April 6, 2012

Mitochondrial DNA revision and the Reconstructed Sapiens Reference Sequence (RSRS)

The authors and maintainers of PhyloTree have produced a new build (no. 14) with a long list of changes. However the most important part is probably in an associated paper:


The Copernican adjective is because they hope to replace the use of the rCRS (revised Cambridge Reference Sequence, with the highly derived haplogroup H2a2a1, and arbitrary yet convenient pick back in the day) with the Reconstructed Sapiens Reference Sequence (RSRS) which is also the haplotype of the matrilineal most recent common ancestor of extant Humankind, alias 'Mitochondrial Eve'.

The RSRS is also quite directly comparable to the RNRS (the 'Neanderthal Eve', see Fig. S1), being separated by 122 mutations of the coding region and a few more of the control region (HVR). However while between the 'Neanderthal Eve' and actual Neanderthal sequences there are some 17 coding region mutations (14-21), in our species the distance to the most recent common ancestor is longer, 40-50 coding region mutations (most commonly, from memory) and even more when we count the HVR, as illustrated in figure S2:

Fig. S2 - Distances in Substitution Counts from the RSRS to Extant Haplotypes


This image is particularly interesting because it illustrates what the authors describe as indications for violation of the molecular clock: differences in the in the length of the various branches, which vary wildly from circa 40 to above 70, a difference of almost 2:1 between the extremes.

Oddly enough, in spite of M being closer to the root than N and having on average more mutations to present day sequences, the authors manage to somehow assign a younger age to this haplogroup than to its sister N. But in any case their estimates must be wrong overall because the age attributed to L3'4'6 (71 Ka BP), L3'4 (64 Ka) and L3 (67 Ka) are more recent than the known archaeological evidence for  the migration out-of-Africa which, at the latest, must have happened c. 90-80 Ka ago. The L3 node must be older than these dates therefore.

The authors also propose some nomenclature terminology, notably the use of superscript n for the nodal haplotypes (as opposed to just unclassified sequences, for which we will still use asterisk). That way we can more easily discern a nodal or root H haplotype (Hn) from a mere random unclassified H haplotype (H*). Other proposals for the nomenclature may be more debatable and in some cases they manage to violate them themselves in the supplemental materials.

Whatever my criticisms (everything is debatable and I love a good discussion), I must say that the PhyloTree team deserves my utmost appreciation and respect: before them understanding the human mtDNA landscape was a total mess, now it is possible even for amateurs with a keen interest like myself. Thanks a lot.

See also: Mitochondrial DNA and molecular clock.

60 comments:

  1. The "n" v. "*" superscript idea is indeed a good one, and the PhyloTree team does deserve kudos.

    The Bell Curve-like substitution charts are pretty much what one would expect to see when the number of substitutions is essentially a binomial function.

    In a case like L0 you can point to the quirkiness of small numbers.

    But, the bimodal distributions at L2 and N are harder to fathom. Is the bimodal in N a function of an N node and an R node interacting? Why would there be a bimodal in L2 - could this be Bantu expansion driven with L2 really needing to be parsed into two subsets (Niger-Congo excluding Bantu, and Bantu perhaps) to fit Bell Curve like distributions?

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    1. The only curve that truly approaches the bell curve is that of M. All the others are messier. N approaches two successive bell curves (humps of different proportions), while the L2 and L3'4'6 charts are like a pointy bell curve followed by a long group of longer-than-average haplotypes. Otherwise the double-hump of N can be loosely compared to that of L2 and L3'4'6 (although their second hump is a lot smaller).

      "Is the bimodal in N a function of an N node and an R node interacting?"

      I don't think so: this duality of length does exist within R (and maybe even more dramatically so): U should makes the bulk of the second hump, while HV the bulk of the first one (see here for a different but easily comparable graph only for R).

      Delete
  2. "Whatever my criticisms (everything is debatable and I love a good discussion)"

    So here goes:

    "Oddly enough, in spite of M being closer to the root than N and having on average more mutations to present day sequences, the authors manage to somehow assign a younger age to this haplogroup than to its sister N".

    I have long been claiming that the distribution evidence strongly suggests that N is older than M in Australia/New Guinea. Even P's arrival in, and spread from, Australia is claimed in this paper as being older than M, at 55,000 years. This date is actually older than the Australian N-derived haplogroups O and S, at 52,000 and 53,000 respectively. The Australian/New Guinea M haplogroups are given the earliest date of 45/46,000 years. To me this all has relevance to the origin and spread of haplogroup R.

    "But in any case their estimates must be wrong overall"

    Quite possibly, but taken at face value their dates do provide some intruiging information. Following from our argument about the Andamans you will note that M31 is dated at 35,000 years, while the Andaman M31a is dated at merely 5900 years ago. And M32 is dated at 43,000 years ago but the Andaman M32a is dated a mere 7452 years.

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    1. "I have long been claiming"...

      Where? Do you even keep any public track of your claims, hypothesis, etc.?

      Just because you have been howling in the night emotionally, without data to support and a properly described model to structure, there is no theory and no claim that I should care about.

      How do you expect me to debunk or agree to a ghostly "theory" that is nowhere to be found but in scattered comments here and there and nowhere properly exposed?

      As for the rest, it is molecular-clock-o-logy of the kind I can't accept (M must be 80-74 Ka old, being the most clear calibration point in the human mtDNA phylogeny per our current archaeological knowledge).

      Delete
  3. "Where? Do you even keep any public track of your claims, hypothesis, etc.?"

    You have a very defective memory. We have argued the case several times on your own blog. Every time you have blogged about early humans in Australia or New Guinea, especially regarding the spread of Y-DNA C and mt-DNA N.

    "Just because you have been howling in the night emotionally, without data to support and a properly described model to structure, there is no theory and no claim that I should care about".

    Maju, the data has always been there, as I've tried many times to point out. But you have made your mind up as to what has happened and consistently refuse to consider any other option until the evidence becomes absolutely overwhelming. The distribution of haplogroups in the McDonald maps can only be explained by the earlier arrival in Australia of the above haplogroups. And the maps came out in 2005.

    "As for the rest, it is molecular-clock-o-logy of the kind I can't accept (M must be 80-74 Ka old, being the most clear calibration point in the human mtDNA phylogeny per our current archaeological knowledge)".

    Surely the paper has some merit but you are simply dismissing the paper because you don't agree with the findings. I agree that inconsistencies have appeared in the data presented in the paper. For example the Central Indian haplogroups (M3, M5, M4''67, M35, M36, M39'70 and M49) all appear to be far too young. Apart from these few geographically limited M haplogroups other M haplogroups (along with N and R) with an apparently young age have a 'stem' several mutations long, and so their spread looks to have been delayed. For example Central Indian haplogroups M6 and M2 each have a stem 4 mutations long. Most non-Indian haplogroups depicted as young have similarly long stems. What was so strange about India?

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  4. "You have a very defective memory".

    Not really but, for what is worth, take that as granted. You can't search the comments' sections: it's not any bug but a feature: all what is there is semi-lost unless you randomly stumble on it.

    That's why you should keep a diary: a blog.

    "The distribution of haplogroups in the McDonald maps can only be explained by the earlier arrival in Australia of the above haplogroups".

    I fail to see how that supports your thesis or contradicts mine. The other way around if anything: if they were so early in Australia, there was no time for them to dally in the remote frozen wastelands of Siberia.

    "... you are simply dismissing the paper"...

    I'm dismissing obviously defective molecular-clock-o-logy (not the paper as a whole but the waste-of-time section of it).

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  5. "That's why you should keep a diary: a blog".

    It so happens that I do have a public track of my claims concerning the different arrival times of N and M in Australia. Here, in this 2009 essay:

    http://humanevolutionontrial.blogspot.co.nz/2009/06/human-evolution-on-trial-mitochondrial.html

    Quote:

    "After an initial expansion a series of mutations in the M and N mtDNA lines gave rise to regional varieties throughout the world, especially in the east. Line N reached Australia, probably more than 50,000 years ago. A later migration brought M’s line, and N’s descendant line P, to New Guinea".

    Of course I would now place the arrival of N and P together, but earlier than M's. And here:

    http://humanevolutionontrial.blogspot.co.nz/2009/06/human-evolution-on-trial-into-australia.html

    Quote:

    "The ancestors of the first Australians moved down the eastern coastal regions of Asia from the north. Their technology already included some basic boating ability which allowed the proto-Pama-Nyungan / Sepik-Ramu people to be the first onto the closer islands. They reached New Guinea and Australia some time between about 70,000 and 50,000 years ago. They probably carried Y-chromosome line C and mtDNA line N and her descendant R’s daughter line P. The fossils found at Lake Mungo represent this physical type".

