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Genetic origin of East Asian thicker hair, denser sweat glands

16 Feb
The single origin of these regional phenotype traits has now been tracked to a single allele of gene EDAR (Wikipedia, SNPedia), specifically to its variant EDAR370A, typical of East Asians, using a genetically modified mouse model.
Yana G. Kamberov, Modeling Recent Human Evolution in Mice by Expression of a Selected EDAR Variant. Cell 2013. Pay per viewLINK [10.1016/j.cell.2013.01.016]

Summary


An adaptive variant of the human Ectodysplasin receptor, EDARV370A, is one of the strongest candidates of recent positive selection from genome-wide scans. We have modeled EDAR370A in mice and characterized its phenotype and evolutionary origins in humans. Our computational analysis suggests the allele arose in central China approximately 30,000 years ago. Although EDAR370A has been associated with increased scalp hair thickness and changed tooth morphology in humans, its direct biological significance and potential adaptive role remain unclear. We generated a knockin mouse model and find that, as in humans, hair thickness is increased in EDAR370A mice. We identify new biological targets affected by the mutation, including mammary and eccrine glands. Building on these results, we find that EDAR370A is associated with an increased number of active eccrine glands in the Han Chinese. This interdisciplinary approach yields unique insight into the generation of adaptive variation among modern humans.

As the summary mentions, it has also been suggested that the variant influences tooth morphology, although this could not be demonstrated in the mouse model. 


The mutation was found in a gene for ectodysplasin receptor, or EDAR,
part of a signaling pathway known to play a key role in the development
of hair, sweat glands and other skin features. While human populations
in Africa and Europe had one, ancestral, version of the gene, most East
Asians had a derived variant, EDARV370A, which studies had linked to
thicker scalp hair and an altered tooth shape in humans.


The ectodysplasin pathway is highly conserved across vertebrates —
the same genes do the same thing in humans and mice and zebrafish. For
that reason, and because its effects on skin, hair and scales can be
observed directly, it is widely studied.


This evolutionary conservation led Yana Kamberov, one of two first
authors on the paper, to reason that EDARV370A would exert similar
biological effects in an animal model as in humans. The HMS research
fellow in genetics developed a mouse model with the exact mutation of
EDARV370A — a difference of one DNA letter from the original, or
wild-type, population. That mouse manifested thicker hair, more densely
branched mammary glands and an increased number of eccrine, or sweat,
glands.

The authors argue for a selective pressure but I find hard to imagine which one could it be. Therefore I rather lean again towards a random founder effect. 
Unless… notice that in the figure accompanying the summary also mammary gland density is shown as increased, what could result in improved nutrition for babies, what would indeed be selected for (assuming the rest of effects are neutral or quasi-neutral).
Anyhow, linking it obliquely to the previous entry (on Neanderthal admixture in East Asians), I have often wondered about the origins of straight hair in general, because it is obviously not ancestral in our species (all “Aboriginal African” populations have thinly curled hair, as do some non-Africans, especially remote Tropical populations like Papuans or Andamanese) and my main hypothesis is that it could be a Neanderthal genetic influence, possibly selected because of less intense need of head ventilation (for which thinly curled “African” hair seems best) and more intense need instead of protection against cold and rain. The thick hair East Asian variant might in this case be just the extreme variant of a more widespread Neanderthal introgression. Just food for thought.

Update (Feb 20): Razib Khan also finds the suggested “selection sweep” dubious, and his discussion of this paper is very interesting to read.

An interesting detail that I could not gather clearly from the abstract is that the allele causes (at least in mice) smaller breasts and not just denser mammal glands.

But surely the most interesting item is this map of the frequencies of the EDARV370A allele through the World, being very much and quite strictly limited to the peoples displaying what is classically described as the Mongoloid phenotype:

An intriguing issue is also the lack of it in Europe, even among peoples of well-known Siberian/East Asian low-level admixture (Northern Russians). I’m tentatively imagining some sort of “racist selection” against the trait among those peoples, as it expresses an exotic, possibly not favored (to put it mildly), very apparent phenotype. Food for thought.

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143 responses to “Genetic origin of East Asian thicker hair, denser sweat glands

  1. princenuadha

    February 16, 2013 at 4:17 pm

    Interesting idea on the neandertals.Also, did the native Americans attain this variant common in East Asia, or had the two already separated by 30 thousand ya?

     
  2. Maju

    February 16, 2013 at 11:08 pm

    Glad you liked it. It can of course be a very successful ex-novo mutation in H. sapiens but it looks a bit suspicious, right?"Also, did the native Americans attain this variant common in East Asia, or had the two already separated by 30 thousand ya?"Not sure. I could not find enough data on this allele's distribution but, if Native Americans have it, they surely must have got it also already in NE Asia 30 or even more Ka ago.

     
  3. Ebizur

    February 16, 2013 at 11:47 pm

    princenuadha wrote,"Also, did the native Americans attain this variant common in East Asia, or had the two already separated by 30 thousand ya?"Yes, the same EDAR variant in question is very common among Native Americans and populations that contain significant amounts of Native American admixture, such as Mexicans:Frequency of ancestral rs3827760 allele (encoding EDAR370V)1.0 Yoruba in Ibadan, Nigeria1.0 Utah residents with Northern and Western European Ancestry0.98 Gujarati Indians in Houston, Texas0.59 Mexican ancestry in Los Angeles, California0.20 Japanese in Tokyo0.08 Chinese in Denver, Colorado0.06 Han Chinese in BeijingFrequency of derived rs3827760 allele (encoding EDAR370A)0.94 Han Chinese in Beijing0.92 Chinese in Denver, Colorado0.80 Japanese in Tokyo0.41 Mexican ancestry in Los Angeles, California0.02 Gujarati Indians in Houston, Texas0.0 Utah residents with Northern and Western European Ancestry0.0 Yoruba in Ibadan, NigeriaThis sample of Mexican Americans from Los Angeles is known to be an approximately 50%/50% admixture of Europeans/Africans and Native Americans in terms of autosomal genetic ancestry, so I would guess that the frequency of the derived EDAR variant in the Native American ancestors of these Mexicans in Los Angeles was probably about the same as the frequency of the derived EDAR variant in Japanese from Tokyo.

     
  4. Ebizur

    February 16, 2013 at 11:55 pm

    Also, note that the derived EDAR variant is not found with significant frequency in Gujarati Americans. The very low-level presence of the derived allele in this population easily could be due to historically recorded invasions of the Subcontinent or even gene flow from populations of the northern fringes of the Subcontinent (Tharus, Lahaulis, Burushos, etc.), which are quite admixed with East Asians.

     
  5. Maju

    February 17, 2013 at 12:43 am

    That's very interesting, thanks.

     
  6. Joy

    February 17, 2013 at 6:17 am

    Given as this variant became regionally dominant in a time when people were quite capable of making headgear that would overcome any advantages of different hair types, this is obviously a trait that spread through sexual selection. Any teenaged european girl in a european dominant social environment can tell you that any hair texture with more than a very relaxed wave lowers social status.

     
  7. Joy

    February 17, 2013 at 6:22 am

    PS: The children born to Vietnamese mothers fathered by (admixed African) "black" US soldiers suffered a dire social fate in Vietnam. Their pariah status was determined by hair texture rather than skin tone, which in many cases was not outside the range of SE Asian norm.

