May 17, 2013

An avalanche of Tibetan genetic data (Qi et al. 2013)

A very impressive data dump on Tibetan genetic variation gives us an excellent picture on both the Y-chromosome and mtDNA side. There are two interesting things about Tibetans -at least to me. First, their mtDNA is dominated by haplogroup M9, which is ~39 thousand years old, suggesting an early settlement after the dispersal of modern humans across Eurasia.

Second, their Y-chromosomes are dominated by Y-haplogroup D, the sister clade of African haplogroup E, which links in some (unspecified, but I'm guessing old) time depth with such diverse peoples as the Andaman Islanders and the Ainu. Mongolians also share haplogroup D, but this is perhaps not surprising given the well-known links between Mongolia and Tibet. One might attribute the high Tibetan D frequency to drift, but drift acts randomly, and I don't think it's a coincidence that it acted in the same way in three quite different and fairly isolated corners of Eurasia to produce the Tibetan/Andaman/Ainu local peaks in an otherwise rather barren haplogroup D landscape.

There are other interesting details, such as the presence of R1a*(xM17) in Tibet, a haplogroup that has a patchy distribution in Asia. In a sample size of ~2,354 it's possible to get one of these less successful relatives of mega-groups like R-M17, and their systematic study may help root in space the earliest history of these lineages.


Mol Biol Evol (2013) doi: 10.1093/molbev/mst093

Genetic evidence of Paleolithic colonization and Neolithic expansion of modern humans on the Tibetan Plateau

Xuebin Qi et al.

Tibetans live on the highest plateau in the world, their current population size is nearly 5 million, and most of them live at an altitude exceeding 3,500 meters. Therefore, the Tibetan Plateau is a remarkable area for cultural and biological studies of human population history. However, the chronological profile of the Tibetan Plateau's colonization remains an unsolved question of human prehistory. To reconstruct the prehistoric colonization and demographic history of modern humans on the Tibetan Plateau, we systematically sampled 6,109 Tibetan individuals from 41 geographic populations across the entire region of the Tibetan Plateau and analyzed the phylogeographic patterns of both paternal (n = 2,354) and maternal (n = 6,109) lineages as well as genome-wide SNP markers (n = 50) in Tibetan populations. We found that there have been two distinct, major prehistoric migrations of modern humans into the Tibetan Plateau. The first migration was marked by ancient Tibetan genetic signatures dated to around 30,000 years ago, indicating that the initial peopling of the Tibetan Plateau by modern humans occurred during the Upper Paleolithic rather than Neolithic. We also found evidences for relatively young (only 7-10 thousand years old) shared Y chromosome and mitochondrial DNA haplotypes between Tibetans and Han Chinese, suggesting a second wave of migration during the early Neolithic. Collectively, the genetic data indicate that Tibetans have been adapted to a high altitude environment since initial colonization of the Tibetan Plateau in the early Upper Paleolithic, before the Last Glacial Maximum, followed by a rapid population expansion that coincided with the establishment of farming and yak pastoralism on the Plateau in the early Neolithic.

Link

18 comments:

Jim said...

"We also found evidences for relatively young (only 7-10 thousand years old) shared Y chromosome and mitochondrial DNA haplotypes between Tibetans and Han Chinese, suggesting a second wave of migration during the early Neolithic."

That looks like a neolithic expansion of Sino-Tibetan. (It's not as tautological as it sounds rom that terminology.) The next thingg is to find when barley cultivation statrs, unless people can grow the millet and whatever the Sino-Tibetans are suppased to have lived off of.

Dr Rob said...

RE Hg D

Yep, most likely the Neolithic and historic expansion of Han chinese 'wiped' its record from mainland China

R1a(xM17) is also found in Europe and western Asia ; so its patchy distribution is not very informative. Overall, one would be hard pressed against a South Asian origin for R, overall.

terryt said...

"The first migration was marked by ancient Tibetan genetic signatures dated to around 30,000 years ago"

Interestingly that is exactly the time suggested for the origin or introgression of the EDAR370A variation into modern humans. Coincidence?

"their Y-chromosomes are dominated by Y-haplogroup D, the sister clade of African haplogroup E, which links in some (unspecified, but I'm guessing old) time depth with such diverse peoples as the Andaman Islanders and the Ainu".

And mt-DNA A is present in both Ainu and Tibetans although not in the Andamans as far as I'm aware. I can't access the article so I don't know what caldes of A the authors found. Perhaps someone can help?

