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Ancient North Chinese from 40,000 years ago closely related to modern locals

21 Jan
Tianyuan Cave (source)
The information is sketchy as of now but the news in the press indicate that an Homo sapiens from Tianyuan Cave, near Beijing, whose fragmented remains were discovered in 2003, was closely related to modern East Asians and Native Americans. 
The paper is not yet online but the information released to the media strongly suggests that East Asians were already distinct from other populations some 40,000 years ago. This would seem to be based on the sequencing of the mitochondrial DNA and the explicit mention of Native Americans indicates that the lineage must be A, B, C or D (X, the fifth and less common matrilineage of Native Americans, is not found in East Asians, with some exceptions from Siberia, so we can exclude it safely). 

Ancient DNA from cell nuclei and maternally inherited mitochondria
indicates that this individual belonged to a population that eventually
gave rise to many present-day Asians and Native Americans, says a team
led by Qiaomei Fu and Svante Pääbo, evolutionary geneticists at the Max
Planck Institute for Evolutionary Anthropology in Leipzig, Germany. 

This would seem to discard some adventurous hypothesis floating around about tremendous demographic changes in the Paleolithic and afterwards, at least for this region. Probably not even when “mode 4” technology arrived to the region (from Altai) c. 30,000 years ago. 
In other words: the seeds of modern populations were already there c. 40,000 years ago in East Asia (and surely also in most other regions) and, even if they may have changed somewhat, they have remained the same at least to some notable degree.
Furthermore, the autosomal DNA also seems to have been sequenced to at least some degree because the researchers state that Denisovan and Neanderthal genetic inputs are at the same levels as modern North Chinese (i.e. some 0% and 2.5% respectively):

The partial skeleton, unearthed in Tianyuan Cave near Beijing in 2003,
carries roughly the same small proportions of Neandertal and Denisovan
genes as living Asians do (SN: 8/25/12, p. 22), the scientists report online January 21 in the Proceedings of the National Academy of Sciences.

Or in the words of the Max Plank Institute:

The genetic profile reveals that this early modern human was related to
the ancestors of many present-day Asians and Native Americans but had
already diverged genetically from the ancestors of present-day
Europeans. In addition, the Tianyuan individual did not carry a larger
proportion of Neanderthal or Denisovan DNA than present-day people in
the region.

This also seems to discard models implying Denisovan admixture happening in Siberia or NE Asia and would indirectly support my own hypothesis of admixture with Homo erectus (for which Denisovans, plausibly an Erectus-Neanderthal hybrid, would be just a proxy) in or near Indonesia.
Sources: Science News, Max Plank Institute.

Update (Jan 22): the paper is already online and is open access (cool!)  I don’t think I have time to discuss it today but will do tomorrow without doubt (other than the sky falls on my head, you know).

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103 responses to “Ancient North Chinese from 40,000 years ago closely related to modern locals

  1. Andrew Oh-Willeke

    January 22, 2013 at 12:46 am

    The Neanderthal admixture percentages are unremarkable. No one supposed that there was significant new Neanderthal admixture at any time after East Eurasian populations had reached China. But, the absence of Denisovan admixture in a 40,000 year old modern human is very significant. Many Asian migration wave theories suppose that first wave Asians had Denisovan admixture which was diluted to essentially zero by subsequent waves of migration everywhere but among Papuans, Australian aborigines and certain Phillipino Negritos. The results greatly constrain those theories requiring the obliterating waves to have run their course by 40,000 years ago – a time frame that predates by more than ten thousand years, for exampe, the archaeologically attested arrival of the Jomon in Japan, or the archaeologically attested appearance of the earliest modern humans in Tibet, two of the places where Y-DNA D is most prevalent. This sample is only about 5,000 years +/- after the proto-Papuans cross the Wallace line. Archaeological evidence for modern humans in China in the timeframe prior to 40,000 years ago is quite sketchy.

     
  2. Ethio Helix

    January 22, 2013 at 4:36 am

    But maybe they didn't really split off that early as meta-populations, but rather West Asians, and therefore Europeans by extension, had experienced heavy African Admixture since OOA? Recall my K2 ADMIXTURE analysis and the significant (1/3) affinity that Europeans and West Asians had with the African cluster. If Africans were mating with West Asians since OOA, but not with East Asians because they are far away, would that not distort what the ancestral West/East Asian population would have been like?

