On the Y-Chromosome Q haplogroup
TThis is the second part (See First Part here) of my ramblings on a possible Out of America migration back into Asia.
I will carry on from where I left off: (Summary) some Asian (specifically Northern, Central and Northeastern Asians - from Siberia, NE China and Mongolia) have a small but noticeable content of specific genes of Amerindian content. Mainstream science has it that these Asians descend from the people that were also the ancestors of Amerindians therefore they do carry some of the same genes.
I posted that the Turkic people moved out from the Altai spreading West towards Europe and North, Northeast into Siberia (Sakha or Yakuts, Kets and Selkups) and that they probably admixed there with aboriginal Siberians who in turn had an American admixture due to an Out of America gene flow.
I pointed out tha the Kets have the highest frequency of Y chromosome haplogroup Q (Q hg) in all of Asia (93.7%), which is only found among Amerindians; The Selkups have the second-highest frequency of haplogroup Q (Q hg) in Asia (66.4%).
Other groups, Tuvans, Oroqen, Mongols, Hadza and Daur carry a much lower Amerindian content and is very likely due to admixing with the other Siberian peoples.
The Y-chromosome Q haplogroup (Q hg) mentioned above is very interesting due to its strong preponderance in the Americas. Could it be a signal of an Out of America back-migration into Asia?
The Y-Chromosome haplogroups in America
A paper analyzing American and Asian lineages of Y-Chromosome (Battaglia V., et al., 2013)  notes that of the two founding lineages of Y-chromosome found in America, (C and Q), Q is the oldest and most widespread (with 75% frequency), while C, is limited to North America and found at a lower frequency . This means that Q haplogroup (Q hg) reached America first and spread from Alaska to Tierra del Fuego, C hg is a later arrival.
Q haplogroup is found in two main lineages in America: Q1a3a1a-M3 (76.8%) and Q1a3a1-L54* (16.7%). It is however interesting to point out the great diversity of Q hg in America: another 8 haplotypes have been discovered, mainly found among Peruvians and Mexicans, and they add up to 6.4% frequency, much greater than the diversity found in Siberia. 
The M3 part of Q1a3a1a stands for the M3 marker which is believed by mainstream geneticists to have arisen in Beringia, except for some extant Far Eastern Siberians (it appears among Koryaks at a frequency of 40%)  it is only found among Native Americans. Its presence among Koriaks (see image below for Q1a3a1a* red and blue square) is believed to be "... the result of a back migration rather than be direct M3 Beringian descendants... [and] could also be due to recent contacts (gene flows) with modern northern Native Americans."  .
An alternative explanation could be that M3 originated in Asia and those that took it into America survived, while the Siberians that carried it, passed away without descent.
The other marker L54, is definitively American (with a higher frequency in Mexico and Central America and lower elsewhere), none were found in the "populations living along the entry route to the Americas"  , and "only a potential Q-L54* has been observed in one Chukchi from Northern Siberia" , the paper cautiously points out that "any interpretation of this result (new Asian lineage, remnant of an ancestral state, trace of forward or back-migration) is premature..." .
Eastern and Southern Siberian peoples, Mongolians from the Altai Region in Western Mongolia and southern Ataians are definded by the Q1a3a1c sub-clade defined by the L330 marker. Asian upstream intermediate is L53* is found in Northern-Altai and Mongolia, at very low frequencies.
The paper concludes that the Altai Mountains were the southern barrier for these people who carried an ancestral form of L54, which "in prehistoric times and long before the peopling of the New Continent, moved eastwards during the Beringian standstill." 
This is reasonable, but the dating of the different branches is very strange:
The Odd phylogenetic tree
What I find perplexing are the dates of the branches of Battaglia et al.'s Phylogenetic tree of Y-chromosome Q hg; where some branches are older than their roots!:
Below is my adaptation of Battaglia et al.'s figure 1; in red I shaded the American haplogroups (M3), and in blue the Asian ones. The number on the right is the age of each haplogroup, (kya). The branches that are "American" are shaded red. All other branches are fully Asian.
