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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.

 

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

  1. Maju

    February 24, 2013 at 4:29 pm

    Ah, alright. Thanks for the explanation.

     
  2. terryt

    February 25, 2013 at 4:33 am

    "these four individuals have been found to be positive for M95, M88, and M111 in addition to PK4". Thaks for that information. I note the four Tharus from Morang District of southeastern Nepal and the single adivasi from Andhra Pradesh may belong to that haplogroup but I presume the Munda O2a definitely does not. Is that still so? "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" However O2a may have introduced both the haplogroup and the language. "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". But we know there has been considerable language shuffling in the region. Tai-Kradai and the Sino-Tibetan languages presumably overly a substrate of Austro-Asiatic and Hmong-Mien languages. Hmong-Mien languages are discontinuously distributed suggesting they are remnants of a once more widely-spoken language group: http://en.wikipedia.org/wiki/Hmong%E2%80%93Mien_languagesAnd Wiki even says: "Early linguistic classifications placed the Hmong–Mien languages in the Sino-Tibetan family, where they remain in many Chinese classifications, but the current consensus among Western linguists is that they constitute a family of their own. The family is believed to have had its origins in central-southern China. The current area of greatest agreement is that the languages appeared in the region between the Yangtze and Mekong rivers, but there is reason to believe that speakers migrated there from further north with the expansion of the Han Chinese". And Austro-Asiatic/Mon-Kmer languages also have a discontinuous distribution: http://en.wikipedia.org/wiki/Austroasiatic_languagesI notice that Pakanic looks to be found in Guangxi Province of southern China. It seems not to be a root Mon-Kmoer languge although there does seem to be disagreement as to its position. http://en.wikipedia.org/wiki/Khasi%E2%80%93Khmuic_languages"However, Sidwell (2009, 2011) notes that Khmuic and Pakanic (or at least Mangic) appear to be independent branches, and that the only valid connection is Khasi–Palaungic.The extent of the recently described Pakanic branch is contested, with some including the Mangic languages and others placing those in Palaungic".

     
  3. terryt

    February 25, 2013 at 4:56 am

    "I personally find your comments so long and combative" My comments are combative because you're absolutely committed to a particular belief, so much so that you're thoroughly inconsistent as to how you interpret data. And when the data conflicts with your belief you simply dismiss it. An example of the latter approach: "Both believed the results produced by MixMapper (but I did not)". Yes. You refuse to believe it because to do so would require you to seriously alter your belief: that haplogroups have not shifted since the Upper Paleolithic. An example of your altering your interpretation to fit your belief: "It indicates specific founder effects in the North". Now. You have consistently claimed that offspring haplogroups cannot replace parent haplogroups while confined to their region of origin because parent haplogroups will dominate numerically and cause offspring haplogroups to drift to extinction. It is generally accepted that novel haplogroups usually develop along the advancing front of a haplogroup's expansion. But here you are claiming the opposite. "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". Any farmer will tell you that although the first cross of any two breeds (F1) tend to all look the same (dominant genes from each breed are expressed) once you interbreed the hybrids (F2) almost any combination can be thrown up. There is no reason at all why two populations formed from even the same two original populations will have the same genes. And the difference will be even more marked if the admixture consists of other than a mixture of other than 50% from each parent population. "It does suggest (awaiting more data) that the coastal populations of around Shanghai have been largely replaced from people from maybe Hunan" Yes. And those 'original' coastal populations look to have been mainly O1. That haplogroup expanded south into Taiwan and beyond. "This might have also been the case with the people of the Yellow River(?? – they were not 02 in any case)" At present we have no idea of what haplogroups were present in the Hwang Ho before the Neolithic. "You should have very clear my viewpoint by now". I am. And I realise no amount of evidence is going to change it.

     
  4. Maju

    February 25, 2013 at 7:45 am

    I have the right to be "wrong" (i.e. in disagreement with you or whoever) and you are not persuading me at all, as you know. Surely because you are too combative and wasteful of words. You have no excuse in any case to be excessive lengthy and unfocused, always bringing too many matters to any single discussion and wasting too much time accusing me of your imagination's "sins" and (sometimes at least intentionally) misunderstanding half of what I say, so you have even more imaginary space to yell at. For example above you waste four paragraphs (two quotes and two of your own) just yelling at me and accusing me of "heresy" or something. En fin I do not expect you to amend at your advanced age but, please, surprise me."… once you interbreed the hybrids (F2) almost any combination can be thrown up".And that supports "racist selection". The farmer acts with intention of picking these or those traits and so does "racist selection", focused on the visible phenotype, some of which are preferred (for example blonds with blue eyes, or, in this case, people who look less East Asian). With no selection against some traits, there should be nothing being "thrown up" at all."And those 'original' coastal populations look to have been mainly O1. That haplogroup expanded south into Taiwan and beyond".Or maybe came from there (from Taiwan and beyond) via the coast. Or are you telling me that you have genetic reasons of diversity or obvious ancestry (in the case of aDNA → modern DNA) that backs a Shanghai area origin for Austronesians? Just because you wish so it does not make it true: look at the two sides of the issue before picking your "truth". "At present we have no idea of what haplogroups were present in the Hwang Ho before the Neolithic". Actually the link you insist on, Hui Li 2007, includes a Yellow River area sample from Taosi (Shanxi, Longshan culture), which 3/4 O3* and 1/4 O3e (the only such finding of today's most common "Sino-Tibetan" lineage). You go half-blind on all this, even in what you could use (in your usual one-sided and sloppy manner) to support your models.

     
  5. terryt

    February 25, 2013 at 7:45 pm

    I was going to leave this topic but then you made this idiotic comment: "And that supports 'racist selection'. The farmer acts with intention of picking these or those traits and so does 'racist selection'" One minute you're stressing the variation within 'racial types' and now you're claiming racial selection has made each type uniform. The F2 human hybrids between groups have maintained considerable diversity. Minimal selection.

     
  6. Maju

    February 25, 2013 at 10:43 pm

    I'm not talking about generalities here but the particular case of Northern Russia, which is anomalous considering what we know about Siberian/East Asian admixture in that area: it is very strange that with a 10% or more such admixture not even a thin red line appears in the map. That requires an explanation and the best I could come up with was "racist selection" in favor of European looking phenotypes. Do you have better ideas on the matter, smartass? No? Well, the don't be so cocky and insulting.

     
  7. terryt

    February 26, 2013 at 3:45 am

    "Do you have better ideas on the matter, smartass?" Yes, I do. 10% East Asian admixture is far less than that of America, Northeast Siberia or Southeast Asia. The anomaly is the Munda. Perhaps they have not admixed with their neighbours much at all since the arrived.

     
  8. terryt

    February 26, 2013 at 5:05 am

    Seems the Munda are not so anomalous after all: http://blogs.discovermagazine.com/gnxp/2010/10/sons-of-the-conquerers-the-story-of-india/#.USwtM_KJmuI"Indian AA speakers have high frequencies of Y chromosome haplogroup O2a" In that blog we find the information that: "The G allele exhibits co-dominance" So its influence is in direct prortion to its presence. Even this paper, which claims the Munda are the 'original' South Asian people (an unlikely hypothesis in fact): http://www.ispub.com/journal/the-internet-journal-of-biological-anthropology/volume-4-number-2/munda-speakers-are-the-oldest-population-in-india.html#sthash.718qY3ts.dpbsSays: "The Munda y-chromosome is O2a (M95)". If the proportion of O2a is as much as 50% of the Y-DNA haplogroups that gives 25% East Asian genes. That is more than twice the level in Northern Russia.

     
  9. Maju

    February 26, 2013 at 3:54 pm

    Which are the admixture levels in Near Melanesia? We do see a 5% or so of this EDAR variant there. But in North Russia: 0%. That is most strange.

