December 23, 2010

Denisova hominins, Neanderthals, Melanesians and so on...

A new "bomb" has been dropped by the Paabo team and their Neanderthal Genome Project. This review is just a very preliminary approach to really heavy material, dealing essentially with the autosomal DNA of the Denisova hominins, now sequenced, but also with their relations with Neanderthals and us.

A tooth found in the same cave carried mtDNA very similar to that of the finger bone. The tooth is morphologically distinct from both H. sapiens and H. neanderthalensis.

David Reich et al., Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 2010. Pay per view (supplementary material is freely available). 


Denisova closer to Neanderthals?

NJ tree
You are by now probably familiar with the Denisova hominin, a mere finger bone found in a cave from Altai (Mousterian context). While the mitochondrial DNA placed Denisova's lineage almost twice as distant as our divergence from Neanderthals, the autosomal DNA makes Denisovans a closer relative to Neanderthals (left). 

However I'd take this with a pinch of salt because autosomal DNA is subject to admixture and may therefore indicate a hybrid population or even individual. 

For example it could well be the case that Denisovans were a hybrid population of H. erectus and H. neanderthalensis (or a related species such as H. heidelbergensis). Or your best guess.

Also you may notice that in the above tree H. sapiens populations appear unusually divergent. This is not a distortion of this graph only, but it is also sustained when the Chimpanzee outgroup is taken into account, yielding age estimates for the autosomal divergence of our species that are several times older than that achieved by comparison of haploid lineages or justified by the archaeological record. 

So I am quite uncertain on how to read this and if errors are happening that cloud our understanding.


Are Melanesians more admixed with Denisovans? Are Native Americans less admixed with Neanderthals?

The possibility of Melanesians being slightly admixed with Denisovans is probably the most explosive aspect of the paper. Following Supplementary Information 8, the authors find some greater similitude between Melanesians and Denisovans than any other Eurasian population.

A visual explanation is in the following eigenvector graphs:

Notice that the second image is nothing but a high resolution zoom of the central clump in the first one (H. sapiens). Only at such high resolution three micro-clusters can be noticed, apparently reflecting different admixture levels with Neanderthals and Denisovans. 

To further clarify this matter, the authors resort to statistical methods that confirm these clusters and maybe add some information on several individual populations' admixture levels (not anymore just the four Eurasian populations represented above but also others). These calculations show that effectively Melanesians are slightly but significantly closer to Denisovans, while also retaining the general Neanderthal admixture of all non-Africans (or almost all). 

And I say almost all because the Karitianas (a Native American nation of Brazil) are found to have much lower Neanderthal blood than other non-Africans.

The estimates for Neanderthal admixture in Eurasians are overall of c. 3%, with the following variations:
  • Cambodian 4.4%
  • Mongolian 4%
  • Han Chinese 3.2%
  • French and Sardinians 2.6%
  • Melanesians 2.5%
  • Karitianas 0.9%
Additionally Melanesians have c. 4.8% of Denisovan genetic contribution, totaling c. 7.4% of archaic admixture.

Update (Dec 25): it may well be only 4.8% of total archaic admixture if Denisovans were hybrids of Neanderthals and H. erectus (see here - scroll to near bottom).

Note: I have a technical doubt because in table S8.2, French appear quite closer to Neanderthals than Sardinians, who seem less admixed than all other non-Africans but the Karitiana, but in table S8.3 they are given the same values of admixture. At the moment I do not understand why this difference in the values, really.

In the same table S8.2 French, Han and Cambodians (and only them) also appear to show some admixture with Denisovans, though maybe a third or fourth of that of Melanesians.


Affinities of the Denisova tooth, chronology of the Denisova cave.

In Supplementary Information 12, the authors deal with the possible paleo-anthropological affinities of the Denisova tooth (a molar), finding that it is closest in morphology to those of Australopithecus sp., H. habilis, African (but not Chinese) H. erectus and (oddly enough) Oase 2 (a H. sapiens that does not cluster with the rest of our species in this aspect).

Indonesian H. erectus is also very close if it is a second molar but not if this is a third molar. 

H. sapiens (other than Oase 2), H. neanderthalensis, Chinese H. erectus, H. georgicus (Dmansi), H. antecessor/heidelbergensis (Atapuerca) do not cluster in any case.

In this section, they also deal with the radiocarbon chronology of the site, concluding that:

... we propose the following scenario: a first hominin occupation of the cave more than 50,000 radiocarbon years ago by the Denisova hominins, and a second occupation during the Upper Palaeolithic, at 30,000 years BP or later, probably by modern humans.

Feel free to discuss.


Update (Dec 23): Denisova mtDNA "modern"?

Dienekes mentions today that Niccolo Caldararo has published an article at Nature (freely available as PDF) suggesting that the Denisova mtDNA sequence may be corrupt. If this would be true, then the sequence would be that of a H. sapiens.

This could explain some of the anomalies in the autosomal NJ tree and related age estimates, that would make Chinese and French (for instance) diverging by more than 500,000 years, what is totally absurd.

However, considering that a very similar sequence was successfully sequenced also for the tooth, this claim seems less likely.

Still many questions remain open because there are issues such as the divergence estimates for various H. sapiens, specially Eurasian H. sapiens, that just do not make any sense at all. So I'd say it's best to lay back a bit and wait patiently for more brilliant insights, which will no doubt come.


Update (Dec 25): see this new review for a more elaborate review of mine on this matter, including some intriguing hypothesis I am launching, partly on feedback provided by commenters.


45 comments:

  1. Hi Maju!

    I found the study very interesting (I can't read it, because I have to pay) but I'm very confused.

    "And I say almost all because the Karitianas (a Native American nation of Brazil) are found to have much lower Neanderthal blood than other non-Africans."

    How can this be possible, if Native Americans are supposedly descendend from an Asian population, akin to East Asians, like the Chinese and Mongolians?
    If N.A. migrated to Americas when neanderthals were already extinct, how is it possible, that the other populations have more neanderthal admixture? Where did they get it from? I think these % can vary a lot, and that low % in the Karitiana can be due to a founder effect.