     
  8. Mike Keesey

    February 17, 2013 at 8:00 am

    If straight hair is a Neandertal trait that introgressed into human populations, then why are there populations with curly/kinky/woolly hair that do have Neandertal DNA (e.g., Papuans)?

     
  9. Maju

    February 17, 2013 at 1:41 pm

    That's not real in my experience. But I live in a country where "more than a very relaxed wave" is very common, even dominant maybe. It seems to reflect some kind of racist(?) prejudice in your particular modern environment and nothing else.

     
  10. Maju

    February 17, 2013 at 1:44 pm

    In some East Asian populations curly hair is relatively common and does not seem to affect social status at all. I have spotted it among Tibetans and among island Koreans. Obviously social status in small communities where everyone knows everyone else is not derived from such minor elements, at least mostly not, but from each one's personality and maybe (where castes are already developed, not in the Paleolithic in any case) birthright (inheritance).

     
  11. Maju

    February 17, 2013 at 1:56 pm

    Neanderthal admixture is in the best case very small in non-Africans, so unless selected for some reason (or lots of luck) it should have not become dominant. That's why I use the term "introgression" which implies a selection for that trait after incorporation by minor admixture. Whatever the case, many Eurasians (including myself) have curly hair, just not the "African" thinly curled type (which is much rarer, although not so rare in beards, never mind pubic hair). This may well be an intermediate type. It's too common, not just in Europe and West Asia but also in India, among Australian Aborigenes, etc. to be considered a secondary introgression from Africa in "recent" times, so straight hair was not fully selected for (or randomly succeeded) in many areas but only somewhat.We may not notice in modern contexts because men often have hair cut very short (more comfortable) and women often alter their hair texture artificially (for whatever aesthetic reasons) but the intermediate phenotype is still very common and even dominant in Southern Europe, West Asia, some parts of India and Australian Aborigines (also often found in SE Asian "Negritos"). Of course, as already mentioned, some non-African populations (Melanesians, Andamanese) still retain the ancestral "African" thinly curled type. Why? Random unknown reasons and/or tropical adaption.

     
  12. Maju

    February 17, 2013 at 4:10 pm

    Ebizur: I was thinking if there's any data on this variant among SE Asians. I ask because one of the traits supposedly regulated is dental morphology (sinodonty I presume) and SE Asians are mostly sundandont. Also it's plausible under various population history models that they might have it in lesser frequency than NE Asians.

     
  13. Grey

    February 17, 2013 at 6:17 pm

    "but the intermediate phenotype is still very common and even dominant in Southern Europe"Quite common in Wales, Ireland, SW England also – dunno about Brittany.It seems likely to me that African-style hair probably serves a particular tropical purpose.Populations that moved out of the tropics might simply not have the same selective pressure so random variation breaks it down.If there was more to it than that then wouldn't the percentage of curly hair have to decline as you moved further from the tropics?

     
  14. Maju

    February 17, 2013 at 7:42 pm

    It could of course be a founder effect. If there's no selective pressure nor randomly selecting bottlenecks involved, why don't most retain the thinly curled "Tropical" hair? Once a variant is fixated, as it seems it happened with thinly curled hair (judging on Africans and other tropical peoples), if no pressure of any sort is applied, it should remain there. Also, as the variant is already fixed, the novel allele must come from somewhere (either ex novo mutation or admixture). So I conclude that, unless I'm missing something, (1) there straight hair allele is either a new variant or one taken from Neanderthals and (2) there was some sort of notable "pressure", either by random bottleneck (founder effect) or by some sort of selection in favor of straight hair. I speculate that it may have to do with a trade-off between ventilation (curly) and warming (straight) but I may be totally wrong.

     
  15. Grey

    February 18, 2013 at 6:28 pm

    "I speculate that it may have to do with a trade-off between ventilation (curly) and warming (straight) but I may be totally wrong."That seems the most plausible.If the west coast of the UK and Ireland is an exception to the rule (and it may just be a perception on my part) it could simply be a coastal effect outweighing a northern latitude effect.

     
  16. Maju

    February 18, 2013 at 6:39 pm

    Ireland was not (or almost not) populated until "a few" thousand years ago (10,000 years?) and the effect does not seem too extreme anyhow. First is the availability of the allele (i.e. does it exist in the population?, how common is it to begin with?) and then the weight of the effect, which in this case I suspect quite weak. Maybe it's about founder effects (and sexual selection?) Who knows.

     
  17. andrew

    February 19, 2013 at 11:05 pm

    EDAR was not a random founder effect. It is the strongest signal of a selective sweep in the entire East Asian genome and would be in the top ten for the entire human genome in the last 100,000 years.I agree that explaining it as a result of temperature and humidity adaptation or arbitrary preferences leading to sexual selection are implausible. Neither is a strong enough selective pressure to produce the nearly complete fixation of this gene in all of East Asia and the Americas.My personal suspicion is that EDAR conferred protection against bubonic plague outbreaks in China to some extent (I outline my reasoning a post at my blog today and comments at Gene Expression), but while that specific hypothesis is speculative, the notion that this was a powerful fitness based selection is not.

     
  18. andrew

    February 19, 2013 at 11:07 pm

    I believe that the paper has data on Southeast Asians. The pie charts on a global map seem to show this. It is a pretty stark divide between SE Asia and S Asia. The Munda in S Asia also have the derived allelle at an elevated frequency relative to other South Asians.

     
  19. Maju

    February 20, 2013 at 12:29 am

    I am skeptic about "selective swaps" when the benefit is not obvious and the allele is concentrated in one specific population. This can also be explained, maybe better, by reason of founder effect, at least partly. This article discusses this one and, at the bottom, another related paper. The second one did find an allele that looks very much as being selected for health reasons (TLRS5) but this one is a gene known to be related to immunology. But EDAR is not apparently immunologic and the best reason for a selective swap (if real) that I can imagine is an increase in breastfeeding capacity (however I never read that East Asian women excel in that so…)

     
  20. terryt

    February 20, 2013 at 2:23 am

    "I am skeptic about 'selective swaps' when the benefit is not obvious and the allele is concentrated in one specific population". It is obvious that what you really mean is that you refuse to accept selective sweeps if accepting them would conflict with what you wish to believe. Just because you (or anyone else) cannot see the reason for the sweep doesn't mean it didn't happen. "It is a pretty stark divide between SE Asia and S Asia". That divide is of long standing, yet Maju can still insist that the route into SE Asia via India was a doddle for early humans of all species. "The Munda in S Asia also have the derived allelle at an elevated frequency relative to other South Asians". Which makes complete sense. The language and the bulk of their haplogroups come from the east. In fact the boundary between South and Southeast asia has been crossed far more often from east to west than in the other direction.

