February 16, 2013

More Neanderthal admixture details

The main conclusion of this new study seems to be that East Asians have normally more Neanderthal admixture than South or West Eurasians. Also the Maasai from East Africa have been shown to have minor Neanderthal admixture, consistent with the also minor Eurasian genetic component they have.

Jeffrey D. Wall et al., Higher Levels of Neanderthal Ancestry in East Asians Than in Europeans. Genetics 2013. Freely accessible at the time of writing thisLINK [doi: 10.1534/genetics.112.148213]

Abstract

Neanderthals were a group of archaic hominins that occupied most of Europe and parts of Western Asia from roughly 30-300 thousand years ago (Kya). They coexisted with modern humans during part of this time. Previous genetic analyses that compared a draft sequence of the Neanderthal genome with genomes of several modern humans concluded that Neanderthals made a small (1-4%) contribution to the gene pools of all non-African populations. This observation was consistent with a single episode of admixture from Neanderthals into the ancestors of all non-Africans when the two groups coexisted in the Middle East 50-80 Kya. We examined the relationship between Neanderthals and modern humans in greater detail by applying two complementary methods to the published draft Neanderthal genome and an expanded set of high-coverage modern human genome sequences. We find that, consistent with the recent finding of Meyer et al. (2012), Neanderthals contributed more DNA to modern East Asians than to modern Europeans. Furthermore we find that the Maasai of East Africa have a small but significant fraction of Neanderthal DNA. Because our analysis is of several genomic samples from each modern human population considered, we are able to document the extent of variation in Neanderthal ancestry within and among populations. Our results combined with those previously published show that a more complex model of admixture between Neanderthals and modern humans is necessary to account for the different levels of Neanderthal ancestry among human populations. In particular, at least some Neanderthal-modern human admixture must postdate the separation of the ancestors of modern European and modern East Asian populations.

There is a sentence in page 8 in which the authors claim that:

By using the high coverage Denisova genome, we are able to show that the admixture rate into East Asians is 40% higher than into Europeans.

However I fail to see it in the D-statistic graphs, which show less than 15% more Neanderthal admixture in Eastern Asians than in Europeans (on average and discounting error margins, which strongly overlap). It may be therefore another case of hair-splitting.

Instead the evidence of weak Neanderthal admixture (via minor Eurasian  genetic influence) in the Maasai of East Africa seems more solid: while error margins of Maasai and Luhya do overlap, the main blocs do not.

Figure 3. Summary of significance tests for average values of D. Positive values indicate that the second sequence is more similar to the Neanderthal genome than the first sequence. In all parts, the box plots indicate the range of D values obtained for pairs of individuals from the populations indicated. Parts A and B are box plots of individual D statistics computed for each individual from the specified population compared with each Yoruban. The p values are from the randomization test, Test 1, of significant differences in the average D values for different pairs of populations. Parts C and D show box plots of individual D statistics computed for every pair of individuals in the specified populations. The p values are from the randomization test, Test 2, of significant differences of the average D from 0. See also Table 2.

It is surely convenient to look carefully at all the data, including the supplementary materials, before jumping to any strong conclusions. Among them I found more interesting fig. S1:

Figure S1: Box plot of the D-statistics for Analyses A and B for the set (Afr, X), where X was any of the non-African populations, CEU or TSI (Europeans, green), CHB or JPT (East Asians, blue), or GIH (South Asian, pink) (PDF, 222 KB).

As we can see here, the error margins continue overlapping very strongly, but, assuming that we can jump to conclusions based on the norm (thick black line), which is assuming some risks indeed but also the only way to (tentatively) agree with the authors' conclusion of greater Neanderthal admixture among East Asians, then the causes should be:
  1. Founder effect among East Asians, known to have less overall genetic diversity and suspected to have undergone some extra (mild?) bottleneck at their ancient origins.
  2. Low-level African (and surely also early OoA residuals from West Asia) admixture among West Eurasians, notably Tuscans (TSI) in these samples but also to some extent all Europeans (incl. CEU). This has the effect of increasing genetic diversity but also of slightly diluting Neanderthal admixture. The control here are Indians (GIH), which show slightly more Neanderthal admixture than Europeans (but are still closer to these than to East Asians also in this aspect).
Indians (who don't seem to have any post-OoA African admixture, unlike Europeans and West Asians, who have it at variable low levels) suggest that factor #2 (dilution) weights only somewhat and therefore that factor #1 (East Asian founder effect) must be considered the main one instead. 

But, unless someone can point me where I am wrong, I fail to see neither the alleged 40% excess Neanderthal admixture in Orientals nor why would these results question the single admixture episode (or period) at the origins of migration out of Africa (OoA).

To finish this entry, it must be mentioned that the authors could only detect at most the tiniest fraction of Denisovan admixture among the sampled populations (i.e. nothing relevant and with no regional differences). However they did not research, admittedly, the South China populations suggested to have slight more Denisovan input by  Skoglund and Jakobsson 2011.


See also:

61 comments:

  1. "Indians (who don't seem to have any post-OoA African admixture, unlike Europeans and West Asians, who have it at variable low levels) suggest that factor #2 (dilution) weights only somewhat and therefore that factor #1 (East Asian founder effect) must be considered the main one instead".

    Exactly.

    "Founder effect among East Asians, known to have less overall genetic diversity and suspected to have undergone some extra (mild?) bottleneck at their ancient origins".

    Doesn't that fit with what I've been trying to tell you for ages? There was at least some movement into East Asia via Central Asia. Surely that is the only possible conclusion considering the lack of either neanderthal or Denisova admixture in South Asian populations. And that movement through central Asia considerably pre-dates any movement into Europe.

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    1. I understand that Central Asia is (before the Metal Ages) in the Western and not the Eastern Asian province and that no archaeological evidence suggest exchange with the East other than (1) Denisovans, if they are, as I think, partly H. erectus from East Asia, and (2) "mode 4" flows already within full Homo sapiens, which have not been demonstrated in any way to be "more Neanderthal" than any other.

      I lean for founder effect unless there are clear indications of something else: the founders of East Asian peoples had on average slightly more Neanderthal input than the founders of South/West Eurasian ones. A mere fluke long ago.

      Prove me wrong, please, but don't try to convince me without evidence because founder effect is a wonderful explanation by default.

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    2. @terryt: There was at least some movement into East Asia via Central Asia.

      I was just reading about the Paleolithic in Central Asia and thought of you. I had not given it much thought, before, but from what I'm seeing in the literature there is no particular reason that some modern humans could not have entered East Asia via an inland route. There certainly seems to have been a Neanderthal presence throughout Central Asia, one that extended through Mongolia and Siberia. At some sites, they've found Mousterian and an Upper-Paleolithic industry in alternating strata, while at others MP and UP industries appear to occur within the same horizon.

      That there were ancient modern humans just west of China proper in the Late Pleistocene is an incontestable fact. The Salawusu culture of Inner Mongolia, for instance, is roughly contemporary with the people of Tianyuan Cave, if not earlier.

      The idea that Central Asia was part of the west, before the metal age, is self-serving rubbish.

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    3. Actually there is a particular reason, Highlander: that all Homo sp. we know at the necessary crossroads, Altai, before c. 40 Ka are not Homo sapiens but other species (Neanderthals and Denisovans). Only after c. 40 Ka we see Homo sapiens (with Aurignacian-like tech) and by then there were already H. sapiens near Beijing with a different flake-based industry (but nothing Mousterian AFAIK). So Homo sapiens almost necessarily arrived to East Asia via SE Asia.

      Tell me if you need links on the literature on the matter.

      "At some sites, they've found Mousterian and an Upper-Paleolithic industry in alternating strata"...

      Mousterian in Mongolia?! That would be totally new to me. Could you produce a link?

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    4. Would you consider reading a book, Maju? Or how about just putting "mousterian" and "mongolia" into a search engine and mashing the "Enter" key? Worked for me.

      The Salawusu formation is at least 35,000 years old and possibly twice that. The scapula found near its base has been interpreted as modern with Neandertal-like features. The Darra-i-Kur temporal bone is likewise interpreted as H sapiens with archaic morphology and was found in a Mousterian context.

      Reports of two Qafzeh-Skhul-type hominids, one in Inner Mongolia and another using a Neandertal toolkit in Afghanistan, suggest that it is at least plausible that Neandertal DNA arrived in China via Central Asia, especially in light of curiously persistent Mousterian industries across the region. Terry could be right on this one. His idea certainly deserves more than the sneering contempt you've shown so far.