     
  3. Maju

    January 22, 2013 at 8:08 am

    "The Neanderthal admixture percentages are unremarkable".In raw preliminary though, it could be less or even 0% and reach current levels later by arrival of more admixed "moderns". Also some have speculated about distinct admixture events in the East and West… it is not totally unremarkable (depends on what you would expect). "But, the absence of Denisovan admixture in a 40,000 year old modern human is very significant".Absolutely."The results greatly constrain those theories requiring the obliterating waves to have run their course by 40,000 years ago"…Absolutely again. Of course, the more we get to know, the better.

     
  4. Maju

    January 22, 2013 at 8:14 am

    "… but rather West Asians, and therefore Europeans by extension, had experienced heavy African Admixture since OOA?"There's something of that indeed but not "heavy", more like "subtle". "Recall my K2 ADMIXTURE analysis and the significant (1/3) affinity that Europeans and West Asians had with the African cluster".I told you already that such phenomenon happens because of (1) Admixture is forced at K=2 to create exactly two clusters and place all anomalies in the intermediate zone (i.e. "neither this nor that") and (2) to mild (tending to subtle) African admixture of West Eurasians. In other examples I pointed to you in that thread, it is Africans (sampled in lesser numbers) who are forced to appear as "Europeans" or "West Eurasians", because in all A vs B comparisons they happen to be slightly (but not much) closer to WEA pops. If you reduce the sample of East Asians enough, they will surely be forced at K=2 to appear as Western Eurasians, the two poles being Africa vs Europe/WEA.

     
  5. Raimo Kangasniemi

    January 22, 2013 at 8:59 am

    There might not be a total absence of Denisovan admixture. Different teams are claiming different things at the moment; some claim no evidence of Denisovan admixture on the Eurasian landmass, others claim very small amounts (well below 1 percent) in East Asia.In China it also seems that the larger number of modern people are included, the more likely the study is to come up with claims of Denisovan admixture.It's kind of same as in Africa with neanderthals. When some teams don't take into account admixture under 1 percent, then we get the claims that there is no Neanderthal heritage in current sub-Saharan African populations.

     
  6. Maju

    January 22, 2013 at 9:09 am

    That's because of a reason: the appearance of Neanderthal/Denisovan admixture is subject to minor error because of normal variance (we are not so distant from our other Homo cousins) and that's why only when we look at the big picture we can ascertain with any confidence that there was admixture (the "most Neanderthal" of Nigerians is clearly much much "less Neanderthal" than any Eurasian-plus and only slightly "more Neanderthal" than any other "purebred" African (i.e. excluding populations with significant Eurasian admixture).IMO very low levels of apparent "admixture" should therefore be ignored as mere noise (normal variance). Of course we can never be 100% sure that they are meaningless but that's the level of precision we can reach objectively.

     
  7. Maju

    January 22, 2013 at 10:12 am

    Erratum: "… is subject to minor error" should better be "… is subject to minor uncertainty".

     
  8. Václav Hrdonka

    January 22, 2013 at 11:19 am

    I think all those haplogroups are possible in those times in north China: M7, D, M8, M9 maybe even G, or N/N9, B, R9/F, maybe even R11. When they talk about native American, M8(as parent of C), D, B are highly probable. I dont think it will be N (parent of A) because they would not talk about difference from Europe in that case.

     
  9. Maju

    January 22, 2013 at 11:37 am

    The articles explicitly mention relatedness to modern East Asians AND Native Americans. The latter have only four matrilineages (excluding X2) so it should be either of them (A, B, C or D). Guess we can be flexible and consider all M8 (which includes C and Z) but all the rest you say should not be (unless both articles has a blatant error, what seems most unlikely), i.e. not any of these you mention: M7, M9, G, N9, R9, R11…

     
  10. Maju

    January 22, 2013 at 11:41 am

    PS- As mere bet (i.e. based only on my educated intuition) I would happily guess that not B, which has a more southernly distribution and, being derived from R may have expanded in a secondary wave (together with Y-DNA O). But then of course that secondary wave may well be before 40 Ka. so it's just a hunch after all. All the rest (D, A and M8/C) may well be very old in NE Asia. An even thinner bet would be D, which I deem the oldest to expand in Northernmost East Asia.