     
  21. andrew

    February 20, 2013 at 2:55 am

    The selective sweep classification follows from the statistical profile. The ancestral allelle is almost completely absent, except as a low frequency recessive carrier gene, in the Han Chinese. It is near 100% from SE Asia to East Asia to the Americas prior to known historic era admixtures (and hence must have reached fixation ca. 15,000 kya). It is absent from populations with Denisovan admixture (except to the extent of their Austronesian admixture). It is almost completely absent (except in Munda populations that arrived in the last few thousands years) in South Asia. A mutation that didn't exist 45,000 years ago has reached fixation ca. 15,000 years ago. Unless the effective size of the founding population is in the single digits, random founder effects involving selective neutral traits don't bring about that kind of total replacement in that time frame without a selective driver, particularly in the Upper Paleolithic where there is no large scale political organization. If the effective size of the entire Asian founding population is even in the high hundreds or low thousands the numbers just don't work for a random founder effect on an autosomal trait in a growing population that is settling virgin territory for the first few thousand years at least.The possibility of an immunological effect is quite real. EDAR governs, among other things, sweat gland density. Sweat glands each hold a lymph node. Lymph nodes are your body's warehouses of white blood cells and microphages. The possibility that more warehouses mean mean immune capacity is quite plausible.But, whatever the selective factor involved is, and we don't know for sure, to get its present distribution, the derived allelle of EDAR needed to be providing a 10% fitness advantage per generation for people who have it relative to people who have the ancestral version of this one gene, which is huge!

     
  22. Maju

    February 20, 2013 at 4:11 pm

    It's obvious that what I'm saying is just that: that the benefit of the "selection" is not obvious and the allele is concentrated in one specific populations, which would have the same "adaptive needs" as many other populations in which there is no such statistical signal at all. There is at least another very reasonable explanation for that and its name is founder effect.You dislike the concept of founder effects and there's where real problem lays, IMO.

     
  23. Maju

    February 20, 2013 at 4:27 pm

    But what is the benefit of the allele and why it has not spread to similar levels by means of introgression to other populations in contact with them? Why is it restricted to a geographically well defined population (NE Asians plus the Native American offshoot) and not widespread along a climate range or something like that across population barriers? Europeans for example have been in contact with this population since long ago (at least the Epipaleolithic judging from recent aDNA data) and live in a similar climatic zone, yet the allele has not spread in any significant manner. Elsewhere you mention that its presence is weak in SE Asia, another contact population (and surely ancestral to NE Asians): if the allele would be so desirable for non-climatic reasons, it would also have spread to them and it has not (not significantly). I understand that most of the ancestry of NE Asians and Native Americans comes from the same founder population, which migrated northwards from SE Asia, if there was a selective swap it seems more likely to me that it was mild (for the reasons mentioned above) and it affected the founder population rather than larger more recent ones, so it surely originated before the end of the LGM. As a side not, if you or someone has the paper, I'd appreciate if I could be sent a copy, if nothing else to peek on the graphs and figures in more detail (lialdalmiz[at]gmail[dot]com). Thanks in advance.

     
  24. Maju

    February 20, 2013 at 6:23 pm

    Update published based on the article and discussion at Razib's blog (includes map of frequencies).

     
  25. terryt

    February 21, 2013 at 7:00 am

    "Update published based on the article and discussion at Razib's blog (includes map of frequencies)". Thanks for drawing attention to that post. Extremely revealing, especially the maps. "An intriguing issue is also the lack of it in Europe, even among peoples of well-known Siberian/East Asian low-level admixture (Northern Russians)". But the map shows just one North European group so we cannot draw valid conclusions concerning that region. "I'm tentatively imagining some sort of 'racist selection' against the trait among those peoples" I don't think so. Look at the other map Razib posted. The gene is centred on where the Hwang Ho(Yellow River) emerges from the hills. Exactly the region where I have suggested that Y-DNA O spread from, and Y-DNA C. And presumably N. "It's obvious that what I'm saying is just that: that the benefit of the 'selection' is not obvious and the allele is concentrated in one specific populations, which would have the same 'adaptive needs' as many other populations in which there is no such statistical signal at all. There is at least another very reasonable explanation for that and its name is founder effect". That 'benefit of the selection' (whatever it was) occurred while the population was confined to its source region though, not during its expansion. The allele's expansion was not through 'adaptive needs' or introgression into neighbouring people, but through the huge expansion of the population containing the allele. That is something I have been trying to convince you of for years. "Elsewhere you mention that its presence is weak in SE Asia, another contact population (and surely ancestral to NE Asians)" In SE Asia the allele has been diluted by the presence of a pre-Mongoloid population. And it is extremely doubtful that the SE Asian contribution to NE Asia was very great. Just your belief that it is so. "I understand that most of the ancestry of NE Asians and Native Americans comes from the same founder population, which migrated northwards from SE Asia" But the allele expanded from around the middle reaches of the Yellow River, not from SE Asia. "But what is the benefit of the allele and why it has not spread to similar levels by means of introgression to other populations in contact with them? Why is it restricted to a geographically well defined population (NE Asians plus the Native American offshoot) and not widespread along a climate range or something like that across population barriers?" You should now know the answer to those questions. Of course I don't expect for a moment that you will agree. The obvious explanation doesn't fit your belief. "The thick hair East Asian variant might in this case be just the extreme variant of a more widespread Neanderthal introgression. Just food for thought". Unlikely because of its geographic distribution. However it could be a variant introduced to modern humans from an archaic population from somewhere within the Yellow River catchment.

     
  26. terryt

    February 21, 2013 at 7:14 am

    Some comments Razib made that I certainly find supportive of what I wrote above: "One thing to note is that the derived East Asian form of EDAR is found in Amerindian populations which certainly diverged from East Asians > 10,000 years before the present (more likely 15-20,000 years before the present). The two populations in West Eurasia where you find the derived East Asian EDAR variant are Hazaras and Uyghurs, both likely the products of recent admixture between East and West Eurasian populations. In Melanesia the EDAR frequency is correlated with Austronesian admixture. Not on the map, but also known, is that the Munda (Austro-Asiatic) tribal populations of South Asia also have low, but non-trivial, frequencies of East Asian EDAR. In this they are exceptional among South Asian groups without recent East Asian admixture. This lends credence to the idea that the Munda are descendants in part of Austro-Asiatic peoples intrusive from Southeast Asia, where most Austro-Asiatic languages are present". "I am perplexed why such an ancient allele, which is found in Amerindians, or Munda populations, is absent in Europeans who have putative East Eurasian admixture". The prortion of East Asian genetic mixture in Europe may be far lower than that in the other regions listed. "In addition to EDAR I’m thinking of the pigmentation loci, such as SLC24A5. I wouldn’t be surprised if there was something similar for the epicanthic fold". And possibly those genes too are from an archaic East Asian population. "If it is visible, and defines between populations differences, it is generally not genomically trivial. There’s usually a story underneath that difference". Not through founder effect or drift. "A climate adaptation is always a good bet. The problem I have with this hypothesis is that modern day gradients in the distribution of this allele are exactly the reverse of what one might expect in terms of adaptation to heat and humidity". Which supports the expansion of a population not introgression of the gene. Razib then launches into the very unlikely explanation of sexual selection.