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    5. IMO MP Palestine remains are all Homo sapiens. There could be one hybrid individual (Skhul 5 if my memory is correct) but that's about it.

      What else? The scapula: this paper says clearly: "This scapula is small and its dimension is similar to that of modern female".

      The alleged Mousterian artifacts. I could find nothing but a cryptozoological book that mentions that claim by passing: "Neanderthal fossils are not known in Central Asia, though Shackley claims to have re- covered, in Mongolia, Mousterian tools normally associated with them".

      A claim is not a fact!

      So rien de rien.

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    6. Sorry, the first paper is: http://csb.scichina.com:8080/kxtbe/fileup/PDF/06ky2110.pdf

      Forgot to insert the link, meh!

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    7. On the other side, as Terry points below, this paper does mention that there seems to be some Mousterian, related to that of Altai, in Mongolia. If so, I stand corrected.

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    8. Ooops, forgot the link again: http://www.cell.com/AJHG/retrieve/pii/S0002929711005453

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  2. Indians (who don't seem to have any post-OoA African admixture, unlike Europeans and West Asians, who have it at variable low levels) suggest that factor #2 (dilution) weights only somewhat and therefore that factor #1 (East Asian founder effect) must be considered the main one instead.

    The Gujarati are predominantly West Eurasian ("ANI"), so that explains the result in their case. Groups like the Onge would probably be different. Onge would also be particularly interesting to examine as they belong to Y-DNA D and mtDNA M, and so any preserved Neanderthal affinity they have may trace back to some of the earliest Eurasians.

    As for Europeans, we must not forget that Ötzi was apparently much more "Neanderthal" than any modern European or Middle Easterner. So it would probably be fallacious to use East Asians as a baseline for the Neanderthal affinity of early Eurasians (if considering the second possibility of African admixure you mentioned), it seems like the story was much more complicated. It will all be known more precisely once some more aDNA is available, I'm sure.

    Another matter that should be looked further into is whether the lower Neanderthal affinity of the Luhya in comparison to Yoruba is a result of their hunter-gatherer or Nilotic admixture.

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    1. Whatever some other bloggers and even the occasional academic researchers say, I'm still very unconvinced of the ANI component being a West Asian backflow and I rather suspect it as signature from before 50 Ka - i.e. North and South India, I suspect, were two differentiated populations mostly separated by an arid Deccan since maybe as early as 80 or 70 Ka ago (although never fully separated because the Western coastal corridor was always permeable - but so were other regional boundaries, so...) Later, maybe as early as c. 55 Ka ago some people from proto-ANI migrated Westward and founded the West Eurasian population which remains, with only minor further admixture, until now.

      As for the Onge, I find their conjectured connection with India proper (the Andaman are a remote SE Asian archipelago even if it politically belongs to the Indian Union) equally oblique: they are IMO a segregated "continental" population on their own right since some time, rather early, in the process of colonization of Eurasia and Australasia.

      That's my understanding, with due caution. Some day I guess I may explore the matter by myself with the help of ADMIXTURE but who knows when - then I'd be very careful to explore all "natural" clusters and not just a few until the cross-validation value is the correct one (normally this step is ignored and too few clusters are used instead, rendering the results relatively useless and confusing), also I'd check carefully genetic distances (Fst) and if the ANI-ASI and ANI-WEA genetic distances are as I expect, then they should be of "continental value", otherwise ANI would be indistinct in this aspect with any other West Eurasian clusters.

      Hope you see my point. I may be wrong but I would not call ANI "West Eurasian" on light of the little I have seen on genetic distances on this aspect. For example, in the 1990s, Cavalli-Sforza already found two distinct South Asian clusters but both were equally distant from West Eurasians (see tree), of course he has been found incorrect in some aspects but still I am not aware of any such genetic distance comparison, just wild speculation on the origins of this ANI/ASI duality.

      ...

      As for Ötzi, that's what John Hawks believed to have found. His method also produced very different results than this paper re. East Asian vs European Neanderthal admixture, so again I prefer to remain cautious until confirmed or rejected. Notice that Ötzi was also "found" to be most similar to modern Sardinians (maybe debatable because there are many isolated populations in the Alps only recently explored for the first time) but Sardinians are not particularly akin to Neanderthals at all.

      So I prefer to remain cautious again.

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    2. As for the Luhya and Yoruba they look quite similar and any apparent difference may well be "splitting hairs". But if there is some of what you say, then it may be caused by Chadic genetic influences in the Yoruba or whatever. Hard to say.

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  3. Whatever some other bloggers and even the occasional academic researchers say, I'm still very unconvinced of the ANI component being a West Asian backflow and I rather suspect it as signature from before 50 Ka - i.e. North and South India, I suspect, were two differentiated populations mostly separated by an arid Deccan since maybe as early as 80 or 70 Ka ago (although never fully separated because the Western coastal corridor was always permeable - but so were other regional boundaries, so...) Later, maybe as early as c. 55 Ka ago some people from proto-ANI migrated Westward and founded the West Eurasian population which remains, with only minor further admixture, until now.

    There is clear evidence of relatively recent admixture in India, mainly in the paternal lineages; especially R1a1a-Z93 and J2. These would be descendants of an "eastern" Neolithic wave, and/or later Indo-Aryan incursions. Compare to the western Neolithic wave reaching Africa, bringing J1, R1b and perhaps T (the eastern counterpart in that case may be L). If the Gujarati are already "more Neanderthal" than West Eurasians, despite their West Eurasian admixture (also suggested by their autosomal affinities), there's every reason to believe that relatively unadmixed South Asians would preserve this element even further.

    You bring no genetic evidence to support your explanation for the regional/caste differences in South Asia. So I don't know what to think about that. I know that mtDNA R, which may be indigenous to South Asia, is also predominant in West Eurasia. But I don't see how the frequency nor diversity of R within India supports your scenario.

    As for the Onge, I find their conjectured connection with India proper (the Andaman are a remote SE Asian archipelago even if it politically belongs to the Indian Union) equally oblique: they are IMO a segregated "continental" population on their own right since some time, rather early, in the process of colonization of Eurasia and Australasia.

    Regardless, their Neanderthal affinity would be very interesting to look at, don't you think? Other isolated tribal groups from the subcontinent could also be used to compare with Indian populations.

    As for the Luhya and Yoruba they look quite similar and any apparent difference may well be "splitting hairs". But if there is some of what you say, then it may be caused by Chadic genetic influences in the Yoruba or whatever. Hard to say.

    The autosomal DNA of Chadic populations is very similar to Nilotic populations, despite the high frequencies of Y-DNA R1b in the former. And the Nilotic influence in the Luhya is certainly much more significant than the Chadic influence in Yoruba (so far undetected AFAIK).

    The Maasai may be Nilotic, but it's well known that they have admixed with Cushites quite heavily. So they are expected to be admixed with Eurasians, and in turn, Neanderthals as well.

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    1. "There is clear evidence of relatively recent admixture in India, mainly in the paternal lineages; especially R1a1a-Z93 and J2".

      Not really sure about when R1a and J2 may have arrived to South Asia but what I know from many other regions and populations is that Y-DNA inheritance hardly ever correlates too strongly with autosomal genetics when mtDNA is contradictory in origins. And the vast majority of South Asian mtDNA, except maybe in parts of Pakistan, looks terribly aboriginal to the subcontinent.

      "Compare to the western Neolithic wave reaching Africa, bringing J1, R1b and perhaps T"...

      Precisely: I have all kinds of doubts about that wave being "Neolithic" and instead I suspect it much much older, maybe early UP/LSA (in NE Africa at least). Notice please that most West Asian populations have a balanced tendency in their J1/J2 correlation, some have more J1, some more J2 but none show only J1 or J2. and yet, as I was discussing with Etiopis at his blog recently, only Lower Egyptians of all African populations show any kind of relevant amount of J2. Hence if it is Neolithic it must be from before J2 migrated towards Levant and Arabia and that would be IMO the PPNB period (most plausible case - or earlier), leaving a very narrow window for the specifically Neolithic propagation to Africa other than Lower Egypt, which does indeed look like having strong "recent" West Asian genetic influence.

      But well... opinions.

      "You bring no genetic evidence to support your explanation for the regional/caste differences in South Asia".

      Nor did the authors of the ANI-ASI study. At first I also accepted their conclusions upfront but, after reading someone protesting them at another blog, I re-read the paper and realized that it was all based on nothing: just an arbitrary interpretation.

      I did bring anyhow the Cavalli-Sforza tree, which so far is the best I have read on the matter. I know it's not enough but it's quite indicative.

