The Altai region of southern Siberia has played a critical role in the peopling of northern Asia as an entry point into Siberia and a possible homeland for ancestral Native Americans. It has an old and rich history because humans have inhabited this area since the Paleolithic.
Today, the Altai region is home to numerous Turkic-speaking ethnic groups, which have been divided into northern and southern clusters based on linguistic, cultural, and anthropological traits.
To untangle Altaian genetic histories, we analyzed mtDNA and Y chromosome variation in northern and southern Altaian populations. All mtDNAs were assayed by PCR-RFLP analysis and control region sequencing, and the nonrecombining portion of the Y chromosome was scored for more than 100 biallelic markers and 17 Y-STRs.
Based on these data, we noted differences in the origin and population history of Altaian ethnic groups, with northern Altaians appearing more like Yeniseian, Ugric, and Samoyedic speakers to the north, and southern Altaians having greater affinities to other Turkic speaking populations of southern Siberia and Central Asia.
Moreover, high-resolution analysis of Y chromosome haplogroup Q has allowed us to reshape the phylogeny of this branch, making connections between populations of the New World and Old World more apparent and demonstrating that southern Altaians and Native Americans share a recent common ancestor. These results greatly enhance our understanding of the peopling of Siberia and the Americas.
Source: Matthew C. Dulik, Sergey I. Zhadanov, Ludmila P. Osipova, Ayken Askapuli, Lydia Gau, Omer Gokcumen, Samara Rubinstein, and Theodore G. Schurr, "Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians", The American Journal of Human Genetics, 26 January 2012 doi:10.1016/j.ajhg.2011.12.014 via Razib Khan at Gene Expression who provides one of the key tables (breaks added in closed access paper abstract above for ease of reading).
The abstract is about as clear as mud in the context of prior research in this area, because when one says "that southern Altaians and Native Americans share a recent common ancestor", it isn't at all clear which Native Americans you are discussing, and methodological issues make the genetic conclusions seen in isolation unconvincing without a rich context to support them.
Wikipedia summarizes the state of the academic literature Y-DNA of indigeneous Americans prior to the latest paper as follows (citations and some headings and portions unrelated to Y-DNA omitted, emphasis added):
Human settlement of the New World occurred in stages from the Bering sea coast line, with an initial layover on Beringia for the small founding population. The micro-satellite diversity and distributions of the Y lineage specific to South America indicates that certain Amerindian populations have been isolated since the initial colonization of the region. The Na-Dené, Inuit and Indigenous Alaskan populations exhibit haplogroup Q (Y-DNA); however, they are distinct from other indigenous Amerindians with various mtDNA and atDNA mutations. This suggests that the peoples who first settled the northern extremes of North America and Greenland derived from later migrant populations than those who penetrated further south in the Americas. Linguists and biologists have reached a similar conclusion based on analysis of Amerindian language groups and ABO blood group system distributions. . . .
Haplogroup Q . . .
Q-M242 (mutational name) is the defining (SNP) of Haplogroup Q (Y-DNA) (phylogenetic name). Within the Q clade, there are 14 haplogroups marked by 17 SNPs. In Eurasia haplogroup Q is found among Siberian populations, such as the modern Chukchi and Koryak peoples. In particular two populations exhibit large concentrations of the Q-M242 mutation, the Kets (93.8%) and the Selkups (66.4%). The Kets are thought to be the only survivors of ancient nomads living in Siberia. Their population size is very small; there are fewer than 1,500 Kets in Russia. The Selkups have a slightly larger population size than the Kets, with approximately 4,250 individuals. 2002 Starting the Paleo-Indians period, a migration to the Americas across the Bering Strait (Beringia), by a small population carrying the Q-M242 mutation took place. A member of this initial population underwent a mutation, which defines its descendant population, known by the Q-M3 (SNP) mutation. These descendants migrated all over the Americas.
Q subclades Q1a3a and Q1a3a1a . . . .
Haplogroup Q1a3a (Y-DNA) and/or Q-M3 is defined by the presence of the rs3894 (M3) (SNP). The Q-M3 mutation is roughly 15,000 years old as the initial migration of Paleo-Indians into the Americas occurred. Q-M3 is the predominant haplotype in the Americas at a rate of 83% in South American populations, 50% in the Na-Dené populations, and in North American Eskimo-Aleut populations at about 46%. With minimal back-migration of Q-M3 in Eurasia, the mutation likely evolved in east-Beringia, or more specifically the Seward Peninsula or western Alaskan interior. The Beringia land mass began submerging, cutting off land routes.
Since the discovery of Q-M3, several subclades of M3-bearing populations have been discovered. An example is in South America, where some populations have a high prevalence of (SNP) M19 which defines subclade Q1a3a1a. M19 has been detected in (59%) of Amazonian Ticuna men and in (10%) of Wayuu men. Subclade M19 appears to be unique to South American Indigenous peoples, arising 5,000 to 10,000 years ago. This suggests that population isolation and perhaps even the establishment of tribal groups began soon after migration into the South American areas.
Haplogroup R1 . . .
