiple eastern states bordering West Virginia, with the probable origin of the rabid coyote being the county of collection. The RRV phylogenetic analyses included cases detected from West Virginia and neighboring states, with most similar RRV sequences collected in a county 80 km to the northeast, within the oral rabies vaccination zone. The combined results suggest that the coyote was infected in an RRV management area and carried the RRV to Lewis County, a pattern consistent with coyote local movement ecology. Distant cross-species transmission and subsequent host movement presents a low risk for onward transmission in raccoon populations. This information helped with emergency response decision-making, thereby saving time and resources.

Diet selection in the Coyote Canis latrans

The Coyote (Canis latrans) is one of the most studied species in North America with at least 445 papers on its diet alone. While this research has yielded excellent reviews of what coyotes eat, it has been inadequate to draw deeper conclusions because no synthesis to date has considered prey availability. We accounted for prey availability by investigating the prey selection of coyotes across its distribution using the traditional Jacobs' index method, as well as the new iterative preference averaging (IPA) method on scats and biomass. We found that coyotes selected for Dall's Sheep (Ovis dalli), White-tailed Deer (Odocoileus virginianus), Eastern Cottontail Rabbit (Sylvilagus floridanus), and California Vole (Microtus californicus), which yielded a predator-to-preferred prey mass ratio of 1:2. We also found that coyotes avoided preying on other small mammals, including carnivorans and arboreal species. There was strong concordance between the traditional and IPA method on scats, but this pattern was weakened when biomass was considered. General linear models revealed that coyotes preferred to prey upon larger species that were riskier to hunt, reflecting their ability to hunt in groups, and were least likely to hunt solitary species. Coyotes increasingly selected Mule Deer (O. hemionus) and Snowshoe Hare (Lepus americanus) at higher latitudes, whereas Black-tailed Jackrabbit (L. californicus) were increasingly selected toward the tropics. Mule Deer were increasingly selected at higher coyote densities, while Black-tailed Jackrabbit were increasingly avoided at higher coyote densities. Coyote predation could constrain the realized niche of prey species at the distributional limits of the predator through their increased efficiency of predation reflected in increased prey selection values. These results are integral to improved understandings of Coyote ecology and can inform predictive analyses allowing for spatial variation, which ultimately will lead to better understandings about the ecological role of the coyote across different ecosystems.

Can a traditional partner preference test quantify monogamous behavior in captive coyotes?

Social monogamy is a unique social system exhibited by only 3-5% of mammalian taxa; however, all wild canid species exhibit this social system. Despite the high prevalence of social monogamy among canids, little is known about how they form selective social attachment relationships among non-kin. Thus, we aimed to quantify monogamous behavior in a highly ubiquitous canid, the coyote (Canis latrans). We adapted the three-chambered partner preference test, which was originally developed for prairie voles (Microtus ochrogaster), to assess social preference in mated pairs of captive coyotes at the USDA Predator Research Facility. We quantified monogamy-related behaviors, such as time spent in spatial proximity to a pair-mate versus a stranger. Our behavioral ethogram also included visual seeking, olfactory investigations, ears down, scent marking, and affiliative behavior. Test subjects showed significantly greater affiliative behavior toward their partner than toward a stranger. However, there was extremely high variability both within and between coyote pairs across behavioral measures. These data suggest the need for larger sample sizes when working with species with high individual variability, as well as the need for species- and facility-specific modifications to this testing paradigm and/or ethogram to better adapt it from its laboratory and rodent-based origins.