      ...

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    2. ...

      "But I don't see how the frequency nor diversity of R within India supports your scenario".

      That's a good ojection: the basal diversity does suggest an origin in South Asia for mt DNA R but the direct connection to West Asia sublineage by sublineage is weak (not totally lacking but unclear in many cases). Still, if SA is at the origin of R and M (and probably SEA at the one of N), where else could the ancestors of West Eurasians come from? Not Africa, which has different lineages, nor via Central Asia which was then inhabited by Neanderthals and other archaic humans. So, on mtDNA alone, it must be South Asia.

      When we look also at Y-DNA and what do we see: all F-derived (except the occasional Siberian or African arrival), which is again original of South Asia based on what we know about its basal diversity. Its descendants P and R also appear to have the greatest diversity in South Asia (most P*, nearly all R2 and lots of R1 - even if it can be argued that R1 is West Asian) - even if their precursor MNOPS might have made a detour via SE Asia (as may also have done mtDNA N), they must have come back via South Asia anyhow.

      Finally we have some still weak but suggestive archaeological evidence like very early stone blades in the subcontinent, which I am not sure how supportive it is but is at least quite suggestive of North SA rather intense interaction with the West Eurasian province at the origins of UP. I cite from Synopsis of Paleo-India, section MP (with H. sapiens?):
      → Patpara, Middle Son Valley <103 ka (100-150 ka): Blade and flake-blade cores; polyhedrons absent (Blumenschine et al 1983) ‘scraper-based industry’ (JH2005)
      → Patne, Maharashtra Late MP Phase 1: blade cores, retouched blades (Sali 1989) (JH2005)
      → Bhimbetka III F-23, near Narmada River, Raisen District, Madhya Pradesh Layers 4 and 5 (EIP Project Preliminary OSL central) 45±8 ka(BR2005): III F-23 (Misra Shelter) : ‘Middle to late phase of MP’: blade and flakeblade cores, scrapers, blades, knives, borers, denticulates, notches,burins (Misra 1985) (JH2005)
      → Chancha Baluch, Indus Valley (Allchin, Goudie, Hegde 1978) Panchmahals (Sonawane
      1984) Godavari Valley (Joshi et al 1979-80) Bhagi Mohari (Paddayya 1982-3) (JH2005):
      Transitional MP-UP: blade-based tools, typically small % of total blank production (Allchin, Goudie, Hegde 1978) (JH2005)
      → Site 55, Pakistan (loess overlying artifacts) ~45 ka (Rendell and Dennell 1987, Dennel 1992) (CP2006, JH2005): Flake blades, microblades; stone lined pit, wall (Dennell et al 1992) (JH2005)
      → Chandresal, Kota, Chambal Valley, Rajasthan Lower Level (14C on eggshell) 38.9±0.7 ka Upper Level (14C on eggshell) 36.55±0.5 ka (Mook 1982) (KG1988): ostrich eggshell beads and fragments, 1 engraved (Mook 1982) (KG1988) Chambal UP: typically
      jasper, chalcedony, chert retouched blades, small and tanged points, scrapers, burins, lunates, flakes (KG1988)

      Etcetera...

      I'm no expert in Indian archaeology but, to my eyes, all this suggests a process of evolution towards "mode 4" in Northern South Asia and maybe especially in the NW. Considering the genetic evidence and that there is no other plausible origin when looking at the overall picture, the conclusion seems relatively straightforward. In any case, it's not impossible that there was a period of SA-WEA interaction at the beginnings of the UP in both regions, even after the colonization of West Eurasia was already ongoing strongly.

      ...

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    3. "[Onge] Neanderthal affinity would be very interesting to look at, don't you think?"

      Sure, why not? Another piece in the puzzle.

      "The autosomal DNA of Chadic populations is very similar to Nilotic populations, despite the high frequencies of Y-DNA R1b in the former. And the Nilotic influence in the Luhya is certainly much more significant than the Chadic influence in Yoruba (so far undetected AFAIK)".

      I take your word in that but it is precisely the R1b among Chadics (necessarily of Eurasian origin) what offers a window of opportunity for increased Neanderthal admixture. On the other side, I fail to see how "decreased" Neanderthal admixture could come from Nilotics (it'd be either increased or neutral but not "decreased").

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    4. Not really sure about when R1a and J2 may have arrived to South Asia but what I know from many other regions and populations is that Y-DNA inheritance hardly ever correlates too strongly with autosomal genetics when mtDNA is contradictory in origins. And the vast majority of South Asian mtDNA, except maybe in parts of Pakistan, looks terribly aboriginal to the subcontinent.

      I agree with you on that general principle, actually. But South Asians look like an exception, considering their autosomal DNA affinities.

      Precisely: I have all kinds of doubts about that wave being "Neolithic" and instead I suspect it much much older, maybe early UP/LSA (in NE Africa at least). Notice please that most West Asian populations have a balanced tendency in their J1/J2 correlation, some have more J1, some more J2 but none show only J1 or J2. and yet, as I was discussing with Etiopis at his blog recently, only Lower Egyptians of all African populations show any kind of relevant amount of J2. Hence if it is Neolithic it must be from before J2 migrated towards Levant and Arabia and that would be IMO the PPNB period (most plausible case - or earlier), leaving a very narrow window for the specifically Neolithic propagation to Africa other than Lower Egypt, which does indeed look like having strong "recent" West Asian genetic influence.

      I strongly disagree with your dating. The spread of the "West Asian" component often seen in ADMIXTURE correlates very well with Y-DNA J2 in Africa, the Middle East, and South Asia. Quite unlike J1 which is "Southwest Asian" and similar to the Neolithic component found in Europeans. West Asian may also be associated with Y-DNA R1a1a in parts of Europe and South Asia.

      Anyway, "West Asian" also looks very much like a Bronze Age phenomenon outside of West Asia, from where it was spread as a result of Semitic and Indo-European migrations. Except maybe in South Asia where some of it may be Neolithic. Across North Africa and East Africa, there is an absence of the West Asian component (excluding Egypt and to a lesser degree Semitic Eritrea/Ethiopia) that correlates with J2. Both are highly prevalent in Semitic Middle Easterners. In Europe, West Asian is present all across except in the non-Indo-European Basques, and it is totally unseen in the ancient DNA so far (unlike the "Southern" or "Southwest Asian" Neolithic component). Clearly, the spread of the West Asian component had nothing to do with the spread of farming. Their time to shine came later.

      Early UP/LSA is of course simply ridiculous, I hope you're not serious about that. The ancient DNA will solve this soon enough, and the dating of Y chromosome lineages will improve greatly as FGS becomes more widespread.

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    5. I found a relevant paper, Metspalu 2011 - "Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia".

      In table 1 we find all kind of Fst distances and Indians have:
      → North vs South: 0.004
      →North vs Center: 0.003
      →South vs Center: 0.005
      →GIH vs North: 0.003
      →GIH vs Center: 0.010
      →GIH vs South: 0.007
      →Pakistan vs North India: 0.010
      →Pakistan vs Central India: 0.020
      →Pakistan vs South India: 0.016

      By contrast:
      → North Indians vs "Near East": 0.036
      → North Indians vs Europe: 0.037
      → North Indians vs Caucasus/Iran (3 values): 0.026-0.036
      → Indians vs SE Asia: 0.049-0.062
      → Indians vs East Asia: 0.057-0.071
      → Indians vs Melanesia: 0.113-0.121 (this may be enhanced by Melanesian isolation?)
      → Indians vs "Sub-Saharan Africa": 0.139-0.145

      Pakistanis are more leaning to WEA however: 0.008-0.019

      Notice that the pop. in Caucasus closest to SA is North Caucasus (intriguingly).

      What can be concluded from this that North India (but not so clearly Pakistan) belongs to a "continental population" of South Asia, which is nevertheless closest in "intercontinental" affinities to West Eurasia, but there is a clear degree of difference between the levels of affinity within South Asia (strong) and with WEA (weak).

      If you want the paper (it may not be freely available online), drop me a line (lialdamiz[at]gmail[dot]com).

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    6. As for the rest I do not have much more to say. Unlike SA, I did study WEA components (with Fst values) on my own 14 months ago and Fst distances (different scale as before, it seems) between components ("pop") is of around 0.100 (0.010 with Metspalu's scale?) for all WEA components: there are some differences but not extreme ones. All the differences therefore should come from, initially, the same period, which I estimate to be early to middle UP, with some polishing afterwards by new waves of course.

