January 23, 2013

Tianyuan, mtDNA B and the formation of Far Eastern peoples

The genetic study of the ancient man of Tianyuan is already online, as I commented yesterday in a quick update.

Qiaomei Fu et al., DNA analysis of an early modern human from Tianyuan Cave, China. PNAS 2013. Open accessLINK [doi: 10.1073/pnas.1221359110]

Abstract

Hominins with morphology similar to present-day humans appear in the fossil record across Eurasia between 40,000 and 50,000 y ago. The genetic relationships between these early modern humans and present-day human populations have not been established. We have extracted DNA from a 40,000-y-old anatomically modern human from Tianyuan Cave outside Beijing, China. Using a highly scalable hybridization enrichment strategy, we determined the DNA sequences of the mitochondrial genome, the entire nonrepetitive portion of chromosome 21 (∼30 Mbp), and over 3,000 polymorphic sites across the nuclear genome of this individual. The nuclear DNA sequences determined from this early modern human reveal that the Tianyuan individual derived from a population that was ancestral to many present-day Asians and Native Americans but postdated the divergence of Asians from Europeans. They also show that this individual carried proportions of DNA variants derived from archaic humans similar to present-day people in mainland Asia.

Mitochondrial DNA

Part of fig. 1
And the old guy (or is it a woman?) happened to carry the matrilineage (mtDNA) B, more specifically B4'5, defined by a relatively long deleted block at positions 8281-8289 (this excludes B6 now linked with R11 and also the other relative of all them R24, see PhyloTree for details). However within B4'5 the lineage could not further be resolved within the modern haplogroups, so it is neither B4 nor B5 but a third branch of the same haplogroup. 

The authors actually talk of "haplogroup B" but they explicitly mention a deletion of a 9-bp motif (5′-CCCCCTCTA-3′, revised Cambridge reference sequence positions 8,281–8,289) as well as a substitution at position 16,189, what makes it unmistakable B4'5 per the current PhyloTree build.

The tree to the right illustrates this fact, placing Tianyuan man's lineage hanging directly from the root of this haplogroup that, beyond reasonable doubt, coalesced somewhere in East Asia (probably SE Asia, with Laos and Hainan being good references judging on diversity) some time before this person lived and died near what today is Beijing. 

What does it tell us? Really nothing new, at least within the parameters I have been managing: it confirms that the expansion of mtDNA B4'5 was already happening back in that time and that it had reached more or less its current area of expansion in East Asia (American and Oceanian B variants expanded later, of course). It also implies that its ancestors R and N, which experienced important successive expansions in the course of the colonization of Eurasia by our species had expanded  at an even earlier date (again nothing new to me but a nice confirmation anyhow).

On the other hand, this person's particular matrilineage went eventually extinct later on. This again does not tell us too much because it is something to expect with the course of time, especially at low population densities, as was the case in the Paleolithic. He can still be ancestral to modern peoples in the area and elsewhere but not by a purely mother-to-daughter line - at least not that we know. 


Chromosome 21 autosomal DNA

Because of the poor state of the DNA, the researchers had a difficult time sequencing it (technical details in the paper), however they managed to reconstruct a good deal of chromosome 21, which they used to compare with modern humans and also with Neanderthals and the so-called Denisovans

The result places Tianyuan closer to modern Far Eastern populations than to the rest of modern humans. This clearly indicates that the process of division in various more or less homogeneous subcontinental-sized populations was already somewhat advanced. 

Fig. 2. Maximum-likelihood tree relating the chromosome 21 sequences of the Tianyuan individual, 11 present-day humans, and the Denisovan genome. The most strongly supported gene-flow event is shown in yellow. Bootstrap support for all internal edges is 100% except for the edge putting Tianyuan outside the four Asians, which is 31%. The scale bar shows 10 times the average standard error of the entries in the covariance matrix.