     
  11. Davidski

    January 22, 2013 at 11:59 am

    Where's the paper anyway? Isn't it supposed to be out by now?

     
  12. Václav Hrdonka

    January 22, 2013 at 12:38 pm

    I guess its B, it seems to have some branches in that time, so it probably expanded earlier than D. Haplogroup A – surely not, its younger. M8 is possible but its also too young. I am pretty sure about B.

     
  13. Millan Mozota

    January 22, 2013 at 2:08 pm

    I'm quite surprised of those results, i did not expected them.

     
  14. Maju

    January 22, 2013 at 3:24 pm

    It was suppossed to be out yesterday but I haven't been able to find it yet. Can't do anything about it, sorry.

     
  15. Maju

    January 22, 2013 at 3:37 pm

    Can't imagine why. They seem to fit well with my own understanding on the expansion of H. sapiens, creating the basis of modern populations already in what I call the Great Eurasian expansion. The admixture event with Neanderthals happened soon after the OoA while the one with H. erectus must have happened in Indonesia, soon before the colonization of Australasia.

     
  16. andrew

    January 22, 2013 at 7:31 pm

    I see reports of very low levels of Denisovan admixture (less than 1%) in SE Asia, but not in Northern China.

     
  17. andrew

    January 22, 2013 at 7:37 pm

    Per Dienkes, quoting from the now available paper: "Thus, it is related to the mtDNA that was ancestral to present-day haplogroup B (Fig. 1), which has been estimated to be around 50,000 y old (18) (50. 7 ka BP; 95% CI: 38.1–68.3 ka BP). We note that the age of the Tianyuan individual is compatible with this date." B is, of course, part of the mtDNA N clade rather than the mtDNA M clade.

     
  18. Millan Mozota

    January 22, 2013 at 8:08 pm

    Well, it is just that tend to think that post-pleistocene human migrations (i.e. of Neolithic chronology, recent prehistory, etc) are of much importance. For Europe & Mediterranean i recently attended to a conference of Eva Fernández Domínguez & Cristina Gamba, at Residencia d'investigadors (CSIC) in BCN. And she gave a preview of unpublished results on ancient DNA (than i cant really glose as i'm not an expert on genetics) that pointed to an important population remplacement between last mesolithic and first neolithic, in some areas & some continental routes. I'm sending to yout email an extremely low quality cellular phone pics (sorry) and the handout for the conference.

     
  19. Maju

    January 22, 2013 at 8:50 pm

    Ah, the paper is already online? Wow! And it's open access – what a luxury! Haplogroup B… not my bet but very interesting anyhow. That means that mtDNA R had already expanded c. 40 Ka ago (something we could also infer from the fact that West Eurasia, including Europe, where it's very dominant, was already in full process of colonization by then). Very cool, I'll comment more extensively when I read it. 🙂

     
  20. Maju

    January 22, 2013 at 9:06 pm

    It is a common belief (and some people are borderline fanatic about it) but I do not share it. It is still possible that some, even many, of Neolithic and post-Neolithic flows were of great importance in many regions (parts of Europe for example) but not in the simplistic way that some assume (i.e. a unique super-wave from Anatolia that almost totally replaced the pre-Neolithic populations); an intermediate approach is probably the most correct one (in Early Neolithic Europe, for example, there were probably bouts of expansiveness followed by admixture and hiatus and then another expansion wave with a different origin, etc.)It is even possible (to be confirmed or not) that there was an specifically Megalithic wave in Atlantic Europe carrying genes from SW Iberia (including some from West Asia and North Africa but not dominantly so) – just saying. Also while in some parts of Europe, like the Basque Country (cf. Paternabidea, Navarre), the Neolithic genetic pool is almost identical to modern one (and some pre-Neolithic lineages also appear to have survived to modern times), in others like Central Europe the modern genetic pools do not appear till the Bronze Age (could well be Chalcolithic however, lacking data) – but still some modern elements appear in the Neolithic and may come from more southernly parts of Europe like Italy or the Balcans. Each of these aDNA studies give us a bit of more info to reconstruct those processes. In any case massive transcontinental migrations of decisive importance across Eurasia can be safely discarded now, the various "racial" stocks probably formed on early Upper Pleistocene (or even Late Middle Pleistocene) seedings. This should be very obvious for anyone familiar with the genetics of modern populations, for example there is a quite large genetic distance (Fst) between West and East Eurasians, not as large as these two with Tropical/Southern Africans but just clearly large enough to be very very old.I got your email, I'll check it now. Thanks.