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  4. This was my comment to the Meyer 2012 paper with regard to the results of the Dinka:

    They are the closest relatives of Eurasians among the African samples. According to Table S24, the French have a D-statistic of 0.6% relative to the Dinka, and 1.0-1.2% relative to the other African samples (Mandenka, Yoruba, Mbuti, San). My initial response to this result was simple; it seems like Dinka have Neanderthal ancestry. Upon further inspection, however, things do not appear that simple.

    The Nea(Europe, Africa) statistic (Table S28) was designed to find excess Neanderthal ancestry in Europeans. Here, the situation is completely reversed. The estimate of Neanderthal ancestry in Europeans is highest with the Dinka reference. So, what's different in this analysis? The Nea(H1,H2) statistic is limited to the parts of the genome where Denisovans carry the derived allele. If Dinka are more different from Denisovans at these positions than all other Africans, then this would mean that other Africans have an increased affinity with the Denisova-Neanderthal branch. Interestingly, John Hawks found a decreased Neanderthal similarity in the Luhya, in comparison to Yoruba. Autosomally, Luhya fit very well a mixture of West African (similar to Yoruba) and Nilo-Saharan (similar to Dinka), with some Pygmy thrown in.


    Actually, it could either mean that Dinka are admixed with hominins more divergent from modern humans than the Denisova-Neanderthal branch, or that other Africans are admixed with hominins from the Denisova-Neanderthal branch. Although I do recognize it could mean a lot of other things as well, or nothing at all. I agree with you that Denisovans themselves may have been admixed with H. erectus.

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    1. I cannot really comment on this. I simply see no way of "decreasing" Neanderthal admixture under the baseline of zero. Decrease can only happen by dilution (admixture with less admixed or no admixed at all populations) in already admixed populations, so unless you imagine that early West Africans were Neanderthal-admixed, I can't agree with your logic.

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    2. I cannot really comment on this. I simply see no way of "decreasing" Neanderthal admixture under the baseline of zero. Decrease can only happen by dilution (admixture with less admixed or no admixed at all populations) in already admixed populations, so unless you imagine that early West Africans were Neanderthal-admixed, I can't agree with your logic.

      I am merely discussing the data for what it is, you're free to come with alternative interpretations if you'd like. The significantly increased "overall" Neanderthal affinity of Dinka (seen in the relatively low D-statistic of the French relative to the Dinka) fits with what you might expect, as East Africans live closer to Eurasia than West Africans. However, it's the complete opposite when looking at parts of the genome where Denisovans carry the derived allele, which seems odd with the current population model.

      Africa has been a hub for much of the evolution within Homo, and some sort of proto-Neanderthal population migrated from Africa originally as well. Nothing should be ruled out here, especially considering the recent discovery of some very ancient Y chromosomes in West Africa whose divergence likely predate the appearance of anatomically modern humans.

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    3. The " proto-Neanderthal population" that "migrated from Africa originally" is the same ancestral population to us: Homo ergaster (with Acheulean tech, which is the last archaeologically documented OoA migration before the one by H. sapiens). Parsimony, please.

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    4. I was referring to Homo heidelbergensis. Or do you consider the common ancestor of Neanderthals and Homo sapiens to go all the way back to the spread of Acheulean technology, well over 1 million years ago? Considering your general preference for older dates, I suppose I shouldn't be surprised.

      Nevertheless, it's certainly possible that there was substructure within Africa, distinguishing the immediate African ancestors of Neanderthals (H. heidelbergensis or H. ergaster if you'd like) and the ancestors of modern humans in that time. And since we know that archaics persisted in parts of Africa until quite recently (see Iwo Eleru, possibly related to Y-DNA A00 found in nearby Cameroon), it's not impossible that this potential substructure may have contributed to modern patterns of variation.

      But this was just a sidetrack of me speculating to try to fit the data. I don't feel very strongly about this either way.

      Delete
    5. "Or do you consider the common ancestor of Neanderthals and Homo sapiens to go all the way back to the spread of Acheulean technology, well over 1 million years ago?"

      Yes, I do. I think that the weight of the evidence is on that side. Only weak disciplines like molecular-clock-o-logy and some currents of anthropometry/palaeoanthropology propose a more recent common ancestor. IMO they lack any sort of weight. A critical revision of molecular clock estimates, using the correct date for the Pan-Homo split (8-13 Ka) really puts the common ancestor around the million years in most cases and the rest is, well, Trinkaus and little more. There are other very respectable palaeoanthropologists that propose a divergence of circa one million years (I've also read from them "1.3 Ma" elsewhere). Finally there's no obvious evidence of any migration out-of-Africa nor into-Africa between the spread of Acheulean and the migration of Homo sapiens.

      "Nevertheless, it's certainly possible that there was substructure within Africa, distinguishing the immediate African ancestors of Neanderthals (H. heidelbergensis or H. ergaster if you'd like) and the ancestors of modern humans in that time".

      I'm very skeptic.

      "we know that archaics persisted in parts of Africa until quite recently"

      But archaics closely related to Homo sapiens, or are we to think that there was no genetic flow, probably also expansions and contractions in Africa before the coalescence of our species? Also A0, if not strictly sapiens (??), should be very close to the root of "sapienskind", so the difference would be minor, specially in comparison with Neanderthals. In addition A0 and A1a are very rare lineages even where they exist and, on top of that, Y-DNA (with no plausible mtDNA counterpart), which is generally much less strongly related to autosomal (overall) genetics than mtDNA.

      As for Iwo Eleru, it looks mostly modern by most variables (fig. 2), so I suspect a case of misidentification or retaining of some "archaic" trait (because of admixture or just diversity, in which Africa is king). Anthropometry is not rocket science, you know.

      Even if you'd be right in some aspect, the influence of such elements should be negligible. I'm really more inclined to consider such extremely subtle "differences" just random noise caused by natural diversity or, if real, rather provoked by Chadic influence in Nigeria (Northern Nigeria is essentially Chadic, even if not dominated by R1b like their relatives of Lake Chad).

      Delete
    6. A00, estimated by Michael Hammer to have diverged 338-563 kya, is older than A0 and A1a. Much older, in fact. If you're willing to attempt to push the African presence of lineages such as J1 and R1b to the early LSA, then I presume A00 should even look "H. ergaster" to your eyes, considering its great divergence from other modern Y chromosomes. So how can you claim it's a H. sapiens lineages, or even close to the root of H. sapiens?

      There are a couple of reasons to believe that A00 may be related to recent admixture with hominins related to Iwo Eleru. This admixture may have occurred as late as the Neolithic.

      A00 is highly rare, in accordance with the possibility that it may have introgressed relatively recently, but was neither lost nor strengthened by genetic drift. And it wasn't spread to other parts of Africa. As a result, it is apparently limited to areas not far from Iwo Eleru (western Cameroon).

      Delete
    7. Vale. I'm not familiar with this A00, which is not even listed at ISOGG as of today. I cannot therefore comment further at this stage.

      Delete
  5. This comment has been removed by the author.

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    1. This you say sounds mostly to demagogy, so I will ignore that part.

      "Since when is blade technology, or specifically of the Levalllois type invented by Neaderthals"...

      There are blades of some sort in South Asia c. 100 Ka ago. It's extremely doubtful that they were made by Neanderthals. There are some Levallois "blades" in Palestine (and other sites) of more recent dates but, even if Neanderthals invented the concept of the blade, it is mostly irrelevant.

      "a proto-Auragnian version of which shows up in the Altai-China region as early as 50K (earlier than in Europe)"

      Reference? I believe I have read by now all the literature on Altai and Mongolia/North China UP and I

      1. First in all that area was in Altai.
      2. The "50 Ka" age you mention has never been confirmed, the oldest dates being 40-something Ka (43 Ka I believe but maybe after calibration it gets somewhat older).
      3. There is "Aurignacoid" tech (Emirian) in Palestine, associated to Homo sapiens remains, since 55 Ka ago.
      4. There is Aurignacian tech in Southern Germany since 49 Ka ago.
      5. The arrival of mode 4 tech to Mongolia and North China (Korea too?) only took place since c. 30 Ka ago (probably associated to the migration Eastward of the proto-Amerindians).

      So you are managing all the wrong data, which I know you stick to (instead of expanding your horizons freely) because of your incorrigible Sinocentrism. Still I must thank you for that vice you have because otherwise I might never have begun blogging (instead of wasting my time with your manipulative manners as petty forum chieftain).

      "... a West Eurasian invention?"