Spatiotemporal relationships of coyotes and free-ranging domestic cats as indicators of conflict in Culver City, California

As habitat generalists, urban coyote (Canis latrans) populations often utilize an abundance of diverse food sources in cities. Within southern California, domestic cats (Felis catus) comprise a higher proportion of coyote diets than in other studied urban areas throughout the United States. However, it is unclear which ecological factors contribute to higher rates of cat depredation by coyotes in this region. While previous research suggests that coyote presence may have a negative effect on free-ranging domestic cat distributions, few studies have determined whether urban green spaces affect coyote or free-ranging domestic cat occurrence and activity within a predominantly urbanized landscape. We placed 20 remote wildlife cameras across a range of green spaces and residential sites in Culver City, California, an area of Los Angeles County experiencing pronounced coyote-domestic cat conflict. Using data collected across 6 months from 2019-2020, we assessed the influence of green space and prey species (i.e., cottontail rabbits (Sylvilagus spp.) and domestic cats) on coyote habitat use and activity. Coyotes exhibited a preference for sites with higher amounts of green space, while domestic cat habitat use was high throughout our study region. Although cottontail rabbit habitat use was also highly associated with urban green space, neither cottontails nor domestic cats appeared to temporally overlap significantly with coyotes. Unlike other cities where coyotes and domestic cats exhibit strong habitat partitioning across the landscape, domestic cats and coyotes spatially overlapped in green space fragments throughout Culver City. We suggest that this pattern of overlap may be responsible for the frequent cases of domestic cat depredation by coyotes in Culver City.

Loggerhead sea turtle nesting and coyote depredation habits in relation to weather and the presence of wolf urine data set

The data in this manuscript are comprised of loggerhead sea turtle nesting records and coyote depredation events on South Island Beach in the Tom Yawkey Preserve, South Carolina, from 2015 to 2019 comprise the data in this manuscript. We compared the nesting and depredation rates with abiotic factors that may have influenced them. We analysed our data using G-tests to determine whether any abiotic factors were associated with coyote depredations or the timing of loggerhead nesting. Data were collected in conjunction with an experiment testing a possible conservation tool to deter coyote depredation of loggerhead sea turtle nests (Wauson and Rogers 2021).

An Excel® file contains the entire data set in the supplemental material. Tables and their corresponding statistics test whether behavioural traits of loggerhead sea turtles and coyotes change based on certain abiotic factors, as well as how coyote depredation rates behaviour change in the presence of wolf urine.

Urbanization's influence on the distribution of mange in a carnivore revealed with multistate occupancy models

Increasing urbanization and use of urban areas by synanthropic wildlife has increased human and domestic animal exposure to zoonotic diseases and exacerbated epizootics within wildlife populations. Consequently, there is a need to improve wildlife disease surveillance programs to rapidly detect outbreaks and refine inferences regarding spatiotemporal disease dynamics. Multistate occupancy models can address potential shortcomings in surveillance programs by accounting for imperfect detection and the misclassification of disease states. We used these models to explore the relationship between urbanization, slope, and the spatial distribution of sarcoptic mange in coyotes (Canis latrans) inhabiting Fort Irwin, California, USA. We deployed remote cameras across 180 sites within the desert surrounding the populated garrison and classified sites by mange presence or absence depending on whether a symptomatic or asymptomatic coyote was photographed. Coyotes selected flatter sites closer to the urban area with a high probability of use (0.845, 95% credible interval (CRI): 0.728, 0.944); site use decreased as the distance to urban areas increased (standardized [Formula: see text] = - 1.354, 95% CRI - 2.423, - 0.619). The probability of correctly classifying mange presence at a site also decreased further from the urban area and was probably related to the severity of mange infection. Severely infected coyotes, which were more readily identified as symptomatic, resided closer to the urban area and were most likely dependent on urban resources for survival; urban resources probably contributed to sustaining the disease. Multistate occupancy models represent a flexible framework for estimating the occurrence and spatial extent of observable infectious diseases, which can improve wildlife disease surveillance programs.