Kristiina said...

For the most part A4 (53.8%) and A11 (44.63%), a little bit of A5, A7and A10 (0.03-1.13%).

terryt said...

"For the most part A4 (53.8%) and A11 (44.63%), a little bit of A5, A7and A10 (0.03-1.13%)".

Thanks for that information. What was the proportion of A overall? The A4 is interesting as that haplogroup has been further subdivided and includes American A2. And A is very definitely a northern haplogroup so presumably has been in Tibet from an early period.

"That looks like a neolithic expansion of Sino-Tibetan. (It's not as tautological as it sounds rom that terminology.)"

I agree.

Ebizur said...

A4 is generally the most common type of mtDNA haplogroup A (technically, even the American haplogroup A2 is a subclade of A4). However, the figure for A11 looks interesting, though I do not know where this subclade has been found outside of Tibet.

As for M9, which seems to be the most common mtDNA haplogroup in modern Tibetans, how might its relationship to mtDNA haplogroup E be explained? Haplogroup E seems to be a fairly typical Austronesian haplogroup, with high frequency in the aborigines of Taiwan, populations of Maritime Southeast Asia (the Philippines, Indonesia, etc.), and especially the Chamorros of the Mariana Islands.

Kepler said...

Well, I wouldn't say it was "Han people" who came with the Neolithic but rather the ancestors of both Han Chinese and Tibetans. There were no Han Chinese 5000 years ago.
Of course and unfortunately, some groups in China would like to see it otherwise and mix politics with science.

terryt said...

"I wouldn't say it was 'Han people' who came with the Neolithic but rather the ancestors of both Han Chinese and Tibetans".

I've been trying to point that out for years. I'm relieved to at last find someone who agrees.

"the figure for A11 looks interesting, though I do not know where this subclade has been found outside of Tibet".

From notes I made while searching the references at Phylotree I see I have written that it has also been found in 'China', but I haven't noted where in China.

"how might its relationship to mtDNA haplogroup E be explained? Haplogroup E seems to be a fairly typical Austronesian haplogroup"

Not really 'Austronesian'. I seem to remember seeing a reference that claimed E probably entered the Philippines and Taiwan from Borneo, perhaps later than the Austronesian expansion. Its arrival in Borneo was possibly pre-Austronesian though, perhaps Hoabinhian, associated with the spread of Y-DNA O2a. M9 split early into M9a'b and E. Then E split into E1 and E2. Which E is from Borneo? And where has the other one been found?

http://mbe.oxfordjournals.org/content/25/6/1209.full.pdf+html

Quote:

"Although all 4 subclades are found in ISEA, so that ISEA
lineages occur throughout the tree, only 2 of the 4 (E1a [fig. 3a] and E2b [fig. 3d]) are found in Taiwan. The remaining subclades, E1b (fig. 3b) and E2a (fig. 3c), are both largely restricted to ISEA, albeit extending occasionally to
New Guinea and the Malay Peninsula, suggesting that both
arose in ISEA and dispersed fairly recently east and west. Of the 2 subclades shared with Taiwan, E2b, which is only 4,300 (±2,300) years old, falls into 2 branches, both present in ISEA, with the Taiwanese lineages forming a clear, shallower founder subclade. In other words, the diversity of
E2b seen in Taiwan is a subset of the clade found in ISEA. This implies an origin in ISEA and subsequent migration to Taiwan.".

So it is not Taiwanese in origin and so not primarily Austronesian. More:

"all subclades of haplogroup
E are present in Borneo but not in Wallacea".

"M9b is more difficult because of its scarcity: it has only been identified twice: once as a complete sequence from western China (Kong et al. 2006) and once as the HVS-I sequence (motif: 16051, 16209, 16223, and 16362) in a Yao speaker from southeast China (Wen, Li, Gao, et al. 2004)".

"Although M9a is restricted to mainland Asia and Japan, the deepest branches in the clade encompassing it (pre-M9a) are found in Indo-China, China, and Taiwan and the next deepest in ISEA".

So M9 may have entered Tibet from the southeast. Or not. The distribution map of M9a given in the paper indicates a more notrtherly origin for that haplogroup at least. The authors were writing at the height of the great southern coastal migration theory and so were probably heavily influenced by that perspective.

Kristiina said...

The proportion of all A is 14.63% in Tibetans. A4 was dated to 15.0 kya in Tibetans. A11 seemed to be a Tibetan-specific lineage and was dated to 13.4 kya.