While it is generally acknowledged that Papuans cluster at very deep level with East Asians, the authors are not fully persuaded of the exactitude of this tree, particularly in this aspect. They declare:

We note, however, that the relationship of the Tianyuan and Papuan individuals is not resolved (bootstrap support 31%). Further work is necessary to clarify whether this reflects the age of the Tianyuan individual relative to the divergence between modern human populations.

The caveat is particularly relevant because the colonization of New Guinea is at least as old as 49,000 years ago, some ten millennia before Tianyuan, what does not fit too well with the tree at that level of detail, assuming (as I do) that modern Papuans are direct unmixed descendants of those early settlers. Papuans do carry at high frequencies a related matrilineage (P also basal descendant from R) but that is also true of modern Europeans and they appear more distant in the tree above.

A good contrast to understand better the difficulties in getting a good picture from autosomal DNA, especially one so old, is table 1:


Here we can appreciate the differences and proximities by another measure. The closest compared modern person to Tianyuan man is a Karitiana, followed closely by the Han and, surprisingly, by the Sardinian and the French, and only then the Dai and Papuan. 

The distance of the Karitiana to Tianyuan man is still greater than that with not just the Han or the Dai but also the Europeans. However this can be argued to be because Native Americans must have a deep dual East Asian and West Eurasian origin, the latter via Altai (Y-DNA Q, mtDNA X2).

Let's check the Han then, who are not believed to have any meaningful West Eurasian admixture. Curiously the paradox happens again: the Han is somewhat closer to Europeans by this measure than to Tianyuan, and even their comparison with the Papuan shows up slightly less differentiated. 

This is admittedly harder to explain but we can conclude that either (a) this method can only grasp affinity/divergence to some degree or (b) that the Tianyuan partial genome indicates a very preliminary level of continental differentiation. Or (c) both. Of course time is the main cause of genetic differentiation and by no means we can imagine that such an ancient individual would be too similar to his modern plausible descendants but, on the other hand, all (including Tianyuan mtDNA) indicates that the process of continental differentiation was already well developed 40,000 years ago (most European ancestry must come from people living in Europe or West Asia back then) so we can either blame subtle flows like Siberian migrations that have kept both genetic pools somewhat closer than in pure isolation or we must assume that the measure is not too exact.



Admixture with other human species

The paper also deals with Denisovan and Neanderthal admixture, finding that Tianyuan man was within the modern range for both parameters in East Asia. 

This is very important because it ratifies the mainstream model of two minor admixture episodes: (1) with Neanderthals at the exit from Africa and prior to the Great Eurasian Expansion (so all non-Africans, including Tianyuan man, have very similar levels of Neanderthal admixture today) and (2) with a relative of Denisovans (Homo erectus?) maybe in Indonesia affecting only (or almost only) the aboriginal peoples of Oceania (and Filipino Negritos but not the other so-called Negritos from Malaysia or the Andaman, who are not particularly related anyhow).

(As a side note notice that the Denisovan-like gene flow into Papuans in fig. 2 appears to hang not from the end of the branch but from a very high position, suggesting it was a relative and not the known Denisovans of Altai themselves who became admixed into Papuans and other Oceanian populations, probably a relative living in the route to Australasia).


Update: Marnie just published a mention of a previous work on Tianyuan 1, which focuses on the isotopic evidence for a fish-based diet. 

24 comments:

  1. Maju, I just called you an eccentric Basque blogger. Hope that's OK.

    http://eurogenes.blogspot.com.au/2013/01/ancient-dna-from-40k-year-old-relative.html

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    1. I take no offense: it's probably an accurate description. Be normal and die of boredom!

      Anyhow, it is B4'5 - at least per PhyloTree (and has been that way for some time). "B" is either an obsolete description (don't think so but I may be wrong in this detail) or most likely just a shorthand.

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    2. It's probably an accurate description of most bloggers anyhow.