    "Additionally Melanesians have c. 4.8% of Denisovan genetic contribution, totaling c. 7.4% of archaic admixture."

    None of the other non-African populatins has any Denisovan DNA? I think that's quite rare for the case of Chinese and other Asians.

    "I have a technical doubt because in table S8.2, French appear quite closer to Neanderthals than Sardinians, who seem less admixed than all other non-Africans but the Karitiana, but in table S8.3 they are given the same values of admixture. At the moment I do not understand why this difference in the values, really."

    Again, that makes no sense. French, Sardinian, Chinese and Papuan are nationalities, it's still possible to find more differences between two French persons than between a French and a Sardinian person. Moreover, how can this be possible? The French are closer to neanderthals than all the other populations or just more than Sardinians? Clearly neanderthals in Europe were completely replaced, or also, Europeans are descended from an Asian population who arrived to Europe when neanderthals were already extinct. That would explain why we see such a small differences, despite neanderthals being an European/West Asian specific population.

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  2. The possibility of serial founder effects and genetic drift producing a low Neanderthal DNA population of a few hundred genetically isolated people in the Karitianas, by random chance (perhaps enhanced by an environment where any Neanderthal genese with selective advantage in Europe were selectively advantageous) deep in the Western Amazon isn't that stunning (particularly if there were one or two esaped post-Columbian African slaves who made their way into the gene pool hundreds of years ago (perhaps removed by a couple of generatioons of admixture with other Amazonians) whose legacy did not survive in the part of the oral tradition communicated to outsiders).

    A diluted Denisovian influence in Han and Camobidan populations of 1.2% to 1.8% also seems plausible to the extent that any of this makes sense.

    But, a 1.2% to 1.8% Denisovian influence in the French (to the exclusion of other West Eurasians and South Eurasians) is hard to fit with any model that makes any sense. I just can't imagine any sensible scenario that makes that happen. The French have too much in common genetically with other Europeans and are too large a population to make sense as an outlier, relative to other European populations.

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  3. "in Europe were not selectively advantageous in the Amazon"

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  4. "How can this be possible, if Native Americans are supposedly descendend from an Asian population, akin to East Asians, like the Chinese and Mongolians?"

    At this moment I do not know, nor I know if the Karitiana case is extensive to all Native Americans. I remember however that Japanese looked much less Neanderthal than Chinese in Green 2010.

    Something to consider is that autosomal DNA is subject to randomized recombination at each reproductive episode, so while you have 50% of your dad and your mum, you do not need to have exactly 25% of each of your grandparents but it can be 30% or even 40%, or less: 20% maybe just 10%. Statistically all this randomization should cancel each other in large populations but Paleolithic hunter-gatherers were not large populations. Founder effects and random allocations may well have happened.

    "None of the other non-African populatins has any Denisovan DNA?"

    I said in the small type note that I have not clear if some populations (Chinese, Cambodians and French) might have maybe 1/4 of the Melanesian component but discerning the stats is quite hard, so unsure.

    "Again, that makes no sense. French, Sardinian, Chinese and Papuan are nationalities, it's still possible to find more differences between two French persons than between a French and a Sardinian person".

    It's possible but, in the cases of homogeneous and somewhat distant populations at least, this is not normal. Sardinians and French are close and French are anything but homogeneous, so it does not apply well.

    "The French are closer to neanderthals than all the other populations or just more than Sardinians?"

    My impression (with doubts) is that Sardinians are less Neanderthal than all other Eurasians, except the Karitiana, while the French are average. But, as I said, I have many doubts.

    "Clearly neanderthals in Europe were completely replaced"...

    I think this is very clear, unless new discoveries find otherwise. For instance I would not mind here to check other Europeans, such as Basques, Spaniards or Swedes, just to be safer. But so far Europeans do not appear to be more Neanderthal than anyone else (except Africans and the Karitiana), so the admixture event happened long before the colonization of Europe by AMHs.

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  5. "But, a 1.2% to 1.8% Denisovian influence in the French (to the exclusion of other West Eurasians and South Eurasians) is hard to fit with any model that makes any sense. I just can't imagine any sensible scenario that makes that happen".

    It's hard to evaluate because very few Europeans were compared and we know nothing about this (these?) French. The French are a very diverse bunch, North French cluster with Central-North Europeans, South French with Iberians, Gascons with Basques, some SE French surely have strong Neolithic Mediterranean input, others not really... Picking a random French is like taking a random West European without further specification.

    "in Europe were not selectively advantageous in the Amazon"

    Really at this moment it is too soon to talk of any advantages. What's the ecological difference between Cambodia and Equatorial South America? Between China and Japan (previous paper)?

    I'm more inclined to ponder random founder effects, recombination, drift... but further comparisons are needed. They will come, no doubt.

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  6. "At this moment I do not know, nor I know if the Karitiana case is extensive to all Native Americans. I remember however that Japanese looked much less Neanderthal than Chinese in Green 2010. "

    As far as I know, the genetics of Native Americans are hotly debated and there's not a consensus. It's likely that they're descended from more than just one group; if that's the case, we'd expect to find differences between different N.A populations.

    "I said in the small type note that I have not clear if some populations (Chinese, Cambodians and French) might have maybe 1/4 of the Melanesian component but discerning the stats is quite hard, so unsure."

    As Andrew points out, finding Denisovan DNA in the French (but not the Sardinians?) has no simple explanation, if the Denisovan admixture is very melanesian-specific, unless the French (and most Europeans) are derived from a south-east Asian population, but I think that's not the case. As you said, more comparisons are needed.

    "My impression (with doubts) is that Sardinians are less Neanderthal than all other Eurasians, except the Karitiana, while the French are average. But, as I said, I have many doubts. "

    Yet Sardinians are very closely related with other Europeans and non-Africans in general, so it may be due to founder effects again, as in the case of the Karitiana.

    "I think this is very clear, unless new discoveries find otherwise. For instance I would not mind here to check other Europeans, such as Basques, Spaniards or Swedes, just to be safer. But so far Europeans do not appear to be more Neanderthal than anyone else (except Africans and the Karitiana), so the admixture event happened long before the colonization of Europe by AMHs."