     
  21. terryt

    January 22, 2013 at 10:30 pm

    "Haplogroup B… not my bet but very interesting anyhow. That means that mtDNA R had already expanded c. 40 Ka ago (something we could also infer from the fact that West Eurasia, including Europe, where it's very dominant, was already in full process of colonization by then)". I wouldn't have picked B either. "It is still possible that some, even many, of Neolithic and post-Neolithic flows were of great importance in many regions (parts of Europe for example)" And in East Asia. "in Early Neolithic Europe, for example, there were probably bouts of expansiveness followed by admixture and hiatus and then another expansion wave with a different origin, etc." And in East Asia.

     
  22. andrew

    January 22, 2013 at 11:14 pm

    Looking at the paper itself, it looks to me like there is some very thin, but non-zero non-Neanderthal archaic admixture in Asians that is not just noise. The Europeans and Africans hover around 0.2-0.25 of a percent Denisovan admixture, while New World and Asian populations reach as much as 1% and this sample is right at the top of that range. The combined archaic admixture is also right at the top of the modern range for Asians and above the highest European individual by a measureable amount, but drops right into the European range when about 0.8% archaic Asian admixture is taken out.If one uses an initial admixture rate of 8% in actually interacting populations found in a prior study for Papuans, this would suggest a roughly 10-1 dilution of a first wave admixing population with a second wave non-admixed population in Asia, which is well short of genocidal. It is on the same order of magnitude of Cro-Magnon v. post-Cro-Magnon admixture in Europe by some estimates. There is room in time for an earlier wave. Dates for a first wave into East Asia in the window of about 75,000 to 45,000 years ago are plausible (particularly given a recent SE Asian mountains date possibly in the 60,000ish years ago) even though the archaeological evidence is thin (I have real doubts about 100,000 years ago, but I suppose it isn't entirely ruled out given what we now know about early Out of Africa dates going back to pre-100,000 years ago by a number of thousands of years).Also, mtDNA haplogroup B derived from N in a second wave, makes somewhat more sense to me than mtDNA haplogroup B in a first wave (which I would be inclined to expect to be M derived).

     
  23. Maju

    January 23, 2013 at 8:27 am

    "… it looks to me like there is some very thin, but non-zero non-Neanderthal archaic admixture in Asians that is not just noise".I can see that too but notice that only one African was used as control, a wider sample may reduce those differences to mere noise. Also PCAs are sometimes confusing, in this case the African is only considered in relation to the Eurasian-Oceanian wider sample and their differences, which must not need to be only a matter of archaic admixture."The combined archaic admixture is also right at the top of the modern range for Asians and above the highest European individual by a measureable amount, but drops right into the European range when about 0.8% archaic Asian admixture is taken out".Maybe but ask John Hawks. Other data says differently, exactly the opposite in fact, so it's threading a bit too thin."There is room in time for an earlier wave. Dates for a first wave into East Asia in the window of about 75,000 to 45,000 years ago are plausible"…I don't see anything in the Sapiens-specific genetic data allowing for two clearly differentiated waves into East Asia, so I'd discard that pretty much. Still the single wave may have been multilayered or otherwise complex (it probably was) but then we see among Papuans pretty much the same great lineages we see in China, India or Europe, so… one single greater wave is the most likely explanation as I see it."Also, mtDNA haplogroup B derived from N in a second wave"…Actually it is derived from R (which in turn is derived from N, yes). I see no particular reason in all to talk of a clear second wave but rather complex rapid dynamic and sometimes bidirectional flows between South and SE Asia. Personally I think that N coalesced in SE Asia and did it very early in the process of Greater Eurasian Expansion (GEE), otherwise why is it the most basally diverse of all macro-lineages reaching that area?