     
  10. terryt

    February 27, 2013 at 3:09 am

    I didn't realise the importance of this research until a few days after you had posted it. It reveals a huge amount abouth East Asian prehistory. "Which are the admixture levels in Near Melanesia? We do see a 5% or so of this EDAR variant there". Razib explains the problem you see: "In Melanesia the EDAR frequency is correlated with Austronesian admixture". Of course Melanesians have minimal amounts of Y-DNA O. But male expansion is not the only vector for the EDAR370A's expansion. Female expansion can be another vector. I realise that you believe mt-DNA B is ancient in Melanesia. But most believe it arrived with the Austronesians. B4's deeper origin is most likely the South China coast. By the time B4a reached Taiwan, and certainly by the time it left, the EDAR370A variant was almost certainly well established through southern China. So Razib is correct: the Austronesians carried the variant into Melanesia. This is probably a good time to respond to some of your doubts about Y-DNA's origin. "Or maybe came from there (from Taiwan and beyond) via the coast. Or are you telling me that you have genetic reasons of diversity or obvious ancestry (in the case of aDNA → modern DNA) that backs a Shanghai area origin for Austronesians?" Yes, I do have good reasons to doubt a movement north from Taiwan to the mouth of the Yangtze rather than in the other direction. O1 is quite rare on the mainland, including the Shanghai region, today. It would be very strange if a SE Asian/Taiwan haplogroup had moved to to make up three quarters of the population near Shanghai to later diminish to almost nothing again. I know Wikipedia insists on a southern origin: http://en.wikipedia.org/wiki/Haplogroup_O-MSY2.2_(Y-DNA)But that insistence leads to the contradictions in the article. Such as: "Neolithic incursions made only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion". We know that what we may prefer to call 'post-Neolithic incursions' must have had a huge impact on the Shanghai region gene pool then. "Approximately 5000 BCE, Haplogroup O-MSY2.2 coalesced at Sundaland and migrated northwards to as far as Taiwan" No. We know that it became very prominent on the mainland way to the north of Taiwan. It seems very likely that O1a has been replaced on the mainland to a large extent by the later expansion of O3 haplogroups. It became virtually confined to Taiwan and SE Asia from where it expanded further as part of the Austonesian movements. "Actually the link you insist on, Hui Li 2007, includes a Yellow River area sample from Taosi (Shanxi, Longshan culture), which 3/4 O3* and 1/4 O3e (the only such finding of today's most common "Sino-Tibetan" lineage)". Have you checked out the region where the Taosi culture developed? http://en.wikipedia.org/wiki/Taosi"Taosi (Chinese: 陶寺; pinyin: Táosì) is an archaeological site in Xiangfen County, Shanxi, China". But there's more: http://en.wikipedia.org/wiki/Shanxi"The name Shanxi literally means 'mountain's west', which refers to the province's location west of the Taihang Mountains.[1] Shanxi borders Hebei to the east, Henan to the south, Shaanxi to the west, and Inner Mongolia to the north and is made up mainly of a plateau bounded partly by mountain ranges". That is the exact same region that the secong map Razib posted is centred on. The region where the EDAR370A gene swept to prominence. It seems most reasonable to me to suppose O3-M122 coalesced in the region that O-M175 had coalesced in the first place. O1 and O2 had coalesced as O-M175 had expanded from that region. What we may be seeing here is evidence that O3 had remained behind in the region of O-M175's coalescence while O1 and O2 had pushed south.

     
  11. Maju

    February 27, 2013 at 4:33 pm

    If you look at autosomal data, the percentage of East Asian influence in Island Melanesians can't be much higher than among Finnic-ancestry peoples of Northern and NE Europe, including Northern Russians. Two examples from Dienekes (global K=5 shows almost 20% but global K=15 makes them a single distinct cluster with 0% apparent admixture, the results may vary somewhat depending on K-level and particular sample anyhow). The same that Melanesians have mtDNA as more outstanding haploid signal of that admixture, Finnic-ancestry peoples have especially Y-DNA N (c. 50% in Finland for example) as such signature. They are clearly comparable. "I realise that you believe mt-DNA B is ancient in Melanesia"…Again you misunderstand and misrepresent my opinion: B is clearly of Austronesian origin – at least I think so."It would be very strange if a SE Asian/Taiwan haplogroup had moved to to make up three quarters of the population near Shanghai to later diminish to almost nothing again".Regardless of the exact origin, that is exactly what the aDNA mentioned above suggests: that the Shanghai area population was dominated by O1a and now it is not. Whether that O1a came from Taiwan or from Mars is irrelevant to its demise/dilution. "[Shanxi] is the exact same region that the secong map Razib posted is centred on".It is not. The red region corresponds to Henan, south of Shanxi. As I mentioned before, without reading the paper, we cannot interpret its real value (it may well be a ghost, an statistical artifact). It is irrelevant anyhow because the relevance of the Taosi sample is that it doesn't either appear as "modern" in any way. You are just over-reading in search for burning nails again.

     
  12. terryt

    February 27, 2013 at 11:48 pm

    "You are just over-reading in search for burning nails again". Sorry, your Majusty. "If you look at autosomal data, the percentage of East Asian influence in Island Melanesians can't be much higher than among Finnic-ancestry peoples of Northern and NE Europe, including Northern Russians. Two examples from Dienekes (global K=5 shows almost 20% but global K=15 makes them a single distinct cluster with 0% apparent admixture" How has that got anything to do with the matter under discussion here? As I understand things from the context the mutation is confined to Austronesian-speaking groups. The only populations Dienekes entry mentions are 'Papuans' and 'Non-Austronesian Melanesians'. "The same that Melanesians have mtDNA as more outstanding haploid signal of that admixture, Finnic-ancestry peoples have especially Y-DNA N (c. 50% in Finland for example) as such signature. They are clearly comparable". No they're not. Austronesian-speaking Melanesians have a considerable proportion of mt-DNA B. Although Nenets and Sami have considerable proportions of N it seems they were not sampled in this study. Do you have any information as to the proportion of N in the Vologda? But aside from that you have consistently maintained that mt-DNA is a better indication of aDNA than is Y-DNA. So it is you here who is clutching burning nails. "Regardless of the exact origin, that is exactly what the aDNA mentioned above suggests: that the Shanghai area population was dominated by O1a and now it is not". Yes. It has been replaced by O3. To claim that a haplogroup that expanded south from Taiwan a mere 4-5000 years ago had, in a completely unrelated expansion, reached the Shanghai area is unsopportable. "Whether that O1a came from Taiwan or from Mars is irrelevant to its demise/dilution". True. But the matter under consideration here is the expansion of the EDAR370A variant. And the sourse of O1 has everything to do with that topic. Unless you're proposing some alternative vector for the variant's expansion? Come on. Out with it. " the relevance of the Taosi sample is that it doesn't either appear as 'modern' in any way". What?! One third of the haplogroups there are O3a2c1, the most widely distributed modern Chinese Y-DNA. And we can only be sure that the two thirds shown as O3* is not O3a2c1-M134 or O3a2b-M7. It could be O3a2a-M159, O3a1-L127 or even O3a2c-P164(xO3a2c1-M134). Burning nails again your Majusty. "The red region corresponds to Henan, south of Shanxi". I don't think so! Check your Chinese geography. The most that could be said is that the red zone is near the Shanxi/Henan border, exactly where the Taosi culture developed. Burning nails yet again.

     
  13. Maju

    February 28, 2013 at 12:24 am

    I just judging on the map, because I have no access to the paper, and the Melanesians with the EDAR "red" variant are Island Melanesians. Papuans do not have it. All Island Melanesians I know of have some apparent (even if variable and generally minor) Austronesian-East-Asian admixture and the red fraction is clearly correlated with admixture. Similarly all Finnic-ancestry Northern Europeans have some apparent (even if variable and generally minor) Siberian-East-Asian admixture but they don't appear to have the EDAR variant (according to what we can see in the maps at least). "No they're not. Austronesian-speaking Melanesians have a considerable proportion of mt-DNA B". And Finnics have a considerable proportion of Y-DNA N. Both have similar autosomal admixture signals from East Asia."Although Nenets and Sami have considerable proportions of N".I'm not talking of Nenets nor Sámi (not of Nenets in any case, who are autosomally much more East Asian than anything else). I'm talking of Finns, Karelians, Northern Russians, Volga Finnics, Estonians and Latvians – read at least Wikipedia before commenting on a matter you seem to know nearly nothing. "But aside from that you have consistently maintained that mt-DNA is a better indication of aDNA than is Y-DNA".But it does not matter here, because at least I (not sure about you) have seen many ADMIXTURE and STRUCTURE analysis that always confirm that those peoples have some 15% Siberian-East-Asian admixture (with whatever particular variations). Equally I have seen a number of such autosomal analysis for Island Melanesians, which give similar apportions. Why to look at the part when you already have the whole?" To claim that a haplogroup that expanded south from Taiwan a mere 4-5000 years ago had, in a completely unrelated expansion, reached the Shanghai area is unsopportable".Why? You are being just knee jerk.Anyhow I don't believe that O1a as a whole expanded from Taiwan: it did first from Indonesia probably, and the Taiwan centered secondary expansion southwards only had a minor impact (mayor in some isolated populations). But do not start a discussion on the origins of O1a, please. It does not matter at all. They may well be unrelated processes, why not? (although IMO the single S→N coastal expansion can well explain both the arrival to Taiwan and to Shanghai region). "But the matter under consideration here is the expansion of the EDAR370A variant".Exactly and it does not seem particularly related to O3, otherwise Native Americans would be drowning in O3, or also Mongolians, Siberians, Burmese, Koreans, Japanese, etc. We know it is not the case and that's why the expansion seems to be from a less specific source and in a less specific process. "One third of the haplogroups there are O3a2c1"… [in Taosi]1/4 or 1/5. But the other 3/4 are O3*, what is inconsistent (today's Sino-Tibetans only have 17% of that). So it is impossible that modern ST Y-DNA pool spawned from Taosi. You just don't seem to be able to see the whole picture and cherry-pick your "evidence" without apparently being aware of any contradictions. Rebating that is for me a waste of time, sorry, a time that I do not have anymore."I don't think so!"I do. I contrasted the maps and it is very clear. But anyhow I don't know yet why the red region would be meaningful: nobody explains that clearly.

