Y‐chromosome evidence supports widespread signatures of three‐species Canis hybridization in eastern North America

There has been considerable discussion on the origin of the red wolf and eastern wolf and their evolution independent of the gray wolf. We analyzed mitochondrial DNA (mtDNA) and a Y‐chromosome intron sequence in combination with Y‐chromosome microsatellites from wolves and coyotes within the range of extensive wolf–coyote hybridization, that is, eastern North America. The detection of divergent Y‐chromosome haplotypes in the historic range of the eastern wolf is concordant with earlier mtDNA findings, and the absence of these haplotypes in western coyotes supports the existence of the North American evolved eastern wolf (Canis lycaon). Having haplotypes observed exclusively in eastern North America as a result of insufficient sampling in the historic range of the coyote or that these lineages subsequently went extinct in western geographies is unlikely given that eastern‐specific mtDNA and Y‐chromosome haplotypes represent lineages divergent from those observed in extant western coyotes. By combining Y‐chromosome and mtDNA distributional patterns, we identified hybrid genomes of eastern wolf, coyote, gray wolf, and potentially dog origin in Canis populations of central and eastern North America. The natural contemporary eastern Canis populations represent an important example of widespread introgression resulting in hybrid genomes across the original C. lycaon range that appears to be facilitated by the eastern wolf acting as a conduit for hybridization. Applying conventional taxonomic nomenclature and species‐based conservation initiatives, particularly in human‐modified landscapes, may be counterproductive to the effective management of these hybrids and fails to consider their evolutionary potential.     

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.     

RAD sequencing and genomic simulations resolve hybrid origins within North American Canis

Top predators are disappearing worldwide, significantly changing ecosystems that depend on top-down regulation. Conflict with humans remains the primary roadblock for large carnivore conservation, but for the eastern wolf (Canis lycaon), disagreement over its evolutionary origins presents a significant barrier to conservation in Canada and has impeded protection for grey wolves (Canis lupus) in the USA. Here, we use 127 235 single-nucleotide polymorphisms (SNPs) identified from restriction-site associated DNA sequencing (RAD-seq) of wolves and coyotes, in combination with genomic simulations, to test hypotheses of hybrid origins of Canis types in eastern North America. A principal components analysis revealed no evidence to support eastern wolves, or any other Canis type, as the product of grey wolf × western coyote hybridization. In contrast, simulations that included eastern wolves as a distinct taxon clarified the hybrid origins of Great Lakes-boreal wolves and eastern coyotes. Our results support the eastern wolf as a distinct genomic cluster in North America and help resolve hybrid origins of Great Lakes wolves and eastern coyotes. The data provide timely information that will shed new light on the debate over wolf conservation in eastern North America.     

Genetic outcomes of wolf recovery in the western Great Lakes states

Conflicting interpretations of the influence of coyote hybridization on wolf recovery in the western Great Lakes (WGL) states have stemmed from disagreement over the systematics of North American wolves. Questions regarding their recovery status have resulted. We addressed these issues with phylogenetic and admixture analysis of DNA profiles of western wolves, WGL states wolves and Wisconsin coyotes developed from autosome and Y-chromosome microsatellites and mitochondrial DNA control region sequence. Hybridization was assessed by comparing the haplotypes exhibited by sympatric wolves and coyotes. Genetic variability and connectivity were also examined. These analyses support the recognition of Canis lycaon as a unique species of North American wolf present in the WGL states and found evidence of hybridization between C. lupus and C. lycaon but no evidence of recent hybridization with sympatric coyotes. The recolonized WGL states wolves are genetically similar to historical wolves from the region and should be considered restored.     