    Of course, more comparisons are needed as we see that the % of either neanderthal or denisovan is not homogeneous. I'd like to sample populations like north Africans, Middle Easterners and australian aborigines, because Europeans seem to be a very closely related population, it's not expected to find any significant difference.

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  7. "autosomal DNA is subject to admixture and may therefore indicate a hybrid population or even individual".

    As you know, I have always been a believer in more admixture between human groups than is generally acknowledged.

    "The possibility of Melanesians being slightly admixed with Denisovans is probably the most explosive aspect of the paper".

    But again, as you know, I have long seen evidence for a human movement across Central Asia and down the east coast to Australia. Y-hap C and mtDNA N fit the pattern.

    "The possibility of serial founder effects and genetic drift producing a low Neanderthal DNA population of a few hundred genetically isolated people in the Karitianas, by random chance (perhaps enhanced by an environment where any Neanderthal genese with selective advantage in Europe were selectively advantageous) deep in the Western Amazon isn't that stunning"

    Exactly.

    "if the Denisovan admixture is very melanesian-specific, unless the French (and most Europeans) are derived from a south-east Asian population, but I think that's not the case".

    But hang on Maju. Didn't we agree some time back that both Y-hap MNOPS and mtDNA R are of SE Asian origin? Surely some autosomal DNA would travel with the haplogroups to some extent.

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  8. congratulations analysis

    However, I have to admit I'm a little confused.

    Do you believe that the end may be right when Maria Martinon Torres through the analysis of teeth concluded that after an initial migration from Africa, the other hominids can be derived from Asian populations georgicus homo type?

    As part of your analysis of these populations would be mixed among themselves giving rise to others, perhaps those of Denisova, and others ...

    After sapiens come in a second migration from Africa and will be mixed in turn with all the species meet on their way.

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  9. @Maria Lluïsa:

    I do not think that the genetics of Native Americans are "hotly debated", nor that there is any clear reason to think they could descend from several ancestral populations. The main possible exceptions, where there might be some uncertainty is in regard to some North American groups, specially Na-Dene and Inuit. But in general it is mainstream that they descend from a single founder population from Beringia.

    However a single sample is not enough to judge a whole continental population, clearly not, because founder effects and other randomizing events might distort the whole picture.

    "...unless the French (and most Europeans) are derived from a south-east Asian population, but I think that's not the case"...

    Actually, if you trace the main haploid lineages of Europeans, they seem to come from SE Asia. That is the case with nearly all mtDNA (derived from N and it's "daughter" R) and with the main Y-DNA lineage R, which is derived from MNOPS, most diverse in Eastern Eurasia (incl. Oceania). However autosomally West Eurasians are closest to South Asians.

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  10. @Terry:

    Altai would be a good place for admixture because it is a crossroads.

    "I have long seen evidence for a human movement across Central Asia and down the east coast to Australia".

    It is likely that Denisovans represent in fact a much larger population, probably Asian H. erectus or, even more likely, a hybrid of H. erectus and H neanderthalensis (or H. heidelbergensis).

    Denisovans would have been extinct by the time our species arrived to the area, per the archaeological record. Maybe the climatic changes triggered by Toba impeded life so far north (a good guess). The radiocarbon dates are all "infinite" (older than 50 Ka) and we'd need some other form of chronological measure such as uranium series or at least a good stratigraphy to know more. In general there are no known H. erectus fossils after 200 Ka., at least in mainland Asia but I think you have mentioned H. erectus survivals in Java much more recently, right?

    I would rather think that the Denisovan component means a mix of Neanderthal(-oid) and H. erectus, and this H. erectus component was picked in Sundaland or nearby areas.

    "But hang on Maju. Didn't we agree..."

    Hang on, Terry: you are replying to a quote of Maria Lluïsa, not mine. ;)

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  11. @David:

    "... I have to admit I'm a little confused".

    You are not the only one, believe me. :D

    I am in general (by default) of the rather mainstream opinion that H. sapiens evolved separately in Africa from H. ergaster (or H. erectus of Africa). The fossil record seems to support it more than other alternative hypothesis (add to these fossils the Africa > Eurasia direction of Acheulean scatter, which would correspond with H. ergaster c. 1 Ma ago, etc.)

    However there are many uncertainties. Of critical importance in my opinion is to properly describe and correlate the oldest large brained human skull known to date, which is not in Africa nor West Eurasia but in India (Narmada hominin).

    On Denisovans, I think that they represent a peculiar hybrid Erectus-Neanderthal(-oid) population, and I also think that they are probably exceptional in this regard because the Altai is a crossroads. Other ancient Altai sites have, AFAIK, Neanderthal remains and the fact that Denisovans used Mousterian tech strongly suggests Neanderthal admixture in them.

    "After sapiens come in a second migration from Africa and will be mixed in turn with all the species meet on their way".

    Up to a point that is what it seems but admixture was small in any case and concentrated in the Neanderthal branch, which were also the closest ones to us (H. ergaster-derived).

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  12. Maju, a couple of days ago I found a paper which seems to claim that there's something strange in the DNA of the X woman. At the moment, I didn't pay too many attention to it, but now, it seems that (according to Dienekes) her mtDNA is... modern!! (Oh my God).

    Here's the paper:

    http://precedings.nature.com/documents/5360/version/1/files/npre20105360-1.pdf

    I can't believe it, because her morphology is clearly archaic, I think it's more likely due to some kind of contamination, and Dienekes seeing what he wants to see, but anyway, I'd like to know your opinion.

    "Actually, if you trace the main haploid lineages of Europeans, they seem to come from SE Asia. That is the case with nearly all mtDNA (derived from N and it's "daughter" R) and with the main Y-DNA lineage R, which is derived from MNOPS, most diverse in Eastern Eurasia (incl. Oceania). However autosomally West Eurasians are closest to South Asians."

    Well, that'd explain the small % of denisovan DNA in non-melanesians, if Denisovans were occupying most Asia.

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  13. I just posted an update on that, Maria Lluïsa. Thanks anyhow.