    Next paragraph:

    "About 30,000 years ago Indo-Pacific, or Non-Pama-Nyungan-speaking, people were able to expand from further south into islands in the area today covered by the Arafura Sea (Sahul Shelf). People in the region had improved the boating technology the earlier immigrants had brought in. Their economy had become primarily coastal, swamp, lake and river. They carried mtDNA lines M and Q and Y-chromosome line K. The Kow Swamp fossils represent this type".

    "I fail to see how that supports your thesis or contradicts mine"

    You cannot be looking at the distribution then.

    "if they were so early in Australia, there was no time for them to dally in the remote frozen wastelands of Siberia".

    So how come basal mt-DNA N(xR) haplogroups are spread so widely outside India and virtually absent from India? Can you not see that from the map? Colourblind?

    "I'm dismissing obviously defective molecular-clock-o-logy (not the paper as a whole but the waste-of-time section of it)".

    That 'waste-of-time section' takes up the bulk of the paper. And by the way, I've noticed Phylotree now has an N3 with the present paper as reference. Any ideas as to where it was found? Perhaps the mysterious 'Ket N'?

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    1. You have not written anything since 2009 and what you may say that is relevant is hidden behind rhetoric and a huge scope. You seem more concerned about your literary style than about writing clear and short and to the point.

      But in any case it's all nothing but "I think that way" therefore "it must be that way". Where's the substance? Where's the evidence? Where's the in-depth discussion?

      Nowhere. I'm still waiting for you to put together your Eurasian (plus) mtDNA modeling, your maps, your explanation of why mtDNA N is clearly older in Australia than in West Eurasia

      "So how come basal mt-DNA N(xR) haplogroups are spread so widely outside India and virtually absent from India?"

      Actually only X of all West Eurasian N-subclades is absent in South Asia (not just "India", some Pakistanis would kill you for much less): N1'5 and N2 are common and basally so. The only "problem", your only "proof" is X.

      But the stem of X is way too long to prove anything, so you invent your own dogmas about how the stem "must" have coalesced in destination and what not. All nothing but a pathetic sophism of the worst kind. I'd rather have the one about the fractal immobility of Achilles.

      Anyhow, I have already debated all that in the relevant posts, for example:

      http://leherensuge.blogspot.com.es/2010/02/reconstruction-of-mtdna-spread-in.html

      http://forwhattheywereweare.blogspot.com.es/2010/10/on-high-mobility-of-mtdna-macro.html

      http://forwhattheywereweare.blogspot.com.es/2010/10/mtdna-stars-notes.html

      See also Mele's paper.

      Delete
    2. mtDNA haplogroup N3 is Middle Eastern (Iranian, Marsh Arab)

      Delete
    3. Hello, G. Horvat.

      That's very interesting to know, thanks a lot.

      Delete
  6. "But in any case it's all nothing but 'I think that way' therefore 'it must be that way'. Where's the substance? Where's the evidence? Where's the in-depth discussion?"

    Your inconsistency is obvious yet again. within the one paragraph you're complaining both of the the length of my argument and the lack of argument. Make up your mind. The 'substance' is in the 'huge scope'. The reason is that the evidence is cumulative, and therefore takes a long time to explain. My conclusions are certainly not simply that 'I think that way'. If you were prepared to start at the beginning you would then be able to follow the accumulating evidence clearly for yourself.

    "your explanation of why mtDNA N is clearly older in Australia than in West Eurasia"

    If yoy were actually interested you would have read the essay and would therefore know exactly my explanation. But clearly you are not actually interested. You have decided what you want to believe and are sticking with that.

    "I'm still waiting for you to put together your Eurasian (plus) mtDNA modeling"

    I did actually post the list at another of your blogs, although I promise I will also put it on your Wiki site.

    "Actually only X of all West Eurasian N-subclades is absent in South Asia (not just "India", some Pakistanis would kill you for much less): N1'5 and N2 are common and basally so".

    Rubbish. Clades of N1'5 and N2 haplogroups are hardly 'common' in South Asia, and it is extremely likely that any members there have arrived there from elsewhere.

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  7. "Anyhow, I have already debated all that in the relevant posts, for example"

    And my arguments there have been subsequently shown to more accurate than were your own. For example:

    "Not only M as such shows clear signs of expansiveness early on, many of its sublineages bi-/multifurcated just after it. Most did in South Asia itself but a handful expanded in Eastern Eurasia (i.e. everything that is East of Bangladesh)"

    That 'handful' has now greatly expanded, although I note you correctly place M32'56 in South Asia. Most of the newly discovered haplogroups are from either NE India or South China.

    "In comparison with the huge starlike structure of M, the one of N is quite modest".

    And you in no way explain how that could have come about. In your last comment on that post you wrote in reply to my comment, 'The evidence is pretty overwhelming that they didn't move along the coast and rivers'.

    "Instead of making such arrogant baseless claims, why don't you bother providing that 'overwhelming evidence'?"

    The haplogroup discoveries mentioned above provide the 'overwhelming evidence' in support of my comment. We have all those inland M haplogroups M11, M76, M13'46'61, M10, M71, M8, M9, M12'G, M7 and M80'D. It is impossible to argue convincingly that these haplogroups entered East asia via the coast. And the same holds true for those haplogroups shared between India and South China (M39'70, M40'62, M49, M50).

    "Update on the debate R had a South Asian coalescence almost for sure, even if this one happened (maybe) closer to Bengal than depicted in the map".

    Well, new R haplogroups have also been discovered. The eastern haplogroups are P, R12'21, R14, R22, R23, R9 and R11'B6/R4'5/R24. That is 7, or perhaps the last could be regarded as 3 separate haplogroups as they are combined by a single mutation in the hypervariable region. Such mutations are not considered accurate representatives of phylogeny. In South Asia we have 6 haplogroups: R7, R8, R6, R5, R31 and R30, the first 2 considered to be associated with munda and austro-Asiatic speaking people. The remaining haplogroups are SW Asian. So that makes the East the region of greatest diversity fo R.

    A few days ago you wrote:

    "I'm dismissing obviously defective molecular-clock-o-logy"

    So you dismiss molecular-clock-o-logy when it fails to fit your belief yet all three of those old posts rely completely on defective molecular-clock-o-logy. Yet again: inconsistent.

    ReplyDelete
  8. "mtDNA haplogroup N3 is Middle Eastern (Iranian, Marsh Arab)"

    Thanks very much for that information. That still leaves South Asia devoid of any basal N haplogroups. Difficult to make a case that N passed through South Asia not just once but twice. Once from west to east and again from east to west. In fact it adds a SW Asian haplogroup to the N collection.

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    1. N1'5, N2 and R are found in South Asia and possibly coalesced there, regardless of what you wish. We know too little about this N3 to say where it's found: the Persian Gulf is closer to Pakistan than France, mind you.

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  9. "We know too little about this N3 to say where it's found"

    The best information we have is that supplied by G. Horvat. I presume that the haplogroup will appear in the paper recently mentioned concerning the origin of N round the Persian Gulf.

    "N1'5, N2 and R are found in South Asia and possibly coalesced there, regardless of what you wish".

    I don't 'wish' anything. I'm merely going on what the phylogeny and distribution might be able to tell us, unlike you. That phylogeny and distribution tells us that N1'5 and N2 are both present in South Asia in derived forms, so unlikely to have coalesced there, and R, for many reasons, is also unlikely to have coalesced in South Asia. All in all the evidence for any haplogroup N(xR) having moved either east or west through South Asia is non-existent.

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    1. The N(xR) haplogroups of the SE Asian Isles and of Australia came from somewhere and not likely East Asia. N5 seems to be Indian-specific.

      Delete
    2. "in derived forms"...

      I all relevant "derived" forms we know of: N5 and N1(both), N2a and W (both), R in multiple variants...

      Furthermore, you may try as hard as you wish to emphasize the West Eurasian oddities like X but that can't hide that the basal diversity of N in Siberia (your alleged "corridor" is zero) and that the genetic variability we find in that area begins only at the level of very derived clades like X2 subhaplogroups, etc. The Siberian corridor was only used since c. 40 Ka ago, not before (when it was occupied by Neanderthals and their Denisovan hybrid relatives); meanwhile humankind was spreading from Arabia to Australia and China and even into Europe (genetically and archaeologically a "Sapiens colony" contemporary of Altai).