Canid hybridization: contemporary evolution in human‐modified landscapes

Contemporary evolution through human‐induced hybridization occurs throughout the taxonomic range. Formerly allopatric species appear especially susceptible to hybridization. Consequently, hybridization is expected to be more common in regions with recent sympatry owing to human activity than in areas of historical range overlap. Coyotes ( Canis latrans) and gray wolves ( C. lupus) are historically sympatric in western North America. Following European settlement gray wolf range contracted, whereas coyote range expanded to include eastern North America. Furthermore, wolves with New World (NW) mitochondrial DNA (mtDNA) haplotypes now extend from Manitoba to Québec in Canada and hybridize with gray wolves and coyotes. Using mtDNA and 12 microsatellite markers, we evaluated levels of wolf‐coyote hybridization in regions where coyotes were present (the Canadian Prairies, n = 109 samples) and absent historically (Québec, n = 154). Wolves with NW mtDNA extended from central Saskatchewan (51°N, 69°W) to northeastern Québec (54°N, 108°W). On the Prairies, 6.3% of coyotes and 9.2% of wolves had genetic profiles suggesting wolf‐coyote hybridization. In contrast, 12.6% of coyotes and 37.4% of wolves in Québec had profiles indicating hybrid origin. Wolves with NW and Old World ( C. lupus) mtDNA appear to form integrated populations in both regions. Our results suggest that hybridization is more frequent in historically allopatric populations. Range shifts, now expected across taxa following climate change and other human influence on the environment, might therefore promote contemporary evolution by hybridization.     

Inter-specific territoriality in a Canis hybrid zone: spatial segregation between wolves, coyotes, and hybrids

Gray wolves (Canis lupus) and coyotes (Canis latrans) generally exhibit intraspecific territoriality manifesting in spatial segregation between adjacent packs. However, previous studies have found a high degree of interspecific spatial overlap between sympatric wolves and coyotes. Eastern wolves (Canis lycaon) are the most common wolf in and around Algonquin Provincial Park (APP), Ontario, Canada and hybridize with sympatric gray wolves and coyotes. We hypothesized that all Canis types (wolves, coyotes, and hybrids) exhibit a high degree of spatial segregation due to greater genetic, morphologic, and ecological similarities between wolves and coyotes in this hybrid system compared with western North American ecosystems. We used global positioning system telemetry and probabilistic measures of spatial overlap to investigate spatial segregation between adjacent Canis packs. Our hypothesis was supported as: (1) the probability of locating wolves, coyotes, and hybrids within home ranges ( $\bar{x}$  = 0.05) or core areas ( $\bar{x}$  < 0.01) of adjacent packs was low; and (2) the amount of shared space use was negligible. Spatial segregation did not vary substantially in relation to genotypes of adjacent packs or local environmental conditions (i.e., harvest regulations or road densities). We provide the first telemetry-based demonstration of spatial segregation between wolves and coyotes, highlighting the novel relationships between Canis types in the Ontario hybrid zone relative to areas where wolves and coyotes are reproductively isolated. Territoriality among Canis may increase the likelihood of eastern wolves joining coyote and hybrid packs, facilitate hybridization, and could play a role in limiting expansion of the genetically distinct APP eastern wolf population.     

Genetic and morphometric analysis of sixteenth century <Emphasis Type="Italic">Canis</Emphasis> skull fragments: implications for historic eastern and gray wolf distribution in North America

Resolving the taxonomy and historic ranges of species are essential to recovery plans for species at risk and conservation programs that aim to restore extirpated populations. In eastern North America, planning for wolf population restoration is complicated by the disputed historic distributions of two wolf species: the Old World-evolved gray wolf (Canis lupus) and the New World-evolved eastern wolf (C. lycaon). We used genetic and morphometric data from 4- to 500-year-old Canis samples excavated in London, Ontario, Canada to help clarify the historic range of these two wolf species in the eastern temperate forests of North America. We isolated DNA and sequenced the mitochondrial control region and found that none of the samples were of gray wolf origin. Two of the DNA sequences corresponded to those found in present day coyotes (C. latrans), but morphometric comparisons show an eastern wolf, not coyote, origin. The remaining two sequences matched ancient domestic dog haplotypes. These results suggest that the New World-evolved eastern wolf, not the gray wolf, occupied this region prior to the arrival of European settlers, although eastern-gray wolf hybrids cannot be ruled out. Furthermore, our data support the idea of a shared common ancestry between eastern wolves and western coyotes, and that the distribution of gray wolves at this time probably did not include the eastern temperate forests of North America.     