     
  14. terryt

    February 28, 2013 at 6:32 am

    "But anyhow I don't know yet why the red region would be meaningful: nobody explains that clearly". Absolute rubbish. Are you really so silly? The red shows where the authors calculated that the variation came to dominance. Have you not read Razib's post? "the Melanesians with the EDAR 'red' variant are Island Melanesians". You seem to have shifted what you're talking about. You said, 'The red region corresponds to Henan, south of Shanxi'. What has that to do with Melanesians of any kind? But to move to what you're talking about here: even though they are 'Island Melanesians' they are specifically 'Non-Austronesian Island Melanesians'. We would therefore expect them to lack the EDAR370A variation. Read the post. Don't simply make things up. "I'm talking of Finns, Karelians, Northern Russians, Volga Finnics, Estonians and Latvians" None of which appear to have been tested in the relevant paper. Read Razib, again if necessary. "Why to look at the part when you already have the whole?" Because when it comes to Melanesia the parts are each very different from each other, even though you consistently lump everything together as 'Australasian'. Read at least something on the subject before commenting on a matter you seem to know nearly nothing about. "Anyhow I don't believe that O1a as a whole expanded from Taiwan: it did first from Indonesia probably" And you believe that because …? Any evidence? "Exactly and it does not seem particularly related to O3" On the contrary, through most of the southern regions where the variant is found it is closely associated with Y-DNA O. "otherwise Native Americans would be drowning in O3, or also Mongolians, Siberians, Burmese, Koreans, Japanese, etc." You are being deliberately obtuse here, your Majusty. Obviously the variant is associated with Y-DNA N and C3, and possibly C1, as well as with O. And you are very well aware of that fact because you keep bringing up the subject of Northern Eurasia. But many mt-DNA haplogroups also look to have expanded, or at least partially expanded, from the region where the variant originated. "We know it is not the case and that's why the expansion seems to be from a less specific source and in a less specific process". In your imagination. We can be almost certain that it is associated with a selective sweep within the region shown in the map at Razib's blog, and a subsequent population expansion from that region. To plead ignorance as to any process is simply a ploy to avoid facing the facts. "But the other 3/4 are O3*, what is inconsistent (today's Sino-Tibetans only have 17% of that)" Yet another ridiculous comment. Most Sino-Tibetans are O3 of some sort. You're closing your eyes to facts again. All we know is that the O3* shown in the map is not O3a2b or O3a2c1. That still leaves a number of possibilities other than the O3* you're insisting on. And surely the fact that O3a2c1 was found only in the Taosi sample yet is now the most widely distributed and common Y-DNA O in China indicates it expanded southwards, not northwards. "You just don't seem to be able to see the whole picture" Your latest comments on this topic show absolutely that you carefully avoid looking at the whole picture.

     
  15. terryt

    February 28, 2013 at 6:51 am

    Seeing you have not actually read Razib's post I'll put some of his comments here: Maju: "But anyhow I don't know yet why the red region would be meaningful: nobody explains that clearly". Razib: "The second figure shows the inferred region from which the East Asian EDAR haplotype expanded over the past 30,000 years". I'm sorry, but I can't explain it any more simply than that. Maju: "the Melanesians with the EDAR 'red' variant are Island Melanesians. Papuans do not have it". Razib: "In Melanesia the EDAR frequency is correlated with Austronesian admixture". In spite of what you claim, not all island Melanesians have Austronesian-East-Asian admixture. Only the Austronesian-speaking populations and their very near neighbours. Maju: "All Island Melanesians I know of have some apparent (even if variable and generally minor) Austronesian-East-Asian admixture" Obviously incorrect.

     
  16. Maju

    February 28, 2013 at 8:13 am

    "Absolute rubbish. Are you really so silly?"Doubly insulting comment. Nth warning!"The red shows where the authors calculated that the variation came to dominance"…While I can't read HOW they calculated it I do not care. I've been begging for a free copy of the paper since comment #1 or so.Their calculation can always be wrong and I refuse to accept any conclusion just because someone says so. Data!"You seem to have shifted what you're talking about. You said, 'The red region corresponds to Henan, south of Shanxi'. What has that to do with Melanesians of any kind?""Red" as in EDAR370A variant marker in the main map above. That is real data and that's what I'm discussing when we talk of admixture. You seem to understand nothing at all, and I'm robbing time from other activities to pay attention to your ignorance and confusion.All you the rest say are one-liners devoid of meaning, words to argue words, without any content, without any single general sense, almost babbling. Seriously…"Most Sino-Tibetans are O3 of some sort."Generic claim devoid of any meaning: your accidental claim that Sino-Tibetans or whatever come from Taosi clashes with the known composition of that sample. O3* in this context is not "03 of some sort" but specifically excluding this and that and that other clade. Also there are other lineages. 1:3 O3e:O3* apportion creates after expansion 1:3 O3e:O3* apportion (plus whatever remnants of assimilated substrate pools), and what we see in modern ST is 2:1 O3e:O3*, what must have other more complex (or simpler but unknown, not Taosi) origins.

     
  17. Maju

    February 28, 2013 at 8:16 am

    That is not any explanation: it is a description of what the authors say. I don't want you to explain more simply but more in depth, detail, with enough data for me to comprehend HOW they reached that conclusion. Meanwhile for me it is trivial, pointless, meaningless. "Razib: "In Melanesia the EDAR frequency is correlated with Austronesian admixture"". Exactly my point as well. But then among Finnic peoples, which have similar amounts of East Asian admixture, that does not happen and it is most strange. We are not discussing Melanesians here but Finnic-ancestry Northeastern Europeans!

     
  18. terryt

    February 28, 2013 at 9:55 pm

    "Generic claim devoid of any meaning" http://forwhattheywereweare.blogspot.co.nz/2011/04/haplogroup-o3-downstream-structure.html"your accidental claim that Sino-Tibetans or whatever come from Taosi clashes with the known composition of that sample. O3* in this context is not '03 of some sort' but specifically excluding this and that and that other clade". Incorrect. Specifically excluding only two clades: O3a2b-M7 and O3a2c1-M134. So their O3* could be O3a2c*, O3a2a, O3a2* or O3a1, most likely O3a1c which makes up 16.9% of the modern Chinese Y-DNA and is widely, and evenly, spread through China (see above link). "Also there are other lineages. 1:3 O3e:O3* apportion creates after expansion 1:3 O3e:O3* apportion (plus whatever remnants of assimilated substrate pools), and what we see in modern ST is 2:1 O3e:O3*, what must have other more complex (or simpler but unknown, not Taosi) origins". Remember that their 'O3e' is actually O3a2c1-M134. That haplogroup now makes up around 30% of Chinese Y-DNA. Again widely and evenly spread through China (see above link). I agree its origin may be complex but that doesn't rule out a northern origin. Note that O3a2c1-M134 was not found in any of the other Neolithic regions tested. It is confined in this study to the Taosi, although that tells us nothing about its earlier history. We can be reasonably sure of some level of continuity though. O3a2b-M7 (O3d in the study) is still concentrated in the Daxi and Hmong Mien. So O3a2c1's concentration in the region from where the later Chinese Han expansion originated may be significant. "Their calculation can always be wrong and I refuse to accept any conclusion just because someone says so. Data!". At present we just have to accept their map. I note Razib seems to accept it at face value. But you are obviously not even prepared to consider the possibility that their conclusion may be extremely sound. Why is that? "But then among Finnic peoples, which have similar amounts of East Asian admixture, that does not happen and it is most strange". You find it 'strange' only because you are confusing two sets of data. You are comparing apples with oranges. I repeat: Dienekes post considers only Papuans and non-Austronesian Melanesians. Both the Papuans and the Melenesians have a level of East Asian admixture, with the Melanesians having more than Papuans. That makes complete sense as it results from introgression from Austronesian-speaking peoople. The level in these non-Austronesian Melanesians is comparable to the level in the North Russians. Neither group has the EDAR variation. Now, have another look at the map you posted above. You will see two population sets from the New Guinea/Melanesia region. One has no EDAR370A even though, presumably, it has some level of East Asian ancestry. The other, as specifically stated by Razib, is 'Austonesian Melanesians'. These do have the variation and presumably have a higher level of East Asian ancestry. Higher than the North Russian population shown in the diagram. Why do you have such difficulty seeing that? Or is it that: "You seem to understand nothing at all"