     
  27. Maju

    February 21, 2013 at 7:51 am

    "But the map shows just one North European group so we cannot draw valid conclusions concerning that region". It's obviously North Russians, very likely the very used sample of Vologda, who are known to have levels of Siberian/East Asian ancestry comparable to those of Finns and other Uralic peoples of Europe. True that it'd be best if Finnic peoples and also West Siberian peoples were detailed, but nope. "The gene is centred on where the Hwang Ho(Yellow River) emerges from the hills. Exactly the region where I have suggested that Y-DNA O spread from, and Y-DNA C. And presumably N". That's not diversity from the allele but surely: an allele is generally defined by a single SNP, which can have no diversity value. It is surely some other sort of diversity (maybe based on the adjacent genetic segment?) and the label actually reads "Probablity Diversity". Also I thought you imagine all those lineages expanding from Mongolia or whatever.I withheld my opinion on this until I can read the paper and see what is it about exactly and in detail. "That 'benefit of the selection' (whatever it was) occurred while the population was confined to its source region though, not during its expansion".Strange to say the least that the benefit of selection stopped being important as soon as the population began expanding. I would call that a founder effect. Assuming your explanation as correct, if the initial fixation was caused by selection or random drift in a small population is extremely hard to discern and mostly irrelevant. If there was a selection sweep why would it lose its effectiveness or even, if ecologically determined, be selected against in other environments? That you say is not what they mean when they talk of selection sweep, clearly not. "In SE Asia the allele has been diluted by the presence of a pre-Mongoloid population".Then why is it as common as in China, Siberia, Japan (excepting in Cambodia it seems). In South China, where your alleged pre-Mongoloids would also have been dominant once they have very high levels, even fixation, so do in Burma. The frequency maps are very compatible with a South to North expansion model in which founder effects (and maybe mild selective pressure of some sort?) would have increased the frequency. "You should now know the answer to those questions".I do not. Otherwise why would I ask them? I repeat:But what is the benefit of the allele and why it has not spread to similar levels by means of introgression to other populations in contact with them? Why is it restricted to a geographically well defined population (NE Asians plus the Native American offshoot) and not widespread along a climate range or something like that across population barriers?"Unlikely because of its geographic distribution".Hmmm… Let's take another look at the map: the dominance of EDAR alleles follows continental/"racial" patterns. The South-West Eurasian region is dominated by the dark blue allele, while Africa is dominated by one or two light blue ones (not sure because I don't have access to the original map), while Melanesia is dominated by a middle blue type. However only the red allele is novel out of Africa, the others existing at lower frequencies in Africa. This pattern seems to me a product of founder effects at the beginnings of each population's expansion. The East Asian variant may be novel mutation or Neanderthal introgression but actually all the others look original from Africa, i.e. ancestral Homo sapiens.

     
  28. Maju

    February 21, 2013 at 7:56 am

    "The prortion of East Asian genetic mixture in Europe may be far lower than that in the other regions listed". It is important enough (many different ADMIXTURE/STRUCTURE studies show it) for the nearly fixated "red allele" to show up at some 10% levels or at least 5% among Northern Russians. But not even a 1% line!The rest I agree that may not have any relevant East Asian admixture, contrary to what some recent MixMapper-based studies claimed."Which supports the expansion of a population"…It does not. If there was a climatic adaption, then the allele would have been selected against in other ecosystems and also introgressed into populations living in similar ones to the favorable case. We see nothing of that. What we see fits best with a quasi-neutral allele favored only by the population dynamics of that continental region.

     
  29. terryt

    February 22, 2013 at 1:38 am

    "What we see fits best with a quasi-neutral allele favored only by the population dynamics of that continental region". Certainly so. The allele was carried from its region of origin in the form of a population expansion mildly, if at all, advantaged by the possession of the genetic variation. But the variation itself had almost certainly originally come to dominance in its region of origin as an advantageous gentic adaptaion, whether it arrived through founder effect or as introgression from an archaic Homo species. "Strange to say the least that the benefit of selection stopped being important as soon as the population began expanding". Surely it is obvious, even to you, that the climatic adaptation involved had almost nothing at all to do with the expansion of the gene. The gene was not 'responsible' for the expansion. The gene was carried into regions that were obviously different from the conditions for which it evolved. "It does not. If there was a climatic adaption, then the allele would have been selected against in other ecosystems and also introgressed into populations living in similar ones to the favorable case". The fact it wasn't selected against in dissimilar habitats, and wasn't selected for in similar habitats, surely further supports the fact that the expansion was not assisted in any meaningful way by the mutation. "If there was a selection sweep why would it lose its effectiveness or even, if ecologically determined, be selected against in other environments?" Again you're letting your beliefs blind you to the obvious. "I repeat: But what is the benefit of the allele and why it has not spread to similar levels by means of introgression to other populations in contact with them? Why is it restricted to a geographically well defined population (NE Asians plus the Native American offshoot) and not widespread along a climate range or something like that across population barriers?" I repeat: because its greater expansion had very little to do with the mutation itself. "Then why is it as common as in China, Siberia, Japan (excepting in Cambodia it seems)". What has Cambodia to do with Japan? I'm prepared to accept its expansion through those northern regions was aided by the genetic adaptation to the climate. "That's not diversity from the allele but surely" No, it represents the spread of the allele from its point of origin. "the label actually reads 'Probablity Diversity'". Yes, of the heterozygosity. The dark red is 100% homozygous for the gene in question. The lighter the red the more the other mutation in the population as it moves towards 0% homozygous for the alternative gene. "Also I thought you imagine all those lineages expanding from Mongolia or whatever". Ahh. Maju. Check your atlas. 'Where the Hwang Ho(Yellow River) emerges from the hills' is within spitting distance of the border with Inner Mongolia. "In South China, where your alleged pre-Mongoloids would also have been dominant once they have very high levels, even fixation, so do in Burma". The Y-DNA O haplogroup is dominant through the whole region. We would surely expect a high level of the gene, although considerably lower than the level further north. "The frequency maps are very compatible with a South to North expansion model in which founder effects (and maybe mild selective pressure of some sort?) would have increased the frequency". You really have to use your imagination considerably though. And why postualte 'founder effects' just to make the evidence fit what you want it to?

     
  30. Maju

    February 22, 2013 at 12:16 pm

    "I repeat: because its greater expansion had very little to do with the mutation itself".For that very reason we cannot talk of "selective sweep". The correct term is "founder effect". We agree in the process but you confuse the correct term to use. http://en.wikipedia.org/wiki/Selective_sweepWhether prior to that founder effect, there was a very localized selective sweep or the quasi-fixation was caused by random drift is not important (nor can probably be discerned easily)."Yes, of the heterozygosity. The dark red is 100% homozygous for the gene in question. The lighter the red the more the other mutation in the population as it moves towards 0% homozygous for the alternative gene". It cannot be that way. Just compare your claims with the allele frequency map. "The Y-DNA O haplogroup is dominant through the whole region. We would surely expect a high level of the gene, although considerably lower than the level further north". Look at diversity, even better: to phylogenetically hierarchical structured diversity (or basal diversity to simplify). Very often regions of great frequency are not the most basally diverse, indicating a founder effect after migration from the most basally diverse region. For example R1b in West Europe is derived from R1b in West Asia, where it is less common but more basally diverse. Change R1b with O, West Europe with NE Asia and West Asia with SE Asia and you have almost the same scenario translocated to the Far East.

     
  31. terryt

    February 22, 2013 at 9:42 pm

    "For that very reason we cannot talk of 'selective sweep'. The correct term is 'founder effect'. We agree in the process but you confuse the correct term to use". We have a 'selective sweep' during the establishment of the gene in the founder population. We then have a population spread that carried the gene into regions beyond that founder population. Perhaps we could refer to that later expansion as spreading the gene through 'founder effect' but there were a large number of them. They outnumbered (or at least came to) any original population in the regions into which they expanded except, of course America and presumably northern Siberia. Can we call such an expansion a 'founder effect'? "Whether prior to that founder effect, there was a very localized selective sweep or the quasi-fixation was caused by random drift is not important (nor can probably be discerned easily)". 'Quasi-fixation'? One hundred percent fixation in the central population. Random drift is unlikely to explain that level. Selective sweep in relation to climate adaptation is a far more reasonable assumption. "It cannot be that way. Just compare your claims with the allele frequency map". The two maps deal with separate issues. The second is an attempt to calculate where the gene first entered the modern human population. Surely you're not claiming that the gene reached its level in the American population through a selective sweep. It presumably made up a reasonable proportion of genes in the first people into America. The element of the population with it have their ultimate origin within the region shown in Razib's second map. "Look at diversity, even better: to phylogenetically hierarchical structured diversity (or basal diversity to simplify)". I have. And there is no way O is an original SE Asian haplogroup. "For example R1b in West Europe is derived from R1b in West Asia, where it is less common but more basally diverse". Exactly.