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  2. Well, I couldn't resist myself to comment such an interesting paper, so I'd like to add:

    "so we can either blame subtle flows like Siberian migrations that have kept both genetic pools somewhat closer than in pure isolation or we must assume that the measure is not too exact. "

    It looks like all non-Africans are closer to Africans than Tianyuan, and all Africans are closer to non-Africans than to this old Asian too, which only can be explained by gene flow from Africa to Eurasia (and the Americas) less than 40K ago.

    "The paper also deals with Denisovan and Neanderthal admixture, finding that Tianyuan man was within the modern range for both parameters in East Asia. "

    But isn't Tianyuan closer to Denisovans than the Papuan is according table 1? Also some Africans appear closer to Denisovans than others: admixture or what?

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    1. "I couldn't resist myself to comment such an interesting paper"...

      Please do. Long time not seeing you around, nor even at your blog - hope that's because of all the good reasons.

      "... which only can be explained by gene flow from Africa to Eurasia (and the Americas) less than 40K ago".

      And vice versa (there are many Eurasian lineages in Africa, and not just in the North). However the flows are (at least in the areas sampled) subtle at best.

      It's a possibility I'm a bit perplex by the table so I can't be certain of what is causing all those apparent anomalies. It may also be a peculiarity of chr 21 or who knows!

      "But isn't Tianyuan closer to Denisovans than the Papuan is according table 1?"

      Yes. Almost the same in fact. But then the tree does not find that nor does the (not copied) fig. 3, which is assumed to be "the real thing" re. Denisovan/Neanderthal affinity.

      Autosomal comparisons are slippery at best. I stumble on this kind of contradictions all the time: the tools may not be the best (after all statistical approaches, the only possible ones with always recombining autosomal DNA unavoidably commit errors, hopefully not too relevant) or the sampling strategy may sideline some key actors or whatever.

      Can't say.

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    2. I know what's the issue, Neanderthalerin: both Tianyuan has been dead from long ago, so Tianyuan has never accumulated this last 40 Ka of human evolution, which may be different in each pop. but has happened anyhow, so it's only logical that "he" is slightly closer to Denisovan, after all a distant relative, than us. What is not so logical is what we see in modern Papuans.

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    1. I doubt I said that: autosomal analysis does not seem able to, at least easily, detect such deep layers, when subpopulation distinctiveness was still preliminary. All I can say is that Y-DNA Q is obviously original from the West, surely Iran.

      "Europeans have 10% ancient Siberian admixture"...

      That's an unlikely high figure: MixMapper and TreeMix are not reliable tools; not just they produce often incredible affinities but also reverse or oversimplify the direction of flows. For me all that you have in mind is junk, noise. Nothing else. Just like molecularclockoloy... useless in the best case, totally confusing in the worst one.

      I do not understand what you mean with the last paragraph. I don't do much anthropometry. West Eurasia is a geographic region, which has genetic an prehistoric homogeneity since c. 55 Ka ago until the Bronze Age.

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    2. " molecularclockoloy" should read "molecular-clock-o-logy".

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  6. http://en.wikipedia.org/wiki/Haplogroup_Q_(Y-DNA)

    Q* India, Pakistan, Afghanistan
    Q1* Iran
    > Q1a* Koryaks
    >> Q1a1 East Asia
    >> Q1a2 Iran
    >> Q1a3* West and South Asia, Europe, Tibet
    >>>> Q1a3a1 Native Americans
    >>Q1b1 West and South Asia, Europe, Uyghurs

    Judge yourself but I'd say it's center of diversity is near Iran. South Asia is also quite obviously ancestral for P and R but Q looks maybe a tad more to the NW.

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  7. Also I think that West Eurasia was colonized from South Asia, long after the OoA. Previously it was mostly in Neanderthal hands. Similarly I understand that all the evidence points to a colonization of NE Asia from SE Asia. The Siberian W-E migration of Q is exceptional but still within the general S-N trend of the late phase of Eurasian colonization by our species.

