Updating the Bibliography of Interbreeding among Canis in North America

Potential Adaptive Introgression From Dogs in Iberian Grey Wolves (Canis lupus)

Invading species along with increased anthropogenization may lead to hybridization events between wild species and closely related domesticates. As a consequence, wild species may carry introgressed alleles from domestic species, which is generally assumed to yield adverse effects in wild populations. The opposite evolutionary consequence, adaptive introgression, where introgressed genes are positively selected in the wild species, is possible but has rarely been documented. Grey wolves (Canis lupus) are widely distributed across the Holarctic and frequently coexist with their close relative, the domestic dog (C. familiaris). Despite ample opportunity, hybridization rarely occurs in most populations. Here we studied the geographically isolated grey wolves of the Iberian Peninsula, who have coexisted with a large population of loosely controlled dogs for thousands of years in a human-modified landscape. We assessed the extent and impact of dog introgression on the current Iberian grey wolf population by analysing 150 whole genomes of Iberian and other Eurasian grey wolves as well as dogs originating from across Europe and western Siberia. We identified almost no recent introgression and a small (< 5%) overall ancient dog ancestry. Using a combination of single scan statistics and ancestry enrichment estimates, we identified positive selection on six genes (DAPP1, NSMCE4A, MPPED2, PCDH9, MBTPS1, and CDH13) for which wild Iberian wolves carry alleles introgressed from dogs. The genes with introgressed and positively selected alleles include functions in immune response and brain functions, which may explain some of the unique behavioural phenotypes in Iberian wolves such as their reduced dispersal compared to other wolf populations.

Coyotes can do 'puppy dog eyes' too: comparing interspecific variation in Canis facial expression muscles

Facial expressions are critical for non-verbal communication. The Canis genus epitomizes the interplay between behaviour and morphology in the evolution of non-verbal communication. Recent work suggests that the levator anguli oculi medialis (LAOM) muscle is unique to dogs (Canis familiaris) within the Canis genus and evolved due to domestication. The LAOM raises the inner eyebrows, resulting in the 'puppy dog eyes' expression. Here, we test whether the LAOM is a derived trait in dogs by (i) examining the facial expression muscles of a closely related and ancestral wild Canis species, the coyote (C. latrans) and (ii) comparing our results with other Canis and canid taxa. We discover that coyotes have a well-developed LAOM like dogs, which differs from the modified/absent LAOM in grey wolves. Our findings challenge the hypothesis that the LAOM developed due to domestication. We suggest that the LAOM is a basal trait that was lost in grey wolves. Additionally, we find inter- and intraspecific variations in the size of the muscles of the outer ear, forehead, lips and rostrum, indicating potential adaptations related to sensory perception, communication and individual-level functional variations within canids. Together, this research expands our knowledge of facial expressions, their evolution and their role in communication.

The value of hybrid genomes: Building two highly contiguous reference genome assemblies to advance Canis genomic studies

Previous studies of canid population and evolutionary genetics have relied on high-quality domestic dog reference genomes that have been produced primarily for biomedical and trait mapping studies in dog breeds. However, the absence of highly contiguous genomes from other Canis species like the gray wolf and coyote, that represent additional distinct demographic histories, may bias inferences regarding interspecific genetic diversity and phylogenetic relationships. Here, we present single haplotype de novo genome assemblies for the gray wolf and coyote, generated by applying the trio-binning approach to long sequence reads generated from the genome of a female first-generation hybrid produced from a gray wolf and coyote mating. The assemblies were highly contiguous, with contig N50 sizes of 44.6 and 42.0 Mb for the wolf and coyote, respectively. Genome scaffolding and alignments between the two Canis assemblies and published dog reference genomes showed near complete collinearity, with one exception: a coyote-specific chromosome fission of chromosome 13 and fusion of the proximal portion of that chromosome with chromosome 8, retaining the Canis-typical haploid chromosome number of 2n = 78. We evaluated mapping quality for previous RADseq data from 334 canids and found nearly identical mapping quality and patterns among canid species and regional populations regardless of the genome used for alignment (dog, coyote, or gray wolf). These novel wolf and coyote genome reference assemblies will be important resources for proper and accurate inference of Canis demography, taxonomic evaluation, and conservation genetics.

Genome-wide variant analyses reveal new patterns of admixture and population structure in Australian dingoes

Admixture between species is a cause for concern in wildlife management. Canids are particularly vulnerable to interspecific hybridisation, and genetic admixture has shaped their evolutionary history. Microsatellite DNA testing, relying on a small number of genetic markers and geographically restricted reference populations, has identified extensive domestic dog admixture in Australian dingoes and driven conservation management policy. But there exists a concern that geographic variation in dingo genotypes could confound ancestry analyses that use a small number of genetic markers. Here, we apply genome-wide single-nucleotide polymorphism (SNP) genotyping to a set of 402 wild and captive dingoes collected from across Australia and then carry out comparisons to domestic dogs. We then perform ancestry modelling and biogeographic analyses to characterise population structure in dingoes and investigate the extent of admixture between dingoes and dogs in different regions of the continent. We show that there are at least five distinct dingo populations across Australia. We observed limited evidence of dog admixture in wild dingoes. Our work challenges previous reports regarding the occurrence and extent of dog admixture in dingoes, as our ancestry analyses show that previous assessments severely overestimate the degree of domestic dog admixture in dingo populations, particularly in south-eastern Australia. These findings strongly support the use of genome-wide SNP genotyping as a refined method for wildlife managers and policymakers to assess and inform dingo management policy and legislation moving forwards.

