Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a.
Malyarchuk B, Derenko M, Denisova G, Maksimov A, Wozniak M, Grzybowski T, Dambueva I, Zakharov I.
Abstract
To investigate the structure of Y chromosome haplogroups R-M207 and Q-M242 in human populations of North Asia, we have performed high-resolution genotyping using both single nucleotide polymorphisms and short tandem repeat (STR)-based approaches of 121 M207- and M242-derived samples from 885 males of 16 ethnic groups of Siberia and East Asia. As a result, the following Y chromosome haplogroups were revealed: R1b1b1-M73 (2.0%), R1b1b2-M269 (0.7%), R2-M124 (1.1%), Q1a(*)-MEH2 (0.5%), Q1a2-M25 (0.1%), Q1a3(*)-M346 (9.2%) and Q1a3a-M3 (0.2%). Despite the low coalescence age of haplogroup Q1a3(*)-M346, which is estimated in South Siberia as about 4.5±1.5 thousand years ago (Ka), divergence time between these Q1a3(*)-M346 haplotypes and Amerindian-specific haplogroup Q1a3a-M3 is equal to 13.8±3.9 Ka, pointing to a relatively recent entry date to America. In addition, unique cluster of haplotypes belonging to Q1a(*)-MEH2 was found in Koryaks inhabiting the Sea of Okhotsk coast (at a frequency of 10.3%). Although the level of STR diversity associated with Q1a(*)-MEH2 is very low, this lineage appears to be closest to the extinct Palaeo-Eskimo individuals belonging to the Saqqaq culture arisen in the New World Arctic about 5.5 Ka. This finding suggests that Q1a(*)-MEH2 likely traces a population migration originating in Northeast Siberia across the Bering Strait.
Link
To investigate the structure of Y chromosome haplogroups R-M207 and Q-M242 in human populations of North Asia, we have performed high-resolution genotyping using both single nucleotide polymorphisms and short tandem repeat (STR)-based approaches of 121 M207- and M242-derived samples from 885 males of 16 ethnic groups of Siberia and East Asia. As a result, the following Y chromosome haplogroups were revealed: R1b1b1-M73 (2.0%), R1b1b2-M269 (0.7%), R2-M124 (1.1%), Q1a(*)-MEH2 (0.5%), Q1a2-M25 (0.1%), Q1a3(*)-M346 (9.2%) and Q1a3a-M3 (0.2%). Despite the low coalescence age of haplogroup Q1a3(*)-M346, which is estimated in South Siberia as about 4.5±1.5 thousand years ago (Ka), divergence time between these Q1a3(*)-M346 haplotypes and Amerindian-specific haplogroup Q1a3a-M3 is equal to 13.8±3.9 Ka, pointing to a relatively recent entry date to America. In addition, unique cluster of haplotypes belonging to Q1a(*)-MEH2 was found in Koryaks inhabiting the Sea of Okhotsk coast (at a frequency of 10.3%). Although the level of STR diversity associated with Q1a(*)-MEH2 is very low, this lineage appears to be closest to the extinct Palaeo-Eskimo individuals belonging to the Saqqaq culture arisen in the New World Arctic about 5.5 Ka. This finding suggests that Q1a(*)-MEH2 likely traces a population migration originating in Northeast Siberia across the Bering Strait.
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I have been looking for something like this...
ReplyDeleteI have been trying to find something in the way of genetics to confirm a link between Yeniseian and Na Dene...more than just very, very compelling linguistic analysis.
This is not about those two languages...but this is very, very compelling in and of itself.
It sheds tremendous light on the genetic situation. Seems that many of the Siberian signatures did not make it across the Bering Strait though.
In all the genetic assays of Native Americans I have seen, they are mostly Q and C with some groups having minor and groups with some major recent European admixture.
In one genetic assay there was some N present...I don't know if that was recent or if that came with them across the Bering Strait.
Dienekes I thought you were against the usage of the evolutionary effective mutation rate.
ReplyDeleteThis is from the study:
Malyarchuk et al(2011)
"The age of STR variation within haplogroups was estimated as the average squared difference in the number of repeats between all current chromosomes and the founder haplotype (formed by the median values of the repeat scores at each STR locus within the haplogroup), averaged over STR loci and divided by means of a mutation rate.25,33 The evolutionary effective mutation rate of 6.9x104 per 25 years based on STR variation within Y chromosome haplogroups in the populations with documented short-term histories was used.33 The upper bound for divergence time of two groups of haplotypes was calculated as divergence time estimate, assuming STR variance in repeat number at the beginning of population subdivision (Vo) equal to zero.34 In the age calculation procedures, only tri- and tetranucleotide markers were used, so, besides the ambiguous loci DYS385a and DYS385b, locus DYS438 with pentanucleotide repeats was excluded from the calculations."
So if we follow your correction for the genealogical rate, and divide the numbers by a factor of 3, then it would mean that divergence time between these Q1a3(*)-M346 haplotypes and Amerindian-specific haplogroup Q1a3a-M3 is equal to 4.6±1.3 Ka, something awfully recently considering the archeological record of the colonization of the Americas. It seems the genealogical mutation rate might have hit a brickwall.
very interesting work
ReplyDeleteDienekes I thought you were against the usage of the evolutionary effective mutation rate.
