C. Lupus and C. Latrans interbreed with regularity, and share most of the genes (the primary reason they can breed). To Identify coyotes vs grey wolves the genetic tests must look at the species exclusive genes, and determine how much of each the sample contians.
I know it's from Wikipedia, but it good info.
Interspecific hybridization
Coyotes will sometimes mate with
domestic dogs, usually in areas like Texas and Oklahoma, where the coyotes are plentiful and the breeding season is extended because of the warm weather. The resulting hybrids, called
coydogs, maintain the coyote's predatory nature, along with the dog's lack of timidity toward humans, making them a more serious threat to livestock than pure-blooded animals. This cross-breeding has the added effect of confusing the breeding cycle. Coyotes usually breed only once a year, while coydogs will breed year-round, producing many more pups than a wild coyote. Differences in the ears and tail are generally what can be used to distinguish coydogs from domestic/feral dogs or pure coyotes.
[28] Breeding experiments in Germany with
poodles, coyotes, and later on with the resulting dog-coyote hybrids showed that unlike
wolfdogs, coydogs show a decrease in fertility, significant communication problems as well as an increase of genetic diseases after three generations of interbreeding.
[29]
Coyotes have also been known on occasion to mate with
wolves, though this is less common than with dogs, due to the wolf's hostility to the coyote. The offspring, known as a
coywolf, is generally intermediate in size to both parents, being larger than a pure coyote, but smaller than a pure wolf. A study showed that of 100 coyotes collected in
Maine, 22 had half or more wolf ancestry, and one was 89% wolf. A theory has been proposed that the large eastern coyotes in Canada are actually hybrids of the smaller western coyotes and wolves that met and mated decades ago as the coyotes moved toward New England from their earlier western ranges.
[24] Ontario Ministry of Natural Resources research scientist Brent Patterson has revealed findings that most coyotes in
Eastern Ontario are wolf-coyote hybrids and that the
Eastern wolves in
Algonquin Park are, in general, not inter-breeding with coyotes.
[30]
The
Red Wolf is thought by certain scientists to be in fact a wolf/coyote hybrid rather than a unique species. Strong evidence for hybridization was found through genetic testing, which showed that red wolves have only 5% of their
alleles unique from either gray wolves or coyotes. Genetic distance calculations have indicated that red wolves are intermediate between coyotes and gray wolves, and that they bear great similarity to wolf/coyote hybrids in southern
Quebec and
Minnesota. Analyses of mitochondrial DNA showed that existing red wolf populations are predominantly coyote in origin.
[31]
