Indeed, I myself have used MCLUST to classify Upper Paleolithic skulls, and a number of them such as Markina Gora get the label of "Australoid". This is usually explained as an consequence of their greater robusticity, which links them to modern Australo-Melanesians, but the finding that a pre-modern population that lived in Eurasia did contribute genes to Melanesians, certainly raises all sorts of questions.
This is not a simple paper to read, if we also add the extensive supplementary material, so I will probably give my impressions and thoughts on it in piecemeal fashion.
The first interesting part comes from Table 1 in the paper. This contains values of the authors' D statistic D(H1,H2,archaic,chimpanzee) which shows how more frequently population H1 matches an archaic group than H2 does. A positive value suggests that H1 is more "archaic"-like.
The authors consider Neandertals (in the form of Vindija and Mezmaiskaya), as well as Denisova as the "archaic" groups of interest.
D values are consistently positive for H1=Papuans/Melanesians and H2 either African or Eurasian. This suggests indeed that Australo-Melanesians have archaic admixture from a population related to Denisova.
It is interesting that the authors are back-pedalling on the idea that specifically Neandertal admixture is responsible for the "archaic" genes found in Eurasians in the previous paper.
I think there are two reasons behind this: first of all, all Eurasians are closer to Denisova than Africans are. Melanesians are even more closer. But, Eurasians are closer to Neandertals than they are to Denisovans.
What this means is that Eurasians did not admix with Neandertals themselves but with a population that was closer to Neandertals than to Denisovans.
The second reason why I think that the idea of specifically Neandertal admixture is rejected is the fact that it makes no sense: the D statistic is 7.5 for Cambodians and 3.3 for Sardinian with standard errors of 1.2 and 1.5.
This means that Cambodians have more "Neandertal" admixture than Sardinians do, which makes absolutely no sense if specifically Neandertal admixture was the reason, as Neandertals were a West Eurasian-distributed species.
So, while not all is well for the Neandertal admixture theory, they also argue (in the supplementary material) that the alternative theory (which I've argued for, of archaic structure) is weakened by the new evidence. I'll think about their argument in a future update.
The authors did not consider the possibility of modern human to Denisova gene flow. Here is their reason (from the supplement):
Gene flow from modern humans into the ancestors of Denisovans is not only unsupported by the D-statistics, but is also historically implausible. The Denisova phalanx is more than 30,000 years old, and in our opinion is likely to be more that 50,000 years old (SI 12). The more ancient age estimate is older, and the more recent age estimate is only slightly younger than the age of the oldest confirmed modern human remains outside of Africa and the Levant. It is difficult to envision a plausible scenario in which the Denisovan population could have ancestry from a modern human group that experienced mixture in an area near where Melanesians live now, and then migrated to Siberia in just a few thousand years.
And, yet, we have evidence now of much older modern humans in South China, in the form of the Zhirendong mandible, which dates from ~100ky.
Looking at supplementary table S8.2 is quite interesting, because it gives the D statistics for intra-African "Neandertal" gene sharing.
The highest one is with H1=Yoruba and H2=Mbuti at 2%. What this means is, in essence, that Yoruba are more Neandertal-like than Mbuti are. How is this possible if a positive D value is reflective of admixture between Eurasians and Neandertals? There are no Neandertals in Nigeria to Neandertalize Yoruba with respect to Mbuti Pygmies.
This either means that Neandertal admixture is not the cause of the positive D statistics, or alternatively, that Yorubans are not pure Africans but have experienced back-migration of Neandertal-admixed Eurasians that Mbuti Pygmies did not experience to the same extent.
How interesting that Mbuti Pygmies (the least "Neandertal") and Papuans (the most "Denisovan") are the two most divergent living humans with an Fst of 0.377. Is it the case the different patterns of archaic admixture are contributing to this?
It is unfortunate that the authors did not sample East Africans yet again. The authors do not consider Z-scores below 3 (in absolute value) significant, so, the Yoruba/Mbuti score (for Neandertals) of 2.4 does not achieve significance, but it is almost there.
If the authors' theory is correct, then we expect to see no variation (or only variation attributed to noise) within native African populations with respect to their inferred "Neandertal admixture", as Neandertals were a Eurasian species.
It is perplexing why yet again East Africans were not sampled: if you are claiming Eurasian-African differences in archaic admixture, sampling East Africans who live in-between Eurasians and Africans is the natural thing to do!
Nature 468, 1053–1060 (23 December 2010) doi:10.1038/nature09710
Genetic history of an archaic hominin group from Denisova Cave in Siberia
David Reich et al.
Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.