I have recently discussed the Denisovan admixture in Melanesians discovered by the Neanderthal Genome Project and I discussed back in its day the Neanderthal admixture in all non-Africans (see here and here).
While the Neanderthal admixture episode may be easy to explain and was thus explained by Green et al. as happening early in the migration out of Africa, probably before arrival to South Asia. The Denisovan admixture in islands far away from Altai is not so easy to understand and has not been satisfactorily explained by anybody I know so far.
What were the Denisovans?
First of all we have not a very clear idea of what kind of hominin were the Denisovans. Well, actually we know that their tooth clusters with Indonesian H. erectus, H. habilis and australopithecines (but also with the H. sapiens of Pestera cu Oase, quite divergent from the rest in this aspect).
We also know that the Denisovan mtDNA belongs to a branch older than that of H. ergaster and descendants, because it is almost twice older in its divergence from that of Neanderthal and Sapiens mtDNA (both derived from H. ergaster c. one million years ago by all accounts that make any sense). What diverges in the common tree of Humankind (senso lato) almost twice that time? Asian H. erectus, believed to derive from a population represented by H. georgicus.
Nothing else does. Hence the Denisovan mtDNA, found in two different individuals (a finger and a tooth actually) must be that of Asian H. erectus.
However the Denisovan nuclear DNA is not so distant from Neanderthals. What does it mean? Most probably that they were a hybrid Erectus-Neanderthal population, what fits well with their presence in Altai (at the crossroads of known homelands of both species), their use of Mousterian technology (typical of Neanderthals) and the presence of Neanderthals in similar dates at nearby sites.
So my theory about Denisovan identity is this one: they were a hybrid population of Neanderthals and H. erectus, with maternal lineages of the latter species and technology of the former.
Melanesians in Siberia? No way!
Quite obviously Melanesian ancestors were never in Siberia. This is not just a matter of the coastal migration model, that also, but specially a matter of pigmentation. The name Melanesia means Islands of the Blacks in modified Greek and, if the ancestors of these peoples would have been in Siberia for any extended period, they would have lost their tropical pigmentation for sure because otherwise they would not be getting enough vitamin D and their children would be extremely unfit for that reason (retarded, schizophrenic, rickety, etc.) And, as the case of Native Americans clearly illustrates, re-evolving black pigmentation, once it is lost, is no easy matter. In maybe 15,000 years tropical native Americans have only got a tan.
So the ancestors of Melanesians and other very dark tropical Asians have definitively not lived in Siberia at any time. Besides, it is totally non-parsimonious in what regards to modern human mtDNA and Y-DNA spread, the tropical route is much more logical and natural.
So they must have admixed with some relative of Denisovans elsewhere, for example in Sundaland, where some Homo erectus are known to have lived in dates that are perfectly compatible with this scenario. An encounter of the first of our species arriving to that area and Homo erectus soloensis is almost sure to have happened.
So we do have a plausible and even likely scenario for this admixture event in the ancestors of Melanesians, not in Altai but in SE Asia.
Admixture detection by proxy... interesting.
Certainly that we can detect admixture happening in Java by studying distant relatives in Altai is interesting. And it makes sense. If you compare a modern French-Vietnamese with French and Altaians it's likely that he will appear as a mixture of French and Altaians, even if the proportions may not be exactly correct.
I'll get to this matter of proportions later on because it is relevant too.
What happens if we get the son of an Punjabi and Vietnamese and compare with French and Altaians? He will surely still show up as admixed. A simplistic conclusion might be that he is descendant from French and Altaians. This conclusion would be wrong, even if the confusion is understandable.
The Narmada hominin and "Neanderthal" admixture
Thinking about this brought me (with some important help from readers - feedback is crucial) to the mysterious Narmada or Hathnora hominin (see here for an open access reference), the oldest of really big-brained humans and possibly a relative of Neanderthals (but not a true Neanderthal, among other reasons because they did not use Mousterian technology but Acheulean). The skeletal record of South Asia is quite scarce but this big-headed hominin is the last people we know about before African-like Middle Paleolithic technology appears c. 120,000 years ago (see here), probably with the first members of our species.