    An issue with Caldararo's criticism is that a second mtDNA sequence has been extracted from the tooth and is similar.

    However I do have many doubts, not so much for the Melanesian admixture but specially for the age estimates based on the NJ tree, which are totally unrealistic for H. sapiens, with Eurasians (and Africans too) diverging from each other at ages of more than half a million year ago. This does not make any sense at all, so I'm getting more and more cautious.

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  14. "An issue with Caldararo's criticism is that a second mtDNA sequence has been extracted from the tooth and is similar. "

    Moreover, anatomically, the X-woman is clearly archaic, showing more affinities with H. erectus and H.habilis.

    "However I do have many doubts, not so much for the Melanesian admixture but specially for the age estimates based on the NJ tree, which are totally unrealistic for H. sapiens, with Eurasians (and Africans too) diverging from each other at ages of more than half a million year ago. This does not make any sense at all, so I'm getting more and more cautious."

    I didn't know this yet, but if true, more studies are needed to clarify the complex and rare affinities of that X-woman to neanderthals and modern humans.

    Maybe the X-woman is a neanderthal-like already admixed with modern humans who in these dates were migrating to Asia? Anyway, I'm going crazy :S

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  15. "Moreover, anatomically, the X-woman is clearly archaic, showing more affinities with H. erectus and H.habilis".

    I am not sure if that can be decided with any safety based only on a finger bone and a tooth. For example Oase 2 clusters well with the Denisova molar (but not the rest of H. sapiens).

    However I do think at the moment that the Denisovans were probably a hybrid Erectus-Neanderthal or Erectus-Heidelbergensis population.

    If this is correct the admixture levels of Melanesians with H. erectus could well be just half of those reported, the rest actually being Neanderthal admixture (and not even sure if they add up or they just overlap).

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  16. "I didn't know this yet"...

    I addressed it in the first section of the review. I wrote:

    "Also you may notice that in the above tree H. sapiens populations appear unusually divergent. This is not a distortion of this graph only, but it is also sustained when the Chimpanzee outgroup is taken into account, yielding age estimates for the autosomal divergence of our species that are several times older than that achieved by comparison of haploid lineages or justified by the archaeological record".

    I wanted to address this matter in a separate post but I am quite unsure of what to say.

    The authors estimate that French and Han have diverged for 404,000 years (!!!) but this is with a low estimate of the Pan-Homo divergence date of only 6.5 Ma. With the most correct date of c. 8 Ma., we get 497,000 years (and this is the smallest divergence of all, except Han-Papuan, which is similar).

    There is something radically wrong in those calculations or the underlying data because it can't be that San are almost as distinct (0.09) from other extant humans as Neanderthals (0.12), figures as fractions of Pan-Homo divergence.

    Even the lowest estimates of Neanderthal-Sapiens divergence make it at least twice or three times older than internal Sapiens divergence and not just (33% larger, which is almost nothing).

    The data is in Supplemental Information 6.

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  17. Thanks for the link, very interesting maps!

    It may not explain me well, I also believe that homo sapiens develops from Homo ergaster in Africa independently in, which I disagree is on the dates or proposed at first migration, which should be sooner than that says, pre-erectus Homo ergaster, based on the remains of Georgia's 1.8 m, which appear hybrids habilis erectus.

    In relation to Denisova, I read a review of caldararo and my confusion has increased even further! In the news published in Nature, the researchers said Denisova man is closer to Neanderthals than modern humans, and now this review is prefers Denisova because mtDNA is modern??

    On the other hand, the new study that comment in the new post suggests that Northeast Asia was colonized by modern humans 40,000 years ago through the mountain range in southern Siberia, ie Denisova areas near where we doubt which species belong these remains, dating from the first study between 30,000 and 50,000 years.

    I think we'll wait a little longer because it seems that the experts can not agree, and there is much confusion about it.

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  18. Maju:
    Do you want to propose, since this contradicts the coastal migration, admixture in Melanesians must be of that Erectus and this Denisovans are a hybrid Erectus and Neanderthals?

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  19. @David: in the linked article (maps), "erectus" means all Homo species, including H. ergaster, except a few. This is a matter of nomenclature and I followed that of my source.

    H. ergaster is not "pre-erectus". H. ergaster is generally considered pre-Sapiens and pre-Neanderthal, via rhodesiensis an antecessor/heidelbergensis respectively (depending on whom you read, there's a lot of debate on these issues). H. ergaster is the "new name" of somewhat evolved H. erectus in Africa, nothing else.

    As for Caldararo, I have already commented above that I believe his caveat is not sustainable now that a second Denisova mtDNA sequence is also available. Denisova mtDNA seems to be one of H. erectus, regardless that this particular population was hybrid with Neanderthals (maybe in the Y-DNA side?) Haploid lineages do not mix, your mtDNA is always your mother's, not your father's.

    "On the other hand, the new study that comment in the new post suggests that Northeast Asia was colonized by modern humans 40,000 years ago through the mountain range in southern Siberia"...

    Yes, but there is some uncertainty on the exact dates and sequences and does not refer specifically to the Denisova cave anyhow.

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  20. @Manju: that's exactly what I am thinking.

    I do not think this contradicts the coastal migration at all. However further research on aDNA from other, more clear, H. erectus may in the future clarify this matter.

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  21. I'm not clear about your theory. And I need to have clear picture of this admixture scenario.

    Do you mean to say, Denisovans are an erectus subspecies. Melanesians admixed with some other subspecies of erectus in Oceania (Let's say Soloensis).

    What should be the divergence age for two human subspecies to show 0% aDNA similarity? I suppose maximum divergence age should be 825 years considering (1) the Sapiens and Nenaderthal aDNA divergence and (2)no admixture of Neanderthals in Homo Sapiens of Africa. I wonder what should be the minimum age.

    Now erectus appeared in east Asia around 1m years ago. I suppose there is every possibility that Denisovans and Soloensis diverged for almost 800 years thus show no 0% aDNA similarity. In such a scenario, Melanesians admixing with Soloensis and shown to be closer to Denisovans is unlikely.

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  22. Now I'm looking at the article's supplementary info.

