Regarding coywolves:
Hi John. This coy-wolf paper is the iceberg tip a a huge, complex, and controversial literature. You describe some correct aspects of it, but here are a couple of rejoinders.
Since wolves existed around the Great Lakes "originally" and coyotes moved in from the south only after white human settlement drove the wolves back, it is probably more correct to say that the local wolves have acquired coyote genes, or at least equally correct. Many indisputably ecologically wolf individuals around the Great Lakes also have coyote mtDNA, including most (perhaps all?) of those on Isle Royale. There have also been critters called the Algonquin wolf and the Tweed wolf, believed initially and controversially to have been good species but more likely rather small wolves with rather fewer coyote genes, rather than "coy-wolves" (coyotes bulked up by wolf genes). Of course it's likely a continuum.
Still controversial is whether all such introgression post-dates white contact.
Several wildlife genetics labs have also had papers about this in the last year. Mike Schwartz did a good invited review of the sampling partialness of much of the evidence to date:
Schwartz MK, Vucetich JA. Molecules and beyond: assessing the distinctness of the Great Lakes wolf. Mol Ecol. 2009 Jun;18(11):2307-9. Epub 2009 Apr 7. PubMed PMID: 19389174.
In another life a student in my bailiwick looked for such introgression in the Rockies as a side-project to other things. The result was negative.
I couldn't readily find a link to the original paper in the the MSNBC page. A bit frustrating.
Ah, very interesting. Thanks! I reviewed the literature on this in 2006 but I can see that much has changed. It's such an encouraging sign that phylogeography is actually going somewhere.