Yes, you read right: 120,000 years ago (more or less), the idea of a much more recent Out of Africa is almost certainly wrong, even if you will surely read such nonsenses for a while: the molecular clock pseudo-science cannot overrule archaeology.
It is at this moment uncertain whether the Narmada specimen and the probably much larger population it belonged to was a descendant of H. erectus or a descendant from H. heidelbergensis (and hence closely related to Neanderthals). Depending on which of these two options is correct, the scenario presented below will make sense or need to be revised.
I will consider, as suggested here by Michael Petraglia, that the Narmada specimen and related Indian population of the Early Paleolithic (which lasted until c. 100,000 years ago) were descendant of H. heidelbergensis, and hence cousins of Neanderthals. Why? Because they had Acheulean technology, which is associated with at least the late H. ergaster.
If this is correct, when we talk (after Green 2010) of Neanderthal admixture at low levels in non-African modern humans we may well be talking of admixture with anything within the broader Neanderthal family, in other words, with its ancestor H. heidelbergensis (cousin of our most direct ancestor H. rhodesiensis) and their descendants (Neanderthals and others, including probably the Narmada hominin and broader Acheulean-using population of South Asia.
A hypothesis strongly consistent with the coastal (or tropical) migration model
And I finally reach here to my hypothesis, to my explanation of the admixture episodes revealed by the Neanderthal Genome Project this eventful year of 2010. And I will do it with few words:
|click to expand|
The first admixture refers to the general non-African admixture with "Neanderthals", which would actually have happened with their Indian cousins instead upon arrival to South Asia. This admixture would have affected all non-Africans, but as the case of the Karitiana (who only show some 0.9% of such admixture, much less than the rest) evidence, maybe not all populations exactly in the same amounts.
The second admixture refers to the specifically Melanesian hybridization with "Denisovans", which would actually have been with their Indonesian pureblood relatives, H. erectus soloensis.
Makes sense? I think so. Of course, it is not set on stone but it seems a good hypothesis and should at least get some people chewing on this.
Special thanks for some key references to Terry T. and Manju (but in general to all readers who take part in the discussions at the comments sections: keep the flow of ideas vibrant, please). I suspect that Terry will not like my conclusions because they end up in the coastal migration model that he hates so much. But well...
Appendix 1: the real apportion of Melanesian admixture with archaic hominins may be lower than suggested by Reich 2010.
They suggest (supp. info 8) that Melanesians would have as much as 7.4% of admixture with archaic species: 4.8% Denisovan plus 2.5% Neanderthal. But, if Denisovans are hybrids of H. erectus and H. neanderthalensis (as seems most likely, see above), then the real admixture with H. erectus would be an undetermined percentage but always less than 4.8%. As we know that the Neanderthal (or Heidelbergensis) component is 2.5%, it is most likely that the actual Erectus admixture in Melanesians is of only 2.3% or 2.4%, totaling 4.8%.
Appendix 2: very serious inconsistencies in the age estimates derived from nuclear DNA in Reich 2010.
In supp. info. 6, the authors provide data of genetic divergence between various modern populations, Neanderthals and Denisovans, expressed as fractions of the Homo-Pan divergence. They use the wrong time frame for this event (6.5 Ma) but even then the results make no sense.
Using a much more correct (according to modern best scientific understanding) of 8 million years, I get that the age of the migration Out of Africa would have happened between 650,000 and 500,000 years ago. The first figure is the distance between Yorubas and non-Africans and the latter the one between non-Africans.
This is a total nonsense (120,000 years makes sense, add some tens of thousands more if you wish but half a million years is simply not possible) and there must be a critical error somewhere. However I have not been able yet to discover what exactly is wrong. In any case, word of warning about accepting molecular clock age estimates in general and in particular when using nuclear (autosomal) DNA for this purpose.