Size‐assortative choice and mate availability influences hybridization between red wolves (Canis rufus) and coyotes (Canis latrans)

Anthropogenic hybridization of historically isolated taxa has become a primary conservation challenge for many imperiled species. Indeed, hybridization between red wolves (Canis rufus) and coyotes (Canis latrans) poses a significant challenge to red wolf recovery. We considered seven hypotheses to assess factors influencing hybridization between red wolves and coyotes via pair‐bonding between the two species. Because long‐term monogamy and defense of all‐purpose territories are core characteristics of both species, mate choice has long‐term consequences. Therefore, red wolves may choose similar‐sized mates to acquire partners that behave similarly to themselves in the use of space and diet. We observed multiple factors influencing breeding pair formation by red wolves and found that most wolves paired with similar‐sized conspecifics and wolves that formed congeneric pairs with nonwolves (coyotes and hybrids) were mostly female wolves, the smaller of the two sexes. Additionally, we observed that lower red wolf abundance relative to nonwolves and the absence of helpers increased the probability that wolves consorted with nonwolves. However, successful pairings between red wolves and nonwolves were associated with wolves that maintained small home ranges. Behaviors associated with territoriality are energetically demanding and behaviors (e.g., aggressive interactions, foraging, and space use) involved in maintaining territories are influenced by body size. Consequently, we propose the hypothesis that size disparities between consorting red wolves and coyotes influence positive assortative mating and may represent a reproductive barrier between the two species. We offer that it may be possible to maintain wild populations of red wolves in the presence of coyotes if management strategies increase red wolf abundance on the landscape by mitigating key threats, such as human‐caused mortality and hybridization with coyotes. Increasing red wolf abundance would likely restore selection pressures that increase mean body and home‐range sizes of red wolves and decrease hybridization rates via reduced occurrence of congeneric pairs.     

Genetic nature of eastern wolves: Past, present and future

Eastern North American wolves have long been recognized as morphologically distinct from both coyotes and gray wolves. This has led to questions regarding their origins and taxonomic status. Eastern wolves are mainly viewed as: (1) a smaller subspecies of gray wolf (Canis lupus lycaon), potentially the result of historical hybridization between gray wolves (C. lupus) and red wolves (C. rufus), (2) a hybrid, the result of gray wolf (C. lupus) and coyote (C. latrans) interbreeding, or (3) a distinct species, C. lycaon, closely related to the red wolf (C. rufus). Although debate persists, recent molecular studies suggest that the eastern wolf is not a gray wolf subspecies, nor the result of gray wolf/coyote hybridization. Eastern wolves were more likely a distinct species, C. lycaon, prior to the eastward spread of coyotes in the late 1800s. However, contemporary interbreeding exits between C. lycaon to both C. lupus and C. latrans over much of its present range complicating its present taxonomic characterization. While hybridization may be reducing the taxonomic distinctiveness of C. lycaon, it should not necessarily be viewed as negative influence. Hybridization may be enhancing the adaptive potential of eastern wolves, allowing them to more effectively exploit available resources in rapidly changing environments.     

Hybridization among three native North American Canis species in a region of natural sympatry

Background

Population densities of many species throughout the world are changing due to direct persecution as well as anthropogenic habitat modification. These changes may induce or increase the frequency of hybridization among taxa. If extensive, hybridization can threaten the genetic integrity or survival of endangered species. Three native species of the genus Canis, coyote (C. latrans), Mexican wolf (C. lupus baileyi) and red wolf (C. rufus), were historically sympatric in Texas, United States. Human impacts caused the latter two to go extinct in the wild, although they survived in captive breeding programs. Morphological data demonstrate historic reproductive isolation between all three taxa. While the red wolf population was impacted by introgressive hybridization with coyotes as it went extinct in the wild, the impact of hybridization on the Texas populations of the other species is not clear.

Methodology/ Principal Findings

We surveyed variation at maternally and paternally inherited genetic markers (mitochondrial control region sequence and Y chromosome microsatellites) in coyotes from Texas, Mexican wolves and red wolves from the captive breeding programs, and a reference population of coyotes from outside the historic red wolf range. Levels of variation and phylogenetic analyses suggest that hybridization has occasionally taken place between all three species, but that the impact on the coyote population is very small.

Conclusion/Significance

Our results demonstrate that the factors driving introgressive hybridization in sympatric Texan Canis are multiple and complex. Hybridization is not solely determined by body size or sex, and density-dependent effects do not fully explain the observed pattern either. No evidence of hybridization was identified in the Mexican wolf captive breeding program, but introgression appears to have had a greater impact on the captive red wolves.     