    Here's an interesting table with 13 regions showing potential neandertal admixture, but I don't know why the authors separate CEU (I suppose they're European Americans) from ASN (Asians?) and Africans, I don't know either how to read the numbers, have you noticed anything strange in them?

    http://www.nature.com/nature/journal/v468/n7327/extref/nature09710-s2.xls

    I noticed that the divergence between two humans in one table (Han vs French) is about 20-25.000, when the divergence between two humans and chimps is only 100.000! Also, there aren't too many diferences between two modern humans and the Denisova hominin nor neanderthals, which is completely crazy, because we know that the French and Han are practically identical, even more if we consider that Europeans are derived from a population who lived in South-East Asia. I don't know how they get these numbers, but something must be wrong.

    Also, it seems that there's some evidence of Denisovan DNA in Melanesians, but the authors didn't explore well this issue.

    All it's pretty confusing. The authors also propose an alternative model to explain the findings, but in my opinion it's extremely complicated.

    I thought that more remains of the X-woman were found, not just a finger and a tooth, which is very few to classify an individual, but all evidence, either from the finger or tooth seem to support the idea of a very archaic component in the X-woman.

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  23. "Also, it seems that there's some evidence of Denisovan DNA in Melanesians, but the authors didn't explore well this issue."

    I mean in non-Melanesians, sorry.

    Apparently all Africans are 0% either Denisovan or neanderthal?

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  24. "The authors estimate that French and Han have diverged for 404,000 years (!!!) but this is with a low estimate of the Pan-Homo divergence date of only 6.5 Ma. With the most correct date of c. 8 Ma., we get 497,000 years (and this is the smallest divergence of all, except Han-Papuan, which is similar)."

    Good catch. Any conclusion like that should raise serious red flags about the entire methodology used. An error of a factor of five or ten is a big problem.

    "There is something radically wrong in those calculations or the underlying data because it can't be that San are almost as distinct (0.09) from other extant humans as Neanderthals (0.12), figures as fractions of Pan-Homo divergence."

    Again, you must be right. This also seems off by a factor of five or ten.

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  25. "H. ergaster is the "new name" of somewhat evolved H. erectus in Africa, nothing else"

    I know it. I would like to say that maybe homo georgicus is ancestor of all asians hominids, who called generally erectus. The distinction of terms is too small based on anatomical differences that coincide with different geographical areas(Ergaster-Africa; Erectus -Asia).

    Anyway thanks for the clarification. :)

    I think that evolution is lineal in Africa up to sapiens, but in Asia is different, there are lots of combinations of populations from smeary first migration that should be older than we think, is only a hypothesis.

    I hope not to be weighed with this discussion ergaster - erectus that goes a little about the subject of the post.

    About discussion , is very good, are very interesting the diferent points of view of all, i´m learning with you, thank you.

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  26. @Manju:

    "Do you mean to say, Denisovans are an erectus subspecies. Melanesians admixed with some other subspecies of erectus in Oceania (Let's say Soloensis)".

    I'm more in the line of Denisovans being an admixed Erectus-Neanderthal population at the Altai crossroads between West and East Eurasia, which makes good sense - IMO.

    Denisovans are way out of the Neander-Sapiens "super-species" (or sub-genus) by mtDNA. By this measure they must be Asian H. erectus, spread, as David says in the times of the Dmanisi specimen (Homo georgicus).

    However by autosomal DNA they fall within this Neander-Sapiens biological set, actually within the Neanderthal branch (but quite distinct). Would not be because of the mtDNA I'd say H. heidelbergensis but because of the mtDNA and the crossroads geography of Altai, I think that a hybrid population is most likely.

    Therefore, my favorite hypothesis right now is that the "Denisovan admixture" detected among Melanesians actually represents a composite of Neanderthal and H. erectus, from either Java or China or something like that.

    (We must not forget also that H. floresiensis was also over there until some 12 Ka ago and that it may also be implicated - though this is confusing because we are not even sure where does H. floresiensis belong in the Homo or even Australopithecine genealogical tree).

    "What should be the divergence age for two human subspecies to show 0% aDNA similarity?"

    I do not understand this question. 0% DNA similarity is impossible even with amoebas. However we should not find much greater similarity with other species than our own in the absence of admixture. The concept subspecies is sloppy, so I'll ignore that.

    "I suppose maximum divergence age should be 825 years considering (1) the Sapiens and Nenaderthal aDNA divergence".

    I understand that there are many reasons to think that the Neander-Sapiens divergence is of 0.9-1.3 Ma. But there are other opinions.

    "Now erectus appeared in east Asia around 1m years ago".

    Maybe but they are generally believed to be descendants from the same population as H. georgicus, which made the first "out-of-Africa" migration c. 1.8 Ma.

    "I suppose there is every possibility that Denisovans and Soloensis diverged for almost 800 years"

    800,000 years you may mean... I really do not know. There is not sufficient fossil nor genetic evidence to decide.

    But IF the fundamental distinction between an Asian H. erectus separated from African H. ergaster some 1.8 Ma ago is accepted, then these would be two distinct populations (and species/super-species), with two distinct mtDNA genealogical trees (that fit well with the Denisova mtDNA).

    In this sense, Denisovans can represent H. erectus (ignoring the likely admixture with Neanderthals) the same that a San can represent all H. sapiens for general comparisons (and even a Neanderthal would do).

    But there are, I guess other possibilities and surely other opinions. Yet this is my default hypothesis:

    1. First OoA by H. georgicus/erectus with chopper industry
    2. Second OoA by H. ergaster/antecessor > heidelbergensis > neanderthalensis with Acheulean and then Mousterian industry
    3. Third OoA by H. sapiens with MSA-derived industries and then also blade-based and maybe other industries as well

    Denisova is a mix of #1 and #2 IMHO, with mtDNA of #1 and industry of #2 (Mousterian) in a context otherwise dominated by #2 peoples (Neanderthals).

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  27. "Apparently all Africans are 0% either Denisovan or neanderthal?"