      @ G. Horvat: exactly but never mind engaging Terry in this: he will be arguing circularly until Hell freezes, as they say. He'd like to be able to "demonstrate" some humankind expansion models of the 20th century and he has a major prejudice against South Asia playing the pivotal role it probably did (and also against mainland SE Asia, insisting all the time on "Wallacea", which for him is the mythical land where humankind learned, not to make better boats able to cross to Australia, but to swim altogether).

      We are that way all the time, pretty much to my desperation. Now and then we get some new info on the table but mostly the debate is circularly pointless.

      Thank for your interest in any case.

      Delete
  10. "The N(xR) haplogroups of the SE Asian Isles and of Australia came from somewhere and not likely East Asia".

    Certainly not likely India.

    "N5 seems to be Indian-specific".

    But it is a very minor haplogroup and is just a branch of N1'5, which is very unlikely to have been originally 'South Asian'.

    "I all relevant "derived" forms we know of: N5 and N1(both), N2a and W (both), R in multiple variants..."

    As I said, N1'5 is unlikely to have opriginated in South Asia, same with N2a'W. And far more variants of R are found east of South Asia.

    "that can't hide that the basal diversity of N in Siberia (your alleged 'corridor' is zero)"

    A is reasonably common through Central Asia, as is some unspecified N in the Uzbeks and Altaians. Besides which there is a very good reason why N haplogroups could have become extinct through that region. On the other hand it is very difficult to explain the relative absence of N in South Asia when both M and R are so diverse there.

    "he has a major prejudice against South Asia playing the pivotal role it probably did"

    What complete rubbish you write. South Asia obviously played a huge role in the expansion of both M and R. Where I don't see a role for South Asia is in the expansion of N.

    "insisting all the time on 'Wallacea', which for him is the mythical land where humankind learned, not to make better boats able to cross to Australia, but to swim altogether)".

    What an idiot you are. The expansion of R after both M and N had expanded must have some explanation other than simply being 'luck'.

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    1. "As I said, N1'5 is unlikely to have opriginated in South Asia"...

      This is why I don't like debating with you anymore: you just anchor yourself to the central tenets of your faith and repeat slogans that support these, without substantiating them.

      There's absolutely no reason to imagine that haplogroup Ñ (hypothetical), having two sublineages Ñ1 and Ñ2, both found in the subcontinental region of Ñame but not in that of Ñoño, where only Ñ1 is found, would be from Ñoño. The first logical conclusion is that Ñame, where diversity is 100% is the origin and not Ñoño, where diversity is only 50% (although the evidence is somewhat weak and context should be considered as well).

      But you think like Goebbels that an idea repeated once and again to exhaustion becomes truth, regardless of its scientific merit.

      "A is reasonably common through Central Asia"...

      But obviously originates in East Asia, probably China. Do you want to anchor your ship to A? Then study the real geography and diversity of A first.

      G or H or X are much more common in Central Asia but we know they did not originate there either: they are immigrants from West and East, even if old ones probably.

      "Where I don't see a role for South Asia is in the expansion of N".

      So you think that N migrated to West Asia via Siberia without leaving a single piece of evidence either genetic or archaeological, right?

      It did leave evidence through South Asia: R, N1'5 and N2 (highly diverse basally). You can imagine whatever you wish for the precursor of X but not for the precursor of the other West Asian N sublineages (I'll leave N3 aside because we know too little of it as of now).

      You can also argue maybe that N2 or N2a might have expanded from Central Asia, after all it is found among the Mansi, Ket and other Siberian tribes but it's hard from demonstrated and I think that, in any case, W looks like original from Pakistan, where it's most common - and could be somewhat associated with Y-DNA L originally).

      But most critically you lack of a single piece of archaeological evidence: Central Asia was Neanderthal Mousterian territory until people with West Eurasian Upper Paleolithic technology, which seems derived from South Asian precursors, arrived there c. 40 Ka ago. There is not a single piece of evidence of an East-to-West migration through Central Asia before the Turks.

      Delete
  11. "The N(xR) haplogroups of the SE Asian Isles and of Australia came from somewhere and not likely East Asia".

    I can't see how you can be so confident of that. R is derived from N, and N certainly reached Australia and East Asia by the time that R formed. R could in practice have coalesced anywhere within the region N had occupied. And, interstingly, there is a gap between East Asian and Australian N haplogroups. It si difficult to understand how N could have reached Australia without leaving some descendant haplogroup(s) along the route.

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    1. I retrieve my support for that statement (misunderstanding). I do think that N coalesced in or near SE Asia, because the basal diversity is highest there.

      What I do not think is that it migrated Westward, at least initially, through Central Asia: it did through the South, at least for the oldest clades: R and N1'5, which have short stems.

      Delete
    2. While this particular subject interests me, I know that it is still pretty early in the game to be trying to determine anything conclusive about the 'N' migration Out of Africa. New haplogroups are still being added regularly and previously unclassified sequences are still in the process of becoming classified. Sampling has not been equal in all continents; nor has the genetic work been of equal standard (partially due to different levels of difficulty) The significance of haplogroups which are absent or found in low frequencies may be greater in some broad regions than others. Siberian sequences are much easier to work with than Australian aborigine, for instance, because the former are not very diverse, easily classified and well-studied. The opposite would be true for the latter.

      In my *opinion*, the N (including R) haplogroups developed in the corridor between [the edge of ?] Europe and Australia. From points along that corridor, they entered mainland East Asia which, in my hypothesis, would have been originally 'M' territory. Consistent with this hypothesis, the most common R haplogroups of the East Asian mainland (F & B) appear to have entered from the south and are now routinely described as "southern-prevalent" in peer-reviewed journals. 'N' haplogroup 'A' is found in its highest frequency (and maybe also diversity?) in Tibet and in Tibeto-Burman speaking populations in general. 'N' related haplogroups N9b and Y1 appear to be connected with the origin of the Jomon and Ainu. 'N' haplogroups O, S, N13 & N14 are Australian aborigine. N8, N10, N21, N22, N11b and Y2 are SE Asian.

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    3. @G. Horvat: these things are indeed subject to each one's point of view but my impression, for whatever is worth, is that the explosion of N (apparently in SE Asia, where known basal genetic diversity and its overall geographic scatter appears to point with a flashing arrow of sorts) should be roughly coincident to the expansion of M in East Asia (and Australasia).

      However no subclade of M in the East shows the kind of star-like explosion that N does, so there should also be some difference among them, for example that the timing of N could be earlier (first to arrive gets best position) or that N had a specially good techno-cultural advantage or even that the M-star in East Asia is "invisible" to us because it is at the M-node level (but in South Asia we find subclades with star-like structures, notably M4'67, which is like "the R of M", so to say).

      As for the distribution you say for N, pretty much in agreement but I know no reason why A should be considered primarily "Tibetan". AFAIK it's an East Asian (tending to the North), Siberian and Native American clade. I only know of a single A subclade among Tibetas, A10, although the reference is an obscure pay per view paper.

      Whatever the case, the "flashing arrow" still points to SE Asia as the coalescence zone from N. And the discussion is how it migrated to West Eurasia, where it so obviously not originate. My notion is that it must have been through South Asia, even if the genetic evidence is not clear for some long-stemmed (young) subclades like X and the reason is that it'd be the only way X would be in time to arrive to Altai in time for the local Aurignacoid techno-cultural festival c. 40,000 years ago.

      But all this was settled years ago. And Terry is still insisting (every day!) that it is otherwise: a bubbly cloud of N-ness stemming from West Eurasia (fetish no. 1) to Wallacea (fetish no. 2) via the (Neanderthal) Altai corridor (fetish no. 3) and NOT through India (fetish no. 4). For that he'll drive you crazy explaining how South Chine is not SE Asia (so it miraculously enters his bubbly trans-Siberian cloud) and how Neanderthals are generic "humans" (so H. sapiens can become Neanderthals and whatever else and then H. sapiens again at convenience).

      His fetish no. 5 is boating ability, which according to his dogma must have been invented in Wallacea and only there. Previously people, he'll say, did not have even the most basic raft technology and were more intellectually ape-like than apes themselves.

      In the previous comment I might have been a bit sarcastic but here I'm exposing his viewpoint in great detail, just emphasizing why the pieces do not fit, what his blurry sloppy discourse does not always make apparent.

      So you know.