     
  24. Václav Hrdonka

    January 23, 2013 at 10:03 am

    Well, my guess was correct. Its B…

     
  25. Maju

    January 23, 2013 at 5:52 pm

    Gratz. I though it was the most unlikely bet but still correct in the range of options (consolation prize, I guess). 🙂

     
  26. Ethio Helix

    January 24, 2013 at 2:07 am

    “There's something of that indeed but not "heavy", more like "subtle".”By 'heavy', I meant heavy enough to obscure the inference of ancestral populations.“I told you already that such phenomenon happens because of “Yes you told me but you did not prove it. In either of your points the intermediateness of West Eurasians when 2 poles have been chosen need to be adequately explained, “neither this nor that” is not really an adequate explanation, IMO. In your second point, this is something that can be easily quantifiable and demonstrated if true, and reducing East Asians only defeats the purpose, the point being, that when East Asians/Amerinds, Africans and West Asians are included in an ADMIXTURE run, West Asians always appear intermediate between the two, similar to their placement in global PCA plots.

     
  27. Maju

    January 24, 2013 at 8:00 am

    "… but you did not prove it".I did not have time nor energies to do it. But above I tell you how to do the test: just put 40 Europeans, 50 Tropical Africans (spare the Pygmies just in case they distort it all) and a mere 10 East Asians and you will see a European and an African cluster and how East Asians fall fully in the European one. That's my prediction and my test setting. Anyhow it's common sense re. ADMIXTURE, which after all only checks for affinity and forces each individual into one of K clusters (two in your case). Two clusters is clearly not optimal for all Earth study, three may do depending on which populations you throw in. "West Asians always appear intermediate between the two"…First, West Asians, especially those from Arabia, have more African admixture than other West Eurasians – whether this is remnants of the OoA or more recent flow, remains to be properly determined in most cases (probably both). But more importantly, if you load the sample with East Asians and Africans, West Eurasians will be forced to more or less intermediate positions because they are not too akin to either cluster (but a bit akin to both). So you have to lighten down the sample in either extreme (Africa, East Asia). For example in Behar 2010 (and others), Africans are comparatively undersampled and therefore they cluster inside the West Asian cluster (there's no gradation among West Eurasians and the W-E duality persists at K=3, etc., after Africans are finally separated). Please, look at all carefully this because I am certain it is the way I say.

     
  28. Václav Hrdonka

    January 24, 2013 at 9:26 am

    My guess was mainly based on this paper: http://www.cell.com/AJHG/abstract/S0002-9297%2809%2900163-3 (you criticized it) I found this paper trustworthy. This case confirmed it again.

     
  29. Maju

    January 24, 2013 at 12:39 pm

    Don't have time to check it in depth now but my criticism was probably about still too recent age estimates at least in some cases. For example that paper gives an age estimate for the divergence Homo-Gorilla of c. 8 Ma, when that is in my understanding the lowest possible bound for Pan-Homo, which is necessarily more recent than the Homo/Pan-Gorilla split. But whatever.

     
  30. Onur

    January 24, 2013 at 6:13 pm

    This comment has been removed by the author.

     
  31. Onur

    January 24, 2013 at 6:24 pm

    This comment has been removed by the author.

     
  32. Onur

    January 24, 2013 at 6:38 pm

    First, West Asians, especially those from Arabia, have more African admixture than other West EurasiansOnly Arab (including the Druze) and some of Iranian (most probably from the south of Iran, it is not clear whether they are Arabic-speaking or Persian-speaking), Jewish and Samaritan West Asians have discernible Negroid admixture according to the results of Behar et al. 2010 and other ADMIXTURE studies, and among Negroid-admixed West Asians almost only Muslim Arabs and Yemen Jews have Negroid admixture in levels worthy of mention according to the same results. Importantly, Cypriots, Turks, Armenians, Georgians, Assyrians and Kurds show no discernible Negroid admixture while most non-Basque Iberians and southern Italians (including Sicilians) show small levels of discernible Negroid admixture in those analyses. For example in Behar 2010 (and others), Africans are comparatively undersampled and therefore they cluster inside the West Asian clusterYou must have meant general West Eurasian rather than West Asian, as that cluster includes Europeans and West Asians equally.