    I don't think that West Asia played any meaningful role, except as mere Arabian corridor or 'pump' in the initial, non-expansive, phase of the OoA. The expansion only began after arrival to South Asia (M, y-dna F) and, scondarily, SE Asia (N, y-dna D, surely also C).

    We seem to have very different concepions of the Eurasian Expansion. Yours sounds very obsolete and confused to me. I can discuss any details but please use mtDNA as primary approach, it's obvious that Y-DNA excessive focus confuses even the best minds.

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    1. First of all spare me please your spurious accusations of emotionally-driven bias. You may not remember but it was this attitude of you which caused me to quite your now-dead forum and begin blogging.

      Second, I have just presented you with the (incredibly accessible) evidence that suggests a near-Iran origin of Y-DNA Q and you have simply dribbled the matter altogether.

      Third, the facts are hand are as follow (briefly):
      → Eurasian mtDNA grand lineages (M, N, R) have all basal diversity centroids in South and SE Asia
      → Eurasian Y-DNA grand lineages (F, C, D, K, MNOPS, even NO and P) all look also original from those areas (similar basal diversity reasons)
      → 21st century archaeology (Petraglia, Rose, Armitage, etc.) have found plausible Arabian and Indian related sites with dates of c. 125-90 Ka in the first case and since c. 80 Ka in the latter. SE Asia is still wanting but will eventually provide the key evidence, I'm sure. We know that Altai, in contrast, was occupied by "archaics" with Mousterian. Altai being the only possible alternative corridor to Tropical Asia was obviously not transited by our kin until c. 40 Ka ago, with technologies similar ("Aurignacoid") to those found in West Eurasia, and which may be rooted in South Asia (evidence is fragmentary so far).

      So cry me a river about my "emotional bias" and whatever you wish to imagine. I follow the trail of the material evidence.

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    1. Am I the one being personal ("insulting")? Please, Ren! You should make a self-criticism even if just of this thread. Nobody can progress in the path of truth, of science, without self-criticism.

      "... to say Q and X is West Eurasian is even problematic. It depends on what you mean by West Eurasian".

      I mean that they are original from West Eurasia (West Asia, Central Asia and Europe, sometimes also including North Africa, a region that is genetically rather homogeneous since the Upper Paleolithic until the Bronze Age). This region was essentially colonized by a single population with "mode 4" tech originating somewhere in South Asia c. 55 Ka ago (Palestine) and later.

      "Thirdly, regarding South Asia, there seems to have been continuously habitable zones in the "Gulf Oasis" of SW Asia"...

      That would be West Asia in any case (South Asia begins at Pakistan usually). But it does not seem to me on light of the genetic data that the remnants of the OoA surviving (possibly) in that region played any major role in the effective colonization of the major West Eurasian region in the early UP. They'd be at best a surviving substrate that may be detected (in fact I believe I have detected an ADMIXTURE cluster in Arabs and Low Egyptians that may be from that period, also some mtDNA lineages of Arabia may be survivors from that period as well).

      "South Asia is diverse because it was able to maintain a large enough population so that there was no bottlenecks".

      AFAIK there were no bottlenecks in WEA either after the UP colonization: following Bocquet-Appel 2005, population may have remained relatively low until the Magdalenian explosion but no contractions are obvious, except probably in the northernmost areas.

      "If West Eurasia was derived from South Asia, we would see deep clades rooted in South Asia".

      We do see them, notably mtDNA R (highest diversity in SA) and Y-DNA F, IJK, P (they look totally South Asian by origin). However the core population starring this process probably went via SE Asia at some point (mtN and yMNOPS nodes), where I speculate they may have got the knowledge of dog domestication (just an idea). But whatever the exact nature of their connection to SEA, the route to the West was surely via SA (they did not cause a major impact in SA for exactly the reasons you say but they did leave a mark).

      I don't have time for more. In fact I'm already late.

