Editing Coyote (section)

====DNA evidence====
[[File:Canis latrans orcutti.png|thumb|A skeleton of a [[Pleistocene coyote]] (''C.{{nbsp}}l. orcutti'')]]

In 1993, a study proposed that the wolves of North America display skull traits more similar to the coyote than wolves from Eurasia.<ref name=goulet1993/> In 2010, a study found that the coyote was a [[lineage (genetic)#Basal lineage|basal]] member of the clade that included the [[Tibetan wolf]], the [[Dog|domestic dog]], the [[Mongolian wolf]] and the [[Eurasian wolf]], with the Tibetan wolf diverging early from wolves and domestic dogs.<ref name=zhang2010/>

In 2016, a [[Whole genome sequencing|whole-genome]] DNA study proposed, based on the assumptions made, that all of the North American wolves and coyotes diverged from a common ancestor about 51,000&nbsp;years ago.<ref name=vonholdt2016/><ref name=virginia2016/> However, the proposed timing of the wolf / coyote divergence conflicts with the discovery of a coyote-like specimen in strata dated to 1&nbsp;Mya.{{sfn|Wang|Tedford|2008|p={{page needed|date=November 2020}}}} The study also indicated that all North American wolves have a significant amount of coyote ancestry and all coyotes some degree of wolf ancestry, and that the red wolf and eastern wolf are highly [[Genetic admixture|admixed]] with different proportions of gray wolf and coyote ancestry.<ref name=vonholdt2016/><ref name=virginia2016/>

Genetic studies relating to wolves or dogs have inferred phylogenetic relationships based on the only reference genome available, that of the Boxer dog. In 2017, the first reference genome of the wolf ''Canis lupus lupus'' was mapped to aid future research.<ref name=gopalakrishnan2017/> In 2018, a study looked at the genomic structure and admixture of North American wolves, wolf-like canids, and coyotes using specimens from across their entire range that mapped the largest dataset of nuclear genome sequences against the wolf reference genome.

The study supports the findings of previous studies that North American gray wolves and wolf-like canids were the result of complex gray wolf and coyote mixing. A polar wolf from Greenland and a coyote from Mexico represented the purest specimens. The coyotes from Alaska, California, Alabama, and Quebec show almost no wolf ancestry. Coyotes from Missouri, Illinois, and Florida exhibit 5–10% wolf ancestry. There was 40% wolf to 60% coyote ancestry in red wolves, 60% wolf to 40% coyote in Eastern timber wolves, and 75% wolf to 25% coyote in the Great Lakes wolves. There was 10% coyote ancestry in Mexican wolves and the Atlantic Coast wolves, 5% in Pacific Coast and Yellowstone wolves, and less than 3% in Canadian archipelago wolves. If a third canid had been involved in the admixture of the North American wolf-like canids, then its genetic signature would have been found in coyotes and wolves, which it has not.<ref name=sinding2018/>

In 2018, [[whole genome sequencing]] was used to compare members of the genus ''Canis''. The study indicates that the common ancestor of the coyote and gray [[wolf]] has genetically [[Genetic admixture|admixed]] with a [[ghost population]] of an extinct, unidentified canid. The "ghost" canid was genetically close to the [[dhole]], and had evolved after the divergence of the [[African wild dog]] from the other canid species. The [[Basal (phylogenetics)|basal]] position of the coyote compared to the wolf is proposed to be due to the coyote retaining more of the mitochondrial genome from the unknown extinct canid.<ref name=gopalakrishnan2018/>