Tracing Eastern Wolf Origins From Whole-Genome Data in Context of Extensive Hybridization

Southeastern Canada is inhabited by an amalgam of hybridizing wolf-like canids, raising fundamental questions regarding their taxonomy, origins, and timing of hybridization events. Eastern wolves (Canis lycaon), specifically, have been the subject of significant controversy, being viewed as either a distinct taxonomic entity of conservation concern or a recent hybrid of coyotes (C. latrans) and grey wolves (C. lupus). Mitochondrial DNA analyses show some evidence of eastern wolves being North American evolved canids. In contrast, nuclear genome studies indicate eastern wolves are best described as a hybrid entity, but with unclear timing of hybridization events. To test hypotheses related to these competing findings we sequenced whole genomes of 25 individuals, representative of extant Canadian wolf-like canid types of known origin and levels of contemporary hybridization. Here we present data describing eastern wolves as a distinct taxonomic entity that evolved separately from grey wolves for the past ∼67,000 years with an admixture event with coyotes ∼37,000 years ago. We show that Great Lakes wolves originated as a product of admixture between grey wolves and eastern wolves after the last glaciation (∼8,000 years ago) while eastern coyotes originated as a product of admixture between "western" coyotes and eastern wolves during the last century. Eastern wolf nuclear genomes appear shaped by historical and contemporary gene flow with grey wolves and coyotes, yet evolutionary uniqueness remains among eastern wolves currently inhabiting a restricted range in southeastern Canada.

Coyotes in New York City Carry Variable Genomic Dog Ancestry and Influence Their Interactions with Humans

Coyotes are ubiquitous on the North American landscape as a result of their recent expansion across the continent. They have been documented in the heart of some of the most urbanized cities, such as Chicago, Los Angeles, and New York City. Here, we explored the genomic composition of 16 coyotes in the New York metropolitan area to investigate genomic demography and admixture for urban-dwelling canids in Queens County, New York. We identified moderate-to-high estimates of relatedness among coyotes living in Queens (r = 0.0-0.5) and adjacent neighborhoods, suggestive of a relatively small population. Although we found low background levels of domestic-dog ancestry across most coyotes in our sample (5%), we identified a male suspected to be a first-generation coyote-dog hybrid with 46% dog ancestry, as well as his two putative backcrossed offspring that carried approximately 25% dog ancestry. The male coyote-dog hybrid and one backcrossed offspring each carried two transposable element insertions that are associated with human-directed hypersociability in dogs and gray wolves. An additional, unrelated coyote with little dog ancestry also carried two of these insertions. These genetic patterns suggest that gene flow from domestic dogs may become an increasingly important consideration as coyotes continue to inhabit metropolitan regions.

The natural history and ecology of melanism in red wolf and coyote populations of the southeastern United States – evidence for Gloger’s rule

Background

Gloger’s rule postulates that animals should be darker colored in warm and humid regions where dense vegetation and dark environments are common. Although rare in Canis populations, melanism in wolves is more common in North America than other regions globally and is believed to follow Gloger’s rule. In the temperate forests of the southeastern United States, historical records of red wolf (Canis rufus) and coyote (Canis latrans) populations document a consistent presence of melanism. Today, the melanistic phenotype is extinct in red wolves while occurring in coyotes and red wolf-coyote hybrids who occupy the red wolf's historical range. To assess if Gloger’s rule could explain the occurrence and maintenance of melanistic phenotypes in Canis taxa, we investigated differences in morphology, habitat selection, and survival associated with pelage color using body measurements, GPS tracking data, and long-term capture-mark-recapture and radio-telemetry data collected on coyotes and hybrids across the southeastern United States.

Results

We found no correlation between morphometrics and pelage color for Canis taxa. However, we observed that melanistic coyotes and hybrids experienced greater annual survival than did their gray conspecifics. Furthermore, we observed that melanistic coyotes maintained larger home ranges and exhibited greater selection for areas with dense canopy cover and wetlands than did gray coyotes.