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota

Most knowledge of the vertebrate gut microbiota comes from fecal samples; due to difficulties involved in sample collection, the upper intestinal microbiota is poorly understood in wild animals despite its potential to inform broad interpretations about host-gut microbe relationships under natural conditions. Here, we used 16S rRNA gene sequencing to characterize the microbiota of wild coyotes (Canis latrans) along the gastrointestinal tract, including samples from the duodenum, jejunum, ileum, caecum, ascending and descending colon, and feces. We used this intestinal profile to (1) quantify how intestinal site and individual identity interact to shape the microbiota in an uncontrolled setting, and (2) evaluate whether the fecal microbiota adequately represent other intestinal sites. Microbial communities in the large intestine were distinct from those in the small intestine, with higher diversity and a greater abundance of anaerobic taxa. Within each of the small and large intestine, individual identity explained significantly more among-sample variation than specific intestinal sites, revealing the importance of individual variation in the microbiota of free-living animals. Fecal samples were not an adequate proxy for studying upper intestinal environments, as they contained only half the amplicon sequence variants (ASVs) present in the small intestine at three- to four-fold higher abundances. Our study is a unique biogeographical investigation of the microbiota using free-living mammals rather than livestock or laboratory organisms and provides a foundational understanding of the gastrointestinal microbiota in a wild canid.

First report of Siphonaptera parasites in Canis latrans in the Flora and Fauna Protection Area, Médanos de Samalayuca Chihuahua, Mexico

Siphonaptera are hematophage parasite vectors of both human and animal diseases. We aimed to identify ectoparasites parasitizing a coyote population (Canis latrans) in the northwest region of the Flora and Fauna Protection Area Médanos de Samalayuca, Chihuahua, Mexico. We captured 21 coyotes (15 males and 6 females) during the summer and winter of 2018. The individuals were anesthetized and thoroughly examined for ectoparasites. We found that 43% of the coyotes were infested. Based on characteristics such as the absence of pronotal and genal combs in the head, we identified 15 specimens as Pulex irritans. This is the first report of P. irritans in coyotes in Médanos de Samalayuca Chihuahua, Mexico.

Detecting co-infections of Echinococcus multilocularis and Echinococcus canadensis in coyotes and red foxes in Alberta, Canada using real-time PCR

The continued monitoring of Echinococcus species in intermediate and definitive hosts is essential to understand the eco-epidemiology of these parasites, as well to assess their potential impact on public health. In Canada, co-infections of Echinococcus canadensis and Echinococcus multilocularis based on genetic characterization have been recently reported in wolves, but not yet in other possible hosts such as coyotes and foxes. In this study, we aimed to develop a quantitative real-time PCR assay to detect E. multilocularis and E. canadensis and estimate the occurrence of co-infections while inferring about the relative abundance of the two parasites within hosts. We tested DNA extracted from aliquots of Echinococcus spp. specimens collected from intestinal tracts of 24 coyote and 16 fox carcasses from Alberta, Canada. We found evidence of co-infections of E. multilocularis and E. canadensis in 11 out of 40 (27%) samples, with 8 out of 24 (33%) in coyote samples and 3 out of 16 (19%) in red fox samples. DNA concentrations were estimated in three samples with Cq values within the range of the standard curve for both parasites; two of them presented higher DNA concentrations of E. multilocularis than E. canadensis. The use of qPCR aided detection of co-infections when morphological discrimination was difficult and quantification of DNA for samples within the standard curve. This is the first molecularly confirmed record of E. canadensis in coyotes and the first evidence of co-infections of E. multilocularis and E. canadensis in coyotes and red foxes.

Setting an evolutionary trap: could the hider strategy be maladaptive for white-tailed deer?

An evolutionary trap occurs when an organism makes a formerly adaptive decision that now results in a maladaptive outcome. Such traps can be induced by anthropogenic environmental changes, with nonnative species introductions being a leading cause. The recent establishment of coyotes (Canis latrans) into the southeastern USA has the potential to change white-tailed deer (Odocoileus virginianus) population dynamics through direct predation and behavioral adaptation. We used movement rate and bedsite characteristics of radiocollared neonates to evaluate their antipredator strategies in the context of novel predation risk in a structurally homogeneous, fire-maintained ecosystem. Neonate bedsites had greater plant cover values compared with random sites (t = 30.136; p < 0.001), indicating bedsite selection was consistent with the hider strategy used to avoid predation. We determined selection gradients of coyote predation on neonate movement rate and plant cover and diversity at bedsites during the first 10 days of life. Interestingly, neonates that moved less and bedded in denser cover were more likely to be depredated by coyotes, meaning that greater neonate movement rate and bedsites located in less dense cover were favored by natural selection. These results are counter to expected antipredator strategies in white-tailed deer and exemplify how an adaptive response could be maladaptive in novel contexts.