      A South Eurasian one possibly. But who cares? Prehistory happened as it did, not as you or I wish it might have happened. In everything new someone has to be the first - not necessarily the Chinese however.

      The sequence of spread of mode 4 (a category that some other, very qualified, readers of this blog question to some extent) is in any case (ignoring the less clear South Asian part, mentioned already in another comment): 55 Ka ago West Asia, 49 Ka ago Europe, 40-something Ka ago Altai (Central Asia!), 40 Ka ago Africa, 30 Ka ago NE Asia.

      East Asians (and Australasians) anyhow managed well without it, quite obviously.

      Delete
    2. PS- For whoever who may read the previous comment, let me be clear that I have absolutely nothing against Chinese or East Asians, just against Ren's arrogant, pointless but still annoying, Sinocentrism.

      Delete
  6. Around 50K between the Irano-Afghan and Altai region maybe.. but how this translates into it being West Eurasian (as people expanding out of the Anatolian Neolithic or even pre-Neolithic Europeans who are morphologically and genetically unlike the Anatolian Neolithic "Caucasoids") is beyond me.

    At 55K, Modern humans were just expanding out of Africa. How you retroactively can apply this period , region, developments into being West Eurasian is like how some Arab camel herder can point to some stone tools he found from that age and say that Arabs invented "Mode 4 " for mankind.

    I've pointed this out to you countless times before on my forum, but you either cannot understand or is buried deep in several layers of bunkers.

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    1. Why did you delete your insulting comment? Why not issue an apology? Your manipulative style again, so now it may look like I'm fighting against windmills or something.

      "At 55K, Modern humans were just expanding out of Africa".

      That's ridiculous! You are getting very rusty. Have you even read Petraglia 2007? Yes you did because I was in your petty forum back then, yet you learn nothing.

      Have you read anything I may have written on the matter since then, mostly based on academic papers? I may suggest you to beging here and then follow the links. Don't forget to check some more recent materials re. to that post, like the Nubian tech of Dhofar or the Homo sapiens of Laos of c. 56,000 years ago.

      Open your mind to the facts.

      The most plausible scenario for the OoA as of now is:
      1. Early migrations to Arabia and Palestine c. 125-90 Ka
      2. Migration to South Asia c. 80 Ka
      3. Migration to East Asia (and later Australasia) some time later (unclear because the archaeology of the region is not too good)
      4. Migration to West Eurasia, incl. Central Asia, (from South Asia) c. 55 Ka ago

      There's also some small chance that the migration to South and East Asia was even older (c. 100 Ka ago) but the archaeological data so far is not clearly supportive. But in any case you cannot claim in this year of 2013 that "at 55K, Modern humans were just expanding out of Africa" and not appear as a fool, much less with your know-it-all attitude.

      Delete
  7. (Emirian) in Palestine

    That is not Aurignacian. By saying it is Aurignacian and that there is Aurignacian in Palestine 55K and Mode 4 is West Eurasian you are conflating several unrelated paths the result of which is a very misleading story.

    You have no credibility on this. That's the problem. The blog is just a tool for your to champion your idealogy. That's why I don't blog. It's just a mouth piece for the blogger with a lot of followers. I'm into research, not propaganda-izing.

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    1. I did not say that Emirian is Aurignacian. I said mode 4, which it is.

      Anyhow, according to Hoffecker 2009, Emirian would be related to Bohunician (in which he includes Bacho-Kirian) while Ahmarian, its successor in the Levant, would be related to proto-Aurignacian. There's of course some debate on all this but to my eyes it seems more and more clear that we can talk of "Aurignacoid" for all early UP (mode 4) techs of that kind (i.e. excluding Chatelperronian-Szletian and Uluzzian) but including Emirian, Ahmarian, Bohunician, proto-Aurignacian, Aurignacian proper and the unnamed "Aurignacoid" tech of Central Asia. All them were made with great likelihood by Homo sapiens and is every day more clear that they are just variants of a greater cultural trend that was, in Europe, homogenized by Aurignacian proper (first in Hungary c. 46 Ka ago) upon the HE-4 cold spell, possibly caused by the Campanian-Ignimbrite huge eruption. All them seem to indicate the expansion of Homo sapiens in the "Neanderlands" of most of West Eurasia (Central Asia included), from South Asia.

      Delete
  8. This whole thing with Amerindians...Physical Anthropology-wise they are more "Mongoloid" than East Asians. You are stuck with common misconceptions involving stereotypes of eye shape, skin color, and a general southern Chinese-SE Asian type of face that has nothing to do with what is really Mongoloid in physical anthropology. The Amerindians are the real Mongoloids and you got the whole thing upside down. Even genetically, this is so. But I've been trying to tell you this for years.

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    1. Look: I do not question that Native Americans are East Asians, not because of often confusing Anthropometry but because of autosomal genetics. But their East Asian legacy comes mostly from the mtDNA (and Y-DNA C3) because Y-DNA Q (and mtDNA X2) is quite obviously West Eurasian by origin.

      Cannot you imagine an originally Western population in Altai, gradually, maybe even rapidly, becoming Eastern by means of repeated admixture with East Asian women but retaining at least some elements of their Western legacy, like a mode 4 technology (and obviously also their dominant Y-DNA lineage)?

      Well, I can. It's what the data says and seems extremely plausible to me. The same in reverse happened with Fino-Ugric peoples, who still have lots of Oriental Y-DNA N but are as Western-looking as anyone in their region. However in this case the admixture seems more recent and many of them they still retain visible traces of the East Asian (or Siberian, if you wish) ancestry in their autosomal DNA.

      Delete
  9. "Actually there is a particular reason, Highlander: that all Homo sp. we know at the necessary crossroads, Altai, before c. 40 Ka are not Homo sapiens but other species (Neanderthals and Denisovans)".

    There is no reason at all that should all be 'non-moderns'. As far as I'm aware we have no human remains from the region to judge the case. We have only your belief that modern humans cannot have used Mousterian technology. But we do know that modern humans had emerged from Africa long before mode 4 industries developed.

    "For anyone who understands a bit of archaeology, this statement is the equivalent of dogma coming out of a Salafi cleric or Christian fundamentalist pastor's mouth".

    No comment.

    "East Asians (and Australasians) anyhow managed well without it, quite obviously".

    So you either believe that early East Asians and Australasians were not modern humans or that mode 4 technology is not the marker of the first modern human presence in any particular region.

    "to my eyes, all this suggests a process of evolution towards 'mode 4' in Northern South Asia and maybe especially in the NW".

    Perhaps that is where mode 4 developed. In any case humans must have occupied some region between Africa and South Asia by the time the technology developed.

    "Groups like the Onge would probably be different. Onge would also be particularly interesting to examine as they belong to Y-DNA D and mtDNA M"

    Human presence on the Andaman Islands is not particularly ancient, possibly not much before 10-12,000 years ago. They certainly do not represent a relict population from the original OoA as was widely believed some years ago.

    "they are IMO a segregated 'continental' population on their own right since some time, rather early, in the process of colonization of Eurasia and Australasia".

    The Onge are interesting precisely because they have absolutely no connection with any Australasian populations at all. On the other hand the people on the neighbouring Nicobar Islands do show connections at least with SE Asian populations.

    "Regardless, their Neanderthal affinity would be very interesting to look at, don't you think?"

    Yes.

    "North and South India, I suspect, were two differentiated populations mostly separated by an arid Deccan since maybe as early as 80 or 70 Ka ago"

    'Arid Deccan'? First I've ever heard of that. The Western Deccan is mostly jungle-covered these days with more open jungle in the Eastern Deccan. The arid region is further north: the Thar Desert, which presumably has expanded and contracted with changing climate.

    "Y-DNA inheritance hardly ever correlates too strongly with autosomal genetics when mtDNA is contradictory in origins".

    They are three separate, and often independent, methods of looking at ancestry. Autosomal DNA is presumably usually the oldest with mt-DNA being often younger and Y-DNA being even younger.

    ReplyDelete
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    1. terryt, I would like to have discussions with you. Can you give an email or some type of contact info or should I give you mine?

      Delete
    2. "There is no reason at all that should all be 'non-moderns'".

      There is: we know of physical remains: obviously Neanderthal ones an then the Denisova ones, whose nature has been revealed only by genetics. Only a very dogmatic person can ignore all that.

      "So you either believe that early East Asians and Australasians were not modern humans or that mode 4 technology is not the marker of the first modern human presence in any particular region".

      The latter, obviously. You know that already, anyhow.

      "In any case humans must have occupied some region between Africa and South Asia by the time the technology developed".