Conclusions

In the southeastern United States, pelage color influenced habitat selection by coyotes and annual survival of coyotes and hybrids providing evidence that Gloger’s rule is applicable to canids inhabiting regions with dense canopy cover and wetlands. Greater annual survival rates observed in melanistic Canis may be attributed to better concealment in areas with dense canopy cover such as coastal bottomland forests. We suggest that the larger home range sizes of melanistic coyotes may reflect the trade-off of reduced foraging efficiency in lower quality wetland habitat for improved survival. Larger home ranges and differential use of land cover by melanistic coyotes may facilitate weak assortative mating in eastern coyote populations, in which melanistic animals may have lower success of finding compatible mates in comparison to gray conspecifics. We offer that our observations provide a partial explanation for why melanism is relatively low (< 10%) but consistent within coyote populations throughout southeastern parts of their range.

The myth of wild dogs in Australia: are there any out there?

Hybridisation between wild and domestic canids is a global conservation and management issue. In Australia, dingoes are a distinct lineage of wild-living canid with a controversial domestication status. They are mainland Australia’s apex terrestrial predator. There is ongoing concern that the identity of dingoes has been threatened from breeding with domestic dogs, and that feral dogs have established populations in rural Australia. We collate the results of microsatellite DNA testing from 5039 wild canids to explore patterns of domestic dog ancestry in dingoes and observations of feral domestic dogs across the continent. Only 31 feral dogs were detected, challenging the perception that feral dogs are widespread in Australia. First generation dingo × dog hybrids were similarly rare, with only 27 individuals identified. Spatial patterns of genetic ancestry across Australia identified that dingo populations in northern, western and central Australia were largely free from domestic dog introgression. Our findings challenge the perception that dingoes are virtually extinct in the wild and that feral dogs are common. A shift in terminology from wild dog to dingo would better reflect the identity of these wild canids and allow more nuanced debate about the balance between conservation and management of dingoes in Australia.

Considering Pleistocene North American wolves and coyotes in the eastern Canis origin story

The evolutionary origins and hybridization patterns of Canis species in North America have been hotly debated for the past 30 years. Disentangling ancestry and timing of hybridization in Great Lakes wolves, eastern Canadian wolves, red wolves, and eastern coyotes are most often partitioned into a 2-species model that assigns all ancestry to gray wolves and/or coyotes, and a 3-species model that includes a third, North American evolved eastern wolf genome. The proposed models address recent or sometimes late Holocene hybridization events but have largely ignored potential Pleistocene era progenitors and opportunities for hybridization that may have impacted the current mixed genomes in eastern Canada and the United States. Here, we re-analyze contemporary and ancient mitochondrial DNA genomes with Bayesian phylogenetic analyses to more accurately estimate divergence dates among lineages. We combine that with a review of the literature on Late Pleistocene Canis distributions to: (a) identify potential Pleistocene progenitors to southern North American gray wolves and eastern wolves; and (b) illuminate opportunities for ancient hybridization events. Specifically, we propose that Beringian gray wolves (C. lupus) and extinct large wolf-like coyotes (C. latrans orcutti) are likely progenitors to Mexican and Plains gray wolves and eastern wolves, respectively, and may represent a potentially unrecognized source of introgressed genomic variation within contemporary Canis genomes. These events speak to the potential origins of contemporary genomes and provide a new perspective on Canis ancestry, but do not negate current conservation priorities of dwindling wolf populations with unique genomic signatures and key ecologically critical roles.

Phylogenomics and the Genetic Architecture of the Placental Mammal Radiation

The genomes of placental mammals are being sequenced at an unprecedented rate. Alignments of hundreds, and one day thousands, of genomes spanning the rich living and extinct diversity of species offer unparalleled power to resolve phylogenetic controversies, identify genomic innovations of adaptation, and dissect the genetic architecture of reproductive isolation. We highlight outstanding questions about the earliest phases of placental mammal diversification and the promise of newer methods, as well as remaining challenges, toward using whole genome data to resolve placental mammal phylogeny. The next phase of mammalian comparative genomics will see the completion and application of finished-quality, gapless genome assemblies from many ordinal lineages and closely related species. Interspecific comparisons between the most hypervariable genomic loci will likely reveal large, but heretofore mostly underappreciated, effects on population divergence, morphological innovation, and the origin of new species.

Species assignment in forensics and the challenge of hybrids

Forensic identification of species is in growing demand, particularly from law enforcement authorities in the areas of wildlife, fisheries and hunting as well as food authentication. Within the non-human forensic genetics expanding applications' field, the major current difficulties result from the lack of standards and genetic databases as well as the poor or absent taxonomic definition of several groups. Here we focus on a forensically important and overlooked problem in species identification: the exclusive use of uniparental markers, a common practice in current genetic barcoding methodologies, may lead to incorrect or impossible assignment whenever hybrids can occur (frequently, not only in domesticates, but also in the wild). For example, if one of these cases involves a mammal, and mitochondrial DNA alone is used (which in instances may be the only type of DNA sequence available in databases), the sample will be wrongfully assigned to the female parental species, completely missing the detection of a possible hybrid animal. The importance of this issue in the forensic contributions to food authentication, wildlife and conservation genetics is analyzed. We present a cautionary guidance on the forensic reporting of results avoiding this error.