The above is a figure from The genetic legacy of the Mongols, and illustrates the concept of a “star-shaped phylogeny.” This is basically a phenomenon where a massively rapid demographic expansion of one particular lineage results in a host of nearly simultaneously mutational events which derive from the ancestral state. It is illustrated by the topology above, where derived states cluster around the ancestral type. Obviously it is harder to characterize the sequential structure of lineage fissions in these circumstances.
I am beginning to think that some of the same issues may apply to the expansion of Homo sapiens sapiens 40 to 60 thousand years. The thought was triggered by the recent abstract at SMBE 2014 on the 45 thousand year old Siberian which was whole genome sequenced:
The complete genome sequence of a 45,000-year-oldmodern human from Eurasia
We have sequenced to high coverage the genome of a femur recently discovered near Ust-Ishim in Siberia. The bone was directly carbon-dated to 45,000 years before present. Analyses of the relationship of the Ust-Ishim individual to present-day humans show that he is closely related to the ancestral population shared between present-day Europeans and present-day Asians. The over-all amount of genomic admixture from Neandertals is similar to that in present-day non-Africans and there is no evidence for admixture from Denisovans. However, the size of the genomic segments of Neandertal ancestry in the Ust-Ishim individual is substantially larger than in present-day individuals. From the size distribution of these segments we estimated that this individual lived about 200-400 generations after the admixture with Neandertals occurred. The age of this genome allows us to directly assess the mutation rate in the different compartments of the human genome. These results will be presented and discussed.
200-400 generations means 5 to 10 thousand years. So the implication is that the admixture event which led to the Neandertal ancestry in non-Africans dates to 50 to 55 thousand years before the present. Australia was settled by modern humans ~45 thousand years before the present, while western Europe was settled ~35 thousand years before the present. Ancient DNA from China 40 thousand years ago already suggests that East Eurasians had begun to diverge as an independent lineage. Joe Pickrell says that when he saw the poster the ancient Siberian seemed more closely related to one of the two dominant Eurasian lineages. I suspect it would be to West Eurasians, as the Ma’lta Paleo-Siberian from 22 thousand years ago was. Overall the picture seems to be that many of the ancestral lineages which are geographically distinct across Eurasia and Oceania had already come into being in the interval between the admixture even with Neandertals 55 thousand years ago the 45 thousand year old Siberian. Because these lineages diverged so rapidly in sequence you see a situation where sometimes have polytomies, where the phylogeny can not be fully resolved. With the emergence of ancient DNA and whole genome sequences I believe that this issue will mostly be overcome, but, it explains why different methods of inference have given someone different results (e.g., the old question with Oceanians are an outgroup to Eurasians or more similar to East Eurasians).
Finally, there’s the issue why these neo-Africans were so rapid in their spread and demographic dominance ~50 thousand years ago. Probably the dominant position, most forcefully articulated by Richard Klein in The Dawn of Human Culture, is that Homo sapiens sapiens has biological competencies which allowed them to marginalize other hominins. This is obviously one reason that some geneticists are trying to find specific differences between the genomes of our own lineage and that of our cousins. But if researchers focused on modern human lineages they wouldn’t present a biological explanation at all, but a cultural one. How do you set up your priors? Because many people presumed that the emergence of sapiens sapiens was a speciation event it seemed that a biological explanation was more plausible. I don’t deny that that’s the case, and that we should weight cultural explanations more strongly when it comes to something like the Austronesian expansion (first, the genetic difference between Austro-Asiatic Southeast Asians and Austronesians is not that great at all). But perhaps we shouldn’t dismiss the possibility of some cultural innovation as being the root of the neo-African advantage? I believe we need to start thinking more systematically about the expansions of hominin lineages since the early Pleistocene.