     
  33. Ethio Helix

    January 24, 2013 at 7:05 pm

    It doesn't matter which West Asian population has more African affinity @ K2, the point is that they all have it at significant amounts relative to East Asians, this African Affinity of West Asians appears in a clinal manner, Yemenis have it at 43%, while Russians have it at 25%, and even South Asian Dalits have it at 21%, the only populations that do not carry this affinity in appreciable amounts are East Asians and Amerinds, that is the whole point.Maju, you are also mistaken in the way you are reading the Behar 2010 ADMIXTURE chart for K2, it is the West Asians that appear in the African cluster and not the reverse, please take a look at it carefully.

     
  34. Maju

    January 24, 2013 at 8:12 pm

    @Onur: if a population has, for example, some Y-DNA E (and all West Eurasian populations I know of do to some extent) they do have some African-specific admixture. Some of course have more and others less but that's not too important because if the ADMIXTURE algorithm produces very low values of affinity with either cluster, that will weight a lot in comparison in every case. What Ethio Helix does is to load ADMIXTURE with various populations from all the Old World and that makes even the Finns to appear intermediate between Africa and East Asia at K=2. I say that that's irrelevant because cross-validation would denounce that K level as mostly meaningless but how it happens is still interesting to understand.@Ethio Helix: It is extremely clear in Behar 2010 (PPV), in the global ADMIXTURE graph, how for example Turks appear exactly the same amount of brown at K=2 as blue at K=3 (and yellow for both). That the brown color is used at K=3 to describe Africans and not Eurasians should not mislead you (it does however) because color coding changes following a sequence that is not defined by continents but by cluster number (or arbitrary choice by the authors). What I say of Turks is the same for most other West Eurasian populations, although some also display minor African admixture at K=3, etc. In that graph it is very clear that Africans (relatively undersampled) are forced to cluster with West Eurasians at K=2 but break apart with their own cluster at K=3. You may say: but then Ethiopians are admixed! And I'll answer: of course, you only have to look at patri- and matrilineages but ADMIXTURE confirms it in case there was any doubt. You may not like it (I personally think that admixture is as cool as anything else, or even more, and in the case of Ethiopians very interesting because of its likely antiquity) but it is what it is. Carry your double ancestry proudly because for what they were, you are.

     
  35. Onur

    January 24, 2013 at 10:31 pm

    Luis (a.k.a. Maju), Ethio Helix/Etyopis confusingly often uses the phrase West Asian to denote West Eurasians, i.e., Caucasoids, in general. You have to take that into account when responding to him.if a population has, for example, some Y-DNA E (and all West Eurasian populations I know of do to some extent) they do have some African-specific admixture.Y-DNA haplogroup E is not a specifically Negroid haplogroup. So it is very normal for a population to carry significant proportion of Y-DNA haplogroup E and at the same time show no Negroid admixture.

     
  36. Ethio Helix

    January 25, 2013 at 1:31 am

    First a correction on my previous comment, the Behar (2010) run was produced by STRUCTURE not ADMIXTURE.Now back to addressing your points Maju,#1) The color coding was most certainly not arbitrary Maju, and you know it, in effect what you are saying is that Africans split off from West Asians, which is utterly ridiculous.#2) Ok, forget the Behar (2010) global run, I have shown that the data-set is imbalanced anyway, here is another one that resembles my run even better,Schlebusch (2012) , an ADMIXTURE run using 270K SNPs and with a better global representation than Behar (2010). Note again the significant African affinity in all West Asians @ K2. #3) Let's try to keep topic of your blog post, which is not about my ancestry but about West and East Asians splitting off from each other > 40KYA. My point is that they while they may have very well split off from each other GEOGRPAHICALLY >40 KYA, what makes these scientists so sure they went their separate ways genetically that long ago? Especially given the fact that modern West Asians today have an African affinity that modern East Asians don't have, and that likely this affinity has always been there and maintained since OOA, thus obscuring any inferred ancestral population for any subset of West Asian populations.

     
  37. Onur

    January 25, 2013 at 1:46 am

    This comment has been removed by the author.

     
  38. Onur

    January 25, 2013 at 2:02 am

    Ethio Helix, please stop referring to West Eurasians as "West Asians", as that is confusing people and, more importantly, is wrong terminology. Also, the Behar et al. 2010 run is an ADMIXTURE run, not a STRUCTURE run.