      Of course, and beyond it, into East Asia and Australasia surely (maybe simultaneously to its development for some particular areas). Mode 4 is overrated. But you know that also.

      "Human presence on the Andaman Islands is not particularly ancient, possibly not much before 10-12,000 years ago".

      We don't know that. I suspect it a case of lack of sufficient archaeological surveillance.

      "They certainly do not represent a relict population from the original OoA as was widely believed some years ago".

      I still think they are a relict of what I call the Greater Eurasian Expansion, so not to confuse with the preliminary OoA into Arabia. The exact timing or whether there may have been two waves is debatable of course.

      "'Arid Deccan'? First I've ever heard of that".

      I have been telling you for months if not years. A clear indicator that you do not read what I write specifically to you.

      "The Western Deccan is mostly jungle-covered these days with more open jungle in the Eastern Deccan".

      For example this Google book suggests a humid parenthesis in Northern Deccan in the 40-25 Ka period, followed by a "distinctly dry" period in 22-16 Ka (LGM), followed by a phase of rapid changes.

      This other book by Michael Petraglia talks instead of arid conditions in the last Ice Age in the Western Deccan, suggesting that Eastern and Central India (not affected) was the preferred habitat for human habitation then.

      Neither of them is my original source, I'm quite certain. But can't recall which one is it, so enough. The key point is that the Indian subcontinent was not demographically a single unit in all the last Ice Age. It was also mentioned in the first source that the Northern Deccan was also arid in the Middle Pleistocene, what affects directly the early population of the subcontinent by our species, which clearly happened long before the late Pleistocene.

      "Autosomal DNA is presumably usually the oldest with mt-DNA being often younger and Y-DNA being even younger".

      That makes no sense whatsoever to me. Autosomal DNA actually is the data where you cannot see the remote past easily - because of continuous processes of homogenization within semi-isolated populations, etc. I generally consider it mostly apt for a relatively recent overview.

      On the other hand both haploid lineage systems may and usually retain information from the remote past (they are at least partly oblivious to homogenization processes). However among the two, mtDNA tends to be the most stable one (because women, unlike men, can only have so many kids).

      Delete
    3. ... also women migrate less than men, if any does.

      Delete
  10. This comment has been removed by the author.

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  11. There is East Asian - Tianyuan 40k BP, already split from Europeans. If we accept that the first admixture for their common predecessor happened around 70k BP in the Near East, the second admixture for already-separated East Asians must have happened on the way from Near East to the East Asia - maybe the same way like Silk road probably around 50k BP. This are was really full of neanderthals in that times. Why Indians have less, even when they originated in East Asia? I think its partly because of the bottleneck, partly because of the later admixture from central Asia (mtDNA X, Chromosome Y Q).

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    1. I do not understand what you say. As Ebizur mentions Indians are people from India (either the Indian Union or sometimes, loosely, the Indian subcontinent, although to avoid confusion I try to use the term South Asians instead).

      If you mean Native Americans, as I explained in a comment above, I think that the genesis of that population implies a migration through Siberia from Altai in which they became, by repeated admixture through millennia, East Asians, but retained elements of their Western origins, notably Y-DNA Q but also some mtDNA X2. IMO this migration could well be related to the appearance of "mode 4" (roughly stone blades but distinct from Levallois "blades" from flakes, which would still be "mode 3") in NE Asia, which begins (AFAIK) c. 30 Ka. in Mongolia, North China, etc.

      Delete
  12. ... I forget one interesting thing: People brought wheat the same way (silk road) from Near east to north China (Yangshao culture) so I think this way was much easier to pass than it is today because of drought.

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    1. "People brought wheat the same way (silk road) from Near east to north China (Yangshao culture) so I think this way was much easier to pass than it is today because of drought."

      Precisely so. Sheep came to the East along the proto-Silk Routes, too, and likely metallurgy as well. The Afanasevo of Siberia owed their material culture to southern Central Asia, not the Eurasian steppe.

      During the Pleistocene, there were periods when Central Asia was more hospitable than in historical or proto-historical times. What we see in the material record is that, whenever this vast region could be occupied by man, it was occupied, even when the environment was marginal at best. It could conceivably have been an area of significant human development and interaction for, not just the thousands of which we know but, several tens of thousands of years.

      Delete
  13. Václav Hrdonka wrote,

    "Why Indians have less, even when they originated in East Asia? I think its partly because of the bottleneck, partly because of the later admixture from central Asia (mtDNA X, Chromosome Y Q)."

    You seem to have misunderstood the word "Indian." When we (and most other English speakers who are not street trash) say "Indian," we are referring to the people of India, a country located in South Asia.

    The aboriginal (pre-Columbian) inhabitants of the American continent are an entirely different metapopulation, rather closely related to the North Asian and East Asian metapopulations. The American, North Asian, and East Asian metapopulations are genetically very distant from the South Asian metapopulation (which includes Indians).

    ReplyDelete
  14. "terryt, I would like to have discussions with you. Can you give an email or some type of contact info or should I give you mine?"

    Email: terrytoohill@yahoo.com

    "That makes no sense whatsoever to me [Autosomal DNA is presumably usually the oldest with mt-DNA being often younger and Y-DNA being even younger]".

    Obviously it does make sense because you then wrote:

    "also women migrate less than men"

    So, make up your mind. Does it make sense or does it not?

    "We don't know that. I suspect it a case of lack of sufficient archaeological surveillance [Human presence on the Andaman Islands not much before 10-12,000 years ago]".

    The Andamans have been subject to 'archaeological surveillance', and we certainly have no evidence that human presence there is any more ancient than that. Just what some people would like to believe:

    http://www.andaman.org/BOOK/chapter25/text25.htm

    Quotes:

    "The handful of Indian archaeological excavations in the islands have so far found an oldest archaeological date for an Andamanese presence of only 2,280 years from the present (with an uncertainty +/-90 years). In prehistory, this is almost yesterday and not old at all".

    "The stone tools found in Andamanese kitchen midden and described in the previous chapter are closely related to a specific stone tool industry, the Toalean (see below). This industry has been found all over the Indonesian archipelago and beyond".

    "The Toalean is defined by B. Bulbeck, Pasqua M., and Di Lello A. for Sulawesi (Celebes) as a "mid-Holocene stone flake and blade industry of a number of caves in southern Sulawesi, Indonesia, c 6000 BC and later. The industry developed out of preceding flake industries and is characterized by small backed flakes and microliths, and well-made Maros points".

    Another interesting snippet from the same source:

    "Was that more or less unified Negrito population broken up and largely destroyed by the Great Migrations of modern groups speaking languages of the Austronesian (Malayan etc), Austroasiatic (Khmer, Nicobari, etc) and Sino-Tibetan (Thai, Burmese, etc) families from the north between 8,000 and 5,000 years ago? Probably it was".

    The author has no difficulty accepting that these langauges came from further north. And some will find this 1955 extract interesting:

    http://www.andaman.org/BOOK/reprints/cipriani/rep-cipriani.htm

    "Human groups physically and culturally comparable to the Andamanese exist only in Asia. They are the Semang of the Malaya Peninsula, and the Aeta of the Philippines. Important is this finding of resemblances between people so widely separated to-day, and without any contact between them now. This similarity is not a chance similarity; it arose certainly because there was contact between these peoples in ages long ago, a contact now destroyed".

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  15. "Terry could be right on this one. His idea certainly deserves more than the sneering contempt you've shown so far".

    Everyone gets sneering contempt from Maju.

    "it is at least plausible that Neandertal DNA arrived in China via Central Asia, especially in light of curiously persistent Mousterian industries across the region".

    Here is a paper Maju has read but others will find it illuminating:

    http://paleo.sscnet.ucla.edu/BrantCA2001.pdf

    Quote:

    "As in western Eurasia, the Initial Upper Paleolithic emerges in Northeast Asia sometime after 45,000 years ago and is characterized by the elaboration of blade technologies showing a mixture of Middle and Upper Paleolithic
    characteristics".

    And:

    "We include the Kara Bom Upper Paleolithic, Chikhen Agui, and Shuidonggou assemblages in the Initial Upper Paleolithic, emphasizing both the striking technological coherence between these assemblages and the technological
    parallels with accepted Initial Upper Paleolithic assemblages from western Eurasia. Moreover, we hold that there is strong continuity between the regional Middle and Initial Upper Paleolithic".