Distribution and host associations of ixodid ticks collected from wildlife in Florida, USA

A tick survey was conducted to document tick-host associations with Florida (USA) wildlife, and to determine the relative abundance and distribution of ixodid ticks throughout the state. The survey was conducted using collection kits distributed to licensed Florida hunters as well as the examination of archived specimens from ongoing state wildlife research programs. Collected tick samples were obtained from 66% of Florida counties and were collected from nine wildlife hosts, including black bear, bobcat, coyote, deer, gray fox, Florida panther, raccoon, swine, and wild turkey. In total, 4176 ticks were identified, of which 75% were Amblyomma americanum, 14% Ixodes scapularis, 8% A. maculatum, 3% Dermacentor variabilis, and < 1% were I. affinis and I. texanus. americanum, D. variabilis, and I. scapularis had the broadest host range, while A. maculatum, D. variabilis, and I. scapularis had the widest geographic distribution. While the survey data contribute to an understanding of tick-host associations in Florida, they also provide insight into the seasonal and geographic distribution of several important vector species in the southeastern USA.

Do the antipredator strategies of shared prey mediate intraguild predation and mesopredator suppression?

Understanding the conditions that facilitate top predator effects upon mesopredators and prey is critical for predicting where these effects will be significant. Intraguild predation (IGP) and the ecology of fear are hypotheses used to describe the effects of top predators upon mesopredators and prey species, but make different assumptions about organismal space use. The IGP hypothesis predicts that mesopredator resource acquisition and risk are positively correlated, creating a fitness deficit. But if shared prey also avoid a top predator, then mesopredators may not have to choose between risk and reward. Prey life history may be a critical predictor of how shared prey respond to predation and may mediate mesopredator suppression. We used hierarchical models of species distribution and abundance to test expectations of IGP using two separate triangular relationships between a large carnivore, smaller intraguild carnivore, and shared mammalian prey with different life histories. Following IGP, we expected that a larger carnivore would suppress a smaller carnivore if the shared prey species did not spatially avoid the large carnivore at broad scales. If prey were fearful over broad scales, we expected less evidence of mesopredator suppression. We tested these theoretical hypotheses using remote camera detections across a large spatial extent. Lagomorphs did not appear to avoid coyotes, and fox detection probability was lower as coyote abundance increased. In contrast, white‐tailed deer appeared to avoid areas of increased wolf use, and coyote detection probability was not reduced at sites where wolves occurred. These findings suggest that mesopredator suppression by larger carnivores may depend upon the behavior of shared prey, specifically the spatial scale at which they perceive risk. We further discuss how extrinsic environmental factors may contribute to mesopredator suppression.