     
  19. Maju

    February 28, 2013 at 10:55 pm

    It seems that I can't speak English anymore or that you just don't care at all about what I say. The Hiu Li paper already has a comparison where we can see that:1. Taosi (Longshan): 75% O3* – 25% O3e – (0% O3d – 0% O2a – 0% O1a)2. Modern Sino-Tib.: 17% O3* – 33% O3e – (1% O3d – 8% O2a – 2% O1a)The signatures do not match. From 75% to 17% is a HUGE difference!

     
  20. Maju

    February 28, 2013 at 11:01 pm

    I'm not "comparing apples and oranges": the two populations are perfectly comparable on their East Asian admixture levels! I don't care what you (mis-)understood about what Dienekes might have said: there are two obviously different pie charts in that map: one for Papuans and another for Island Melanesians (from maybe New Brunswick?) And those Island Melanesians are who are perfectly comparable in this aspect of minor but noticeable East Asian admixture with NE Europe's Finnic-ancestry peoples.By the Monkey King Sun Wukong, Equal to Heaven!

     
  21. terryt

    March 1, 2013 at 10:34 pm

    "The signatures do not match. From 75% to 17% is a HUGE difference!" Are you claiming haplogroup proportions in a particular region never change? Come on. Anyway, even here you are comparing apples with oranges. Taosi is just one small sample within a whole Sino-Tibetan-speaking region. The figures do not tell us the O3(xO3d,o3e) figure in the immediate vicinity of Taosi today. "there are two obviously different pie charts in that map: one for Papuans and another for Island Melanesians" Maju. I repeat: non-Austronesian Melanesians. "I'm not 'comparing apples and oranges': the two populations are perfectly comparable on their East Asian admixture levels!" Where on earth did you get that idea from? You have seen the first of these papers before. The last is an extract from a Bellwood book: http://mbe.oxfordjournals.org/content/25/7/1362.long"Thus, the Austronesian language replacement on the Admiralties (and elsewhere in Island Melanesia and coastal New Guinea) was accompanied by an incomplete genetic replacement that is more associated with mtDNA than with NRY diversity". Leaving non-Austronesian Melanesians with less of the EDAR variation. http://www.ncbi.nlm.nih.gov/pubmed/15009807Again showing a distinction between Austronesian and non-Austronesian Melanesians. http://www.ncbi.nlm.nih.gov/pubmed/18208337Quote: "A small 'Austronesian' genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages, and is entirely lacking in Papuan-speaking groups". http://books.google.co.nz/books?id=Ovm_HRqOJH0C&pg=PA110&lpg=PA110&dq=austronesian+melanesian+genes&source=bl&ots=UP3DRrGHi9&sig=0L0dRm8piywsinNjiiRqTBSSwf0&hl=en&sa=X&ei=8BkxUZvbG-qSiQfSsoCQBg&ved=0CGEQ6AEwBw#v=onepage&q=austronesian%20melanesian%20genes&f=false

     
  22. Maju

    March 1, 2013 at 11:43 pm

    "Are you claiming haplogroup proportions in a particular region never change?"Everything eventually changes but, when it does, it is for some reason. So if YOU are claiming such a change, which is very extreme, up to the point that the two genetic pools don't look the same AT ALL, you first need to offer a very good explanation. "Where on earth did you get that idea from?"If you would have read what I said (with informative links) previously about the autosomal genetics of Island Melanesians, you'd knew by now. I'm not willing to repeat myself once and again because you write faster than read. "A small 'Austronesian' genetic signature (always <20%) was detected in less than half the Melanesian groups that speak Austronesian languages"…Exactly my point. A small East Asian genetic signature <20% is also present in all Finnic-ancestry peoples of NE Europe.

     
  23. terryt

    March 1, 2013 at 11:49 pm

    "Modern Sino-Tib.: 17% O3* – 33% O3e – (1% O3d – 8% O2a – 2% O1a)" Here is the paper the data Liu used in his table comes from: http://www.ncbi.nlm.nih.gov/pmc/articles/pmc1288383/The phylogeny has been considerably altered since 1999, and so little as to the the significance of O3*' distribution can be gained. "The signatures do not match". Why should they? The Liu paper says: "A rare haplogroup, O3d, was found at the Daxi site in the middle reachesof the Yangtze River, indicating that the Daxi people might be the ancestors of modern Hmong-Mien populations, which show only small traces of O3d today". So the signatures do not match for the Daxi either. In fact they also say: "The absence of O3d in the historical samples from the Daxi site (it might not have been found because of the small sample size), and the migration ofmodern Hmong-Mien populations to the southwest might indicate that the prehistoric population in the Three Gorges area has been replaced". So O3a2b has been completely replaced in the region where it was present 6500-5500 years ago. And the authors obviously accept that the Daxi/Hmong Mien and their Y-DNA have moved south, not north. And, lastly: "at least 62.5% of the individual remains (30 out of 48) belong to O haplogroup, which is still the major haplogroup of today’s East Asians". That is actually somewhat less than the proportion today. The smallest proportion of O shown in the modified Y-DNA O phylogeny paper is 69.2%, in 'Northern China'. So the overall proportion of O in China has changed since the Late Neolithic. And we are talking small sample size in the Neolithic study. Just five individuals from Taosi.

     
  24. terryt

    March 1, 2013 at 11:57 pm

    "A small East Asian genetic signature <20% is also present in all Finnic-ancestry peoples of NE Europe". Much less than 20% is my understanding. Less than 10% even. About the same level as the non-Austronesian Melanesians have. And they don't have the EDAR variation either. Be consistent. "If you would have read what I said (with informative links) previously about the autosomal genetics of Island Melanesians, you'd knew by now". I have read a lot more on the subject than just your links and all consistently claim a genetic distinction between Austronesian-speaking Melanesians and non-Austronesian-speaking Melanesians. Of course the genetic boundary is actually in the form of a cline as genes have seeped each way across but the distinction holds. So you cannot compare the level of either Mongoloid or EDAR between non-Austronesina and Austronesian Melanesians.

     
  25. terryt

    March 2, 2013 at 12:00 am

    Correction. You cannot claim the two Melanesian populations are the same. And: "Everything eventually changes but, when it does, it is for some reason. So if YOU are claiming such a change, which is very extreme, up to the point that the two genetic pools don't look the same AT ALL, you first need to offer a very good explanation". Are you not aware that there has been considerable population movement in China over the last few thousand years? otably the Han expansion, but others as well.

     
  26. Maju

    March 2, 2013 at 2:03 am

    You're trying to be overly complicated for things that are fairly simple: the SNPs tested by Liu are not just meaningful for all the paper's data (and that's why it's best to compare within it first) but also fit well with your mention of 16% some other O3 clade whose name I can't recall right now. "Much less than 20% is my understanding".The figure I manage is c. 15%, 10-20% depending on specific populations and methods. Certain recent study (that I contested) claimed as much as 20-40% East Asian/native American admixture in most European populations anyhow. "You cannot claim the two Melanesian populations are the same".They tend to use the same samples once and again but of course I am not sure, nor are you of the opposite. You're just trying anyhow to make complicated (without any clear foundation) something that is very simple in the outline: both Melanesians and Finnics have notable but >20% East Asian admixture but ones display the EDAR variant in reasonable amounts and the others do not, what is puzzling. You just keep fighting and fighting without foundation nor purpose but the fact is that one.