Haplogroup R1 (Y-DNA) is the second most predominant Y haplotype found among indigenous Amerindians after Q (Y-DNA). The distribution of R1 is believed to be associated with the re-settlement of Eurasia following the last glacial maximum. One theory put forth is that it entered the Americas with the initial founding population. A second theory is that it was introduced during European colonization. R1 is very common throughout all of Eurasia except East Asia and Southeast Asia. R1 (M137) is found predominantly in North American groups like the Ojibwe (79%), Chipewyan (62%), Seminole (50%), Cherokee (47%), Dogrib (40%) and Papago (38%). The principal-component analysis suggests a close genetic relatedness between some North American Amerindians (the Chipewyan and the Cheyenne) and certain populations of central/southern Siberia (particularly the Kets, Yakuts, Selkups, and Altays), at the resolution of major Y-chromosome haplogroups. This pattern agrees with the distribution of mtDNA haplogroup X, which is found in North America, is absent from eastern Siberia, but is present in the Altais of southern central Siberia.
Haplogroup C3b . . .
Haplogroup C3 (M217, P44) is mainly found in indigenous Siberians, Mongolians and Oceanic populations. Haplogroup C3 is the most widespread and frequently occurring branch of the greater (Y-DNA) haplogroup C. Haplogroup C3 decedent C3b (P39) is commonly found in today's Na-Dené speakers with the highest frequency found among the Athabaskans at 42%. This distinct and isolated branch C3b (P39) includes almost all the Haplogroup C3 Y-chromosomes found among all indigenous peoples of the Americas. The Na-Dené groups are also unusual among indigenous peoples of the Americas in having a relatively high frequency of Q-M242 (25%). This indicates that the Na-Dené migration occurred from the Russian Far East after the initial Paleo-Indian colonization, but prior to modern Inuit, Inupiat and Yupik expansions.
Analysis of Dating
There are a couple of different methodologies for mutation dating. Pedigree mutation rates support a most recent common ancestor between Native American and South Altaic populations ca. 5,170 to 12,760 years ago (95% confidence interval, median 7,740 years ago), and a most recent common ancestor between North Altaic and South Altaic populations that is only a bit more recent (a 95% confidence interval 3,000 to 11,100 years ago, median 5,490 years ago). Evolutionary mutation rates support a most recent common ancestor of North Altaic and South Altaic of a median 21,890 years ago, and a statistically indistinguishable most recent common ancestor of Native Americans and South Altaic of a median 21,960 years ago.
Of course, all of the interesting inferences from the dates flow from the method you use and its accuracy. The evolutionary mutation rates suggest a split just before the Last Glacial Maximum and is suggestive of a scenario in which part of a population retreats to the South from the glaciers, while the other seeks a refuge in Beringia.
The pedigree date (which usually is closer to the historical corrolates that make sense) would be a decent fit for secondary Na-Dene migration wave that is before the original Native American population of the New World, but is before more recent circumpolar population migrations in and after the Bronze Age. The pedigree date also makes the possibility that there is an authentic Na-Dene to Yenesian linguistic link far more plausible than the older evolutionary date. Linguistic connections ought to be impossible to see at a time depth of 21,000 years, but is conceivable with a link that could be less than a third as old.
The "median split time" using pedigree dates is 4,490 years ago for N. Altaians v. S. Altaians, and 4,950 years ago for Native Americans v. S. Altaians, which would coincide with Uralic language expansion and the first of three major waves of Paleoeskimo migration to the New World. The evolutionary dates give a 19,260 years ago "median split time" for N. v. S. Altaians, and 13,420 years ago for Native American v. S. Altaians, an order reversal from all the other dates apparently driven by a wide and old date biased confidence interval. The very old genetic dates don't make a lot of sense, however, given that megafauna extinction dates in Siberia suggest a modern human arrival there ca. 30,000 years ago, plus or minus.
The indications that the northern Altaians are less strongly genetically connected than the southern Altaians to Native Americans is quite surprising. Linguistically and culturally the Northern Altaic populations would seem closer, but those are things that are more succepible to change over time and the southern populations may have faced stronger cultural pressures than the more remote and isolated northern populations.
The reasoning here matters a great deal, of course, and with a closed access paper isn't easy to evaluate. The abstract seems to indicate that the linkages are being based on the phylogeny of non-recombining Y-DNA haplogroup Q (the dominant one in Native Americans) without necessarily relying much on the mtDNA part of the analysis. In particular, it isn't easy to tell from the abstract how succeptible the data are to a multiple wave, as opposed to a single wave migration model.
There are really no sensible models for the arrivals of modern humans in the New World that can fit with a split between Native Americans and Siberian populations any later than 13,000-14,000 for the predominant haplogroups of Y-DNA haplogroup Q found in South America (Q-M3 and its descendants). But, a link of a secondary subtype of Y-DNA haplogroup Q that is pretty much exclusively found in North America at a later date is quite possible to fit consistently with plausible population models. Evolutionary mutation rate dates would strongly disfavor this scenario, but pedigree mutation rate dates could comfortably accomodate this scenario.