Wolves in the Great Lakes region: a phylogeographic puzzle

Empirical studies demonstrate that natural hybridization in animals is more common than thought so far ( Mallet 2005 ), particularly among species that originated recently through cycles of population contraction–expansion arising from climate changes over the last glacial period, the Pleistocene. In addition, the post‐glacial global growth of human populations has fostered anthropogenic hybridization events, mediated by habitat changes, the persecution of large predators and the introduction of alien species ( Allendorf et al. 2001 ). The Canis lineage shows cases of both natural and anthropogenic hybridization, exacerbating the controversy about the number of species that should be formally validated in the taxonomic lists, the evolutionary role of genetic introgression and the ways to manage hybrids with invading wild or domesticated populations. The study by Wheeldon et al. (2010) , published in this issue of Molecular Ecology, adds a new piece to the intricate puzzle of evolution and taxonomy of Canis in North America. They show that sympatric wolves (C. lupus) and coyotes (C. latrans) are not (extensively) hybridizing in the western North American Great Lakes region (GLR). Widespread hybridization between coyotes and a genetically distinct, but closely related, wolf‐like population (the eastern wolf) occurred in the northeastern regions of North America. In Wheeldon et al.’s (2010) opinion, these data should prove definitely that two different species of wolf (the western gray wolf C. lupus and the eastern wolf C. lycaon) and their hybrids are distributed across the GLR.     

Environmental variation,hybridization, and phenotypic diversification in Cuatro Ciénegas pupfishes

Hybridization can generate novel phenotypes, and in combination with divergent selection along environmental gradients, can play a driving role in phenotypic diversification. This study examined the influence of introgressive hybridization and environmental variation on the phenotypic diversity of two pupfish species (Cyprinodon atrorus and Cyprinodon bifasciatus) endemic to the Cuatro Ciénegas basin, Mexico. These species occupy opposite environmental extremes and are comprised of multiple, intraspecifically isolated populations. However, interspecific hybridization occurs to various degrees within connecting, intermediate environments. Using geometric morphometric analysis, extensive variation of body shape was observed between and within species, and phenotypic variation was strongly correlated with environmental conditions. Furthermore, some introgressed populations exhibited unique phenotypes not found in either of the parents, and overall morphospace occupation was significantly higher in introgressed populations when compared to the parentals. Overall, we find environmental variation and transgressive segregation both appear to have been important in shaping phenotypic variation in this system.     

Apex predators and the facilitation of resource partitioning among mesopredators

Apex predators may influence carnivore communities through the suppression of competitively dominant mesopredators, however they also provide carrion subsidies that could influence foraging and competition among sympatric mesopredators when small prey is scarce. We assessed coyote Canis latrans and red fox Vulpes vulpes winter diet overlap and composition from scats collected in two study areas with 3‐fold difference in grey wolf Canis lupus density due to a wolf control program. We hypothesized that differences in diet composition would be driven by the use of carrion, and tested whether 1) apex predators facilitate resource overlap, or 2) apex predators facilitate resource partitioning. We estimated the available biomass of snowshoe hares and voles based on pellet density and vole capture rates in each study area. We used molecular analysis to confirm species identification of predator scats, and used microscopic evaluation of prey remains to analyze diet composition of 471 coyote and fox scats. Ungulate carrion, voles and snowshoe hares comprised 73% of coyote and fox diet, and differences in use of carrion and microtines accounted for nearly 60% of the dissimilarity in diet among these canids. Carrion was the top‐ranked item in the coyote diet in both study areas, whereas carrion use by red foxes declined 3‐fold in the study area with higher wolf and small prey abundance. Diet overlap tended to be lower and diet diversity tended to be higher where wolves were more abundant, though these trends were not statistically significant. Taken together, our findings indicate that carrion provisions could facilitate resource partitioning in mesocarnivore communities by alleviating exploitation competition for small mammals.     

Assessment of coyote–wolf–dog admixture using ancestry‐informative diagnostic SNPs

The evolutionary importance of hybridization as a source of new adaptive genetic variation is rapidly gaining recognition. Hybridization between coyotes and wolves may have introduced adaptive alleles into the coyote gene pool that facilitated an expansion in their geographic range and dietary niche. Furthermore, hybridization between coyotes and domestic dogs may facilitate adaptation to human‐dominated environments. We genotyped 63 ancestry‐informative single‐nucleotide polymorphisms in 427 canids to examine the prevalence, spatial distribution and the ecology of admixture in eastern coyotes. Using multivariate methods and Bayesian clustering analyses, we estimated the relative contributions of western coyotes, western and eastern wolves, and domestic dogs to the admixed ancestry of Ohio and eastern coyotes. We found that eastern coyotes form an extensive hybrid swarm, with all our samples having varying levels of admixture. Ohio coyotes, previously thought to be free of admixture, are also highly admixed with wolves and dogs. Coyotes in areas of high deer density are genetically more wolf‐like, suggesting that natural selection for wolf‐like traits may result in local adaptation at a fine geographic scale. Our results, in light of other previously published studies of admixture in Canis, revealed a pattern of sex‐biased hybridization, presumably generated by male wolves and dogs mating with female coyotes. This study is the most comprehensive genetic survey of admixture in eastern coyotes and demonstrates that the frequency and scope of hybridization can be quantified with relatively few ancestry‐informative markers.     