     
  27. terryt

    March 2, 2013 at 3:24 am

    "The figure I manage is c. 15%, 10-20% depending on specific populations and methods [presumably regarding East asian admixtuer in the Vologda]". But this is what you wrote in the comments section here some time back: "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". That is much less than the 20% you are now claiming. "both Melanesians and Finnics have notable but >20% East Asian admixture" No. Finnics and non-Austronesian Melanesians have around 10% East Asian admixture. Austronesian Melanesians have around twice as much. "They tend to use the same samples once and again but of course I am not sure, nor are you of the opposite". ALL the articles and books I have read on the subject claim a genetic difference between Austronesian and non-Austronesian Melanesians. "but ones display the EDAR variant in reasonable amounts and the others do not, what is puzzling". Only 'puzzling' because you are determined to make it so. I think you would agree that we have three points on the periphery of the East Asian EDAR variant's geographic spread, where the variant, the haplogroups and the East Asian genetic influence dwindles away to virtually zero (or four points if we include America). They are: the Munda, the Austronesian Melanesians and Northern Russia. In each region the end result of the mixing of genes and haplogroups is different. The Munda have preserved both the East Asian Y-DNA and the EDAR gene but seem to have largely lost any particular East Asian genetic similarity. The situation in island Melanesia is fairly straightforward. Y-DNA O has almost died out, to be replaced by C2, but mt-DNA B remains prominent. The East Asian genetic similarity has been noticed for some time but a Papuan influence is more prominent in Melanesia. Yet apparently the EDAR mutation survives as a minor presence. In Northern Russia the EDAR gene has failed to survive but East Asian Y-DNA, some mt-DNA, and a substantial East Asian genetic influence survives. Why would we expect all regions to behave in exactly the same manner?

     
  28. Maju

    March 2, 2013 at 10:28 am

    I can't recall the context of that quote that you bothered searching for but I guess I was younger and naiver back then and I was discussing with a (racism-motivated) admixture-denialist. Whatever the case the figure is c. 15% for Vologda Russians, with minor individual variation. Let's see:Here Russians (from Vologda) show exactly 15% (1.5 cm in a 10 cm tall graph in my screen) of East Asian and Native American admixture (50-50). The 75% of 15% is more than 10% but we see 0% of the EDAR thick hair & small breasts variant, when in Eastern Asia and among Native Americans it is at 75-100% frequencies.It needs an explanation!Here, the very same sample show ~1/7 of the length of the graph (a bit more in fact) in all K levels, measure it with a ruler, and 1/7 is ~14%. So it is a very clear case. "Finnics and non-Austronesian Melanesians have around 10% East Asian admixture. Austronesian Melanesians have around twice as much".Neither what you say is true (not to any relevant level of exactness) nor it would matter if it would because 10%-20% of EA/NA admixture should show 7-20% of the EDAR variant, and in the case of North Russians it is apparently zero. And that demands an explanation!

     
  29. Kristiina

    March 2, 2013 at 2:01 pm

    According to Wikipedia, the age of haplogroup NO is 34.600±4.700 years BP and the estimated age of EDAR seems to be 30000 years. So, the lack or paucity of EDAR in Siberia could be explained by the more Central-Asian origin of haplogroup NO. If N arose outside China or in Western parts of China at a time when this EDAR gene was not yet around, it is natural that the gene is absent or almost absent in Russians and Finno-Ugric peoples of Northern Eurasia. The interesting thing is that, according to Wikipedia, the age of haplogroup O is 28,000-41,000 years BP, although haplogroup NO must be older than haplogroup O. The gap in these age estimates could be due to the huge difference in population sizes. What if this EDAR gene arose in Central China at a time when the area was dominated by other YDNA haplogroups than O type haplogroups and was passed on to East Asians maternally. This would also explain why it is present in Native Americans who are paternally haplogoup Q.

     
  30. Maju

    March 2, 2013 at 2:30 pm

    Well, there is at least one key study that estimates the age of O3 in that time-frame (c. 30 Ka ago), so it is most hard for me to believe that NO is so young. Instead I would estimate 50 Ka or more. In any case molecular clock as it has been used so far is not evidence of anything, just an educated guess.

     
  31. Maju

    March 2, 2013 at 3:24 pm

    Another thing, maybe more important, Native Americans lack Y-DNA NO altogether, the only specifically East Asian patrilineage they have is C3 and is very secondary to the, originally West/Central/South Eurasian, lineage Q. This one has a branch in NE Asia that is ancestral or directly related to the Native American subclades but it is still not NO. So associating these traits with any particular lineage is going to fail, same for matrilineages. The ancestral population where this allele originated must have included at some point several patri- and matrilineages: at least Y-DNA NO (or its subclades), C3 and D (still very strong among Japanese and Tibetans but not affecting the frequencies of this EDAR allele). On the mtDNA side there are also many different important lineages: M8 (incl. CZ), D, F, B, A, M7, M9, G, etc. which should have been involved since very early. So IMO this points to an ancestral population with diverse lineages in SE Asia (incl. South China), maybe 70 or 60 Ka ago, where this allele would have been gradually established (by drift or selection) and which would have expanded with them all, as they migrated northwards. The fact that Cambodians have relatively low levels of the allele, suggests that they, as well as other peoples from Indochina, etc. would have retained greater diversity, as corresponds to founder populations that have not gone through the founder effects (migrant bottlenecks) of the migrations northwards.My opinion anyhow.

     
  32. Kristiina

    March 2, 2013 at 9:29 pm

    When you say that in the Americas C3 is very secondary to the lineage Q, it is all the more intriguing that EDAR is present in America but not in Western Siberia. According to Wikipedia, the age of MNOPS node is 35,000-45,000 years BP, and O and N must be younger than that. I would not be surprised if the age of macro-haplogroup O tends to be overestimated and that of N underestimated due to the huge population size of the former group and much smaller numbers of the latter. There is an interesting map on the distribution of NO and different N clades (http://www.nature.com/ejhg/journal/v15/n2/fig_tab/5201748f2.html#figure-title). My guess is that N and NO did not develop in the area where this EDAR gene arose and started expanding. Anyhow, that would be a logical explanation to your question why Russians and Finno-Ugric peoples do not have this gene. In North-Eastern Russia and Finland you have really a tiny amount of Eastern MtDNA present (By the way, my own haplo is I, my husbands's haplo H and my father's haplo U4 and we are all entirely Finnish). It is fascinating how diverse East-Asia is! Maternally both M and N are present and paternally you have haplogroups C, D and F (basal F and all MNOPS clades). I know how difficult it is to link any macro-haplogroup with particular physical looks. MNOPS clades cover almost the whole world, M and S in Indonesia and Melanesia, N in North Eurasia, O in East Asia, P in South Asia, Eurasia, Middle East and the Americas. Also macro-haplogroup DE covers an astonishing variety of ethnic identities on a huge area, African bantus, Afro-Asiatic speakers of Middle East and Africa, Jarawa people and Tibetan as well as Japanese and Ainu. In spite of the deep ancestry, people usually end up looking like their neighbours!

     
  33. Kristiina

    March 2, 2013 at 9:32 pm

    Correction: I did not mean North-Eastern Russia and Finland but North-Western Russia and Finland!

     
  34. terryt

    March 2, 2013 at 10:42 pm

    "According to Wikipedia, the age of MNOPS node is 35,000-45,000 years BP, and O and N must be younger than that" I know Maju is not a fan of 'molecular-clockology' (and neither am I generally) but interestingly Dienekes posted some time ago an age estimate for various basal Y-DNAs: http://dienekes.blogspot.co.nz/2012/08/dates-of-major-clades-of-y-chromosome.htmlHe has NO at 33,000 years and the O diversification into the three haplogroups at a little less than 30,000 years 27-28,000). That is stunningly close to the time the EDAR variant first appeared in the modern human species either by mutation or introgression. He doesn't have an age for MNOPS but the Wiki age fits. "My guess is that N and NO did not develop in the area where this EDAR gene arose and started expanding". Perhaps not where NO originated, but I think it is extremely likely that the EDAR gene arose where NO diversified. Unlike Maju I see no problem with the EDAR307A's absence in northern Russia. "but we see 0% of the EDAR thick hair & small breasts variant, when in Eastern Asia and among Native Americans it is at 75-100% frequencies". As I said, 'Why would we expect all regions [on the margins of a gene's expansion] to behave in exactly the same manner?' I can't understand why you insist that the proportion of each gene should exactly reflect the overall proportion of the whole genetic contribution. Especially when we're talking here of just small proportions. Anything can happen in such situations. "because 10%-20% of EA/NA admixture should show 7-20% of the EDAR variant" Why would that automatically be so? In fact it is extremely unlikely the proportions would be exactly the same, or even necessarily close when we're talking about such low levels in the first place.

