In a late 2018 genomic analysis by Dr. Mikkel-Holger S. Sinding and his team who analyzed samples of wolves and coyotes collected across North America, the team found that every North American inland wolf carries some levels of coyote markers including the Yellowstone and the Mexican wolves as well as other gray wolves from areas far beyond the ranges of the eastern timber wolves and red wolves, both of which some biologists suspect may have bridged geneflows between what were previously thought to be non-hybridizing gray wolves and coyotes in areas where they overlapped.
"We used f4 ratios to investigate proportion of coyote and grey wolf ancestries in the North American wolf-like canids, setting aside the Polar wolf (‘Daneborg’) and coyote (‘Mexico’) as references. These samples were chosen based on their respective distance to the coyote or wolf cluster in the PCA which suggests they may represent the “purest” examples of coyote and North American wolf in our dataset."
" The f4 ratio estimates showed that the coyotes from Alabama, California, Quebec and Alaska harbour negligible wolf ancestry, while those from Missouri, Illinois and Florida contained between 5–10% wolf ancestry. Much higher levels of wolf versus coyote admixture were observed in red wolves (40%:60%), the Eastern timber wolves (60%:40%), and the Great Lakes wolves (75%:25%). Within wolves, coyote ancestry was highest in the Mexican wolves and the Atlantic Coast wolves (10%), followed by the Pacific Coast and Yellowstone wolves (~5%). The wolves from the Canadian archipelago showed less than 3% coyote ancestry. "
It's actually surprising to see that Canis lupus ligoni from the Canadian Archipelago actually carried any coyote markers at all considering that we have no records of any coyotes ever crossing into those islands in the Pacific Northwest. However, it is understood that both the Vancouver Island wolves and Alexander Archipelago wolves have had prior interactions with inland gray wolves so there's a possibility that the inland western wolves may have been responsible for passing those coyote genes into the island wolves.
The authors further stated in the study: "Based on our analyses, it is clear that Mexican wolves are divergent from all other North American wolf populations, and given they form a sister group to all other populations regardless of how they are analysed, they have likely been isolated from other grey wolf populations represented in this study. This divergence is well described, and hypotheses to explain this could be that their presence in the Americas arises from a different colonization history to that of the remaining North American grey wolves. An alternative explanation could be that Mexican wolves diverged early on in a single colonisation event, and have since been isolated from the other populations. In addition, Mexican wolves carry substantial coyote admixture. The admixture from coyotes could also play a role in the basal phylogenetic placement of the Mexican wolves. Similar levels of coyote admixture are present in Atlantic wolves, but do not have the same phylogenetic impact. The wolf diversity in Atlantic wolves seems closely related to diversity in neighbouring wolf populations, giving the lineage affiliation with other Northern American wolves. However the Mexican wolves have no surviving neighbouring wolf populations, a factor further contributing to their distinctness compared to the available references. While clearly distinct, we find that Mexican wolves have the same cladistic ancestry as other American grey wolves, and note that ancient samples will be highly relevant in addressing whether the last common ancestors of North American wolves were within or outside the continent."
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