      Delete
    4. One more comment: I think Altaian X traces back to Georgia.

      Delete
  12. You did not look very hard for the Tibetan articles. :-) Here are urls to two recent ones but I think the second is better than the first:

    Mitochondrial genome evidence reveals successful Late Paleolithic settlement on the Tibetan Plateau
    Zhao et al. (2009)
    http://www.pnas.org/content/106/50/21230.full

    A Mitochondrial Revelation of Early Human Migrations to the Tibetan Plateau Before and After the Last Glacial Maximum
    Qin et al. (2010)
    http://comonca.org.cn/LH/Doc/A58.pdf

    "Haplogroup A is one of the most common haplogroups in northern and eastern Asia with a moderate frequency from 5 to 10% (Derenko et al., 2007)... This haplogroup was found at 14.4% on average in our Tibetan population samples, with the highest frequency in Monba (20.8%) and the lowest in Tibetans from Chamdo (3.3%)."

    Less than half belong to A11 (used to be A10)

    You should be able to access the supplementary files. Zhao's Table S4 contains frequency data for 'A" and other haplogroups.

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    1. I'm sorry but I do not have time to look the matter in depth (not right now certainly). I noticed that all the A subclades together never amount to more than 25% and that only two A sublineages are found in each of the Tibetan subpopulations, when A has at least four subclades: A3'4'7'9'11, A5, A8 and A10 (per PhyloTree's latest build).

      I had not time to check but if, as you say, A11 used to be A10 (??), then all the diversity of Tibetans in this clade is within A3'4'7'9'11. In any case they seem to lack key clades A5, A8, A3 and A9 (and either A11 or A10), so I would not bet for a Tibetan coalescence for A as such.

      With all doubts I feel that A is more original from "generic China" (imprecise, I know) or even NE China (Manchuria and surroundings). But slightly unsure.

      In any case, thanks for the links.

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    2. "I noticed that all the A subclades together never amount to more than 25%"

      For Asia, that is very substantial.

      "and that only two A sublineages are found in each of the Tibetan subpopulations, when A has at least four subclades: A3'4'7'9'11, A5, A8 and A10 (per PhyloTree's latest build)."

      The mtDNA tree is very helpful but it really is nothing more than a reflection of the complete sequencing that has been performed *thus far*. Where much complete sequencing has been performed (i.e. Japan), there are many branches on the tree (see A5a, for instance, which is Japanese-specific). On the other side of the coin, many branches on the tree only apply to a few people's sequences. They might have even paid for the work themselves as I think is the case for A10. It's frequency in my collection of HVR sequences is 1/21,000.

      A8 is a minor sub-haplogroup mainly restricted to Siberia.

      "I had not time to check but if, as you say, A11 used to be A10 (??), then all the diversity of Tibetans in this clade is within A3'4'7'9'11. In any case they seem to lack key clades A5, A8, A3 and A9 (and either A11 or A10), so I would not bet for a Tibetan coalescence for A as such."

      A3 and A9 have no unique HVR I mutations. Since RFLP has not been performed to search for the coding region mutations they contain, we do not know if they are present in Tibetan sample.

      "With all doubts I feel that A is more original from "generic China" (imprecise, I know) or even NE China (Manchuria and surroundings). But slightly unsure."

      Thanks for explaining how you came to that opinion. Could use more of that around here. :-)

      Delete
    3. You're welcome. I don't have a strong position on this matter in any case, just that I don't see any clear support for Tibet, much less as most of Tibet was only colonized in the Holocene (although less high areas by the East, in Sichuan and such have probably been inhabited since very early in modern humankind's prehistory).

      "A3 and A9 have no unique HVR I mutations. Since RFLP has not been performed to search for the coding region mutations they contain, we do not know if they are present in Tibetan sample".

      They would show up as A* and they do not in the second paper (Qin 2010), which is the one I used as main reference: only three A sublineages are mentioned and they may all belong to a single A basal subclade.

      Delete
  13. "There's absolutely no reason to imagine that haplogroup Ñ (hypothetical), having two sublineages Ñ1 and Ñ2, both found in the subcontinental region of Ñame but not in that of Ñoño, where only Ñ1 is found, would be from Ñoño. The first logical conclusion is that Ñame, where diversity is 100% is the origin and not Ñoño, where diversity is only 50%"

    Your logic is faulty here. The diversity of both N1 and W is greater outside South Asia.

    "I do think that N coalesced in or near SE Asia, because the basal diversity is highest there".

    I have never been able to agree with your idea that N coalesced in the east. So I'm pleased to see that you've changed your mind on that.

    "But obviously originates in East Asia, probably China [mt-DNA A]".

    On what grounds 'obviously'?

    "So you think that N migrated to West Asia via Siberia without leaving a single piece of evidence either genetic or archaeological, right?"

    There is archeological evidence for humans right across Central Asia at the appropriate time. There is an obvious reason why the haplogroup diversity in the region would have been greatly reduced: the ice age.

    "It did leave evidence through South Asia: R, N1'5 and N2 (highly diverse basally)".

    N1'5 and N2 are basically confined to the northeast of South Asia and so quite likely entered from somewhere to the west. Subclades of R are the only N haplogroups found in northeast India, and if you concede for a moment that R may not have coalesced in South Asia, you're left with a distribution problem.

    "In my *opinion*, the N (including R) haplogroups developed in the corridor between [the edge of ?] Europe and Australia".

    That's a huge corridor where N is barely present, unless the corridor is in Central Asia.

    "they entered mainland East Asia which, in my hypothesis, would have been originally 'M' territory".

    Which makes the mystery of lack of survival of N haplogroups through South Asia all the greater. I tend to agree that M may have been earlier in the southern part of East Asia, but basal N haplogroups are reasonably numerous through China and so must have occupied a different ecological niche from M there. N certainly reached Australia rapidly, as did R.

    "Consistent with this hypothesis, the most common R haplogroups of the East Asian mainland (F & B) appear to have entered from the south"

    Agree 100%. My best guess is that R9 (containing F) coalesced around the Gulf of Siam (old terminology) and R11'B around the South China Sea. Both coalesced at a time when sea level was much lower than at present. From R11'B we get R24 in the Philippines, R11'B6 in Southeast China and B4'5 along the shore of Sunda.

    "'N' haplogroup 'A' is found in its highest frequency (and maybe also diversity?) in Tibet and in Tibeto-Burman speaking populations in general".

    That's my understanding.

    "'N' related haplogroups N9b and Y1 appear to be connected with the origin of the Jomon and Ainu".

    In other words: largely Northeast Asia rather than East Asian.

    "N8, N10, N21, N22, N11b and Y2 are SE Asian".

    I understand that N8, N10 and N11 are actually South Chinese rather than being strictly 'Southeast Asia'.

    "the explosion of N (apparently in SE Asia, where known basal genetic diversity and its overall geographic scatter appears to point with a flashing arrow of sorts) should be roughly coincident to the expansion of M in East Asia (and Australasia)".

    On what grounds do you believe that?

    "However no subclade of M in the East shows the kind of star-like explosion that N does"

    M's main 'starlike explosion' is actually in the hill country of 'Zomia'. Not South Asia or East Asia.

    ReplyDelete
    Replies
    1. "I have never been able to agree with your idea that N coalesced in the east. So I'm pleased to see that you've changed your mind on that".

      What the fuck?! I have been proposing a SE Asian origin for N for decades (or a Bengali one in some cases). Instead you have been appealing for a West Asian one.

      "There is archeological evidence for humans right across Central Asia at the appropriate time".

      This is exactly the kind of rhetoric BS that makes you an undesirable partner for discussion: vagueness hiding outright lies: there are no Homo sapiens in Central Asia before c. 45 Ka.

      You will understand if I do not read nor reply any further. And if you do not understand, I could not care less.

      Delete
  14. "You did not look very hard for the Tibetan articles. :-) Here are urls to two recent ones"

    I have several times drawn Maju's attention to both, but he insists that he knows more about the subject than the authors do.

    "One more comment: I think Altaian X traces back to Georgia".

    Most probably. And X coalesced from basal N somewhere near Georgia.

    "And the discussion is how it migrated to West Eurasia, where it so obviously not originate".

    Obvously did not originate? Come on. It is African L3 in origin after all.

    "My notion is that it must have been through South Asia, even if the genetic evidence is not clear for some long-stemmed (young) subclades"

    It 'is not clear' for any subclades, long-stemmed or short-stemmed. And yet you insist that it did not merely move through South Asia once, but twice.