     
  32. Maju

    February 22, 2013 at 10:20 pm

    "We have a 'selective sweep' during the establishment of the gene in the founder population".No, we do not. You hypothesize that such is the case but you fail to demonstrate it in any way. And, in any case, that is not what the authors mean. "One hundred percent fixation in the central population".I have no reason to believe that such population is the origin. You arbitrarily just decided so but that's probably not the case." The second is an attempt to calculate where the gene first entered the modern human population".Have you read the paper? Neither you nor I know what that map means, you are just making things up as you go. "Surely you're not claiming that the gene reached its level in the American population through a selective sweep".Not me: the authors of this paper are saying that.

     
  33. terryt

    February 22, 2013 at 10:26 pm

    "Change R1b with O, West Europe with NE Asia and West Asia with SE Asia and you have almost the same scenario translocated to the Far East". Possibly. So let's examine the distribution of O using your belief in basal diversity mutation tails but ignoring molecular-clockology. In some unknown region, or while wandering, NO accumulated a string of at least 6 mutations before O-M175 wents its own way. O then developed a string of at least 4 mutations before members of it formed O1-MSY2.2, O2-P31 and O3-M122. Presumably the three haplogroups each developed in separate regions within O-M175's geographic range. O1 seems to have quickly formed O1a-M119, and then O1a1-P203 and O1a2-M110 formed within O1a-M119's geographic region. We can deduce a fair bit about these two haplogroups' expansion over the last few thousand years. The two were almost certainly involved in the Tai-Kradai/Austronesian language expansion. That expansion is not Paleolithic. A recent paper on Chinese Neolithic haplogroups from the three Gorges region placed O1 at that time at the mouth of the Yangtze. Unlike O1 O2-P31 accumulated at least 3 mutations before O2a-PK4 and O2b -M176 formed. Again O2a and O2b presumably developed within the margin of O2-P31' geographic range. O2a look likely to have been involved in the expansion of the Hmong-Mien and the Austro-Asiatic language expansion, but in several regions the local inhabitants later adopted either Tai-Kradai or Austronesian languages. O2a1a carried Munda into India and even reached the Pashtun. Presumably it is responsible for introducing the EDARV370A allele into India. O2b is the northern version of O2. And let's not forget that its inclusion shifts O2's centroid fairly well north. In fact a recent paper made a convincing case for O2a to have spread south from the Three Gorges region of the Yangtze. That region is where the Yangtze emerges from the hills. A similar environment to where the EDARV370A allele emerged a little to the north. So O3-M122. It looks to have remained in the same place for a considerable time, perhaps where it had first coalesced from O-M175. Perhaps even where O-M175 itself had first coalesced. After at least 7 mutations O3a1-L127, O3a2-P201, O3a3-M300 and O3a4-M333 formed. The above mentioned paper presented a case for O3 to have developed upstream from the Three Gorges. That makes sense. Members of the haplogroup seem to have been involved with the (perhaps periodic) expansion of the Sino-Tibetan languages and the Chinese Neolithic. The last two of the four O3 haplogroups have just a single mutation listed. I have no idea where O3a4-M333 has been found. Although O3a3 is associated with Sino-Tibetan speakers it has been found in Japan. O3a1 developed a tail of at least 3 mutations before members of the haplogroup formed O3a1a-M121, O3a1b-M164 and O3a1c–002611. The last was the only haplogroup to have anything that could realistically be called 'an expansion'. It is spread fairly evenly through China, making up 20% of East asian Y-DNA. Its expansion certainly looks Neolithic. To O3a2-P201. It is the Y-DNA haplogroup with the widest expansion, with members of O3a2c probably associated with the Austronesian/Polynesian expansion into the Pacific. But th ehaplogroup is most closely associated with populations speaking Sino-Tibetan languages and makes up the majority of Chinese Y-DNA. O3a2b is scattered through China although possibly concentrated in South China. That is hardly convincing evidence for the whole O Y-DNA haplogroup having originated in South China let alone SE Asia.

     
  34. terryt

    February 22, 2013 at 10:39 pm

    "No, we do not. You hypothesize that such is the case but you fail to demonstrate it in any way. And, in any case, that is not what the authors mean". Of course you don't know what the authors mean. To accept what they suggest conflicts with your belief. The authors do use the term 'selective pressure'. "I have no reason to believe that such population is the origin". Possibly not. But it makes sense. Again the only reason you refuse to accept it is that such an acceptance conflicts with your belief. Arguing with you is certainly like arguing with a fundamentalist preacher. "Have you read the paper? Neither you nor I know what that map means, you are just making things up as you go". Neither of us has read the paper but Razib seems to have access to more than we do. He obtained the map from somewhere and he says it is an attempt to find the region from which the EDAR mutation expanded from in the last 30,000 years. Why didn't you read what he wrote? "Not me: the authors of this paper are saying that". No they're not. Read what Razib wrote.

     
  35. Maju

    February 22, 2013 at 10:45 pm

    You cannot count SNPs at ISOGG and pretend to measure something with such a count. The Y chromosome is very large and AFAIK no haplogroup has ever been counted in all its length (it will happen, soon maybe, but not yet). That's a method that so far can only be used with mtDNA (and with caution in the case of less well-studied clades). The only thing you can count is STR diversity and haplogroup diversity (the latter being more important but not always sufficiently understood). O3 and O1 originate in SE Asia (O1 is obvious and for O3 there is Hong Shi 2005), O2 is ambiguous, N originates in South China… Hence NO originated in SE Asia and so did O and N (South China). That's all there is to this issue.

     
  36. Ebizur

    February 23, 2013 at 1:29 am

    terryt wrote,"Unlike O1 O2-P31 accumulated at least 3 mutations before O2a-PK4 and O2b -M176 formed. Again O2a and O2b presumably developed within the margin of O2-P31' geographic range. O2a look likely to have been involved in the expansion of the Hmong-Mien and the Austro-Asiatic language expansion, but in several regions the local inhabitants later adopted either Tai-Kradai or Austronesian languages. O2a1a carried Munda into India and even reached the Pashtun. Presumably it is responsible for introducing the EDARV370A allele into India. O2b is the northern version of O2. And let's not forget that its inclusion shifts O2's centroid fairly well north. In fact a recent paper made a convincing case for O2a to have spread south from the Three Gorges region of the Yangtze. That region is where the Yangtze emerges from the hills. A similar environment to where the EDARV370A allele emerged a little to the north."Since the publication of the paper by Shi Yan, Chuan-Chao Wang, Hui Li et al., "An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4" (European Journal of Human Genetics (2011) 19, 1013–1015), the PK4 mutation has been regarded as a marker of a newly defined Haplogroup O2a ("pre-M95"), with the former O2a-M95 being demoted to O2a1-M95. The PK4-carrying Y-chromosomes in the Tharus, Pashtuns, and some other populations of South Asia were published before the aforementioned update to the phylogenetic tree, and they belong toO2a1a-M88. Munda Y-DNA is predominantly O2a1*-M95(xM88), with the remainder being comprised of typically South Asian clades (R-M17, H-M82, etc.); no published sample of Munda Y-DNA has included any representatives of O2a1a-M88.O2a1a-M88 is rather a modern Southeast Asian clade, found especially in Vietnamese and populations of southern China (including Hans). I do not have a good explanation for its marginal presence in Indo-Iranian-speaking populations of South Asia, but until M88 is identified in a sample of Munda speakers, a hypothesis linking it to a Munda intrusion into South Asia is untenable.