     
  35. terryt

    March 2, 2013 at 10:43 pm

    "What if this EDAR gene arose in Central China at a time when the area was dominated by other YDNA haplogroups than O type haplogroups" That would require an even greater displacement of haplogroups than the small level I am suggesting. Maju won't have a bar of it. And I have trouble accepting the idea. "This would also explain why it is present in Native Americans who are paternally haplogoup Q". I agree that the EDAR variant was carried to America mainly by mt-DNAs. The information I have seen suggests that Y-DNA Q picked up the East Asian mt-DNA haplogroups as they passed to the north of the region Y-DNA O and those mt-DNA haplogroups already occupied. That explanation certainly makes sense to me. "Native Americans lack Y-DNA NO altogether, the only specifically East Asian patrilineage they have is C3 and is very secondary to the, originally West/Central/South Eurasian, lineage Q". This is one thing (actually one of many) that Maju and I agree on. "The ancestral population where this allele originated must have included at some point several patri- and matrilineages: at least Y-DNA NO (or its subclades), C3 and D (still very strong among Japanese and Tibetans but not affecting the frequencies of this EDAR allele)". We agree on that too, but perhaps I would exclude D from the original grouping. D is present on the Andamans where there is almost no East Asian admixture as far as I'm aware. "On the mtDNA side there are also many different important lineages: M8 (incl. CZ), D, F, B, A, M7, M9, G, etc. which should have been involved since very early". Once more we are largely in agreement although I would definitely exclude B and F from the core region. And add N9. "So IMO this points to an ancestral population with diverse lineages in SE Asia (incl. South China), maybe 70 or 60 Ka ago, where this allele would have been gradually established (by drift or selection) and which would have expanded with them all, as they migrated northwards". That's where we completely disagree. The EDAR variant almost certainly arose in northern China/Inner Mongolia according to this paper. "The fact that Cambodians have relatively low levels of the allele, suggests that they, as well as other peoples from Indochina, etc. would have retained greater diversity" Again I think otherwise. To me it is yet another indication that the gene didn't originate anywhere near there. "My opinion anyhow". Thank you.

     
  36. Maju

    March 3, 2013 at 1:37 am

    In general age estimates are just that: very rough estimates that have zero value as data or evidence. IMO they are generally too recent and that is partly because of systematic underestimation of the chimpanzee-human divergence date, often cited as 7, 6 and even 5 Ka, when it actually is c. 8-13 Ka, according to several recent studies (Landgraeber for example). With that alone, and assuming all other factors are correctly evaluated, all age estimates should be almost double (minimal error is 15% older, max. 130% older). But there are also other factors that introduce errors. It'd be too cumbersome to discuss here so suffice to say that the molecular clock products so far are pretty much useless, they can be a compass but hardly anything like a reliable map. "it is all the more intriguing that EDAR is present in America but not in Western Siberia".We do not know, at least I do not, if EDAR370A is present in West Siberia or how much. (EDAR is the gene, so we all have it, EDAR370A is the variant allele specific of East Asians and Native Americans). "In North-Eastern Russia and Finland you have really a tiny amount of Eastern MtDNA present"…But as discussed above, the autosomal admixture signal is of c. 15% in Vologda Russians specifically, maybe a bit larger among Finns from Finland. I don't know too much about the rest but it's easy to imagine considering that it is associated with levels of almost 50% Y-DNA N in many of those populations. You are right in that Oriental mtDNA is nowadays relatively rare but ancient DNA shows that it was more common in the past. The general understanding is that these peoples gradually absorbed other European gene pools but much more intensely by the side of women, retaining identity and language via patrilocality, what is still very visible in the Y-DNA. "It is fascinating how diverse East-Asia is!"True. IMO, after Africa, second only to South Asia and not by much. This surely reflects that when the early Eurasians (or Asians if you wish) expanded (probably from South Asia), they quickly colonized also East Asia (and then most of Australasia as well). To my eyes at least mtDNA N and Y-DNA C and D should have been present in very low frequencies and only succeeded in some locations. Another possible explanation might be that Toba supervolcano (c. 74 Ka ago) could have pruned some less common lineages in South Asia, which was the most affected by the ash fall. We know from Petraglia 2007 that people with African-like stone tech, MSA, lived in parts of India before and after the ash rain, so they were already there and at least some survived. But that means (to my eyes at least) that they could also have reached SE Asia, a region poorly understood archaeologically so far, at least for those time depths. "I know how difficult it is to link any macro-haplogroup with particular physical looks".I think that the problem is certain "pop" misunderstanding of haplogroups as always equating one single prehistorical population in a 1:1 relation. I think that is very unlikely in most cases, unless you restrict the concept population to that of extended family or clan, what is very extreme. Conversely I understand that, in most cases, populations must have included diverse lineages. Exceptions would be in very low density areas, where genetic drift would be very strong, or areas reached first by a very small founder population (founder effect).

     
  37. Maju

    March 3, 2013 at 1:39 am

    "Why would that automatically be so?"The actual question is why would it not be so "automatically"?

     
  38. Maju

    March 3, 2013 at 1:41 am

    "That's where we completely disagree".And in almost everything else, I know. I'm tired today.

     
  39. Kristiina

    March 3, 2013 at 11:26 am

    Maju, you say that “autosomal admixture signal is of c. 15% in Vologda Russians specifically, maybe a bit larger among Finns from Finland”, but I would bet that it is the opposite. The article on ancient MtDNA: http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003296 is very interesting and illuminating in this respect. I suppose that you refer to it in your comment. There you can see people moving along different routes, via Volga Ural (aUzPo, Apo) and the northernmost route (aBOO). In figure 3A you can see that there is similarity between aUzPo (with a lot of haplogroup C) and Central Asian people, excluding China. In figure 3B you can see a strong connection between aBOO (with a lot of C, D and Z) and North East Asia. However, it is interesting that Sami people who live today in the same area are not direct descendants of these aBOO people, although haplogroups D and Z have been absorbed specifically to Finnish Sami MtDNA pools. When you say that there are levels of almost 50% Y-DNA N, I can tell you that it is even more, 78% in North Savo (in Eastern Finland) and 60% in South Western Finland (Länsi-Suomi). It would be weird if all MtDNA originally associated with YDNA N virtually disappeared in such a large area as Finland, the Baltic area and North Western Russia. I still think that it is plausible that the archaic N people and their women who eventually reached Finland did not possess this gene. In Finland many people are desperate about their thin hair – I am one of them – and in the whole world the frequency of thin silky hair must be the highest just in Finland.Terry, your justification for exclusion of D from original EDAR370A carriers might be irrelevant, as this gene probably did not yet exist when Andamanese D was separated from the rest of East Asian D http://www.sciencemag.org/content/311/5760/470.2.full. As for your comment on the origin of NO, I would agree with you if you said that it is extremely likely that the EDAR370A gene arose where O diversified! When you want to exclude B and F from the core region, I am wondering what you think were the Y haplos that were expanding with these MtDNA clades.What we physically look like at the moment is probably a result of quite late local developments, in which a host of different haplos have been involved. I think that 50,000 years back we all looked pretty archaic!

     
  40. Maju

    March 3, 2013 at 1:10 pm

    In the comment just before you, Kristiina, began posting (and I was hoping that you had read it but seems not), I linked to two different ADMIXTURE panels which evidence that the Vologda Russians (just "Russians" by label) have 15% admixture from Siberia (or East Asia+Native Americans). The panels are: here and here. Use a ruler to measure the percentages (I did myself). An mtDNA comparison will not help you with that as clearly as a direct autosomal one (probably because in this case it is more strongly related to Y-DNA for reasons of apparent prehistorical patrilocality). "It would be weird if all MtDNA originally associated with YDNA N virtually disappeared in such a large area as Finland, the Baltic area and North Western Russia".It did not completely disappear but was clearly reduced a lot. The exact mechanisms I can't say but I it seems evident that, in the long run, they outmarried with their southern neighbors once and again within a patrilocal scheme. It's also possible that the more "europeanized" populations from the southern fringes of the Finnic (or Fino-Ugric?) area had some sort of advantage (being better connected) and also they may have been pressed in northward direction by their southern neighbors in a chain effect along time. Speculating a bit here but I hope that you get my point.