    So the Initial Upper Paleolithic is intrusive but accommodating of locals. The Initial upper Paleolithic would probably have been introduced by Y-DNA Q and mt-DNA X. But these were obviously not the first 'modern' human haplogroups in the region. So the IUP does not represent the first modern humans in the region. Turning to the Middle Paleolithic:

    http://ejournal.anu.edu.au/index.php/bippa/article/viewFile/85/76

    "In Mongolia, Acheulian-like bifaces were first reported occurring within the surface collections at such open-air sites as Bottom-of-the-Gobi and in the vicinity of Mount Yarkh (Okladnikov 1983, 1986)".

    And:

    "The cultural continuity apparent in the development of the Mongolian Paleolithic suggests the formation of Mousterian traits on the basis of a local Lower Paleolithic tradition with Levallois technology. The analogous features of the major Mousterian variants allow us to include Mongolia, primarily the Mongolian and Gobi Altai regions, and the Russian Altai in a single geographic unit representing the development of a distinctive Middle Paleolithic culture".

    "The occupation of the Altai by early humans was most likely connected with a northern migration wave of Homo erectus who expanded beyond the boundaries of the African continent and reached Asia. According to the dates that have recently been generated from loess and soil samples of the Kuldara, Khonako-2, and Obi-Mazar-6 sites in Tajikistan, H. erectus arrived in Central Asia in the range of 600,000 to 900,000 years ago (Ranov 2001; Ranov and Schäfer 2000)."

    So the authors assume H. erectus could survive that far north, yet maju insists H. sapiens could not. It is uncertain when 'modern' humans arrived there. The authors state:

    "The evidence available has not yet provided reliable grounds for associating the technological variants of the Altai Middle Paleolithic with distinct prehistoric human populations bearing independent cultural traditions".

    We can perhaps accept from here:

    http://ac.els-cdn.com/S0002929711005453/1-s2.0-S0002929711005453-main.pdf?_tid=0d552c56-7977-11e2-9ff1-00000aacb362&acdnat=1361156480_cf82ae9b09a0f34d6156ea6ed99257f1

    that mt-DNA N began diversifying in SW Asia around 60,000 years ago. So modern humans may have reached Altai soon after. Incidently, the last paper has some really useful distrubution maps of mt-DNA haplogroups N1'5, N2 and X. Specifically X as a whole, both N2a and W and N1b, N1a3 (called 'N1c' in the paper), I and N1a1'2(xI) (called 'N1a' in the paper). A further interesting, and probably relevant, point is that apart from the remote possibility that mt-DNA R originated in South Asia India has no basal representatives of mt-DNA N at all.

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    1. "Does it make sense or does it not?"

      No.

      "The Toalean"...

      Is original from SE Asia and surely not the technology brought by the Andamanese. It's probably more related to the Nicobarese, who speak an Austroasiatic language. The presence of pottery and polished adzes would suggest so (this entry suggest a Great Andamanese heritage but did they ever have pottery and adzes?)

      In any case three shell middens are hardly a good knowledge of the islands' prehistory. So I would prefer to use genetic inference and suggest a very old divergence at unknown but clearly Paleolithic time.

      "So the authors assume H. erectus could survive that far north, yet maju insists H. sapiens could not".

      We have already debated that. Homo erectus was in Eurasia, gradually adapting by whichever means to cold climates, since c. 1.8 Ma ago. So for 900,000 or more years they were not able to adapt to Siberia, yet you expect me to believe (without any evidence or rather a lot of evidence against it) that our species chose that harsh route, via deserts and some of the coldest places of Earth, first and foremost. C'mon!

      "The cultural continuity apparent in the development of the Mongolian Paleolithic suggests the formation of Mousterian traits on the basis of a local Lower Paleolithic tradition with Levallois technology."

      That bit is interesting. It would add weight to Highlander's claim. Its alleged similitude with Altai Mousterian may allow us to speculate (but not be certain yet) about Neanderthals or their hybrid "Denisovan" relatives (also users of Mousterian, it seems) to have inhabited both regions.

      "... mt-DNA N began diversifying in SW Asia around 60,000 years ago".

      It seems to me still a bit late. After all we should expect its descendants to be all around and certainly in West Asia c. 55 Ka ago. A bit too fast maybe? I rather favor a near 70 Ka chronology instead in spite of the weakness of the archaeological evidence as of today.

      "So modern humans may have reached Altai soon after".

      At least 15,000 years later. That's not "soon".

      Delete
  16. http://paleo.sscnet.ucla.edu/BrantCA2001.pdf
    I actually posted on my forum and that's where Maju first came in contact with the situation in that region.
    I'm not making any comments, except to give a context for all of Maju's ideas. I haven't seen anything new; they are all versions of what I said with a Basque flavor.

    ReplyDelete
  17. Read Derevianko (2003?).

    The MP-UP inhabited (or known to have been inhabited) Altai district is just West/SW of Gorno Altaisk. Two areas can be discerned:

    1. South (Kara Bom, river Ursul): MP dates: 62.2 to >42 Ka BP; UP dates: 43.3 and 43.2 Ka BP.

    2. North (Anui River, Ust-Karakol and Denisova mainly, very close to each other, further North Okladnikov that I'll treat separately for good reasons). MP dates: 282-46 Ka; UP dates: (a) the very anomalous RTL one of 50,000 but with a brutal error margin of ±12,000 years (it may therefore be as recent as 38 Ka) and (b) more trustworthy C14 dates since >37.2 Ka BP until 29.7 Ka BP.

    It is therefore safe, considering the whole and not just cherry picking the evidence, that the earliest UP dates are not older than those from Kara Bom, what leaves us at c. 43 Ka BP, at most 44.9 Ka BP (but could also be more recent, up to 41.7 Ka BP).

    43 Ka BP = c. 47 Ka ago (calibrated) and 45 Ka BP = c. 48 Ka ago (calibrated). This is what we have after a realistic review.

    As for Okladnikov cave, further North, it is interesting not for its UP dates, which do not exist, but for its very late MP ones: 48.8-33.5 BP, what makes it a likely last stand for either Neanderthals or Denisovans after displacement by our kin from their more traditional settlements further south. The three areas are separated by 60 Km the two mentioned above and by some 45 Km between Denisova and Okladnikov. So there must have been some contact between both populations, even if sporadic and cautious, and possibly even hostile (they retain different techno-cultures, so not really loving each other IMO).

    That (and maybe a little more in the details is what we get from the MP-UP transition in Altai).

    47 Ka ago (after calibration) is still an early date for Aurignacoid cultures but not earlier than the 49 and 48 Ka dates scattered through Europe, much less the 55 Ka ones of Palestine. So it is reasonable to say, as I do, that both phenomena ("Aurignacian" in Europe and Altai are contemporary and originate in the same West Asian older population/culture. We can discuss the details of this but the overview is very clear.

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  18. "No".

    You obviously need to brush up on your knowledge of population genetics then. Autosomal DNA preserves genetic elements older than either mt-DNA or Y-DNA. I would have thought that was obvious to anyone.

    "Is original from SE Asia and surely not the technology brought by the Andamanese. It's probably more related to the Nicobarese, who speak an Austroasiatic language".

    Possibly, but the settling of both island groups could be almost contemporary with each other. After all you know as well as I do that technology can be passed to other groups. The boating technology that allowed SE Asian groups to reach the Nicobars would obviously also have passed along the mainland coast allowing south Burmese populations to reach the Andamans. I'm not claiming that is exactly what happened but there is certainly no reason for it to be impossible.

    "I would prefer to use genetic inference and suggest a very old divergence at unknown but clearly Paleolithic time".

    But genetic evidence doesn't 'suggest a very old divergence at unknown but clearly Paleolithic time'. Andaman Y-DNA D is considered closely related to Indian Y-DNA D and Andaman mt-DNA Ms both have close relations in India. M32 is even found in Madagascar which was settled no more than some 2000 years ago.

    "It seems to me still a bit late"

    Well it does rely on molecular-clockology so I'm prepared to accept an earlier date for SW Asian N's diversification if you so wish.

    "It is therefore safe, considering the whole and not just cherry picking the evidence, that the earliest UP dates are not older than those from Kara Bom, what leaves us at c. 43 Ka BP, at most 44.9 Ka BP (but could also be more recent, up to 41.7 Ka BP)".

    You're still assuming, without any evidence whatsoever, that the first modern humans to enter the region carried a fully-developed Upper Paleolithic technology. On what grounds do you make that assumption?

    "As for Okladnikov cave, further North, it is interesting not for its UP dates, which do not exist, but for its very late MP ones: 48.8-33.5 BP, what makes it a likely last stand for either Neanderthals or Denisovans after displacement by our kin from their more traditional settlements further south".

