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.
Denisova closer to Neanderthals?
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
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.