     
  41. terryt

    March 4, 2013 at 3:39 am

    "Terry, your justification for exclusion of D from original EDAR370A carriers might be irrelevant, as this gene probably did not yet exist when Andamanese D was separated from the rest of East Asian D" I very much doubt that the Andamans were inhabited as long as 30,000 years ago. From your link: "The Andamanese sequences of these two haplogroups shared their most recent common ancestor (MRCA) within these haplogroups at time depths 3000 years [confidence interval (CI) 2] and 12,000 years (CI 4), respectively" But the authors do say, 'the MRCA with continental Indian mtDNA lineages nested within haplogroup M at a time depth of 65,000 years'. But we have no idea if that time has anything to do with the arrival on the Andamans. "I would agree with you if you said that it is extremely likely that the EDAR370A gene arose where O diversified!" I'm fairly sure that is in fact what happened. "When you want to exclude B and F from the core region, I am wondering what you think were the Y haplos that were expanding with these MtDNA clades". Possibly NO itself along with other K and F clades. "The actual question is why would it not be so 'automatically'?" Because migrations do not occur instantaneously. People mix with others along the way diluting and redistributing genes. The proportion of particular genes would alter along the route and we're dealing here with the margins of expansion. Once more you are demonstrating your Garden of Eden obsession. But you know that, because you said: "I think that the problem is certain 'pop' misunderstanding of haplogroups as always equating one single prehistorical population in a 1:1 relation". Yet in the matter of EDAR370A in northern Russia you ignore your own comment.

     
  42. terryt

    March 4, 2013 at 8:27 am

    "When you want to exclude B and F from the core region, I am wondering what you think were the Y haplos that were expanding with these MtDNA clades". I thought I'd better clarify what I meant above. Of course in the early days only one mt-DNA B clade made it as far north as where the EDAR variant appeard. That was the B4b branch of B4b'd'e'j. Other B haplogroups look to have stayed in southern China or SE Asia. The same is basically true for F. Just one F clade expanded widely: F1. And only a small proportion of that haplogroup. I'm not sure what branch(es) of F1 are found in such regions as Tibet, North China, Korea and Japan.

     
  43. Kristiina

    March 5, 2013 at 9:20 am

    Maju, I agree with you when you say that ”two different ADMIXTURE panels which evidence that the Vologda Russians (just "Russians" by label) have 15% admixture from Siberia (or East Asia+Native Americans)”, I just meant that Finns might have less Siberian admixture than Vologda Russians but, actually, this admixture might be the same, little less or more, but it does not change the big picture.Terry, I love you when you say that you’re ”fairly sure that is in fact what happened”. 🙂 You are also right when you say that Y haplo D could be excluded from the original grouping. It is true that Japan and Tibet are not in the core area where this gene arose according to the map. You were interested in the percentage of N haplo in Volgoda Russians. They have 35.5% of N3 and 3.3% of N2 and the percentage of R1a is 33.1% (http://www.sciencedirect.com/science/article/pii/S0002929707000250). After a lot of rethinking, I propose that NO arises somewhere in Yunnan from MNOPS node (http://www.nature.com/ejhg/journal/v15/n2/fig_tab/5201748f2.html#figure-title). O arises somewhere between Yunnan and Three Gorges area and starts expanding. OMSY2.2 and OP31 may arise somewhere near this area. OM122 may also arise in Three Gorges area expanding in the first place in the North. NO, N* and different O subclades expand at least with MtDNA N (R9, R11) that will develop into F and B respectively and with MtDNA M9 (?). These O clades or part of them may be present in the area of origin of EDAR307A gene when this gene arises and starts expanding. You give the time frame of 27-28,000 years for the diversification of this hg.N arises later on in Yunnan (or North of it), and a part of these N men are heading North (There are also important frequencies of N* in Indo-China). North is much less crowded and this is why this haplo becomes an important player in the North and Siberia. According to this recent Chinese research (http://eurogenes.blogspot.fi/2013/01/lots-of-ancient-y-dna-from-china.html#comment-form), there were a lot of N haplo men, as well as Q and R haplo men, in Xinjiang and northernmost part of China 3000 – 5000 YBP. However, it seems to me that they are moving on the outer fringe (or outside) of the core area of EDAR307A gene. I propose that N haplo men heading West did not get this EDAR variant and this leads to the division between more eastern looking Uralic people and Western looking Uralic people.To get an insight into which Mtdna haplos might have been around where N expands in the North, this research is illuminating: arose http://dienekes.blogspot.fi/2012/01/aapa-2012-abstracts-part-1.html. I would pick up C and Z (M8), D, U2 and U4 as possible candidates. These haplos are still present in Uralic speaking peoples of Eurasia and figure in this recent research I referred to in my previous mail (http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1003296). It is interesting that they found C1 haplo in Northwestern Russia! It is rare in Asia and present in America. As for this process of diminution of Eastern MtDNA in Europe, it seems that these N men took H and U5a women when they came to Europe. In this recent research they confirmed the presence of MtDNA H and U5a in northwestern Russia 7,500 (uncal.) years ago. I do not know if you have noticed that Davidski has also recently commented this saying ”I think this ancient admixture is something Central Siberian or Central Asian, and it's shared by Europeans, Amerindians and East Asians. It might well be the same thing as what the proto-Uralics were before they mixed with Europeans and East Asian EDAR carrying eastern Siberians.” (http://eurogenes.blogspot.fi/2013/02/ancient-amerindian-like-admixture-in.html)

     
  44. Maju

    March 5, 2013 at 12:34 pm

    For Finns specifically, you may want to check Bauchet 2007, specifically fig. 1, where it seems obvious that they have some notable Siberian admixture(represented by the light orange component (Altaians themselves are not purely Oriental, so they also display European components) again in the order of 1/7 or 15%. Anyhow, I see no reason why Finnish would be less Oriental than russified populations. Again arguing on the haploid genetics is not as informative as the autosomal data itself. This is not the same elusive and contexted Oriental admixture at levels of 20-40% claimed by a recent paper, on very dubious grounds, for all Europeans or at least most. But a much more clear admixture specific of Finnic and related peoples of NE Europe.

     
  45. Maju

    March 5, 2013 at 3:23 pm

    As for the origins of N, Kristiina, they are probably somewhere in Central or Southern China (highest diversity), although the highest frequencies are further North in Buryat (a Mongol ethnicity of Siberian) and then in the truly Northern fringes of Siberia. This paper only gives data on EDAR370A in Eastern Siberia, so indeed that the allele is more diluted to the West of Siberia is a serious possibility and an alternative option to that of "racist selection" in European peoples of minor Siberian ancestry."It is interesting that they found [mtDNA] C1 haplo in Northwestern Russia! It is rare in Asia and present in America".That may have to do with the fact that both share the Siberian connection rather than a strictly East Asian one, in different ways but Siberian anyhow."I do not know if you have noticed that Davidski has also recently commented this saying ”I think this ancient admixture is something Central Siberian or Central Asian, and it's shared by Europeans, Amerindians and East Asians. It might well be the same thing as what the proto-Uralics were before they mixed with Europeans and East Asian EDAR carrying eastern Siberians.”"Naturally. I am subscribed to that comment section. I agree that it is an alternative possibility but only a wider survey of the relevant peoples re. EDAR will give us a proper answer.