We see an incongruity in the "main" branch MEH2 whose branches M120, MEH2* and M25 (with ages that range from 2.7 to 15.4 kya) are all younger than the offshoots of branch M346 which is at their same level.
Furthermore, M346 (dated by Zhong et al.,  at 17.77 +⁄- 4.4 ky, then branches succesively into branch L53 which then branches into L54 and this one then branches into M3 which is the oldest in the tree with maximum ages between 21 and 23.6 kya.
Lets look at the details:
Dates (I round off the dates from Tables 2 and 3, in ):
- Q1a3a1a-M3*. Most (from 66 to 100%) Amerindians belong to it: 22 kya for Central and Southern Americans, 3.4 kya for Na-Denes and 7.4 kya for Eskimo-Aleuts. Which is reasonable since the last two populations belong to a more recent migratory wave into Northern North America.
- Q1a3a-L54*. The remaining American Natives belong to it: 23.6 kya old, except Na-Dene which, again, are younger: 5.6 kya.
- Q1a1-M120 and Q1a2 - M25. Mongols were not dated in , however Table 1 in  gives 15.4 and 2.7 ky respectively.
- Q1a*-MEH2. Koryaks = 3.5 kya and also the remains of the "Saqqaq" man from Greenland (Morten Rasmussen et al., 2009)  which are about 4,000 years old but belong to a later wave into America.
- Q1a3a1c-L330. Mongols = 6.5 kya and Altaians: 2.9 kya.
- Q1a3a*-M346, is dated at 17.77 +⁄- 4.41 kya 
Below I reproduce the data from Table 3 , showing the "average" ages for all Q haplogroups:
Once more, American Q hg are between 21.1 and 23.4 ky old. The Asian ones range from 10.3 to 22.4 ky with a decreasing age cline as you move East to West from America into Siberia.
This would suggest that these Asian Q lineages originated in America and dispersed West, diversifying (mutating) along the way since the youngest are deeper in central Asia.
But that assumption is apparently wrong, because the markers follow the opposite order (that is, Americans have markers that Asians don't, implying that these markers appeared later, in Americans).
I guess I am going to have to do some deeper research into specific Haplogroup markers, but first, let's look into the Siberian Q haplogroups.
Siberian ancestors (?)
The presence of haplogroup Q (Q hg) among Siberians was pointed out in 2002 (Karafet et al., 2002)  at relatively low frequencies of 18.8% (when compared to Native Americans). Two populations concentrate 79.5% of the ocurrences: the frequency reached 93.8% among Kets and 66.4% among Selkups. The age of haplogroup Q was estimated at 17,700 +⁄- 4,800 years , in tune with the mainstream theory (it is just a bit older than the 15 kya date for entry into America).
These high frequencies were due to "intergenerational genetic drift coupled with founder effects... supported by very low levels of Y-STR diversity associated with haplogroup Q in both populations (0.149 and 0.159, respectively)..." 
In other words it was not natural selection, but chance that acted upon the small population sizes and their high mobility allowing Q hg to become predominant; therefore its frequency grew (intergenerational genetic drift), add to this the fact that small groups with Q hg survived while other haplogroups just died out (bottleneck); outcome: Thus the Q hg became the prevailing line among these people.
Different to Americans and different to each other
But, as we have already seen, these haplotypes are not the same as those found in Native Americans; a Russian language paper (Volkov, 2013)  provides an interesting phylogenetic tree, reproduced below:
At the split between Americans and Asians (Q1a3a-L53), two branches appear, one leading to all Siberian groups in blue. Another one, in orange one leads to American Natives (red branch M3) while another (yellow) leads to the Q haplogroup found in certain Europeans: Q1a2a2 L804, L805 (Sweden, Norway and via Vikings: UK) - this is worth looking into! 