     
  37. terryt

    February 23, 2013 at 1:59 am

    "Munda Y-DNA is predominantly O2a1*-M95(xM88) … no published sample of Munda Y-DNA has included any representatives of O2a1a-M88". Thanks for that clarification. I assumed that just a single clade of O2a had made it into and beyond India. "until M88 is identified in a sample of Munda speakers, a hypothesis linking it to a Munda intrusion into South Asia is untenable". That is very interesting. "You cannot count SNPs at ISOGG and pretend to measure something with such a count. The Y chromosome is very large and AFAIK no haplogroup has ever been counted in all its length" I did say 'at least' so many mutations. "Have you read the paper? Neither you nor I know what that map means, you are just making things up as you go". This is what Razib wrote regarding the second map: "The second figure shows the inferred region from which the East Asian EDAR haplotype expanded over the past 30,000 years. The authors utilized millions of forward simulations with a host of parameters to model the expansion of EDAR, so that it fit the distribution pattern that is realized (see the supplements here for the parmeters). To make a long story short they infer that there was one mutation on the order of ~30,000 years before the present, and that it swept up in frequency driven by selection coefficients on the order of ~0.10 (10% increase relative fitness, which is incredibly powerful!). This is on the extreme end of selective sweeps" I hope that helps you understand the situation in East Asia, but I'm sure it won't. "O3 and O1 originate in SE Asia" Only in your opinion. There is no evidence that they did so. In fact it's difficult to make such a case with the updated phylogeny so quoting a 2005 paper cannot be used as 'evidence'. In fact I'm sure you have blogged on that paper and I tried to point out the problems with it at the time. If you insist I will go through it once more for your benefit. "N originates in South China…" How on earth do you come to that conclusion? I presume you're basing it on the presence of some downstream N clade that has a very minor presence in SE Asia. "That's all there is to this issue'. If you're determined to ignore the evidence I suppose that statement is correct.

     
  38. terryt

    February 23, 2013 at 2:47 am

    "O1 is obvious and for O3 there is Hong Shi 2005)" OK. Let's look at the paper. An early statement: "In East Asian populations, there are three regionally distributed (East Asian–specific) Y-chromosome haplogroups under the M175 lineage (fig. 1)—O3-M122, O2-M95, and O1-M119—together accounting for 57% of the Y chromosomes in East Asian populations (table 1)". So their O2 excludes O2b, the northern version of O2. Note Ebizur's comments above. And the paper shows O3a branching into multiple separate basal clades, but we now know that O3 forms just four basal clades. Their O3a1, O3a2 and O3a4 form one of those clades as do their O3a3, O3a4 and O3a5. O3a6 and O3a7 are the only basal clades remaining from the phylogeny in the paper. So that takes care of a large proportion of the 'southern diversity' they claim for a start. Another thing to notice from their map is that the majority of groups they studied were from southern China. And they admit as much: "Most of the populations sampled were from southern and southwestern China, where ~80% of the Chinese ethnic populations live" So they ignore the majority of the Chinese population. Well done. Surely that would bias their data. Or had they decided in advance what they wanted to find? "The Yangtze River was used as the geographic border to separate the SEAS and NEAS". The Yangtze River is hardly a natural boundary, especially for any Neolithic flows. We actually know that it was a region of early presence of the Chinese Neolithic and source of expansion in fact. "In the SEAS, there are 14 Tibeto-Burman–speaking populations with a recorded history of migration from northern China ~3,000 years ago (Wang 1994). The three Altai-speaking populations in Yunnan (southwestern China) were recent immigrants from northern China, <1,000 years ago" They actually eliminate these populations from their calculations, thus adding further bias to their conclusions: "To remove the influence of relatively recent population admixture, we constructed the STR network excluding the Tibeto-Burman, Altaic, Hmong-Mien, and southern Han populations". And they say: "In general, the distribution of the O3-M122 haplotypes did not show distinctive divergence between southern and northern populations, with all the major subhaplogroups shared between them—except for O3-M7, which was observed only in the southern populations and therefore indicates a recent common ancestry of the O3-M122 lineage in East Asia". Hmmm … I doubt you would agree with that very last bit! And then: "Using the STR data, we calculated the gene diversities; no significant differences were observed between SEAS and NEAS or among different language groups (data not shown). The AMOVA analysis did not show significant between-group divergence either" 'No significant difference'? And: "However, the MDS analysis showed that the NEAS are closely related by clustering together, whereas the SEAS showed relatively loose connections with larger variance, indicating that SEAS are genetically more polymorphic than are NEAS" Isn't that what we would expect if the whole O3 haplogroup had originated in a small region somewhat to the north and then expanded sparodically into the southern hills? "the O3-M122 lineages were probably dominant in the population involved in the initial northward migration; therefore, no obvious bottleneck occurred for the O3-M122 lineage, in contrast with the skewed distribution of the O2-M95 and O1-M119 lineages" Now that should surely have put them on their guard against making too many rapid conclusions. Their claim doesn't actually make sense. I would suggest that it was the southward movement of O3 that was not subject to bottlenecks.

     
  39. Maju

    February 23, 2013 at 11:42 am

    It does not make any sense that the only sample with the novel EDAR variant is fully fixated is the origin… unless you presuppose that a massive population replacement must have happened. You're biting your tail once again, Terry.

     
  40. Maju

    February 23, 2013 at 11:54 am

    [Terry citing Razib:] "To make a long story short they infer that there was one mutation on the order of ~30,000 years before the present, and that it swept up in frequency driven by selection coefficients on the order of ~0.10 (10% increase relative fitness, which is incredibly powerful!)".Precisely. That has nothing to do with what you say. The authors claim that allele expanded because it gave an extremely useful survival kit, 'an offer no one could reject', so to say. That is a selective sweep! But of course the authors fail to convince (neither Razib nor me at least) very especially because none of the traits produced seems that kind life-or-death useful at all. We are not in the survival kit department of biology here but in the accessories one, which may make people look different but gives no or pretty trivial survival edges instead."I hope that helps you understand the situation in East Asia, but I'm sure it won't". I understand it reasonably well. I would hope instead that some of our conversations would help you to understand that science demands humility and self-criticism but, sadly, I'm pretty sure by now that you won't ever incorporate these traits into your personality much less your analytical thought.

     
  41. Maju

    February 23, 2013 at 11:58 am

    "Isn't that what we would expect if the whole O3 haplogroup had originated in a small region somewhat to the north and then expanded sparodically into the southern hills?"No. It indicates specific founder effects in the North.