     
  39. Ethio Helix

    January 25, 2013 at 2:54 am

    By West Asia I mean the ENTIRE western part of the massive continent known as Asia, which includes the European peninsula, I do not mean just the Middle East as for example the United Nations defines West Asia. I actually find the term Eurasia confusing and erroneous as Europe is only a tiny fractional part of the Asian continent, but, whatever.With respect to Behar (2010), yes it was an ADMIXTURE run, I was correct the first time, but I confused it with another study later.

     
  40. Onur

    January 25, 2013 at 8:38 am

    If you do not like the term Europe, then do not use the term Asia either, as Asia by definition exludes Europe since the Antiquity, and only use the term Eurasia. That would not confuse people.

     
  41. Maju

    January 25, 2013 at 8:41 am

    I have no personal problem other than confusion with using the shorter and rather realistic geographical term "West Asia" instead of the more common and easy to understand "West Eurasia" but I prefer the latter for the sake of mutual understanding. Also when I say "West Asia" I mean the "Near" or "Middle East", another unfortunate misnomer but…But there is no point in discussing "races" as Onur does so aggressively. I wouldn't dare to proclaim that there is a "Negroid race". What is clear is that haplogroup E (Y-DNA) is by origin and much of its downstream processes purely African and that original Africans were more or less "Black", even if later Eurasian inputs have changed that reality in some parts of Africa (the North mostly).The presence of Y-DNA E and other lineages (more and more L(xM,N) shows up in West Eurasia, sometimes with very old dates of arrival, others more recent maybe) imply African admixture ("Negroid" if you wish, not my choice of words anyhow) at minor but very real levels. Let's get real!@Ethio Helix: "The color coding was most certainly not arbitrary"… Either arbitrary or automatic it is meaningless. You have used ADMIXTURE: you know how it is: how clusters which are obviously the same change colors from one K-level to the next just because of the change in numeration. "… in effect what you are saying is that Africans split off from West Asians"..Not at all! What I say is that you cannot reconstruct a genetic tree of Humankind with ADMIXTURE. You should know that too. You need haploid DNA for that, or maybe other autosomal techniques like the not-too-trustworthy TreeMix.No time for more. Later…

     
  42. Maju

    January 25, 2013 at 9:42 am

    "… here is another one that resembles my run even better,Schlebusch (2012)"…That one acually resembles your run in that West Eurasians are split (even if the resulting proportions are quite different) between the East Asian (not "Asian" nor "Eurasian") cluster and the African one. As it happens to you at K=3. What differentiates both from Behar's approach is that in his run, Africans are relatively undersampled: they weight less overall and therefore they become the "victims" of K=2 oversimplism: this or that, being this or that in Behar's case: West Eurasian or East African. And because mutual secondary (mostly minor) genetic influences, all Africans end up as apparent West Eurasians (only at K=2). Notice please that unlike in your run or that of Schlebush, in Behar's West Eurasians do not appear as part-and-part. That is very important to know that that cluster is primarily West Eurasian."Let's try to keep topic of your blog post"…I beg you, indeed.

     
  43. Onur

    January 25, 2013 at 9:57 am

    What is clear is that haplogroup E (Y-DNA) is by origin and much of its downstream processes purely African and that original Africans were more or less "Black", even if later Eurasian inputs have changed that reality in some parts of Africa (the North mostly).Incorrect. Africa was racially much more diverse before the relatively recent rise to domination of the Negroid race in its Sub-Saharan part. There were Caucasoids as far south as what is now South Africa (e.g., the Hofmeyr man) during the Upper Paleolithic. Caucasoids arrived much of Africa before the arrival of Negroids to those regions. In fact, the Negroid race seems to be a relatively late formation (originally from western Sub-Saharan Africa? modern-archaic hybrids?). Thus, the original Y-DNA Hg E carriers were probably Caucasoid. The fact that Y-DNA Hg E is descended from Y-DNA Hg DE, which most likely originated somewhere between Africa and East Asia, further supports that.

     
  44. Maju

    January 25, 2013 at 10:17 am

    This comment has been removed by the author.

     
  45. Maju

    January 25, 2013 at 10:18 am

    This comment has been removed by the author.

