The Gambler's House blog has a new post reviewing a large share of all published work on the subject (almost all of which is not open access and has vague abstracts that provide no substantive detail) with a wealth of New World ancient mtDNA information from the American Southwest, which other posts at the same blog have placed in archaeological, anthropological, and linguistic context.
The data cement the prevailing view that all Native Americans in the Southwest are descended either from a small founding population of the Americas ca. 14,000 years ago, or from a later Na-Dene migration wave (Navajo and Apache) that reached the American Southwest ca. 1,000 years ago.
The ancient mtDNA data also clarify that in several cases where it had not been clear that a change in archaeological culture corresponded to substantial demic replacement, that there was indeed a demic replacement (i.e. different groups of people arrived and replaced the people who practiced the old archaeological culture), and that two groups that were linguistically related despite substantial geographic separation where indeed genetically related.
The post also clarifies the genetic linkages of some groups in the American Southwest and with other Native American populations and provides some nice baseline data regarding how the founding mtDNA haplogroups of the Americas are distributed amongst various Native American populations.
I will try to expand further on the results and their context if I can find time to do so.
He also notes that ancient autosomal and Y-DNA data is unavailable at this time from samples in the American Southwest despite the availability of many scores of ancient mtDNA samples, and that there are only a small number of mtDNA studies that provide precision haplogroup subtypes beyond that available in the hypervariable region of mitochondrial DNA.