The Q frequency (L330) among Siberians is in agreement with Karafet et al: Kets: 84%, Northern Selkups: 66.4% (and drops to: Evens: 4.2%, Nenets: 1,4%, Kanthy: 1%). 
But they are not the same Q haplotypes: Selkups, who originally lived in the Urals, share the same haplotype with the Chechens of the Caucasus (which is close by). On the other hand, the remaining Siberian populations and among them the Kets belong to another haplotype, with other downstream mutations: DYS347=14, and DYS437=13, DYS390=23 ("DYS" stands for DNA Y chromosome Short Tandem Repeat, with a lenght of "n").
Considering that Altai was the source of Amerindian Q haplogroup, Dulik at al., (2012)  explored the differences between the Q hg of Southern and Northern Altaian's (this is also reflected in the image above). They found that the latter were quite recent (Bronze Age) the former older -early Bronze Age or late Neolithic.
Then they calculated the divergence times between Southern Altaians and Native Americans, but their TMRCA ages fluctuate widely; from a too recent 7.74 kya (Pedigree Based) to a more reasonable 21.96 ky (Evolutionary-Based); the Split Time values were 4.95 and 13.42 kya for Pedigree based and Evolutionary based, respectively.
Seeing this 3 fold difference between the ages and taking into account that America was peopled more than 8 kya, the authors dismissed the Pedigree based values arguing ("that the evolutionary rate provided a more reasonable estimate.... making the use of the pedigree-based mutation rate questionable." ).
These "average" values are to young (even more recent than the 23 kya age estimated further up for the M3 and L54 haplotypes found in America. And, in my opinion it is due to the fact that the 95% confidence intervals for the Bayesian analyses are extremely broad: they range from 12,260 to 42,690 ya. for TMRCA and 5,220 to 30,430 ya. for Splilt Time.
Taking the oldest figures would mean that the ancestors of Americans could have shared a common ancestor with Altaians 42,690 years ago, which is really much more reasonable and consistent with the earliest dated Upper Paleolithic industries from Altai: 43.3 kya .
Dating and TMRCA values: Are they reliable?
Looking at these disparities it seems that a key issue is the dating, the timeline, the estimation on when groups split or when they shared a common ancestor.
As seen above, Pedigree estimations differ substantially from those based on evolutionary estimations. And these depend on the mutation rates adopted.
When reading the papers that deal with this subject, my doubts intensify. For instance, a paper by Poznik et al., (2013)  estimates mutation rates by adopting, as a "calibration point, the initial migration into and expansion throughout the Americas", based on the dates of known archaeological sites (Paisley Cave and Buttermilk Creek in the US and Monte Verde in Chile) they find Goebel et al. estimation that " humans colonized the Americas around 15 kya” acceptable, and use it for calibration purposes. 
But what if instead of 15 kya the date was really 30 kya or 45 kya? This would introduce a strong bias in their estimations. Once again we see how a "recent date" for the peopling of America impacts upon other branches of formal science.
The authors then use the Y haplogroup Q for their calibrations and assume that M3 arose "shortly subsequent to initial entry to the Americas", and in doing so, underestimate the impact that an earlier divergence (Between L54 and M3) in Siberia, prior to the entry into the New world could have had on their calibration. 
The strange dates produced by these estimations are higlighted by the case I mentioned in a Previous post on the useless mtDNA clock, where the dating of a novel Y-chromosome haplogroup (Mendez et al, 2013) named A00, gave a very old age: " 338 thousand years ago (kya) (95% confidence interval = 237-581 kya). Remarkably, this exceeds current estimates of the mtDNA TMRCA, as well as those of the age of the oldest anatomically modern human fossils..." , strangely old date indeed. The clocks need to be checked.
Another example can be found in a paper on a Q hg sublineage (Q5) detected in India (Sharma et al., 2007) ; the ate estimated for it was 47.1 kya (34.2 – 75.6 ky), but the authors believe that it is "an over estimate than the age of haplogroup Q (15,000–18,000 Years Before Present)" and try to explain the distorted "old" age they calculated as caused by "enhanced diversity, probably as an effect of population expansions and severe bottlenecks or might be due to later migrations and admixture" , they then recalculate it as 14.4 ky old! (fitting it nicely into the assumed age range).