    This is the default assumption and seems consistent when Africans and archaic Eurasians (Denisova/Neanderthal) are compared in triplets. There are small variations but within the expectations of randomness and no peculiar direction (not significant at all). This small variation range of Africans are the baseline on which non-Africans are measured and in all cases (but arguably Karitianas) they are significantly distinct for the Neanderthal comparison (closer to Neanderthals) but not the Denisovan comparison (except Melanesians).

    @Andrew:

    "Good catch. Any conclusion like that should raise serious red flags about the entire methodology used. An error of a factor of five or ten is a big problem".

    Yes, it really projects a serious shadow of doubt on all the paper, however, the paper is in fact a conglomerate of "micro-papers", each one by a smaller team (supplemental material sections), so I'm unsure if section 6 (where the problem is) really affects section 8 (where the substance is) and, if so, how much.

    Hopefully they are sufficiently independent as the failure in section 6 not really affecting the substance of "Denisovan admixture" in Melanesians. I want to believe it is the case, but I would not mind confirmation.

    @David: alright, I did not understand well your question. You seem to be right (see my reply to Manju).

    "I hope not to be weighed with this discussion ergaster - erectus that goes a little about the subject of the post".

    Actually it is central to understanding what Denisovans were or might have been. At least I think so and it makes things clearer than when talking of a "mystery hominin" (though of course there's some mystery, probably not as much as often portrayed).

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  28. @Maria Lluïsa:

    Yes, CEU are the HapMap sample of white non-hispanic US citizens from Utah. Who are mostly of English self-reported ancestry by US census data, also some Danish and other British. In fact Utah is like an island of English ancestry in an ocean of German and Hispanic ancestry. They are consistently representative of NW Europeans. CEU stands for Caucasoid-Europid from Utah or something like that.

    ASN surely represents the combined CHB and JPT (Chinese from Beijing and Japanese from Tokyo), AFR surely represents YRI (Yoruba from Ibadadan, Nigeria). These are the four classical HapMap samples. Nowadays HapMap is being expanded, see the explanation at SNPedia).

    The really interesting part of the paper is the supplmentary material but the PDF part, which is freely accessible, and, within it, most of the substance is in section 8.

    You can surely skip the highly technical info in the excel spreadsheet. I did myself (at least by the moment).

    However I got this morning a copy of the main paper thanks to a reader, so if someone wants one, email me (email at my profile, remove the anti-spam "DELETETHIS" protection). But it's just a synthesis of the supplemental material, having little or nothing that it's not in the supplemental PDF.

    "I noticed that the divergence between two humans in one table (Han vs French) is about 20-25.000, when the divergence between two humans and chimps is only 100.000!"

    Not sure what is this, sorry.

    "Also, there aren't too many diferences between two modern humans and the Denisova hominin nor neanderthals, which is completely crazy, because we know that the French and Han are practically identical, even more if we consider that Europeans are derived from a population who lived in South-East Asia. I don't know how they get these numbers, but something must be wrong".

    This seems to be the same major issue spotted elsewhere in regard to section 6 and the fractions of Pan-Homo divergence, mentioned above and also in the first section of my review. I want to read all this more calmly and then I may post something.

    "Also, it seems that there's some evidence of Denisovan DNA in [non]-Melanesians, but the authors didn't explore well this issue".

    I have that feeling too but admittedly is not sufficiently clear.

    "I thought that more remains of the X-woman were found, not just a finger and a tooth".

    Only a finger and a tooth are mentioned. They belong to different individuals.

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  29. Maju said:

    “However I do have many doubts, not so much for the Melanesian admixture but specially for the age estimates based on the NJ tree, which are totally unrealistic for H. sapiens, with Eurasians (and Africans too) diverging from each other at ages of more than half a million year ago. This does not make any sense at all, so I'm getting more and more cautious.”

    Separate post:

    “Denisovans are way out of the Neander-Sapiens "super-species" (or sub-genus) by mtDNA. By this measure they must be Asian H. erectus, spread, as David says in the times of the Dmanisi specimen (Homo georgicus).”

    This makes sense to me. In fact, they appear to be following my research.

    Both of the below links are listed at http://www.worldfamilies.net/surnames/nolan/

    http://discovermagazine.com/2010/jan-feb/082

    Humans Took Care of the Disabled Over 500,000 Years Ago

    https://www.23andme.com/user/signin/?redirect=Pu7GSudPRuM5_19n_Z14D88KTJuxlPx8EOjzN6dwxthh1ZJu55o63_TBdfFdswkx&r=1

    My one and only foray into Anthropology

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  30. 800,000 years you may mean...

    Yes, both numbers should have been 825K and 800K. Sleepy eyes around 12 in the night(other time I'll be in trance).

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  31. "I think you have mentioned H. erectus survivals in Java much more recently, right?"

    Correct. possibly as recently as 30k, but almost certainly 50k.

    "I'm more in the line of Denisovans being an admixed Erectus-Neanderthal population at the Altai crossroads between West and East Eurasia, which makes good sense"

    I'm very much inclined to agree.

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  32. @Glenn: I do not see how your links have anything to do with my quotes. In fact I think you are spamming but as you did so elegantly that it looks almost like you are not, I'll let it pass for today.

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  33. Just another comment with regard to the nomenclature and regions:

    True Asian erectus is largely seen as a subspecies that (i) did not evolve in conjunction with Europe and Africa, and as such remained archaic (few important changes from 1.5 to 0.5 million years ago), and that (ii) lacked an entire group of advanced skills (proper generation and handling of fire, making of fur clothing, making tents and huts, post-erectus tool making) that were developed just before and during antecessor / early Heidelbergensis times and similar stages in Africa.

    On the other hand, we know that heidelbergensis-like people moved eastwards just when climate changed in Europe and homo became more specialized as Neanderthals, there. Thus, these people were much advanced over local Asian erectus (by about 1 million years, and by that much time of gene flow with Africa that Asian erectus did not have.

    In addition, there is evidence of first AMHs in the Levant, Saudi Arabia, perhaps India, and also now China by about ~100,000 years ago.

    Thus, if anything, Denisovans are either representative of this advancing wave of unmodified (un-Neanderthalized)heidelbergensis, or they may represent a complicated mixture, including very early AMHs and perhaps some Neanderthal. I very much doubt any Asian erectus contribution, which genetically would show up as 1.5 to 2.0 million years old.

