There are now three separate "certified" Mexican wolf lineages. The original McBride lineage is the most extensively bred and studied. It is derived from three founders and now consists of 133 individuals. The Ghost Ranch lineage is derived from two founders taken from the wild in 1959 and 1961. This line was previously uncertified because of claims that the founding male was a wolf/dog hybrid. The Aragon lineage is derived from wolves found in the Chapultepec Zoo in the 1970's. The wild origins of the Aragon line are a mystery. This lineage was previously uncertified because morphological analysis alone is not enough to verify true Mexican wolf ancestry.
Phil Hedrick and others reviewed genetic investigations of all three lineages and found that all three were pure Mexican wolves and that they were unrelated. Three separate molecular genetic analyses were used and comparisons were made between the sequences of Allozyme, mitochondrial and microsatellite DNA. In each case the three Mexican wolf lineages were compared to Northern gray wolves, Coyotes and dogs .
The data from Allozyme comparison is inconclusive. At nineteen of twenty two loci examined, all six lineages were monomorphic. In the other three, the Mexican wolves did not group any closer together than they did to gray wolves, they were however distinct from dogs and Coyotes. In any case, three loci are probably not enough to make a statistically significant comparison. Further, because allozyme loci have such low mutation rates and the split between gray wolf lineages is probably recent in evolutionary terms, there is no reason to expect much variation between Mexican and other gray wolves.
Analysis of mitochondrial DNA did not prove to be much more enlightening. Sheilds et al.  and Wanye et al . carried out separate analyses on 55 and 95 restriction sites respectively, representing approximately 21% of the mtDNA genome. MtDNA is limited in that it is maternally inherited and does not account for any contributions of male founders. It is therefore possible that a male from another species could insert genes that would be undetected by this method. Sequence data matched the Ghost Ranch lineage to the McBride lineage and put the Aragon lineage very close with only three substitutions and an 11 base inversion separating them. However, only a very few gray wolves of any sub-species were sampled and variation between them is undefined. Quantifying the expected variation within the species is critical to this analysis so that differences between them can be weighted. Without weights the data is inconclusive in either direction, Certainly some variation is expected in geographically distinct populations, but how much represents a different sub-species?
Microsatellite tests done by Garcia-Moreno et al  and Wayne  examined 20 individual loci. Microsatellite loci are fast evolving introns that are easy to sequence and they are currently the preferred analytic tool for determining the ancestry of closely related organisms. These tests used 38 Mexican wolves, 55 gray wolves, 39 Coyotes and 27 dogs. The McBride and Ghost Ranch lineages were more closely related than the Aragon lineage, but all three grouped closer than any of the outgroups, based on Nei's genetic distance. The evidence from these studies was conclusive enough to convince Hedrick that genetic mixing of the three should begin immediately.
Although it was a necessary precaution, the separation of the three lineages has led to extensive inbreeding in the McBride line.
In one sense it is a bonus that the three lineages were kept separate for so long; small isolated populations tend to fix different alleles by drift. Thus, the genetic diversity of the species is all the better for having been divided. Because all three lineages were completely unrelated, interbreeding among them has been implemented and the resulting increase in genetic diversity should benefit the species recovery.
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