Y chromosome Q hg predominates in America, most of it belongs to the M3 subtype, the rest is L54. There is a very small presence of these two subtypes in East Beringia (Asia), most likely due to a back migration into Siberia from America.
Greater diversity within Q hg is found in America than in North East and central Siberia, this hints at a deeper and more ancient origin for the American lineages.
However the ages of the oldest Amerindian haplotypes are quite recent and have been calculated as being 22 -23 kya. Asian strains contrary to what would be expected from the theory of a trans-Beringian peopling of America appear to be much younger. Suggesting instead a migration Out of America and into Asia, carrying Q hg. We will see in a future post that there is additional proof from mtDNA and language of a migration from America into Eastern Siberia.
Despite doubts regarding age calculations, the oldest mainstream date of 43 kya for a split between the ancestors of Altaians and Americans seems to allow for an early peopling of America.
There is something with the ages that I find strange. But that will be the subject of another post, where I will deal with the dating methods (in particular after reading how Anzic-1 remains from Montana US were dated. By the way, he was a Q-L54*(xM3) 12,600 years old.
I will review the markers that indicate splits in Q hg, because a radiation out of America seems highly probable. I will also take a look at those odd Q hg found in Europe which some attribute to the Huns, but may have more ancient roots, the same ancient roots that Amerindian Q hg has... (I am thinking about Neanderthal here... however Neanderthal Y chromosome would be even older than the A00 haplogroup mentioned above, and quite different from the current Q hg that descends from A00).
 Morten Rasmussen et al., (2010). Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463, 757-762 (11 February 2010) | doi :10.1038/nature08835
 Battaglia V, Grugni V, Perego UA, Angerhofer N, Gomez-Palmieri JE, et al., (2013). The First Peopling of South America: New Evidence from Y-Chromosome Haplogroup Q.. PLoS ONE 8(8): e71390. doi:10.1371/journal.pone.0071390
 Hua Zhong et al., (2010). Extended Y-chromosome investigation suggests post-Glacial migrations of modern humans into East Asia via the northern route. Oxford Journals.
 Tatiana Karafet et al., (2002). High Levels of Y-Chromosome Differentiation among Native Siberian Populations and the Genetic Signature of a Boreal Hunter-Gatherer Way of Life, Human Biology, December 2002, v. 74, no. 6, pp. 761–789.
 VG Volkov, (2013). Ancient Samoyeds of Yenisey, and migration in light of Genetic Data. Tomsk magazine Ling. and Antropo. 2013. 1 (1) 79-96
 International Society of Genetic Genealogy
 Matthew C. Dulik, et al., (2012). Mitochondrial DNA and Y Chromosome Variation Provides Evidence for a Recent Common Ancestry between Native Americans and Indigenous Altaians. Am J Hum Genet. Mar 9, 2012; 90(3): 573. doi: 10.1016/j.ajhg.2012.02.003
 G. David Poznik et al., (2013). Sequencing Y Chromosomes Resolves Discrepancy in Time to Common Ancestor of Males Versus Females. Science 2 August 2013: vol. 341 no. 6145 pp. 562-565 S. Inf. page 13. DOI: 10.1126/science.1237619
 Mendez et al., (2013). An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am J Hum Genet. 2013 Apr 4;92(4):637.
 Swarkar Sharma et al., (2007). A novel subgroup Q5 of human Y-chromosomal haplogroup Q in India. BMC Evol Biol. 2007; 7: 232. doi: 10.1186/1471-2148-7-2327
 Morten Rasmussen, et al., (2014). The genome of a Late Pleistocene human from a Clovis burial site in western Montana. Nature 506, 225–229 (13 February 2014) doi:10.1038/nature13025
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