    "But all this was settled years ago".

    No it wasn't. You still insist on believing in a very unlikely scenario.

    "a bubbly cloud of N-ness stemming from West Eurasia (fetish no. 1) to Wallacea (fetish no. 2) via the (Neanderthal) Altai corridor (fetish no. 3) and NOT through India (fetish no. 4)".

    Sums it up quite well. That 'bubbly cloud of N-ness' is basal N. Your belief is that some pre-N took a space ship to SE Asia where N coalesced. Whereupon clades of N took another space ship to Pakistan/Northwes India and then emerged into SW Asia. I'm sure I know which scenario is much more likely to be the case.

    "For that he'll drive you crazy explaining how South Chine is not SE Asia"

    If you believe that South China and Southeast Asia are the same place I can tell you now that you had a very poor geography teacher when you went ot school.

    "In the previous comment I might have been a bit sarcastic but here I'm exposing his viewpoint in great detail, just emphasizing why the pieces do not fit"

    Which pieces do not fit?

    ReplyDelete
  15. "I do think that N coalesced in or near SE Asia, because the basal diversity is highest there".

    Sorry. I misread your comment. I saw a 'not' in there as the third word. So I take back my earlier comment. You still believe in miracles.

    "What I do not think is that it migrated Westward, at least initially, through Central Asia: it did through the South, at least for the oldest clades: R and N1'5, which have short stems".

    I certainly have never claimed that N(xR) moved 'west' through South Asia from anywhere. However I do think R moved west through South Asia. The distribution of R haplogroups indicates exactly that.

    ReplyDelete
  16. "What the fuck?! I have been proposing a SE Asian origin for N for decades (or a Bengali one in some cases). Instead you have been appealing for a West Asian one".

    And your evidence in favour of 'SE Asian origin for N' just does not stack up.

    "there are no Homo sapiens in Central Asia before c. 45 Ka".

    We know there were some sort of Homo species in Central Asia long before 45 Ka. We cannot be sure of what they were at this stage.

    G. Horvat, thanks for the information regarding A.

    ReplyDelete
    Replies
    1. We are sure and you know it: H. neanderthalensis and "Denisovans" (in the Northernmost caves) with Mousterian tech. You have read the relevant papers: you know it!

      Delete
    2. "And your evidence in favour of 'SE Asian origin for N' just does not stack up".

      A moment ago you were (mistakenly, deviously, confusedly?) cheering that I claimed a SE Asian origin for N and saying arrogantly "I told you so" and now you change your mind (with no evidence to back you up again).

      C'mon!

      Delete
  17. "A moment ago you were (mistakenly, deviously, confusedly?) cheering that I claimed a SE Asian origin for N"

    You don't read peoples' comments very carefully. I was cheering because, like you, I had misread what you actually wrote. I thought you had written, 'I do [not] think that N coalesced in or near SE Asia, [just] because the basal diversity is highest there'. Certainly it is impossible to claim that N's basal diversity is in any way 'highest' in South Asia, and especially not in Bengal. And on the other hand how can you claim that R's basal diversity is highest in South Asia? Three R haplogroups in western India (R5, R30 and R31), three in eastern India (R6, R7 and R8), and five either side of and in Wallacea (P, R12'21, R14, R22 and R23) with two more within spitting distance of it (R11'b and R9). Why is basal diversity not relevant in the case of mt-DNA R? Surely it is only your eurocentric bias that necessitates your pushing R as far to the west as possible.

    "We are sure and you know it: H. neanderthalensis and "Denisovans" (in the Northernmost caves) with Mousterian tech. You have read the relevant papers: you know it!"

    I have read the relevant papers, and surely you are aware of the fact that technology does not equal species.

    ReplyDelete
  18. Krause et al. 2007. 'Neanderthals in central Asia and Siberia' (ppv).

    From the abstract:

    "To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation".

    I hope you can remember this in the future.

    I also hope that your mind is not as stale as I suspect, and that you can finally accept, from this and other complementary data, that the Altai corridor played no role in the spread of H. sapiens before the Upper Paleolithic.

    Let's settle this for good.

    ReplyDelete
  19. "Let's settle this for good"

    OK.

    "I have been proposing a SE Asian origin for N for decades (or a Bengali one in some cases)".

    So which are the basal N haplogroups that demonstrate N originated in Bengal?

    ReplyDelete
    Replies
    1. We have discussed this before.

      Delete
  20. "To determine how far to the east Neanderthals ranged, we determined mitochondrial DNA (mtDNA) sequences from hominid remains found in Uzbekistan and in the Altai region of southern Siberia. Here we show that the DNA sequences from these fossils fall within the European Neanderthal mtDNA variation".

    So? I know you won't bother reading this, but here goes anyway:

    http://ejournal.anu.edu.au/index.php/bippa/article/viewFile/84/75

    Seems generally accepted by Russian scientists that there was no sharp separation between the Middle and Upper Paleolithic in Central Asia. What's more, until 100,000 years ago the climate in the region was actually more inviting than it is at present. So if you're going to have 'modern humans' emerging from Africa some 100,000 years ago they would have had no problem living as far north as Altai. The presence of Neanderthals in the region more recently than that period looks likely to be explained as replacement, just as in the Levant.

    This too is interesting:

    http://creap.academia.edu/NicolasZwyns/Papers/619857/Burin-Core_technology_and_Laminar_Reduction_sequence_in_the_Initial_Upper_Paleolithic_from_Kara-Bom_Gorny-Altai_Siberia_

    Quote:

    "Regardingtheoverallcharacterof theassemblage,thereisamixof features usually considered typical of Middle Paleolithic (i.e.morphology of the blade core in theirfinal stage of reduction,technique of percussion, pointed laminar blank production) andUpper Paleolithic (i.e. volumetric reduction of blade cores, use of crestedelements atvariousstagesofreduction,occurrenceofsmallelements from a ramified reduction sequence, ornament items)".

    And this one claims the same:

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

    ReplyDelete
    Replies
    1. We have also debated all this in the past. Today the evidence is that there is an hiatus in Altai between the Neanderthal-Musterian remains, all them dated before 50 Ka (beyond the power of C14 dating) and Sapiens-Aurignacoid ones from c. 40 Ka (or less) onwards.

      Neanderthals w/ Mousterian in Central Asia are before the C14 dating boundary of c. 50 Ka uncalibrated. H. sapiens is quite later and there is a hiatus.

      Delete
  21. "We have discussed this before".

    Very inconclusively. With absolutely no solution offered on your part.

    "Today the evidence is that there is an hiatus in Altai between the Neanderthal-Musterian remains, all them dated before 50 Ka (beyond the power of C14 dating) and Sapiens-Aurignacoid ones from c. 40 Ka (or less) onwards".

    No hiatus, yet continuity of technology? And when you write 'these days' you obviously haven't noticed that the first paper is from 2007 and the quote is from a 2011 paper, near enough to 'these days'. I'll admit that the last peper is from 2001. Also, as far as I'm aware the Denisovan fossil is dated at just 40,000 years ago. And I haven't been able to find the dating of the Neanderthals referred to in the Krause paper. If they are round 40-50 Kya we have at least two Homo sprecies in the Altai region at the same time. A third in the mix would hardly be surprising.

    ReplyDelete
    Replies
    1. There is NO "continuity of technology", unless you consider all stone tools to be the same: one is Mousterian (MP tech, no blades) and the other Aurignacoid (UP tech on blade and bladelet largely). Mode 3 and mode 4.

      "you obviously haven't noticed"...

      No. It tires me to read your chaotic and ideological nagging every single day, sorry for existing and having emotions: in my next life I'll be an emotionless robot.

      "the quote is from a 2011 paper"...

      The quote is about blades (mode 4: not Mousterian!), which the author considers somehow transitional between MP and UP techs, what is typical of Aurignacoid techs anyhow.

      Did you even read the paper? From the discussion:

      (...) First, it seems that the technological features observed in both OH5 and 6 are not a result of mixture with the underlying Middle Paleolithic levels. The presence of sterile strata in between OH6 and MPH1 is reinforced by the occurrence of a sterile layer between the two. The 14C results obtained from MPH1 indicate a minimal age circa 44 ka 14C BP, and a maximal age of 62.2 ka calendar years. When calibrated, using both IntCal09 and Marine09 curves (Reimer et al., 2009), the 14C results obtained for OH5 and 6 still show, at two sigma, a 10 ka gap with the first EPR results which were sampled just below MPH1, in a similar sediment matrix (...).