ReplyDeleteI am against the indiscriminate usage of the evolutionary rate. Populations that have maintained a constant and small size are likely to lose Y-STR variance due to drift (this may apply to Siberians). So are populations that experienced a severe bottleneck (this may apply to the ancestors of native americans).
Also, it's not clear from the excerpt you provided how divergence between Siberian and Native American Y-chromosomes was estimated, or which markers were used.
jeanlohizun, that was a very good observation. No wonder Dienekes didn't make any mention of the evolutionary mutation rate when he wrote his post about this study, despite that he always mentions that issue when writing about a y-dna study that makes age estimates.
ReplyDeleteDienekes said:
ReplyDelete"I am against the indiscriminate usage of the evolutionary rate. Populations that have maintained a constant and small size are likely to lose Y-STR variance due to drift (this may apply to Siberians). So are populations that experienced a severe bottleneck (this may apply to the ancestors of native americans).
"
So you don't think this situation could possibly apply to any European population?
Perhaps you would find this interesting:
Malyarchuk et al(2011)
“To obtain a better resolution of phylogenetic relationships between Y chromosomes, we have analyzed haplotypes at 12 STR loci (Supplementary Table S1).Median joining network of haplogroup Q1a demonstrates subdivision of STR-haplotypes in accordance with their haplogroup affiliation into three clusters corresponding to haplogroups Q1a3*-M346, Q1a3a-M3 and Q1a*-MEH2 (Figure 1).
Coalescence age of South Siberian Q1a3*-M346, based on the average squared difference in the number of tri- and tetranucleotide repeats, is about 4.03±1.25Ka, while the age of the Koryak Q1a*-MEH2 appears to be only 1.0±1.0Ka. Median network of haplogroup R1b1b1-M73 shows that there are two subclusters of haplotypes in Siberian populations studied. One of them (designated as a in Figure 2) is determined by median haplotype 14-13-16-13-17-22-11-13-13-15-10-13 (for all loci studied: DYS19, DYS385a, DYS385b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439) and another one (B) by haplotype 14-13-13-14-16-19-11-13-13-15-10-13 (Figure 2). The coalescence age of R1b1b1-M73 in South Siberia, based on tri- and tetranucleotide repeats, is estimated as about 8.2±10.5Ka. The ages of subclusters A and B are amounted to 4.4±1.5 and 5.6±4.0Ka, respectively.”
http://i1133.photobucket.com/albums/m582/jeanlohizun/Malyarchuketal2011Table-1.jpg
http://i1133.photobucket.com/albums/m582/jeanlohizun/Malyarchuketal2011Table-2.jpg
This report looks like one confirming previous expectations. A good thing in science, but not a worldview changing one.
ReplyDelete"So if we follow your correction for the genealogical rate, and divide the numbers by a factor of 3, then it would mean that divergence time between these Q1a3(*)-M346 haplotypes and Amerindian-specific haplogroup Q1a3a-M3 is equal to 4.6±1.3 Ka, something awfully recently considering the archeological record of the colonization of the Americas. It seems the genealogical mutation rate might have hit a brickwall."
ReplyDeleteIn the New World, evolutionary mutation rate is not supported by archaeology either. There're NO archaeological signatures of arrival of NE Asians to the New World. The earliest well-defined archaeological complex in the New World, namely "Clovis," has its roots in southern North America (per the recent find at Buttermilk) and not in NE Asia or Alaska. There's no string of archaeological sites connecting Buttermilk back to NE Asia in pre-Clovis times. Moreover, the age of fluted projectile points decrease from south to north, so that Mesa culture in Alaska is likely evidence of a back-migration of Paleoindians in the direction of NE Asia. Then, of course, we have Monte Verde II, Monte Verde I and a host of other potentially valid sites. Sky is the limit there.
If the New World was colonized from Siberia sometime after 20,000 YBP, we would've found microblades all over America, as they are found all over Siberia. But microblades don't penetrate further south than Vancouver and northern Alberta. Hence, it's of course possible that populations were going east and west, north and south, a migration out of Asia after 20,000 years can't explain the peculiarity of the New World archaeological record.
Hence, the evolutionary rate is just as useless as genealogical rate. Most likely, mutation rate is much slower in small isolated populations, so that Amerindian Q1 lineage can be much older than it is usually assumed. Dienekes just believes that if he cuts a rotten apple into three pieces it will make it fresh.
jeanlohizun
ReplyDeleteWhen M346 was first discovered in India, the entry of Q into India was estimated at between 34K and 75K years BP using the "effective rate" of 6.9 per 10,000 for Y-chromosome mutation. (Swarkar et al) So issues with the issues with the "effective rate" are not confined to the last 1000 years or so.
I hope Q will be found between turk tribes who moved to Carpathian Basin on the second half of first thousand.
ReplyDelete