Dr Rob said...

"There were no Han Chinese 5000 years ago."

Yes, of course. Poor wording on my behalf.

Lathdrinor said...

I reckon that an older population stratum, which was absorbed by a faster expanding O in between its present loci, is logical for D, which is present in small quantities in East Asian populations outside of Tibet and Japan. The loci that preserved the older stratum are all geographically located - in Tibet's case, a plateau; in Japan and the Andaman Islanders' case, islands. O out expanded D everywhere else in its domain, which I imagine spanned a vast space between eastern South Asia and northern East Asia.

terryt said...

Thanks Kristiina. That is very useful and revealing information. It does seem that A was not amoung the first arrivals at 13-15 kya. though.

Dr Rob said...

I guess I meant Sino-Han-like phenotype, not culturally or politically. Compared to older strata of Oriental phenotypes, although of course haplogropus certainly do not correlate in any straightforard and unambiguous way with 'looks'

terryt said...

"O out expanded D everywhere else in its domain, which I imagine spanned a vast space between eastern South Asia and northern East Asia".

That has long been my conclusion. Just as N's expansion has over-run that of Q in northern Eurasia. O has also over-run regions in SE Asia which until its arrival contained other branches of KMNOPS along with F2-M427.

"I guess I meant Sino-Han-like phenotype, not culturally or politically. Compared to older strata of Oriental phenotypes, although of course haplogropus certainly do not correlate in any straightforard and unambiguous way with 'looks'"

I knew what you meant actually. And I agree. Have you seen the information on the derivation and expansion of the EDAR370A mutation? If not:

http://forwhattheywereweare.blogspot.co.nz/2013/02/genetic-origin-of-east-asian-thicker.html

I still very much believe that Y-DNA O was responsible for the gene's southward spread from its region of origin. Razib has supplied a map of the postulated origin of the haplogroup, accessible through the link Maju has provided, in the comments section.

Al West said...

The expansion of Sino-Tibetan into Tibet in the Neolithic was already well-established on the basis of linguistic and archaeological evidence (ie, millet farming, ceramics, etc), but it's good to know that there is genetic evidence to support it as well. Very interesting stuff.

Shelle said...

I'm curious if any of you can help me. I have a daughter who was adopted from southern Hunan, China. We recently had her DNA tested with 23andme for both health and ancestry information. We know nothing about her family background but I'm interested to know if her DNA results could identify whether she is from a Chinese minority group or if she is Han Chinese. She is from an area of Hunan with a sizeable Yao population but not sure on other minorities in the area. Of course many are also Han Chinese. We only have her preliminary ancestry information as of now, her mtDNA haplogroup is M9b for which I am not finding much information and obviously we are not going to have any paternal info to help since we do not know who her birth parents are.
Also in the 23andme.com ancestry tools on the "Global Similarity Map" she is showing up in the Miaozu (Miao minority) box- no clue how accurate that is. They don't have a box for Yao so likely they don't have any representatives from that minority group yet in their database and maybe Miaozu on the next closest thing to Yao- no idea or maybe she is Miao (Hmong).
Any help would be much appreciated.
Thank you.
Michelle

Shelle said...

I'm curious if any of you can help me. I have a daughter who was adopted from southern Hunan, China. We recently had her DNA tested with 23andme for both health and ancestry information. We know nothing about her family background but I'm interested to know if her DNA results could identify whether she is from a Chinese minority group or if she is Han Chinese. She is from an area of Hunan with a sizeable Yao population but not sure on other minorities in the area. Of course many are also Han Chinese. We only have her preliminary ancestry information as of now, her mtDNA haplogroup is M9b for which I am not finding much information and obviously we are not going to have any paternal info to help since we do not know who her birth parents are.
Also in the 23andme.com ancestry tools on the "Global Similarity Map" she is showing up in the Miaozu (Miao minority) box- no clue how accurate that is. They don't have a box for Yao so likely they don't have any representatives from that minority group yet in their database and maybe Miaozu on the next closest thing to Yao- no idea or maybe she is Miao (Hmong).
Any help would be much appreciated.
Thank you.
Michelle

Curt Warner said...

Shelle, Miao and Yao are indeed closely related, and their languages have only been diverging for a little over 2000 years. Southwest Hunan also has a large Miao population (centered around Chengbu County in Shaoyang), while Yongzhou and Chenzhou are mostly Yao. Also, in case you didn't know, the Yao diaspora in the West calls themselves Mien.
Hope that helps.