      It is a good paper on Altaian early UP (or local Aurignacoid technology) and it emphasizes that there is a marked hiatus with the Middle Paleolithic, which collapsed c. 44Ka BP (C14) at the latest (what, once calibrated is c. 47 Ka in calendar years).

      The local UP is not older than 34 Ka BP (C14), what is c. 39 Ka in calendar years. There is a hiatus of many millennia, corroborated by archaeologically sterile sediments.

      Now, please take a sheet of paper a thick red marker and write: ALTAI: HIATUS MP-UP CONFIRMED, then nail it above your work desk or somewhere where it's very visible so you do not forget.

      And do not bother me again with this, please.

      Delete
    2. Why am I not getting a reply from you here, Terry? Because I know what you do: drop the matter, "forget" and then charge again months later with the same tired argumentation that has been demonstrated wrong.

      Are doing the red marker thing or what?

      Delete
  22. "Why am I not getting a reply from you here, Terry?"

    I had very limited time yesterday as I had to go up north for a gig.

    "It is a good paper on Altaian early UP (or local Aurignacoid technology) and it emphasizes that there is a marked hiatus with the Middle Paleolithic, which collapsed c. 44Ka BP (C14) at the latest (what, once calibrated is c. 47 Ka in calendar years)".

    The hiatus is at 47,000 years and perhaps lasts until 34,000 years ago. Now, how long ago did mt-DNAs M and N expand? Surely some time before 47,000 years ago. And isn't it generally accepted that mt-DNA has basically an eastern and a western set of haplogroups? I think you've just pin-pointed the timing of that separation.

    "There is NO 'continuity of technology', unless you consider all stone tools to be the same: one is Mousterian (MP tech, no blades) and the other Aurignacoid (UP tech on blade and bladelet largely)".

    The authors of all three papers are definite that the later technology was basically an add-on to the earlier one, as shown by the lines you quote:

    "First, it seems that the technological features observed in both OH5 and 6 are not a result of mixture with the underlying Middle Paleolithic levels. The presence of sterile strata in between OH6 and MPH1 is reinforced by the occurrence of a sterile layer between the two".

    The authors stress that the similarities are not 'a result of mixture with the underlying Middle Paleolithic levels'. Why would they mention that if they didn't think it was important in the context? You are intent on ignoring the fact that the technology before and after the hiatus is much the same, similar to the situation in India pre- and post- Toba. Surely that indicates that the people were most likely the same. They had simply adopted elements of blade technology while they were not able to occupy the region. I'll remind you of the comment in the paper:

    "Regarding the overall character of the assemblage,there is a mix of features usually considered typical of Middle Paleolithic (i.e.morphology of the blade core in their final stage of reduction, technique of percussion, pointed laminar blank production) and Upper Paleolithic (i.e. volumetric reduction of blade cores, use of crested elements at various stages of reduction,occurrence of small elements from a ramified reduction sequence, ornament items)".

    And further:

    "Therefore, it is not relevant to consider OH5 and 6 as a Transitional or Late Middle Paleolithic assemblage. Rather, the data set presented here supports the attribution to an Initial Upper Paleolithic (IUP)assemblage"

    Why would the possibility that it might be transitional between the Late Middle Paleolithic and Upper Paleolithic if the separation was as clear-cut as you like to believe?

    "Regarding the overall assem-blage, it seems to illustrate one of the oldest sets of Upper Paleo-lithic features in this area, however, it also shows some techno-typological aspects more commonly associated with the MiddlePaleolithic. This evidence suggests that Kara-Bom OH5 and 6should be considered as Initial Upper Paleolithic".

    Seems that it is very difficult to decide. The Upper Paleolithic and the Middle Paleolithic overlap considerably in the region, just as the human types do. You are surely aware that Neandertahls in the region are for more 'modern-looking' than are contemporary Neanderthals from further west. What was happening in Central Asia was fairly complicated, not the simple story you would like it to be.

    "Kara-Bom OH5 and 6 can be seen as resulting from a series of human occupations taking place around 43 ka 14C BP".

    So you believe it was not made by 'modern humans?'

    ReplyDelete
  23. What they are saying is that the local UP Aurignacoid tech shows "archaisms", what is just normal: it is an early UP tech, you can easily consider it "transitional" just as happens with other Aurigancoid industries in Europe and elsewhere.

    But critically they are saying that there is NO continuity between this early UP tech, which is surely of Sapiens manufacture (from overall context) and the pre-existent MP Mousterian one (Neanderthal and "Denisovan" made). They emphasize that an sterile layer, of almost 10 millennia thickness, separates both, so they are not really related: they can't be, not in that particular cave certainly.

    From the other paper you mention (Derevianko 2007), table 1:

    Denisova cave:
    > latest MP: 46 Ka (entrance's L9, C14)
    > earliest UP: 37 Ka (main chamber's L11, C14)
    Hiatus: c. 9 Ka

    Okladnikov cave (farthest North site):
    > latest MP: 33.5 Ka (layer 1, C14) or 28.5 Ka (layer 3, C14)
    > earliest UP: none

    Ust Karakol 1:
    > latest MP: 90 Ka (layer 18A, RTL)
    > earliest MP: 50 Ka? (layer 9C, RTL) or more likely 35 Ka (layer 10 C14)
    Hiatus: 40-55 Ka.

    Kara Bom: data overriden by Zwynns 2011, who states a clear hiatus of c. 10 Ka. as described above.

    So we have a quite apparent first UP (and surely Homo sapiens) occupation of Altai sites c. 34-37 Ka BP (C14). Okladnikov cave could well be a late persistence of Neanderthals but otherwise the archaic species seem to vanish some 10 Ka. before the arrival or consolidation of our species some 40 Ka ago (after calibration). This arrival is too late to represent either migration eastwards or back-migration westwards (there are sites in Europe that approach the 50 Ka calBP dates and in Palestine of RTL 55 Ka with modern human remains).

    "So you believe it was not made by 'modern humans?"

    There are genetically described Neanderthal and "Denisovan" remains in those caves, please!

    Krause 2010: "... individuals carrying Neanderthal mtDNA were present less than 100 km away from Denisova Cave in the Altai Mountains".

    That's Okladnikov:

    Zwynn 2011: ... "it seems clear that Neanderthal fossils are associated
    with the Mousterian assemblage from Okladnikov Cave (Krause
    et al., 2007)"...

    There are also Neanderthals associated with Mousterian in Uzbekistan and then we have the "Denisovan" hybrids (partly Neanderthal, partly erectus surely) in Denisova. But not a single hint of our species: neither suggestive technology, nor bones nor DNA!

    Not before UP, that is.

    ReplyDelete
  24. Just in case:

    "Why would the possibility that it might be transitional between the Late Middle Paleolithic and Upper Paleolithic if the separation was as clear-cut as you like to believe?"

    The MP features are not necessarily (nor likely) locally rooted: our species also used MP techs (Levallois, MSA and others surely, even Mousterian in the Palestinian case!) Europe early "Aurignacoid" UP also shows such transitional features, as do many other early UP techs. It's absolutely normal and does not indicate transition from Mousterian, much less from the Mousterian made by Neanderthals.

    ReplyDelete
  25. "What they are saying is that the local UP Aurignacoid tech shows 'archaisms', what is just normal: it is an early UP tech, you can easily consider it 'transitional' just as happens with other Aurigancoid industries in Europe and elsewhere".

    Not so very long ago you were claiming that 'blades' were an indication of 'modern' humans. So now, when that doesn't suit your belief, you are claiming that the Initial Upper Paleolithic of the region was made by Neanderthals/Denisovans even though it contains blades. Your inconsistency again shines brightly.

    "There are also Neanderthals associated with Mousterian in Uzbekistan and then we have the "Denisovan" hybrids (partly Neanderthal, partly erectus surely) in Denisova. But not a single hint of our species: neither suggestive technology, nor bones nor DNA!"

    Only blades.

    "But critically they are saying that there is NO continuity between this early UP tech, which is surely of Sapiens manufacture (from overall context) and the pre-existent MP Mousterian one (Neanderthal and 'Denisovan' made)".

    But they are saying that the Initial Upper Paleolithic appears before this hiatus, 'taking place around 43 ka 14C BP'. At this stage I think it's valuable to remember that the paper that is the subject of this blog claims N expanded 58,859 years ago. It presumably began to break up into its subclades soon after as R had formed by 56,523 years ago. I realise you refer to the paper as 'molecular-clockology' but your disagreement is usually that the time is too short. So that places N's expansion and diversification considerably before the hiatus in Central Asia.