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  34. "On the other hand, we know that heidelbergensis-like people moved eastwards just when climate changed in Europe"...

    Do we know that? I lack information that could support that H. heidelbergensis was ever outside Europe.

    "Thus, these people were much advanced over local Asian erectus"....

    I just cannot believe that Asian H. erectus did not have their own evolution. Nothing remains static and certainly their brain size increased in parallel to that of Western species.

    Actually, I'm often more comfortable with just using "H. erectus" as catchall term for all Homo before the big headed species (Neanderthal, Sapiens and Narmada hominin). However for phylogenetic terms it's surely better to make the distinction between Asian H.erectus and African H. ergaster. And then between African H. rhodesiensis and European H. heidelbergensis.

    "Thus, if anything, Denisovans are either representative of this advancing wave of unmodified (un-Neanderthalized)heidelbergensis, or they may represent a complicated mixture"...

    They cannot be 100% Heidelbergensis because their mtDNA is clearly pre-Ergaster (i.e. it branched out long before Neanderthal and Sapiens lineages did), so, barring some extremely unlikely and convoluted hypothesis (i.e. following the criterion of parsimony), their maternal lineage was one of Asian H. erectus.

    This means that Denisovans were most likely a hybrid of H. erectus and H. neanderthalensis, which we could well call X Homo denisovensis or altaicus (the X indicates inter-species hybrid).

    "I very much doubt any Asian erectus contribution, which genetically would show up as 1.5 to 2.0 million years old".

    Only in the absence of admixture. Remember that we are dealing here with autosomal DNA. The mtDNA does look to me as having an age of c. 1.8 million years, fitting perfectly in the history of Asian H. erectus, even if it has been happily claimed much lower ages (1.3 million) but based on wrong, very very low and highly unrealistic, estimates of the Pan-Homo split.

    Autosomal DNA age estimates (seldom if ever calculated in other contexts) anyhow do not make any sense, as mentioned several times in this discussion. If we'd take such estimates seriously we'd have to accept that the OoA of H. sapiens happened some 650,000 years ago and the Eurasian divergence into various populations c. 500,000 years ago. This is not any acceptable conclusion on light of all the available archaeological and genetic data and needs a radical revision.

    What we do see in the autosomal data is that Denisovans nuclear DNA is much closer to Neanderthals than expected by mtDNA (which has no relation with Neanderthals at all) and the most reasonable conclusion is that of a hybrid population, what makes total sense considering where is Altai, that Neanderthals were living in nearby areas and that Denisovans used "Neanderthal" Mousterian tech and not Erectus nor Heidelbergensis technologies.

    This could be confirmed by analyzing the aDNA of several Asian H. erectus specimens. And I can only imagine that it will be eventually done.

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  35. Notice also, that if Denisovans are, as I think, an Erectus-Neanderthal hybrid, then the non-Neanderthal archaic contribution to Melanesians may be just 4.8%: 2.5% Neanderthal and 2.3% Erectus (and not 7.4%).

    This would be within the range of some East Asians (Cambodians 4.4%, Mongolians 4%), though these seem only Neanderthal-admixed.

    A big issue for me anyhow is always the Narmada hominin, which makes likely that other Homo species, of uncertain affinity but of quite large brains in any case, may have existed in Asia. But barring this (on lack of data and no other reason), the previous theory is what makes best sense.

    I mention the Narmada hominin because, by the coastal or tropical route and with the likely first South Asian homeland for the Eurasian subset of Humankind, this species (?) would be a likely factor of admixture and could be a cause of confusion easily.

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  36. Erratum: "then the non-Neanderthal archaic contribution to Melanesians may be just 4.8%: 2.5% Neanderthal and 2.3% Erectus (and not 7.4%)" should read either:

    (a) "then the total archaic contribution to Melanesians may be just 4.8%: 2.5% Neanderthal and 2.3% Erectus (and not 7.4%)".

    or

    (b) "then the non-Neanderthal archaic contribution to Melanesians may be just (...) 2.3%, totaling maybe 4.8% for all archaic genetic input (and not 7.4%)".

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  37. Do we know that? I lack information that could support that H. heidelbergensis was ever outside Europe.

    I suppose Narmada hominin was H. heidelbergensis.

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  38. I guess my comment got deleted.

    Narmada hominin were thought to be H. Heidelbergensis.
    http://news.nationalgeographic.com/news/2005/11/1114_051114_india_2.html

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  39. Trying again.
    http://news.nationalgeographic.com/news/2005/11/
    1114_051114_india_2.html

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  40. Your comment did not get deleted: it went to the spam folder (complain to Google). Now it's back.

    Narmada should not be Heidelbergensis because it has a much larger cranial capacity, more like Sapiens or Neanderthals (almost) but it's older by some 250,000 years.

    All the papers on the matter are pay-per-view but you can clearly see that it's being classified as H. sapiens (Kennedy 2005), when there were no known H. sapiens (nor Neanderthals) anywhere, and that the clavicle is described as that of a modern adult Pygmy (Sankhyan 1996).

    "... almond-shaped hand axes" essentially mean Acheulean and hence H. ergaster probably (but not necessarily its heidelbergensis descendant of Europe). There's no reason why H. ergaster could not have colonized India, independently from what happened in Europe.

    But, if you'd be right, "Neanderthal admixture" would be not possible to take apart from Heidelbergensis admixture (at the current level of knowledge), because both are in the same branch diverging from us at in the same timeline.

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  41. Per Petraglia 2010 ("Out of Africa to India" - see here), the Acheulean-MP transition happened c. 120-100 Ka ago, with MP sites of MSA-like tech from Rajasthan to Madhya Pradesh.

    This actually offers a possible place for "Neanderthal" admixture without Neanderthals if the Indian hominins were relatives (H. heidelbergensis or derived). We would not be able to tell the difference.

    Here there's a copy of the clavicle paper, where the Narmada hominin is described to have a Pygmy-like body but much more robust. Neanderthals were like that, what suggests a possible relation.

