By now you have read the paper in Nature, Genome sequence of a 45,000-year-old modern human from western Siberia. In The New York Times Carl Zimmer has an excellent write up, Man’s Genome From 45,000 Years Ago Is Reconstructed. The two major findings that are getting a lot of attention are that the Neandertal ancestry tracts in his genome are considerably longer than in modern humans and that he is basal to modern non-African populations. In regards to the first the distribution of Neandertal ancestry in the genome allowed them to infer backward to the point at which a pulse admixture might have occurred. Seeing as this individual has been dated to ~45,000 years before the present, Neandertal admixture occured 50-60,000 years ago. This happens to right around the time of the “Out of Africa” expansion.

But for me the Neandertal aspect is not the most interesting, as that simply refined our prior understanding. Rather, it is the relationship to modern human beings. The same first author gave us DNA analysis of an early modern human from Tianyuan Cave, China a few years ago, and in it she reported that a 39,000 year old individual found in China already exhibited clear affinities to eastern Eurasians and Oceanians. Now, one of the inferences which fit the results in this paper is that this 45,000 year old Siberian derives from a period when west and east Eurasians were not fully diverged (or, that divergence had been a recent event). Is ~6,000 years sufficient to account for drift away of the Tainyuan sample? My intuition is that it isn’t (they had ~85,000 positions at chromosome 21 to make the inference about the ancient Chinese sample, more than sufficient). I suspect that the dating is off somewhere here, though I don’t know which (if only one) sample.

Second, the issue of Basal Eurasians comes up again in the paper, and more extensively in in the supplements. I have a very hard time not believing that there is a paper on Basal Eurasians in the works, because they are very sketchy on specifics (also, Lazaridis did not really talk about the Basal Eurasians in the ASHG presentation). From page 60 of the supplements:

We caution that the TreeMix model is sensitive to which present-day populations are used for the analysis and the tree changes when we use different present-day human populations (Tabl S10.1). In particular, the analysis is sensitive to which African individuals are included. When we including only one African individual and all available Eurasian individuals, the Ust’-Ishim individual separates before the Eurasian split (position a) with bootstrap support between 68% and 100% depending on which population the individual is from (Table S10.1). These results suggest that recent gene flow between African and from European populations may influence the placement of Ust’-Ishim in the maximum likelihood tree. Nevertheless, the TreeMix models typically find that the Ust’-Ishim individual separates either before Eurasian split (position a in Figure S10.7) or just after the split and already on the eastern non-African lineage (position c in Figure S10.7).

The Sardinians have a bit of Sub-Saharan ancestry from the Roman era, but is this what they’re talking about? The Basal Eurasians are part of the greater Eurasian clade. That is, they are a branch of “Out of Africa.” But who knows where they are localized? No one knows. Thinking about it it probably is the case that they’re talking about recent African gene flow into Europe, even if it’s a few percent in Sardinia. But who knows? It’s all quite mysterious.

We’re at a very confused and exciting time right now. About a decade ago there was a stylized model of a rapid “Out of Africa replacement” all across the world. Mitochondrial Eve had even convinced people that Africans were subject to this. That is not the case. It seems clear that the Khoisan people diverged from the rest of the human lineages on the order of 200,000 years before the present. This predates any “Out of Africa” event. Much of Africa’s genetics has been reshaped by massive demographic expansion by the Bantus. There have long been hints out of the Reich lab about “Out of Africa” gene flow back into Africa that isn’t obvious (i.e., not Ethiopia or North Africa) leading to the genesis of contemporary Sub-Saharan populations, but excluding the hunter-gatherers. Such hints don’t emerge from a vacuum. The results are perplexing. It strikes me that now we know a fair amount about the demographic events which reshaped the Holocene, but the period before the Last Glacial Maximum is now far more clouded. Attempting to reconstruct the deep past with the algebraic variables of the recent past might be part of our problem here….

Update: From the comments:

It’s very likely Tianyuan was not really closer to East Asians than Ust-Ishim. U-I branches with East Eurasians with 100% bootstrap support, but branches off before Oceanians and Asians (supplements, page 57-58). This is similar to how Tianyuan branched, which was the main basis for that paper claiming it’s proto-East Eurasian. I think they did not realize during the Tianyuan paper’s writing that this could be simply because Tianyuan lacked the Middle Eastern/Basal/African admix of Europeans used in the tree (French and Sardinians). Formal testing (f-statistics from Rasmussen et al 2014) which were not done in Tianyuan’s own paper show no difference between Tianyuan’s relation to East Asians and Europeans. http://www.nature.com/nature/journal/v506/n7487/fig_tab/nature13025_SF5.html

(F & G)

This sounds reasonable to me. On the other hand this possibility is not acknowledged in the supplements to the paper.