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  10. "what makes it unmistakable B4'5 per the current PhyloTree build".

    Thanks for that information.

    "I think that West Eurasia was colonized from South Asia, long after the OoA".

    Agreed.

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  12. Maju, as I said, just because of modern inhabitants of SW Asia are from the Anatolian Neolithic dispersal doesn't mean the are was always "West Eurasia". If we define West Eurasian as Anatolian Neolithic, then Q and X were pre_neolithic and not West Eurasian.

    "This region was essentially colonized by a single population with "mode 4" tech originating somewhere in South Asia c. 55 Ka ago (Palestine) and later."

    Does this mean the Neanderthals (who invented this Mode 4) and people in East Asia all the way to the Korean peninsula are also of this single population coming from South Asia? Your statements are sentiments without hard evidence, so I find it useless to discuss.

    "That would be West Asia in any case (South Asia begins at Pakistan usually). But it does not seem to me on light of the genetic data that the remnants of the OoA surviving (possibly) in that region played any major role in the effective colonization of the major West Eurasian region in the early UP. They'd be at best a surviving substrate that may be detected (in fact I believe I have detected an ADMIXTURE cluster in Arabs and Low Egyptians that may be from that period, also some mtDNA lineages of Arabia may be survivors from that period as well)."
    I can't say Q and X are directly from the original dispersal, but they certainly are a different strata from the later Neolithic strata. NRY haplogroup R was also originally like Q, but it attached itself to certain expansions, such as Indo-European. I have foudn the archaeology for all this even a few years back, but I don't think you are interested.

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    1. "modern inhabitants of SW Asia are from the Anatolian Neolithic dispersal"...

      I do not believe in that hyper-gross oversimplification but, even if you do, that would still be "internal West Eurasian affairs", so to say. The continuity of the region's genetic pool, at least in part, from the early UP would be confirmed, not denied.

      "If we define West Eurasian as Anatolian Neolithic"...

      I don't. I define it as the populations of the West Eurasian region of Earth since UP. I also claim that since that time, because of founder effects, there is certain homogeneity in this region (parallel for example to the one we see in East Asia, etc.)

      Besides, I also think, and have good reasons to think that "Anatolian Neolithic replacement" models are pathetic ideological junk with zero empirical support. Said that, of course that there is a number of concentric waves of demographic flows with Western Neolithic, which originated more in Kurdistan than Anatolia Peninsula in fact but then there were many other subcenters. Neolithic (at least in this part of the World but AFAIK also elsewhere) is a very complex phenomenon even if some minds insist in oversimplifying it (because of their own emotional biases??)

      ..."then Q and X were pre_neolithic and not West Eurasian".

      I beg you please not to try again to trick an old devil with this sophism. mtX2, which is the same clade (at that phylogenetic level) that we find among some North American Natives is actually a very much Neolithic lineage in Europe. X1, its "ancient sister", is essentially an Egyptian lineage and has been probably there since early in the UP/LSA (Druze X1 comes from Egypt IMO because one of the two main founder effects of Druzes, who are not "archetypal Levantines" but recent arrivals of 1000 years ago, is from Egypt as acknowledged by their own often ignored historical records). Whatever the case both Q and X1 appear to have been in West Eurasia since the early UP and coalesced here (or in the case of Q maybe South Asia) so calling them West Eurasian lineages is totally correct.

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    2. "Neanderthals (who invented this Mode 4)"...

      Unsure. The evidence is weak and not clear. A problem is that occasionally archaeologists describe "blades" but these are actually Levallois flakes used as such, and therefore mode 3. At this point I'm uncertain of who ultmately may have "invented" the mode 4. It's not very important because in any case the wave of colonization of West Eurasia by Homo sapiens is clearly linked to this technological method, aka (in that specific context) "Aurignacoid" (sometimes even loosely said "Aurignacian").

      "... people in East Asia all the way to the Korean peninsula are also of this single population coming from South Asia?"