     
  46. terryt

    March 6, 2013 at 3:41 am

    "As for the origins of N, Kristiina, they are probably somewhere in Central or Southern China (highest diversity), although the highest frequencies are further North in Buryat (a Mongol ethnicity of Siberian) and then in the truly Northern fringes of Siberia". Diversity is as likely, or even more likely in many cases, to ba a product of multiple enry of a haplogroup rather than being an accurate indicator of origin. I am not claiming that to be the case here but I still think you should consider the possibiliy. As I understand the situation N is quite uncommon in China and where present most prominent in the northwest. And the clades found there are actually widespread clades, not basal ones. "You were interested in the percentage of N haplo in Volgoda Russians. They have 35.5% of N3 and 3.3% of N2" Thanks for that. "I propose that NO arises somewhere in Yunnan from MNOPS node" Yes. I think it very likely that MNOPS's geographic range extended that far north. "O arises somewhere between Yunnan and Three Gorges area" I certainly see O as having originated further north than that. Certainly well within the region where the EDAR370A variant developed and reached fixation. "OMSY2.2 and OP31 may arise somewhere near this area [Three Gorges]". That holds reasonably well for O1-MSY2.2, but one clade of O2-P31 is definitely a northern haplogroup. It is very difficult to make a case for O2b having originated anywhere near the Three Gorges region. "OM122 may also arise in Three Gorges area expanding in the first place in the North" I can't see a northward movement for O-M122. That region would have early become occupied by N and O2b, and probably C3. That places O3's origin either north or west of the Three Gorges. "These O clades or part of them may be present in the area of origin of EDAR307A gene when this gene arises and starts expanding. You give the time frame of 27-28,000 years for the diversification of this hg". I agree that the O clade was present in the region when the gene arose but probably not in an already diversified condition. Its expansion carried the gene south while other haplogroups carried it north and into America. "N arises later on in Yunnan (or North of it), and a part of these N men are heading North (There are also important frequencies of N* in Indo-China)". I am very sure that N is actually just the northern version of NO while O is the southern branch. "there were a lot of N haplo men, as well as Q and R haplo men, in Xinjiang and northernmost part of China 3000 – 5000 YBP. However, it seems to me that they are moving on the outer fringe (or outside) of the core area of EDAR307A gene". On the northern fringe, yes. Have you seen Razib's second map? Maju hasn't posted it for some reason or other: http://blogs.discovermagazine.com/gnxp/2013/02/is-girls-generation-the-outcome-of-the-pleistocene-mind/"I propose that N haplo men heading West did not get this EDAR variant and this leads to the division between more eastern looking Uralic people and Western looking Uralic people". Possible. But it is certainly not necessary to postualte any such thing. The prortion of various genes in a population would change as it expanded and mixed with locals it met along the way. As you say: "it seems that these N men took H and U5a women when they came to Europe".

     
  47. Kristiina

    March 6, 2013 at 6:59 pm

    Maju, according to this Bauchet 2007 research, Finns have more Asian admixture than Poles and Altai people considerably more than Finns. I think that this level of admixture is well in line with the scenario I proposed above, although Russians do not figure in this study. I did not say that russified populations have more Asian admixture than Finns. I just meant that Volgoda Russians, who have a strong Finno-Ugric substrate, might have more Asian admixture because Finland is further West than Volgoda.I do not know how you get at that bigger southern diversity for HG N. Here http://www.nature.com/ejhg/journal/v15/n2/fig_tab/5201748f3.html#figure-title the Chinese samples are near the root of N*, but there is no geographic indication. In the research they say about N3 that “although the frequency of hg N3 is low in northern China and restricted to a few small populations, its STR variance is higher (0.26, averaged across eight loci: DYS19; DYS389I&II; DYS391; DYS392; DYS393 and DYS439 …) than in Altai and in Volga-Ural region (0.16 and 0.17, respectively), thus again pointing to northern China rather than southern Siberia as a possible place of expansion of hg N3.” But in fact they continue that “One may notice that while STR variation is relatively low in the Volga-Ural group, some north-European populations have high STR variance (eg, 0.32 in Finns: data from, 36 without DYS385ab). The high STR variation among the latter, however, might not be a result of a long-term in situ differentiation of the founder lineage, but, rather a consequence of an admixture of separate N3 founder types.” I think that Terry referred to this explanation in his comment. The researchers however postulate a possible southern origin when they say “the phylogeography of the NO* and N* lineages … and the presence of N* chromosomes in southern East Asia (South China and Cambodia …) suggests that this region could be the source of the initial spread of hg N. In this scenario, the Altay/Sayan/southern Siberia region might have been a place of transition of hg N westward as all major subclades of hg N are still to be found there. “When you say that the highest frequencies are further North in Buryat, I don’t quite understand it. Here you have an impressive list of frequencies (http://www.docstoc.com/docs/130265674/Research-Institute-of-Medical-Genetics-at-the-Tomsk-Scientific-Center) and the Buryat N3 frequencies are about 30% and 50% and they seem to lack N* and NO* (with only a small amount of N2). Yakuts have the highest frequencies of N3, 81,9% and 94,3% respectively.Terry, I am much less acquainted with O clades and Chinese geography, so I do not insist. You are right that often it is the basal type that expands first and the diversified clades pop up in different parts of the area concerned. By the way, do you think that O-M122 arose very near the EDAR370A hot spot? Yes, I have seen Razib's second map and I would be interested to know how it is obtained. I proposed in my mail that MtDNA R11 or B is connected to the expansion of O clades in East Asia. Now I am however wondering if B is as old as Wikipedia says, 50 000 years, and NO arises 33,000 years ago, with whom did it arrive in East Asia?Do you happen to know if it is possible that this EDAR gene disappears in a population where both sexes initially have this gene but later on men marry more and more women who do not carry this gene.

     
  48. Maju

    March 6, 2013 at 7:51 pm

    Re. Admixture, Altaians are probably not the best proxy because they are themselves admixed. But if you are so interested just google "Finn admixture East Asia" and you will see a large list of Admixture runs, pro and amateur. With a little patience you can even run your own using Amixture on the 1000 Genomes Project data, as described by Razib here. As for N I won't contest anything of all you have clearly documented very well. I was thinking, wrongly, that N was more common in Buryats than that but still 30% is a quite notable frequency, suggesting a route for the lineage via that region. Otherwise N's great success was clearly in Siberia and even in the North of that region, strongly suggesting that the success of N (mostly N3 and N2) was linked to adaption to the most extreme climates of the Far North. To some extent at least it is also related to Uralic languages. Further South they are instead a small scattered lineage, even if surely more basally diverse.As for the origin of N, I'd accept "somewhere in or near China" as a perfectly valid answer. The problem of relying on N* is that it can be one single haplogroup ("N4") or many (something like "N4, N5, N6, N7 and N8). Unless that small but potentially diverse fraction is clarified, some uncertainty remains. The presence of NO* is also interesting, although again it is scattered between South China and Mongolia (and even some in Japan and Malaysia, although there's no N over there).

     
  49. Maju

    March 6, 2013 at 7:52 pm

    Also notice that I strongly disagree with Terry about the origins of O, which for me are between Indochina and South China, i.e. in the South.

     
  50. terryt

    March 8, 2013 at 3:26 am

    "Do you happen to know if it is possible that this EDAR gene disappears in a population where both sexes initially have this gene but later on men marry more and more women who do not carry this gene". I'd guess it was unlikley unless there was selection against the gene. But I think in the case of northern Russia we are dealing with a situation where a minority of mt-DNA carried the EDAR370A variant and it was drifted out. And even the Y-DNA N men who arrived may have bred with non-EDAR carrying populations along their route. "thus again pointing to northern China rather than southern Siberia as a possible place of expansion of hg N3". Following from our discussion re. Y-DNA N I have begun looking at it, at last. I notice that in ISOGG 'N3' from the paper is now 'N1c1'. It is the main N haplogroup that expanded, with N1c2-L666 a long way behind. An origin in North China makes sense. "The high STR variation among the latter, however, might not be a result of a long-term in situ differentiation of the founder lineage, but, rather a consequence of an admixture of separate N3 founder types". Most likely through the arrival of large numbers as an already-diverse scattering of haplogroups. That is very often the cause of apparent diversity. I am reasonably sure that individual haplogroups arise in separate regions, often on the advancing front of a haplogroup's distribution. "The researchers however postulate a possible southern origin when they say 'the phylogeography of the NO* and N* lineages … and the presence of N* chromosomes in southern East Asia (South China and Cambodia …) suggests that this region could be the source of the initial spread of hg N'". As I said, I can accept NO being from there but N looks much more likely to be somewhat north. "the Buryat N3 frequencies are about 30% and 50% and they seem to lack N* and NO* (with only a small amount of N2)". In ISOGG 'N2' is now 'N1c2b'. Somewhere I found the information that the haplogroup forms two clusters: one in Ural/Volga and the other one further east. "do you think that O-M122 arose very near the EDAR370A hot spot?" I think it extremely likely. And the same holds for the whole O-M175 haplogroup although I could accept that O-M119 and O-P31 arose on the southern boundary of the hotspot if it can be shown to be so. I also think N arose very near the hotspot. The EDAR370A gene is very much associated with N in eastern and northeastern Siberia. And C3 may be involved. "Now I am however wondering if B is as old as Wikipedia says, 50 000 years" It could very well be that old, but I'm very sure it is a south China, or even SE Asia, haplogroup originally. As is mt-DNA F. "NO arises 33,000 years ago, with whom did it arrive in East Asia?" At least some clades of mt-DNA D and CZ. And possibly the northern clade of B. You may be interested in this link where Maju and I have posted our versions of where the mt-DNA haplogroups arose. We agree on the region each haplogroup arose although we disagree as to the explanation for the distribution. Here is mt-DNA R: http://ourorigins.wikia.com/wiki/Mt_R_east_to_west

     

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