Phylogeny of the large extinct South American Canids (Mammalia,Carnivora, Canidae) using a “total evidence” approach

South America currently possesses a high diversity of canids, comprising mainly small to medium‐sized omnivorous species, but in the Pleistocene there were large hypercarnivorous taxa that were assigned to Protocyon spp., Theriodictis spp., Canis gezi, Canis nehringi and Canis dirus. These fossils have never been included in phylogenies based on quantitative cladistics, but hand‐constructed cladograms published in the 1980s included some of them in the South American canine clade and others in the Canis clade. In this work, the phylogenetic position of the large extinct South American canids was studied using a large sample of living and extinct canids, as well as different sources of characters (e.g. DNA and 133 osteological characters). The phylogenetic analysis corroborates the inclusion of Theriodictis and Protocyon in the “South American clade”, where C. gezi is also included. In addition, the position of C. dirus as a highly derived Canis species is confirmed. The simultaneous analysis supports hypercarnivory having arisen at least three times in Caninae and once in the “South American clade”. The combination of the phylogenetic analyses, the fossil record and divergence dates estimated in previous works suggests that at least three or four independent lineages of the “South American clade” invaded South America after the establishment of the Panama bridge around 3 million years ago, plus other events corresponding to the immigration of Urocyon and Canis dirus.
© The Willi Hennig Society 2009.     

Locating hybrid individuals in the red wolf (Canis rufus) experimental population area using a spatially targeted sampling strategy and faecal DNA genotyping

Hybridization with coyotes (Canis latrans) continues to threaten the recovery of endangered red wolves (Canis rufus) in North Carolina and requires the development of new strategies to detect and remove coyotes and hybrids. Here, we combine a spatially targeted faecal collection strategy with a previously published reference genotype data filtering method and a genetic test for coyote ancestry to screen portions of the red wolf experimental population area for the presence of nonred wolf canids. We also test the accuracy of our maximum-likelihood assignment test for identifying hybrid individuals using eight microsatellite loci instead of the original 18 loci and compare its performance to the Bayesian approach implemented in newhybrids. We obtained faecal DNA genotypes for 89 samples, 73 of which were matched to 23 known individuals. The performance of two sampling strategies - comprehensive sweep and opportunistic spot-check was evaluated. The opportunistic spot-check sampling strategy required less effort than the comprehensive sweep sampling strategy but identified fewer individuals. Six hybrids or coyotes were detected and five of these individuals were subsequently captured and removed from the population. The accuracy and power of the genetic test for coyote ancestry is decreased when using eight loci; however, nonred wolf canids are identified with high frequency. This combination of molecular and traditional field-based approaches has great potential for addressing the challenge of hybridization in other species and ecosystems.     

Geographic patterns in morphometric and genetic variation for coyote populations with emphasis on southeastern coyotes

Prior to 1900, coyotes (Canis latrans) were restricted to the western and central regions of North America, but by the early 2000s, coyotes became ubiquitous throughout the eastern United States. Information regarding morphological and genetic structure of coyote populations in the southeastern United States is limited, and where data exist, they are rarely compared to those from other regions of North America. We assessed geographic patterns in morphology and genetics of coyotes with special consideration of coyotes in the southeastern United States. Mean body mass of coyote populations increased along a west‐to‐east gradient, with southeastern coyotes being intermediate to western and northeastern coyotes. Similarly, principal component analysis of body mass and linear body measurements suggested that southeastern coyotes were intermediate to western and northeastern coyotes in body size but exhibited shorter tails and ears from other populations. Genetic analyses indicated that southeastern coyotes represented a distinct genetic cluster that differentiated strongly from western and northeastern coyotes. We postulate that southeastern coyotes experienced lower immigration from western populations than did northeastern coyotes, and over time, genetically diverged from both western and northeastern populations. Coyotes colonizing eastern North America experienced different selective pressures than did stable populations in the core range, and we offer that the larger body size of eastern coyotes reflects an adaptation that improved dispersal capabilities of individuals in the expanding range.     

