Could you please clarify your previous comment?

Thanks.

Previous Y-DNA and mtDNA studies have shown that there are some Y-DNA phylogenies (e.g. Q-M3 and its descendants) and some major mtDNA haplogroups (A2, B2, C1b, C1c, C1d, and D1) that are very old and found throughout the Americas.

There are other Y-DNA and mtDNA haplogroups that are found predominantly only in certain North American groups (Y-DNA Q-M242 (xM3), R1 -M127, C3b, mtDNA X2a, D2a1, A2a. A2b) that seem to be traceable to later migrations (the case of R1-M127 being absent from the first wave or part of a serial founder effect in early first wave Native American migrations is less than clear). Na-Dene and Circumpolar populations tend to have lots of atypicality, Northeast North American populations are rich inY-DNA R1 -M127 and mtDNA X2a but not necessarily some of the other atypical New World Y-DNA haplogroups like Q-M242 (xQ-M3) and C3b that are pretty specific to the Na-Dene and Circumpolar populations. The indigeneous American form of R1 sometimes called R1* splits off before the R1a v. R1b break and is also associated with Indonesia and the Phillipines (arguing for its presence in the first wave indigneous population followed by serial founder effects as that population spreads out, as does the presence of R1* in indigeneous people of South America).

A link between the Na-Dene and Circumpolar Q-M242(xQ-M3) populations and South Altaian populations at a recent date would make sense and could plausibly be refined by an improved South Altaian phylogeny of Y-DNA haplogroup Q (Q-M3 is basically a private American haplogroup so new phylogenies in Siberia should have much of an impact on it to show linkage). A link between all Native Americans via Q-M3 and South Altaian populations makes less no sense at pedigree mutation rates which tend to be more accurately calibrated to historical dates (although the whole Y-DNA dating scheme is fundamentally problematic) but could fit the evoluationary dates.

“The idea of fitting allele frequency differentiation to historical models was first explored by Cavalli-Sforza and Edwards [35], and here we extend it to trees with mixture. This approach contrasts with the STRUCTURE algorithm, which fits data without a tree [36], or a tree in which many groups split simultaneously from an ancestral population followed by mixture [37]. Although STRUCTURE is accurate for estimating individual mixture proportions in recently mixed groups, it is not clear whether its estimates of ancient mixture are biased because it does not model hierarchical relationships among groups, which could lead to inaccurate estimates of allele frequencies in ancestral populations. In contrast, we use a more realistic tree model, and provide a test of fit.”

Supplemental notes 3 and 4 to the study flesh out the idea. Phylogenetic trees yield demonstrable phylogenetic inferences it would seem to me. My 2c.