    Another unjustified assumption. We know that Neanderthals replaced modern humans in the Levant as climate cooled around 70,000 years ago yet you insist that Central Asian Neanderthals and Denisovans remained exactly where God had placed them until being replaced by modern humans.

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    1. Neither M31 nor M32 look particularly derived from M, not more than your famous X is from N for example (in the case of M31, quite less in the case of M32). I conclude that they are therefore very old, maybe of 70 Ka ago for M32 and a little less 60-50 Ka for M31. Certainly not "recent". Y-DNA is less obvious to look at but D is not "recent" in any case.

      "You're still assuming, without any evidence whatsoever, that the first modern humans to enter the region carried a fully-developed Upper Paleolithic technology. On what grounds do you make that assumption?"

      What?! Sorry I'm talking of Aurignacian-like industries all them mode 4. "Fully developed" is a category I don't understand well in this context. All I say is that they are related techno-cultures of a kind that can be safely associated with H. sapiens in those regions (documented in Palestine and Altai).

      "Another unjustified assumption".

      If you say so...

      We also know that Homo sapiens replaced Neanderthals in the dates discussed here or a bit later in all West Eurasia, what's your problem then? What part don't you understand?

      Delete
  19. "You obviously need to brush up on your knowledge of population genetics then".

    Yet you can say:

    "In addition A0 and A1a are very rare lineages even where they exist and, on top of that, Y-DNA (with no plausible mtDNA counterpart), which is generally much less strongly related to autosomal (overall) genetics than "

    So what is your difficulty in seeing that Autosomal DNA is presumably usually the oldest with mt-DNA being often younger and Y-DNA being even younger? Or is it just that you can't see it when it suits your purpose to not be able to see it?

    "On the other side, as Terry points below, this paper does mention that there seems to be some Mousterian, related to that of Altai, in Mongolia. If so, I stand corrected".

    And you will have even more to stand corrected on as time goes by.

    "The key point is that the Indian subcontinent was not demographically a single unit in all the last Ice Age".

    Yet you insist on considering it one unit when considering basal haplogroup diversity in the continent. For example yopu said:

    "The basal diversity does suggest an origin in South Asia for mt DNA R"

    So which region within South Asia exhibits this basal diversity?

    "It was also mentioned in the first source that the Northern Deccan was also arid in the Middle Pleistocene, what affects directly the early population of the subcontinent by our species, which clearly happened long before the late Pleistocene".

    The paper does say that the Thar Desert is 'arid' and the North Deccan is 'semi-arid'. Any time that the North Deccan was semi-arid it is likely to be a result of the expansion of the Thar desert, making anywhere north of the Deccan uninhabitable except for the upper reaches of the Ganges. That does actually make sense of the apparent centre of dispersal of mt-DNA M though. Several branches were eventually able to move south into Madhya Pradesh while most journeyed east north of the Ganges into Northeast India and Zomia.

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  20. "Neither M31 nor M32 look particularly derived from M"

    Of course they're derived from M. That's why their name starts with 'M'. If you're meaning to say they are not basal M then I agree. That was my point. They are not particularly early in M's diversification.

    "I conclude that they are therefore very old, maybe of 70 Ka ago for M32 and a little less 60-50 Ka for M31. Certainly not 'recent'".

    How on earth do you come to that conclusion? Andaman M31 is M31a1, sister to Orissa M31a2. The combined M31a haplogroup is sister to M31b'c. So by the time we get to M31a1 we are considerably downstream from M31. Andaman M32 is M32a, sister to M32c from Madagascar. The combined M32 haplogroup is siter to Indian M56, so again we are dealing with a downstream haplogroup.

    "not more than your famous X is from N for example"

    X branches directly off basal N. What are you talking about?

    "All I say is that they are related techno-cultures of a kind that can be safely associated with H. sapiens in those regions (documented in Palestine and Altai)".

    So I assume you're prepared to share with us the characteristics that distinguish the technologies of the first modern humans in the Levant from the later Neanderthals that occupied the region. That will be a very useful piece of information because no-one else has yet been able to do so. I agree that mode 4 is a characteristic of Homo sapiens but its absence is not evidence of Homo sapiens absence.

    "We also know that Homo sapiens replaced Neanderthals in the dates discussed here or a bit later in all West Eurasia, what's your problem then? What part don't you understand?"

    You are the one who fails to understand that the first humans to emerge from africa did not have a mode 4 technology. Thereforee you cannot use the expansion of mode 4 technology to chronicle Homo sapiens' spread. We also cannot assume that Neanderthals did not replace early modern humans beyond the Levant as climate cooled. A factor to keep in mind here is that Central asian Neanderthals were shifted phenotypically towards Homo sapians as compared with Neanderthals from further west. This is most parsimonioulsy explained as being the product of hybridization between the two 'species'. In fact many individuals have been difficult to classify as either species, only defined by the mt-DNA extracted. For example note the headline of this post:

    http://anthropology.net/2008/05/26/new-hominin-remains-from-uzbekistan-are-kinda-sorta-neandertal-like/

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    1. Oh great, another post to the trash bin!

      Consider yourself replied because I did in length and it did not go through.

      Delete
    2. Anyhow you must know well the answers I was going to give to your many polemicist questions. We have been discussing for way too long.

      Delete
  21. "Read it again".

    So I did, and what I picked up is something you have always dissagreed with. The Petraglia book specifically states that humans prefered the 'deciduous woodland savanna ecosystems'. Bot extracts emphasise the connection between aridity in the north deccan as being part of more widespread climate changes.

    "This other book by Michael Petraglia talks instead of arid conditions in the last Ice Age in the Western Deccan, suggesting that Eastern and Central India (not affected) was the preferred habitat for human habitation then"

    But he also says that hominids seasonally exploited even what he calls the 'isolated areas' during arid times. Talking of inhospitable conditions in India:

    "the founders of East Asian peoples had on average slightly more Neanderthal input than the founders of South/West Eurasian ones. A mere fluke long ago".

    Doesn't make sense. A route through Central Asia is the only possible explanation for some observed phenomena. For example the absence of any basal mt-DNA N haplogroups in South Asia as well as the lack of any evidence for any technological connection between South and East Asia until somke time after the Tianyuan individual's presence . Here's a paper on human occupation of Central Asia:

    http://anthropology.colostate.edu/pdf/GlantzHistoryHomininOccupationCentralAsiaReview.pdf

    The author does say:

    "Given that the new dates from the Nihewan basin in northern China place hominin occupation of this region at roughly 1.6 Ma (Zhu et al. 2004) the relatively younger dates from Central Asia are surprising, as the region represents a possible corridor to the east. The observation that paleoclimatic reconstructions support a general similarity between the savanna conditions of Africa, the Levant and southern Eurasia (i.e., Dmanisi) with those of the foothill regions of Central Asia makes the relative absence of Early Pleistocene sites in the latter area even more unexpected."

    The author is obviously not convinced by the usual explanations for that absence.

    "it seems hominin groups lived in Central Asia during the coldest and
    driest periods of the Late Pleistocene".

    "Lithic techno-typology as well as hominin morphology (see discussion below) point to Central Asia as a zone of interaction during the Middle Paleolithic, with contacts to the north, east, and west".

    Note, even to the north.

    "Evidence that supports potential isolation/separation of Central Asian hominins from northern and eastern Asian populations is not easily delineated. Geographic barriers like the high mountain zones of the Tien Shan and Pamirs did not seem to impede faunal dispersals across Eurasia (see
    Keates 2004). In this regard, the notion that Neandertals moved east from their core area in Europe and stopped in Central Asia because of being geographically hemmed in is unsupported, certainly in light of Middle Paleolithic evidence from the Siberian Altai and other sites in China".

    "In any event, there is some evidence of the continuous occupation of Central Asia during the Late Pleistocene and perhaps across the Middle to Upper Paleolithic divide. A continuous occupation of the Siberian Altai also has been suggested and seems to be supported at sites like Kara Bom (Derevianko et al. 2000; Derevianko and Markin 1992)".

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    1. I just suggested that the dry Deccan acted as buffer, not barrier, to generate two somewhat different populations in India. They are not that different according to Fst distance values (read previous relevant comment), so maybe it's not that relevant anyhow.

      Delete
  22. "Anyhow you must know well the answers I was going to give to your many polemicist questions. We have been discussing for way too long".

    I agree we 'have been discussing for way too long' but you have consistently ignored the many problems I point out in your belief and concentrate on irrelevant trivial nin-picking.

    ReplyDelete

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