    ReplyDelete
    Replies
    1. "... you are claiming that the Initial Upper Paleolithic of the region was made by Neanderthals/Denisovans"...

      Not at all. I'm claiming that the Middle Paleolithic (no blades) of the region is Neanderthal/Denisovan and the Upper Paleolithic is Homo sapiens.

      (Note: in other contexts Neanderthals have also made blade industries, like Chatelperronian, but in Altai it does not seem to be the case).

      "But they are saying that the Initial Upper Paleolithic appears before this hiatus, 'taking place around 43 ka 14C BP'".

      The only site with dates like that in Derevianko 2007 is Kara Bom but Zwynn 2011 argues for more recent dates. I'm taking Zwynn as reference here because he's more recent and he states very clearly that there is a sterile layer between the MP and UP and a hiatus of c. 10 Ka between the two occupations.

      Got that? It's very important.

      "N expanded 58,859 years ago. It presumably began to break up into its subclades soon after as R had formed by 56,523 years ago".

      Assuming that would be correct, they could have never used the Altai route, which only has Neanderthal/Denisovan evidence so early.

      Anyhow I can't agree with those estimates: N must be c. 70 Ka old and R surely older than 60 Ka. But this disagreement is not that important for the matter at hand.

      Delete
  26. "Anyhow I can't agree with those estimates: N must be c. 70 Ka old and R surely older than 60 Ka".

    That places N's expansion even further back before the hiatus you claim destroyed all humans in the Altai.

    "But this disagreement is not that important for the matter at hand".

    It is really. If you accept that N's expansion was some 70,000 years ago that leaves plenty of time for plenty to happen. What regions were Upper Paleolithic that long ago? And what was N doing all those years that provides no trace through Eastern South Asia?

    "I'm claiming that the Middle Paleolithic (no blades) of the region is Neanderthal/Denisovan and the Upper Paleolithic is Homo sapiens".

    But blades appear in the Initial Upper Paleolithic, and that occurrs before the hiatus, at least according to the 2011 paper.

    "Assuming that would be correct, they could have never used the Altai route, which only has Neanderthal/Denisovan evidence so early".

    They don't need to use the Altai route. They do not have to be anywhere near as far north as that to be able to move east during periods of climate amelioration. In adverse conditions they can move south as far as Afghanistan. But you just carry on believing what you want to believe.

    "but Zwynn 2011 argues for more recent dates. I'm taking Zwynn as reference here because he's more recent and he states very clearly that there is a sterile layer between the MP and UP and a hiatus of c. 10 Ka between the two occupations".

    But he states very clearly that the Initial Upper Paleolithic is dated at more than 40,000 years ago. Read the abstract:

    Using a taphonomic and techno-economic approach, we describe the laminar reduction sequences from levels 5 and 6 of Kara-Bom, Gorny Altai, Siberia. The reconstructed technological system includes the production of large laminar blanks, convergent laminarflakes, and small laminar blanks, transcending analytic categories such as blades and bladelets. The burin-core technology is integrated into the general knapping strategy using byproducts from the large blade production as core blanks. The Kara-Bom Initial Upper Paleolithic is associated with the production of ornamental items such as perforated ungulate teeth and is dated around 43 ka uncal. BP."

    And in the conclusion :

    "Kara-Bom OH5 and 6 can be seen as resulting from a series of human occupations taking place around 43 ka 14C BP."

    So we can be sure 'modern humans' were in the region by then?

    "So we have a quite apparent first UP (and surely Homo sapiens) occupation of Altai sites c. 34-37 Ka BP (C14)".

    Wrong.

    ReplyDelete
    Replies
    1. ... "even further back before the hiatus you claim destroyed all humans in the Altai".

      I don't "claim" that.

      The hiatus clearly marks in the relevant caves a lack of occupation in the MP-UP transition. Apparently some Neanderthals survived at the northernmost cave, Okladnikov, until after Sapiens occupation.

      Your usage of the ambiguous "all humans" is only intended to confuse the matter so you can cling to some straws. Or fantasize that you can: you are not deceiving anyone but yourself with this, Terry.

      "If you accept that N's expansion was some 70,000 years ago that leaves plenty of time for plenty to happen".

      Sunshine, lollipops and rainbows... :D

      Sorry but that's what comes to my mind when I read this kind of elusive fantasies in which even elves and goblins and what not could be included... it's all up to claim that there is a blank of knowledge and fill it up with whatever one wishes: God, dragons... N-clan black people wandering in the snow... but then arriving to Australia with the most perfect Afro-tan after millennia of negating Evolution its right to exist in the name of Terry's stubborn beliefs. Darwin's worst nightmare.

      But, in addition to all that, there is another problem: there is no such blank: the region is full of archaeological remains that are fully consistent with a Neanderthal (and Denisovan) occupation but not a single one suggesting the presence of Homo sapiens until much later.

      So you are mercilessly and quite dishonestly bending the evidence in order to make a hole large enough to push your dragons through.

      Sorry, not credible.

      "They don't need to use the Altai route. They do not have to be anywhere near as far north as that to be able to move east during periods of climate amelioration".

      First, the period between c. 74 Ka and c. 60 Ka was one of the coldest in the recent geological history (because of Toba surely).

      Second, the area between the Altai corridor and the Hymalayas is barely able to support life even today, much less in the dry and cold spell of the Ice Age, when Tibet was complete covered in ice and the deserts of Uyghuristan and Mongolia were even more arid than now.

      Third, further south in your hypothetical "Paleolithic Silk Route", in Uzbekistan, the inhabitants were also Neanderthals.

      Fourth, your grasping for straws is becoming quite pathetic. Why don't you put the cart behind the horses for once and stop assuming things without any evidence?

      "But he states very clearly that the Initial Upper Paleolithic is dated at more than 40,000 years ago. Read the abstract"...

      You may be right in this. I will have to check the details because Derevianko 2007 considers this layer to be still Middle Paleolithic. This can mean two things: (1) Neanderthals developing on their own or importing the blade concept from neighboring H. sapiens (just as in Europe in the same period) or (2) the earliest tentative arrival of H. sapiens to the region.

      "Kara-Bom OH5 and 6 can be seen as resulting from a series of human occupations taking place around 43 ka 14C BP."

      It does not really make a big difference and still cannot support your hypothesis either. It would just push the H. sapiens penetration earlier, more in accordance to what we know of the colonization of Europe nowadays, which is even older than that probably, at least in is first stages.

      Delete
  27. You're definitely rambling here:

    "N-clan black people wandering in the snow... but then arriving to Australia with the most perfect Afro-tan after millennia of negating Evolution"

    Isn't the haplogroup evidence reasonably convincing that people arrived in Australia relatively rapidly after N began to expand?

    "Derevianko 2007 considers this layer to be still Middle Paleolithic. This can mean two things: (1) Neanderthals developing on their own or importing the blade concept from neighboring H. sapiens"

    'Middle Paleolithic' does not define 'not modern human'.

    "But, in addition to all that, there is another problem: there is no such blank: the region is full of archaeological remains that are fully consistent with a Neanderthal (and Denisovan) occupation but not a single one suggesting the presence of Homo sapiens until much later".

    On what grounds do you claim that to be so? The absence of blades? If so you need a rethink.

    "I'm claiming that the Middle Paleolithic (no blades) of the region is Neanderthal/Denisovan and the Upper Paleolithic is Homo sapiens".

    So the Australian Aborigines are not 'modern humans' by your definition. They did not have a blade technology until some 6000 years ago.

    http://une-au.academia.edu/MarkMoore/Papers/454683/Australian_Aboriginal_blade_production_methods_on_the_Georgina_River_Camooweal_Queensland

    And:

    http://www.janesoceania.com/australia_aboriginal_arrivalofthedingo/index1.htm

    Quote from the last:

    "Included within the small tool tradition are backed blades, points, tulas and burren adzes. These tool types vary considerably, both in terms of geographic location and the timing of their appearance. It is generally agreed that these small tools were added to the existing Australian tool kit some time between about 6000 and 4000 BP, but there is much debate about the exact chronology, distribution and origin of each type".

    ReplyDelete
  28. Australia was surely colonized soon after N expanded... in SE Asia. You can't take the evidence and the model by parts at your convenience.