ECO-EPIZOOTIOLOGIC STUDY OF FRANCISELLA TULARENSIS, THE AGENT OF TULAREMIA, IN QUÉBEC WILDLIFE

In Canada, Francisella tularensis , the zoonotic bacterial agent of tularemia, affects mostly snowshoe hares ( Lepus americanus ), muskrats ( Ondatra zibethicus ), and beavers ( Castor canadensis ). Despite numerous studies, the ecologic cycle and natural reservoirs of F. tularensis are not clearly defined. We conducted a cross-sectional study to estimate the prevalence of F. tularensis in snowshoe hares, muskrats, and coyotes ( Canis latrans ) in four regions of Québec, Canada, and to describe the risk of infection in relation to host and environmental characteristics at three spatial scales. Between October 2012 and April 2013, trappers captured 345 snowshoe hares, 411 muskrats, and 385 coyotes. Blood samples were tested by microagglutination tests, and DNA extracts of liver, kidney, lung, and spleen of snowshoe hares and muskrats were tested by real-time PCR to detect past and active infection to F. tularensis , respectively. Individual host characteristics, including body condition, age, and sex, were evaluated as risk factors of infection, along with ecologic characteristics of the location of capture extracted from geographic databases. Prevalences of antibody to F. tularensis and 95% confidence intervals were 2.9% (1.4-5.1%) in coyotes, 0.6% (0.1-2.1%) in hares, and 0% (0.0-0.9%) in muskrats. Francisella tularensis DNA was not detected by real-time PCR in the pools of four organs from muskrats and hares, but F. tularensis type AI was detected during testing of the individual organs of two antibody-positive hares. Exact logistic regression analyses showed that age was a significant predictor of antibody detection in coyotes, as were the proportion of forest and the proportion of area considered as suitable habitat for hares in the environment around the location of capture of the coyotes. Our results suggest a terrestrial cycle of F. tularensis in the regions studied.

Nutritional effects on reproductive performance of captive adult female coyotes (Canis latrans)

Interactions between animals and their environment are fundamental to ecological research. Field studies of coyote (Canis latrans) reproductive performance suggest mean litter size changes in response to prey abundance. However, this relationship has been assessed primarily by using carcasses collected from trappers. The objective of this study was to assess whether nutritional manipulation prior to mating affected reproduction in adult female coyotes. We examined the effects of caloric restriction during the 7 months prior to estrus on the reproductive rates of 11 captive female coyotes and the subsequent initial survival of pups through two reproductive cycles. This was a 2-year study with a cross-over design so each female was monitored for reproductive performance on each of the two diet treatments. We assessed the number of implantation scars, number of pups born, sex ratios of pups, average pup weight at birth and 2- and 6-weeks of age, and the survival rates between implantation and 2-weeks of age for two diet treatments. We found the mean number of implantation sites and pups whelped during a reproductive cycle was influenced by food-intake prior to conception. Additionally, we found evidence suggesting the effects of nutritional stress may persist for additional breeding cycles. We also provided evidence suggesting well-fed females tended to have more male pups. Understanding how environmental factors influence reproductive output may improve model predictions of coyote population dynamics.

Y-chromosome evidence supports asymmetric dog introgression into eastern coyotes

Hybridization has played an important role in the evolutionary history of Canis species in eastern North America. Genetic evidence of coyote–dog hybridization based on mitochondrial DNA (mtDNA) is lacking compared to that based on autosomal markers. This discordance suggests dog introgression into coyotes has potentially been male biased, but this hypothesis has not been formally tested. Therefore, we investigated biparentally, maternally, and paternally inherited genetic markers in a sample of coyotes and dogs from southeastern Ontario to assess potential asymmetric dog introgression into coyotes. Analysis of autosomal microsatellite genotypes revealed minimal historical and contemporary admixture between coyotes and dogs. We observed only mutually exclusive mtDNA haplotypes in coyotes and dogs, but we observed Y-chromosome haplotypes (Y-haplotypes) in both historical and contemporary coyotes that were also common in dogs. Species-specific Zfy intron sequences of Y-haplotypes shared between coyotes and dogs confirmed their homology and indicated a putative origin from dogs. We compared Y-haplotypes observed in coyotes, wolves, and dogs profiled in multiple studies, and observed that the Y-haplotypes shared between coyotes and dogs were either absent or rare in North American wolves, present in eastern coyotes, but absent in western coyotes. We suggest the eastern coyote has experienced asymmetric genetic introgression from dogs, resulting from predominantly historical hybridization with male dogs and subsequent backcrossing of hybrid offspring with coyotes. We discuss the temporal and spatial dynamics of coyote–dog hybridization and the conditions that may have facilitated the introgression of dog Y-chromosomes into coyotes. Our findings clarify the evolutionary history of the eastern coyote.