      I can't be sure if you can eventually discern two late MP layers in East Asia but I do not share the oversmplistic view that they all come from a single Neolithic flow - that's IMO quite ridiculous, and Tianyuan's matrilineage being B4'5 rather supports my view in fact. Incidentally North China Neolithic peoples seem more linked archaeologically to non-Neolithic proto-Tibeto-Burmans of Sichuan than to the Neolithic core of South China. In Indochina Peninsula also the Austroasiatic Neolithic seems relatively autonomous. Even most of the so-called Austronesian lineages are actually original from former Sundaland and Philippines and not from Taiwan, which may have been first colonized from those areas south of it.

      "... so I find it useless to discuss".

      In that case, I have no idea why you do.

      "Q and X (...) certainly are a different strata from the later Neolithic strata".

      As I said above, X2 is clearly a Neolithic stratum lineage in Europe, according to both modern and ancient DNA. Other such mtDNA lineages are J2, W, possibly T, K...

      "NRY haplogroup R was also originally like Q, but it attached itself to certain expansions, such as Indo-European"...

      That also seems incorrect but aDNA is still not clear on the matter. R1a in India is at the latest Neolithic. Indoeuropean expansion cannot be attributed the NSA austosomal cluster in any case (and therefore neither can R1a) - but I personally would seriously consider a deep Paleolithic division of South Asia in two mostly segregated regions, separated by the then arid Deccan highlands and only linked by the Western coastal corridor. But, as I say, in doubt in this particular case.

      Claims of R1b in Europe being linked to Neolithic simply don't fit the available phylogenetic data (example reference).

      If you wish to believe differently, up to you... but I'm not going to agree unless clear evidence is presented.



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  13. "But it does not seem to me on light of the genetic data that the remnants of the OoA surviving (possibly) in that region [West Asia] played any major role in the effective colonization of the major West Eurasian region in the early UP".

    Perhaps not more than a minor role, but haplogroups of the OoA such as N1, X and N2 do look to have expanded from there, and not from South Asia, with the Y-DNA P/mt-DNA R group.

    "We do see them, notably mtDNA R (highest diversity in SA) and Y-DNA F, IJK, P (they look totally South Asian by origin)".

    You know what I think about that comment.

    "However the core population starring this process probably went via SE Asia at some point (mtN and yMNOPS nodes), where I speculate they may have got the knowledge of dog domestication (just an idea). But whatever the exact nature of their connection to SEA, the route to the West was surely via SA (they did not cause a major impact in SA for exactly the reasons you say but they did leave a mark)".

    I suggest that mt-DNA R and Y-DNA R did have a major effect in South Asia. I'm not sure about the importance of dog domestication in the spread though.

    "I define it as the populations of the West Eurasian region of Earth since UP".

    I'd go further and use it to refer to any humans in the region, not just UP ones.

    "If we define West Eurasian as Anatolian Neolithic, then Q and X were pre_neolithic and not West Eurasian".

    How can you suggest we should 'define West Eurasian as Anatolian Neolithic' yet agree that haplogroups 'Q and X were pre_neolithic and not West Eurasian'? Surely those haplogroups are as much 'West Eurasian' as are any haplogroups that spread with the Anatolian Neolithic

    "NRY haplogroup R was also originally like Q, but it attached itself to certain expansions, such as Indo-European".

    I think you should be much more specific. 'Some' R haplogroups expanded with Indo-European, not all of them by any means.

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    1. "I'd go further and use it to refer to any humans in the region, not just UP ones".

      But other Homo sapiens have only left a residual genetic signature (unlike you, I do not think that Western N subclades are from that source but backflows from further East, where mtDNA N seems to have coalesced and first expanded), interesting no doubt but residual nonetheless. Other Homo sp. we usually say just "Neanderthals" (or more generically "archaics") and there is nothing obviously specific from them in the modern West Eurasian genetic pool.

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