     
  42. terryt

    February 24, 2013 at 12:52 am

    "No. It indicates specific founder effects in the North". To me the evidence indicates founder effects from the north. You appear to have conveniently forgotten this paper: http://comonca.org.cn/lh/doc/A37.pdfRemember though that their O2 is just O2a. And O3* is O3(xO3a2b,O2a2c1), O3d is O3a2b, and O3e is O3a2c. "It does not make any sense that the only sample with the novel EDAR variant is fully fixated is the origin…" Surely that is the most likely scenario. Why would it not be, and how could it not be? The only other option is that it introgressed from another population where it may have formed somewhere within that population's geographic range. But the implies breeding with an Archaic population. The gene has to be fixated somewhere before it can expand, especially if it is recessive. "unless you presuppose that a massive population replacement must have happened. You're biting your tail once again, Terry". And this paper shows that such replacement is extremely likely to have occurred. The real problem arises for you because you assume a huge Paleolithic population in South China, but I believe you are very much mistaken in that assumption. "The authors claim that allele expanded because it gave an extremely useful survival kit, 'an offer no one could reject', so to say". But we both know very well that the later stages of the expansion did not involve any advantage at all from the gene itself. So when they say, 'there was one mutation on the order of ~30,000 years before the present, and that it swept up in frequency driven by selection coefficients on the order of ~0.10 (10% increase relative fitness, which is incredibly powerful!)' they're almost certainly talking about the original selective sweep within the region shown on the second map. If that was not the authors' intention why would they bother with the second map at all. They must have compiled it to demonstrate something, surely. But of course for you a consideration of that map would require a re-evaluation of your belief, and we can't possibly have that, so you are forced to ignore it. "the authors fail to convince (neither Razib nor me at least) very especially because none of the traits produced seems that kind life-or-death useful at all". Because you misunderstand what they're saying. You assume the gene spread through a static population, but that is not the case. Much of its expansion was by migration, and you are well aware of that fact but it doesn't fit your belief when it comes to South China and SE Asia. How could a 'selective sweep' have occurred in America when there was no-one there until the population that already had the gene arrived? I'm sure the authors are aware of that fact but you are determined to ignore it. "I understand it reasonably well". You've just proved you don't understand it at all.

     
  43. terryt

    February 24, 2013 at 3:34 am

    "But of course the authors fail to convince (neither Razib nor me at least) very especially" The difference between you and Razib is that he says: "There is a weak point in one or more of my assumptions". Now you would never admit that. I have never noticed any adherence to the 'science demands humility and self-criticism' on your part. But presumably his weak point is similar to your own so hopefully you will soon be able to explain things to him. He does say: "If it is visible, and defines between populations differences, it is generally not genomically trivial. There’s usually a story underneath that difference". You refuse to even consider the possibility that there is a story underneath the regional human difference, just random drift, bottlenecks and founder effects. "The two populations in West Eurasia where you find the derived East Asian EDAR variant are Hazaras and Uyghurs, both likely the products of recent admixture between East and West Eurasian populations. In Melanesia the EDAR frequency is correlated with Austronesian admixture". So again, unlike you, he accepts that some of the gene's distribution is a result of population expansion rather than of a selective sweep. "And yet one thing that jumps out at me is that there is no East Asian EDAR in European populations, even in Russians. I am a bit confused by this result, because of the possibility of Siberian-affiliated population admixture with Europeans within the last 10,000 years, as adduced by several researchers" This is not as much of a problem as either you or he makes of it. Of course any admixed population will not carry the same representative sample of genes from both parent populations. "Much of the elegance and power of the paper applies to the discussion section as well, but to be frank this is where things start falling apart for me". So, unlike you, he accepts the body of the research. It is just some of the conclusions the authors propose that he disagrees with. "A climate adaptation is always a good bet. The problem I have with this hypothesis is that modern day gradients in the distribution of this allele are exactly the reverse of what one might expect in terms of adaptation to heat and humidity". I agree 100% with Razib here. The authors themselves are off target with their explanation of how the gene provided a selective advantage. "the derived EDAR mutant is found in high frequencies went through the incredible cold of the Last Glacial Maximum, and groups like the Yakuts are known to have cold adaptations today. Not only that, but the Amerindians from the arctic to the tropics all exhibit a cold adapted body morphology" The evidence actually suggests that adaptation to seasonal cold is a much more likely explanation for the selective advantage. The 'sexual selection' hypotheses tell us more about the people proposing the hypothesis than about any selective sweep. As Razib says: "The main question on my mind is how seriously prominent population geneticists such as Joshua Akey actually take sexual selection to be as a force driving variation and selection in human populations. It seems that quite often sexual selection is presented as a deus ex machina. A phenomenon which can rescue our confusion as to the origins of a particular suite of traits".

     
  44. Ebizur

    February 24, 2013 at 4:08 am

    Erratum:I have reviewed the original sources, and it appears that the four Tharus from Morang District of southeastern Nepal and the single adivasi from Andhra Pradesh reported to be O-PK4 by Fornarino et al. 2009 have been assumed to belong to O-M88 in accordance with the version of the Y-DNA phylogenetic tree that had been accepted at that time. These five individuals were found to be positive for M95, so they certainly do belong to O2a1-M95. However, their status regarding O2a1a-M88/M111 is undetermined.On the other hand, the four Pathan individuals carrying PK4 belong to a subtribe (AusoKhel) of one of the major Pathan tribes (Yousafzai) from the Dir area in the North West Frontier Province (NWFP) of Pakistan, and these four individuals have been found to be positive for M95, M88, and M111 in addition to PK4. This is the source of the original misplacement of PK4 downstream of M88/M111.Thus, it is certain that O2a1a-M88/M111 is found in at least one tribe of Pashtuns in the northwestern extremity of South Asia, but this subclade has not been confirmed in any sample that I have seen from the eastern parts of the Subcontinent. Kumar et al. (2007) did not find this subclade even in their samples of Khasis and Garos from Meghalaya in Northeast India.