    But neither of these scenarios would explain the pre-Ergaster admixture expressed by the "Denisovan" genes among Melanesians. So I am beginning to think in the following scenario:

    1. H. sapiens arrives to India and hybridizes at low levels not with Neanderthals directly but with a relative from the subcontinent.

    2. Some H. sapiens arrive to Sundaland and hybridize at low levels not with "Denisovans" but with a pureblood relative, H. erectus soloensis.

    Makes total sense. It's in fact a lot simpler and fits perfectly with the data.

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  42. "we know that heidelbergensis-like people moved eastwards just when climate changed in Europe and homo became more specialized as Neanderthals, there. Thus, these people were much advanced over local Asian erectus (by about 1 million years, and by that much time of gene flow with Africa that Asian erectus did not have".

    But that doesn't necessarily preclude the SE Asian Home erectus from having hybridised with 'modern' humans when they arrived there. This seems to be what Maju is hinting at:

    "2. Some H. sapiens arrive to Sundaland and hybridize at low levels not with 'Denisovans' but with a pureblood relative, H. erectus soloensis".

    I think that explanation is largely correct.

    "Actually, I'm often more comfortable with just using 'H. erectus' as catchall term for all Homo before the big headed species (Neanderthal, Sapiens and Narmada hominin)".

    Likewise. I'm sure that H. erectus and H. ergaster were barely 'subspecies', and probably quite capable of hybridising where-ever they met.

    "Autosomal DNA age estimates (seldom if ever calculated in other contexts) anyhow do not make any sense, as mentioned several times in this discussion".

    Presumably because individual genes have individual ages of origin. The original Australopithecus population presumably carried several different genes from the population from which it had evolved. Therefore individual autosomal genes may go back as far as the original chimp/human split. And we share genes with them anyway, eliminated in comparisons of course.

    "Narmada should not be Heidelbergensis because it has a much larger cranial capacity, more like Sapiens or Neanderthals (almost) but it's older by some 250,000 years".

    Doesn't that further support a hypothesis that African H. sapiens evolved from a back-movement into that continent from Asia? The modern human haplogroups all appear to be younger than 250,000 years, so we have no knowledge of their deeper ancestry.

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  43. "Doesn't that further support a hypothesis that African H. sapiens evolved from a back-movement into that continent from Asia?"

    It is a possibility but I'd like to see clear evidence of some sort first. So far all techno-cultural innovations of the Early Paleolithic begin in Africa and expand to Eurasia, not the other way around. There is no single piece of evidence of back-migration to Africa at those stages.

    Searching for references on Narmada hominin, I could spot some where it suggested that the age of the fossil is not as old as usually believed anyhow.

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  44. They cannot be 100% Heidelbergensis because their mtDNA is clearly pre-Ergaster (i.e. it branched out long before Neanderthal and Sapiens lineages did), so, barring some extremely unlikely and convoluted hypothesis (i.e. following the criterion of parsimony), their maternal lineage was one of Asian H. erectus.

    Maju,

    Part of this is nomenclature, part of it is which dates you adhere to: outside of Spain, antecessor/ heidelbergensis are not really distinguished (their separation time is minuscule; their main difference is growing and larger brain size in heidelbergensis), which means the earliest heidelbergensis or its immediate "antecessor" are about 0.8 to one million years old, whereas Neanderthals only start to diverge ~400,000 years ago, with full-blown features by ~150,000 to 250,000 years ago. So, if you consequently date the autosomal separation time ("split" - not last common ancestor - to both humans and heidelbergensis) at 400,000 years ago, some heidelbergensis mtDNA lines would be expected to be much older (twice as old or older), since originally, Neanderthals were geographically quite restricted, with severe bottlenecks. This is all in agreement with the Reich et al. paper (~1 million year mtDNA divergence time for Denisova).

    Non-neanderthalized heidelbergensis arrived in China ~200,000 years ago (sometimes classified as early Homo sapiens to get around the issue of stating relation). So, outside of some tropical pockets left with erectus, this population IMO makes a much better candidate for mating with newly-arriving AMHs than Asian erectus does.

    Human occupation at Denisova started at ~280,000 years ago, again in agreement with the suggested wave of heidelbergensis eastward (starting in Europe around 400,000 years ago, and arriving in China by 200,000 years ago).

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  45. What happens is that I do not consider H. sapiens to be descended from H. heidelbergensis (or antecessor) but from a relative in Africa: H. rhodesiensis. Both branches derive from H. ergaster but that's all.

    So Neanderthals and us should have diverged c. 1 Ma ago, maybe even 1.3 million years ago, if we follow Atapuerca palaeontologists, like Aida Gómez.

    So an older mtDNA lineage such as that of Denisovans should be pre-Ergaster, hence H. erectus.

    "Non-neanderthalized heidelbergensis arrived in China ~200,000 years ago".

    I would need clear evidence. Bodo and Dali are sometimes described as H. heidelbergensis but I think this is abusive. Only presence of H. ergaster/heidelbergensis technology (or a clear DNA comparison, yet to be done) could lean the scales in favor of such risky terminologies. For me they are just evolved Asian H. erectus.

    In fact Bodo is so old (600 Ka) that it should not be H. heidelbergensis (which is only dated in Europe to c. 400 Ka). It is also not known to be associated with Acheulean, so it should not even be in the Ergaster sub-genus. Dali is almost identical to Bodo, except maybe less prognathous, (but 400 Ka younger).

    However all H. erectus senso lato (incl. ergaster, heidelbergensis, rhodesiensis) are very similar in many aspects, particularly their low vault and prominent browridge. So confusion is understandable and only a very detailed, technical analysis may establish the differences, if that is even possible.

    "Human occupation at Denisova started at ~280,000 years ago, again in agreement with the suggested wave of heidelbergensis eastward (starting in Europe around 400,000 years ago, and arriving in China by 200,000 years ago)".

    You are the second person to suggest a migration of Heidelbergensis eastwards at those dates, roughly. But I'd like to see any evidence of at least Acheulean tech, other than the disconnected, discontinued and much older Bose basin sites.

    ReplyDelete

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