A survey of the parasites of coyotes (Canis latrans) in New York based on fecal analysis

Coyotes (Canis latrans) have colonized northeastern North America only within the past 10-80 yr. We examined feces of coyotes in 2000-01 at three sites in New York (USA) to survey parasites in the region. Two cestodes, nine nematodes, five protozoa, one trematode, and two arthropods were identified from 145 coyote fecal samples. Parasite component community diversity was higher (n = 16 species) in southern New York than in middle and northern sites (nine species each) and infracommunity species richness was greater in southern New York than at the other sites. These differences may reflect the variable diets of coyotes, as well as recent colonization of the region and the mixing of component communities from expanding coyote populations.     

Poor health is associated with use of anthropogenic resources in an urban carnivore

Rates of encounters between humans and wildlife are increasing in cities around the world, especially when wildlife overlap with people in time, space and resources. Coyotes (Canis latrans) can make use of anthropogenic resources and reported rates of conflict have increased in cities across North America. This increase may be linked to individual differences in the use of human food and developed areas. We compared the relationships between coyote age, sex or health and the use of anthropogenic resources, which we defined as using developed areas over large home ranges, being active during the day, and consuming anthropogenic food. To do so, we applied GPS collars to 19 coyotes and sampled hair for stable isotope analysis. Eleven coyotes appeared to be healthy and eight were visibly infested with sarcoptic mange (Sarcoptes scabiei), a mite that causes hair loss. Diseased coyotes used more developed areas, had larger monthly home ranges, were more active during the day, and assimilated less protein than coyotes that appeared to be healthy. We speculate that anthropogenic food provides a low-quality but easily accessible food source for diseased coyotes, which in turn may increase reliance on it and other anthropogenic resources to promote encounters with people.     

Historical and present distribution of coyote (Canis latrans) in Mexico and Central America

Aim Coyote (Canis latrans) distribution in Mexico and Central America has expanded recently reaching the Yucatan peninsula, Belize and Panama, probably promoted by deforestation of tropical areas. Historically, the southern distribution of coyotes prior to European settlement in America was described as reaching only as far south as central Mexico and that introduction of livestock favoured migration of coyotes to southern Mexico and Central America. However, coyote fossil records in Central America and Yucatan, as well as observational records of travellers during the sixteenth century suggest that the coyote's arrival to the region was earlier. Because of the uncertainty of past coyote distribution and the possible economic and ecological impacts due to recent range expansion, the objectives of this study were to confirm if paleontological and historical evidence support the hypothesis that the southernmost limit of coyote distribution before the arrival of European settlers was the centre of Mexico, to discuss the possible factors that have influenced historical shifts in coyote distribution, and to model the present distribution of the coyote in Mexico and Central America, determining the areas where they could invade in the near future. Location The research area comprises continental Mexico and the Central American Isthmus countries: Guatemala, Belize, El Salvador, Honduras, Nicaragua, Costa Rica and Panama. Methods The historical distribution (Pleistocene–Early Holocene, Pre‐Columbian, sixteenth to nineteenth centuries and twentieth century) was established from coyote records obtained from museum collections and specialized literature. Present coyote distribution for Mexico and Central America was modelled using the Genetic Algorithms for Rule‐set Prediction (GARP). Results Historical coyote records show that this species was distributed in southern Mexico and Central America during the Pleistocene–Early Holocene, the Pre‐Columbian period, and during the arrival of Europeans in the sixteenth century. Coyote records indicate a continuous range expansion during the twentieth century. Historical advance and regression of tropical forests in southern Mexico and Central America produced by natural and human events such as climatic changes and variation in human densities could help us understand the historical coyote distribution. The modelled present‐day coyote distribution included the north of Belize, the north of Panama, the north of the Yucatan Peninsula and a corridor on the Gulf costal plain of Campeche in Mexico. Also, the model predicted a region north of the Darien in southern Panama as appropriate for the presence of coyotes, although they have not been detected there so far. Main conclusion Coyote records in southern Mexico and Central America during the Pleistocene–Early Holocene, the Pre‐Columbian period, and early arrival of European settlers to the area indicated that coyotes were probably already present there and did not recently disperse from the north of Mexico to the south due to livestock introduction.