     
  46. Maju

    January 25, 2013 at 10:21 am

    @Etio Helix:"My point is that they while they may have very well split off from each other GEOGRPAHICALLY >40 KYA, what makes these scientists so sure they went their separate ways genetically that long ago? Especially given the fact that modern West Asians today have an African affinity that modern East Asians don't have, and that likely this affinity has always been there and maintained since OOA, thus obscuring any inferred ancestral population for any subset of West Asian populations".Actually the main OoA population (M, N mtDNA haplogroups) migrated to South and SE Asia before colonizing West Eurasia (parts re-colonized, with plausible remix with other minor OoA pops with L(xM,N) lineages, but mostly anew, taking it from Neanderthal hands).The Eurasian colonization did not directly spawn from West Asia but from South Asia (and SE Asia). West Asia (parts of it, Arabia Peninsula mostly) only acted as initial corridor or "pump", it was not the real source of the Great Eurasian Expansion.In approx. chronology:· c. 125-90 Ka preliminary "pump" out of Africa (to Arabia)· c. 80 Ka arrival to South Asia and first expansion (M explosion)· c. 70-50 Ka secondary expansions in SE Asia and surroundings (Australasia, East Asia in general, backflow to South Asia)· c. 55-40 Ka colonization of West Eurasia (mostly in Neanderthal hands before that) and probably also back-flow into parts of Africa.So there was a period of at least 30 Ka in which both populations ("Africans" and "Asians") were quite strictly separated. That explains why WEA and EA pops. have relatively high Fst values when compared but not quite as high as either do when compared with Africans. This isolation from Africa has persisted in "Eastern Eurasians" (when I say this I mean to include Oceanian and American aborigines) and mostly also in South Asians as well. But not quite in West Eurasians who regained direct contact with Africans and hence became somewhat "African" (post-OoA Africans) ourselves (not much maybe but still meaningful).So the affinity (other than being human) has not "always" been there but was regained with the colonization of West Eurasia (and parts of Africa) from South Asia c. 55-35 Ka ago.

     
  47. Maju

    January 25, 2013 at 10:33 am

    @Onur: nonsense! There were no "Caucasoids" in South Africa (before European colonization), that's a total nonsense proper of ridiculous Hitlerian propaganda, nor "Caucasoid" is any sort of absolute category but just a relatively homogeneous range of phenotypes which, logically, is approximately coincident with a zone of relatively homogeneous genetic ancestry.You already have warnings (did I not banish you altogether?) for racist-mongering. Beware your steps. Certainly I can pass with none of your racialist babbling.

     
  48. Onur

    January 25, 2013 at 10:38 am

    It is scientifically proven that the Hofmeyr Skull (a 37,000-year-old skull from what is now South Africa) is a Caucasoid skull (of the Cro-Magnoid variety of the Caucasoid race):http://en.wikipedia.org/wiki/Hofmeyr_Skull

     
  49. Onur

    January 25, 2013 at 12:25 pm

    The Negroid race seems to be partially descended from the Caucasoid race. This explains the general genetic affinity between Caucasoids and Negroids relative to Mongoloids, Australoids and ASI.

     
  50. Ethio Helix

    January 25, 2013 at 5:51 pm

    Ok I will use Eurasia to avoid confusion, however, I disagree with it as it is simply nothing more than another manifestation of European cultural hegemony rather than any objective geographical description.Anyway, first let me mention something with respect to haplogroup E, since it is once again being dubiously implicated as having non-African origins, the Plaster thesis that I had posted on my blog a few months back found two cases (out of 69) where E-M96 (x P147, M75) were found in Ethiopia, specifically amongst the Amhara dataset. This is significant as it proves, again, the antiquity of E* in East Africa, previously, only one find in Southern Africa was found by Karafet (2008) , an additional 2 finds were reported by Abu-Amero (2009) in their Saudi Arabian dataset, but these could have very easily been transported from nearby Africa in recent times. In addition, the database of private genetic testing company FTDNA reports one additional case of E-M96 (x P147, M75) from Ethiopia. So this is in addition to all the subclades of E-M96 that are found in Africa, most of which are exclusively found in Africa. Therefore, people who implicate E-M96 having non-African origins do so, on not only very flimsy data, but also on grounds that are questionably parsimonious.I will be getting back to the Autosomal issue a little bit later Maju, after I get some other work done.

     

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