     
  45. Ebizur

    February 24, 2013 at 4:34 am

    O2a1a-M88/M11120/29 = 69.0% Xinhmul (Laos/Khmuic?)15/34 = 44.1% Hani (Yunnan/Loloish)12/39 = 30.8% Suy (Laos/West Katuic)23/76 = 30.3% Kinh (Hanoi, Vietnam/Vietic)9/31 = 29.0% Lowland Yao (NE Guangxi/Mienic)10/37 = 27.0% Kataang (Laos/Ta'Oi–Kriang branch of Katuic)5/23 = 21.7% Zhuang (Yongbei, C Guangxi/Tai branch of Kradai)8/37 = 21.6% Zaomin (N Guangdong/Mienic)6/35 = 17.1% Buyi (Guizhou-NW Guangxi/Tai branch of Kradai)5/30 = 16.7% Alak (Laos/Central Bahnaric)6/38 = 15.8% Aheu (Laos/Vietic)5/36 = 13.9% Bunu (NW Guangxi/Hmongic)4/31 = 12.9% Southern Mien (SW Guangxi/Mienic)6/50 = 12.0% So (Laos/West Katuic)3/25 = 12.0% Lao (Luang Prabang, Laos/Tai branch of Kradai)4/34 = 11.8% Han (Chengdu, Sichuan/Sinitic)2/19 = 10.5% Zhuang (Yongnan, C Guangxi/Tai branch of Kradai)1/11 = 9.1% Top Board Mien1/11 = 9.1% Thin Board Mien5/59 = 8.5% Cham (Binh Thuan, Vietnam/Malayo-Polynesian branch of Austronesian)4/50 = 8.0% Mal (Laos/Khmuic)3/39 = 7.7% Zhuang (Hongshuihe, C Guangxi/Tai branch of Kradai)3/41 = 7.3% Lowland Kimmun (NE Guangxi/Mienic)12/166 = 7.2% Zhuang total (Guangxi & vicinity/Tai branch of Kradai)1/15 = 6.7% Zhuang (Shangsi, SW Guangxi/Tai branch of Kradai)2/33 = 6.1% Northern Mien (NW Guangxi/Mienic)3/51 = 5.9% Hmong Daw (Laos/Hmongic)3/51 = 5.9% Khmu (Laos/Khmuic)1/17 = 5.9% Thai (Northern Thailand/Tai branch of Kradai)1/18 = 5.6% Cambodia & Laos (Underhill et al. 2000)1/19 = 5.3% Flower-head Mien (SW Guangxi/Mienic)2/39 = 5.1% Taiwan (aborigines) (Taiwan/Austronesian)5/100 = 5.0% Miao (Hunan/Hmongic)1/20 = 5.0% Mountain Straggler Mien (Hunan/Mienic)1/20 = 5.0% China (Underhill et al. 2000)1/21 = 4.8% Zhuang (Guibei, NE Guangxi/Tai branch of Kradai)1/22 = 4.5% Banjarmasin (Borneo, Indonesia/Malayo-Polynesian branch of Austronesian)1/28 = 3.6% Bo (Laos/Vietic)1/32 = 3.1% Brau (Laos/West Bahnaric)2/65 = 3.1% Kota Kinabalu (Borneo, Malaysia/Malayo-Polynesian branch of Austronesian)1/33 = 3.0% Qiang (Sichuan/Qiangic)1/34 = 2.9% Li (Hainan/Hlai branch of Kradai)1/35 = 2.9% Yao (Liannan, Guangdong/Mienic)1/35 = 2.9% Talieng (Laos/Central Bahnaric)1/41 = 2.4% Native Mien (NE Guangxi/Mienic)1/49 = 2.0% Miao (Guizhou/Hmongic)1/50 = 2.0% Bai (Dali, Yunnan/Tibeto-Burman? Sinitic?)1/50 = 2.0% Laven (Laos/West Bahnaric)1/50 = 2.0% Oy (Laos/West Bahnaric)2/160 = 1.3% Han (Wuhan, Hubei/Sinitic)O2a1a-M88/M111 appears to be distributed geographically rather than ethnically, with highest concentration in a contiguous area centered on Guangxi Province of southern China. Frequencies of this haplogroup are high in most of Guangxi, in southern Yunnan (judging from the Hani), and in populations of the neighboring countries of Vietnam and Laos, pretty much regardless of ethnolinguistic affiliation. The frequency gradually fades out into Thailand, northern Yunnan, Sichuan, Guizhou, Hunan, Hubei, Guangdong, Hainan, Borneo, Taiwan, etc. Burma and Bangladesh are large blanks in my knowledge of haplogroup distributions, but the apparent total lack of O2a1a-M88/M111 in Nepal, Tibet, and (at least most parts of) Northeast India makes me suspect that this haplogroup probably does not spread much to the west of Shan-inhabited areas of Burma.

     
  46. Maju

    February 24, 2013 at 11:22 am

    Why don't you write a blog post at your blog with all you "know" about the origins of O? Seriously: it is infinitely more efficient than once and again here and there writing everything out from the blue. Just a link and a lot of work you don't have to do anymore.I personally find your comments so long and combative (most often about the wrong things and with the wrong evidence) that I'm losing interest. You don't even seem to read and then reply anymore but you begin replying (confronting) as soon as you read the first sentence or almost.The result are extremely and unnecessarily lengthy comments. Half of them empty personal accusations.

     
  47. Maju

    February 24, 2013 at 11:34 am

    Hui Li 2007 is not too relevant here by the way, we see a lot of O3, still more diverse towards the South and we know nothing about other locations, notably Indochina, Sundaland… but also within modern China the blanks are huge. It does suggest (awaiting more data) that the coastal populations of around Shanghai have been largely replaced from people from maybe Hunan (SE Asian -i.e. "not NE Asian"- province of China distinguished for being the origin of the Neolithic and birthplace of Mao) or elsewhere. This might have also been the case with the people of the Yellow River(?? – they were not 02 in any case) but it says nothing at all about any migration southwards and it specifically seems to deny a Yellow River origin for any outstanding migration. As for the rest, more than enough. You should have very clear my viewpoint by now.

     
  48. Maju

    February 24, 2013 at 11:41 am

    "This is not as much of a problem as either you or he makes of it".I borrowed the idea from David "Polako" (a comment at GNXP and later also at his blog Eurogenes). Razib also sees it as a problem. Both believed the results produced by MixMapper (but I did not). "Of course any admixed population will not carry the same representative sample of genes from both parent populations". It should carry them in approximately equal apportions. Something is wrong here: either West Siberians lack the allele or there was some sort of "racist selection", there's no other reasonable explanation. Just stating something, as you do here (and do too often) does not make it true.

     
  49. Maju

    February 24, 2013 at 11:45 am

    This is all very interesting, generally speaking, Ebizur. But, honestly, I'm not even sure anymore (or even to begin with) why O2a1a is relevant to this debate. Could you explain?

     
  50. Ebizur

    February 24, 2013 at 1:50 pm

    It is only relevant in a very tangential manner (if at all), which was my original point. If you review my comments in this thread, you should see that I started posting in response to the following comment by terryt:"Unlike O1 O2-P31 accumulated at least 3 mutations before O2a-PK4 and O2b -M176 formed. Again O2a and O2b presumably developed within the margin of O2-P31' geographic range. O2a look likely to have been involved in the expansion of the Hmong-Mien and the Austro-Asiatic language expansion, but in several regions the local inhabitants later adopted either Tai-Kradai or Austronesian languages. O2a1a carried Munda into India and even reached the Pashtun. Presumably it is responsible for introducing the EDARV370A allele into India. O2b is the northern version of O2. And let's not forget that its inclusion shifts O2's centroid fairly well north. In fact a recent paper made a convincing case for O2a to have spread south from the Three Gorges region of the Yangtze. That region is where the Yangtze emerges from the hills. A similar environment to where the EDARV370A allele emerged a little to the north."I was refuting terryt's hypothesis of a connection among Y-DNA haplogroup O2a1a-M88, Munda languages, and the presence of the derived EDAR allele in mainstream populations of South Asia (e.g. Gujaratis) at very low frequencies. It is still possible that the people who have introduced the ancestral form(s) of the Munda languages to India may have been responsible for introducing some (or all) of the derived EDAR allele that is marginally found there, but terryt's attempt to additionally link Y-DNA haplogroup O2a1a-M88 to this hypothetical Proto-Munda expansion into India is unfounded, since O2a1a-M88 has not beenfound in speakers of Munda languages nor in any other population of India as far as I know. In the greater South Asian region, O2a1a-M88 seems to have been confirmed only in a certain tribe of Pashtuns who presently inhabit an area in the northwest of Pakistan, with Chitral to the north and Kunar Province of Afghanistan to the west.

     

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