    In Altai we have:
    1. Mousterian with Neanderthal/Denisovan skeletal remains
    2. Aurignacoid UP with Homo sapiens' skeletal remains

    Plus the process is linked conceptually and chronologically to a very similar one in Europe and West Asia.

    Barring some strange surprise (let's see it first), the conclusions are very straightforward.

    Associating Mousterian with Homo sapiens is not really acceptable unless you'd have some evidence, which you do not, much less in this case which is so clear-cut.

    The cultural sequence in Eastern Asia and Australasia is different but there is no Mousterian either, so your attempt of comparison is just another attempt at falsifying the terms of the discussion - something that I do not have to put up with.

    Both the Mousterian MP with Neanderthals and the Aurignacoid UP with Sapiens that we find in Altai are totally consistent, even in chronology, with the processes we see elsewhere in West Eurasia (but not in other regions like Southern Africa or Australia, logically). Similarly is the genetic that we find even today, for the largest part.

    Comparing with Australia is pointless when everything points to being part of the same processes that we see in Europe and West Asia (and not any other).

    ReplyDelete
  29. You know: your intellectual cheating really annoys me: I say "Mousterian" and you say "no blades". Why do you think that you can deceive me with such lowly petty discursive tricks?

    That's why I'm getting to dislike you more and more: you are a cheater and not any honest debate partner.

    ReplyDelete
  30. "you are a cheater and not any honest debate partner".

    Not true. How about this:

    "Australia was surely colonized soon after N expanded... in SE Asia. You can't take the evidence and the model by parts at your convenience".

    It is you who is taking evidence apart at your own convenience. N1'5 is also only one mutation from basal N so must have arrived somewhere in northwest India/SW Asia soon after N expanded. And the same holds for N2 and X even though they have long stems. N must have expanded widely at roughly the same time as it reached Australia.

    "your intellectual cheating really annoys me: I say 'Mousterian' and you say 'no blades'. Why do you think that you can deceive me with such lowly petty discursive tricks?"

    I'm doing no such thing. I'm merely relying on your previous distinctions such as:

    "one is Mousterian (MP tech, no blades) and the other Aurignacoid (UP tech on blade and bladelet largely). Mode 3 and mode 4".

    And this one:

    "The quote is about blades (mode 4: not Mousterian!), which the author considers somehow transitional between MP and UP techs, what is typical of Aurignacoid techs anyhow".

    So you obviously consider 'blades' as defing modern human technology. And claim modern humans cannot have been present in any region before blades appear.

    "Associating Mousterian with Homo sapiens is not really acceptable unless you'd have some evidence, which you do not, much less in this case which is so clear-cut. The cultural sequence in Eastern Asia and Australasia is different but there is no Mousterian either, so your attempt of comparison is just another attempt at falsifying the terms of the discussion - something that I do not have to put up with".

    I know you prefer to ignore the difference in Eastern Asia and Australasia because it doesn't fit your belief, but how about this quote in a textbook from my university days (may be dated, but I don't think it's disputed):

    "In territories relatively remote from those in which innovations first appeared old forms of technology might survive from the mere fact that they remained without challenge. Industries in mode 1, which must have been practised over an immensely long period of time, are found over the whole territory occupied by early man. Mode 2 industries on the other hand failed to reach south-east Asia or China. Mode 3 industries still did not penetrate these regions in the Far East, but on the other hand extended northwards into European Russia and Inner Asia. This makes it less of a surprise that when for example men first spread into Australia by way of Indonesia they should have carried with them a lithic tradition in mode 1."

    So do yoy still believe either that the Australian Aborigines are not 'modern human', or that modern humans cannot be associated with anything before the Aurignacoid UP?

    "Comparing with Australia is pointless when everything points to being part of the same processes that we see in Europe and West Asia (and not any other)".

    That statement is obviously incorrect. N's expansion has to be older than the Aurignacoid UP.

    ReplyDelete
    Replies
    1. I'm going to try to save my time when discussing with you so, sythetically:

      1. N1'5 is just one of several short-stem basal derivates from N: you can't finish a puzzle with just one piece.

      2. Don't you know what Mousterian is? Or are you rather just being insultingly cynic?

      3. I do not "consider 'blades' as defing modern human technology". You're making things up with a long shot of hypocrisy and circular reasoning.

      4. I do think that Australian Aborigines are modern humans like you or me. Your resort to gratuitous accusations of "racism" (twice in the day, twice made up and false and only to underline an equally false pseudo-logic of you) is not acceptable. I'd punch your nose at this time or at least throw a beer to your face.

      4.b. As soon as I migrate to Wordpress (which I'm more and more determined to do), I'll have the ability to individually censor commenters and, unless you radically change your manners soon you will be in that list.

      5. You obviously misunderstood me at least once but it'd take too long and would be too useless to dispel your confusion and I cannot care anymore.

      Delete
  31. "1. N1'5 is just one of several short-stem basal derivates from N: you can't finish a puzzle with just one piece".

    But that is exactly what you were trying to do. I have consistently been trying to get you to look at all the evidence. I find it interesting that you have for so long accepted Behar (and the other authors of the current paper) as experts for so long, but now that they have provided fairly convincing dates in their molecular clockology you dismiss them. The dates they offer for the several of the basal N haplogroups are particularly interesting. N at 58,859 years, N1'5 at 56,547 years (even N1 at 51,642 years), N2 (with a 4 mutation tail) at 44,477 years, N9 at 45,709 years, N10 (with a 2 mutation tail) at 50,443 years, N11 at 56,272 years, O (with a 2 mutation tail) at 52,053 years, S at 53,483 years and R at 56,523 years. So we can be sure that N had reached India/SW Asia, South China and Australia before the hiatus in the Altai, and before the appearance of anything that could be considered Upper Paleolithic.

    "2. Don't you know what Mousterian is? Or are you rather just being insultingly cynic?"

    You are obviously trying to avoid the issue here. The Australian Aborigines did not have a culture that could in any way be termed Upper Paleolithic, however you might wish to define such a technology.

    "3. I do not 'consider 'blades' as defing modern human technology'. You're making things up with a long shot of hypocrisy and circular reasoning".

    You seem to have changed your mind then. What do you now regard as the defining characteristic of modern humans?

    "4. I do think that Australian Aborigines are modern humans like you or me".

    Thank you.

    "Your resort to gratuitous accusations of 'racism'

    And you've just demonstrated that I have been correct in those accustaions. You've just suggested that the Australian Aborigines cannot be considered modern humans. I've been trying to tell you for some time now that technology is not the defining characteristic of modern humans but, your obstinate insistence on maintaining otherwise has led you to this ridiculous situation.

    ReplyDelete
    Replies
    1. It's you who is trying to dodge the issue by calling up Australia, where neither Mousterian nor Aurignacian of any kind have ever existed.

      If that would be the slip of a less knowledgeable person who is not an annoying arrogant prick, I'd have no problem in explaining it again, but in your case it's obvious that you are just fooling me, whoever other readers and maybe yourself with ill intent.

      _|_

      Delete
  32. "It's you who is trying to dodge the issue by calling up Australia"

    No Maju. You are dodging the issue by choosing to ignore Australia.

    "where neither Mousterian nor Aurignacian of any kind have ever existed".

    Nor anything that can be called diagnostic of classic Upper Paleolithic. And yet the people surely cannot be considered other than being genetically 'modern' humans.

    "in your case it's obvious that you are just fooling me"

    No, you are fooling yourself. For example:

    "As for the rest, it is molecular-clock-o-logy of the kind I can't accept (M must be 80-74 Ka old, being the most clear calibration point in the human mtDNA phylogeny per our current archaeological knowledge)".

    The only reason you disagree with the dates provided in the paper is because those dates cannot be made to fit your belief. Surely it is time for you to step back and reconsider your belief. The dates fit perfectly with what we know of Australia and neighbouring regions. For example dates of 52,053 and 53,483 years for O and S fit very well what seems to be the most likely dating for the entry into Australia. But of course acceptance of the dates fails to fit what you think you know of South Asia. On the other hand if you were prepared to accept the dates given you would come to quite a different conclusion regarding human expansions.

    "Oddly enough, in spite of M being closer to the root than N and having on average more mutations to present day sequences, the authors manage to somehow assign a younger age to this haplogroup than to its sister N".

    Why are you unable to accept that? Makes sense to me.

    ReplyDelete
  33. Mousterian in Australia? Neanderthals in Australia? Aurignacian in Australia?

    NOPE!

    You know that perfectly well. Nothing of what is found in Altai has any direct relation with Australia!

    ReplyDelete

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