The recent big paper on ancient DNA from East Asia has opened up a bit of a semantic can of worms. If you read all these ancient DNA papers with their stylized models you start to develop a sense of the big overall framework, but even in a big sprawling preprint with copious supplements, it is hard to make sense of things if you haven’t read what’s come before. With that in mind, I did a twitter thread where I outlined my own view and interpretation of how non-Africa was populated by modern humans in the last ~50,000 years with a focus on eastern Eurasia.
But I shouldn’t just leave it at Twitter. So I here I stand.
Above is a simple map, and to the right a stylized phylogram, that shows you the general gist of my thinking and what I’ve gleaned from the papers. First, we know that around 50,000 years ago there was a massive expansion from Africa or its margins all across Eurasia, and, that it reached Oceania really early.
Before that expansion it seems one group, we now call them “Basal Eurasians,” split off before the lineage that led to the peoples of Europe, Siberia, East Asia, South Asia, and Oceania. I set that at 60,000 years ago. Then around 50,000 years ago a group of populations that give rise to the peoples of Pleistocene East and South Asia, and Oceania, split off from groups that became the early Siberians (“Ancient North Eurasians”) and Pleistocene European hunter-gatherers.
In South Asia about half the ancestry derives from populations with affinities or origins in western Eurasia, whether that be West Asia (Iranian-related farmers who occupied the northwestern fringe of the subcontinent expanding south and east), or further north in Central Eurasia and Eastern Europe (Sintashta-Andronovo). The balance is often termed “AASI”, or “Ancient Ancestral South Indian.” The mitochondrial evidence (lots of basal M) suggests deep and diversified lineages in South Asia, so I am willing to agree that this group descends from the first of the recent Out-of-Africa or Out-of-Africa-liminal* pulse of migrants 50,000 years or so ago. But, I do think it is not implausible that some of the ancestry of AASI derives from back-migration from Southeast Asia, which would be prime human habit during the dry and cold Pleistocene.
Further east, you have groups in Southeast Asia proper. If you listen to The Insight podcast you know that Pleistocene Southeast Asia was a much larger landmass due to lower sea levels. Not only was there more territory, but much of it was open wooded savannah, which often supports higher human populations than a tropical rainforest. In any case, most of the human population that lives in this region today descend mostly from farmers who occupied what is today the Yangzi river valley in China. There are exceptions. The Negritos of Malaysia and the Andamanese seem to be reflections of the peoples who were dominant in the region in the Pleistocene and most of the Holocene. Further east, there are Negritos in the Phillippines, who are distantly related to those further west but seem somewhat more connected to the Oceanians, even further eastward.
We know that the humans were in Australia by 40-45,000 years ago, at the latest. This establishes a timeline for the point of divergence of all these lineages. Though Andamanese are used as proxies for AASIs in population genetic analyses, it turns out they are very distantly related to them. All of these dark-skinned people across southern Eurasia and into Oceania are more related to each other than they are to East Asians, but only very distantly and marginally.
Speaking of which, the 40,000-year-old sample from Tianyuan near Beijing is the oldest representative of the human groups which we now term East and Southeast Asian. We know from this sample, and how it relates to other people in eastern Eurasia, that there was already significant differentiation across the region. I assume this had to have happened around 45-50,000 years ago. The time is less important then to note that the split between East Eurasians and West Eurasians, and within East Eurasians and West Eurasians, occurred in very rapid succession. This is the hallmark of an expanding species which occupies “empty” landscapes and fills all the possible niches very fast, and then stabilizes.
An easy dichotomy would be to label the Tianyuan people the northern clade, and what is often termed “Australasian” the southern clade. But it’s not that simple. The most recent paper, aligning with earlier results, argues that the Jomon people of ancient Japan (related to or ancestors of the Ainu) are about a 50:50 mix between the “northern” (Siberian?) and “southern” lineages. But Japan is in northern East Asia! Additionally, they also find that the oldest modern layer in Tibetans is also more closely related to the “southern” lineage. Finally, we know some populations in Amazonia are more closely related to the “southern” lineage than they “should” be, indicating that some “southern” ancestry came over Beringia.
The Jomon culture dates to ~16,000 years ago, right after the Last Glacial Maximum. We don’t know when the two distinct populations mixed, but I wouldn’t be surprised if it was quite early, as Siberian populations moved toward the coast. I assume that haplogroup D, found in both Tibet and Japan, has some origin among the “southern” people. Physical anthropologists have long noted some broad similarities in morphology between some “Australoid” people in India, Australian Aboriginals, and the Ainu of Japan. As the divergence between these groups is 45,000 years ago, the similarities may still be coincidences, but perhaps they are share ancestral characters?
We also need to think about Native American peoples. It looks like this group is a mixture of “northern” East Asians, related to the Devil’s Gate population, and ANE populations. This situates some of the post-Tianyuan groups in Siberia, but recall some Amazonians have “Australasian” affinities. The reality is that I think “southern” lineage population was long present along the Pacific fringe. The Jomon heritage is clear evidence of that. It is not implausible that there was structure in ancient Beringia, and some coastal populations with “southern” ancestry moved on earlier than the inland groups, and were mostly replaced except in the deep Amazon.
Finally, we can mention the strange Paleo-Tibetan “southern” ancestry. Again, there are peculiarities in Tibetan morphology which don’t make them in the same class as East Asians, but that can be attributed to high altitude adaptation. If the Paleo-Tibetans were the earliest population, they probably may have mixed with the Denisovans to obtain EPAS1. But, the majority of Tibetan ancestry seems to date to successive waves of “northern” populations that moved onto the plateau from the north and east. So who were the Paleo-Tibetans most closely related to? If I had to guess, I would say AASI. They may have moved onto the plateau from the south.
This is obviously exceedingly simple. There are many likely details I got wrong, as well as details I left out (I think that “southern” lineages were very common in the southern half of China deep into the Holocene, spanning the region between Tibetan and Jomon Japan). But, it gets across the gist of the broader framework in East Asia.
Here is the one-sentence version: rapid expansion, diversification, stabilization, then much more recent mixture between all the lineages.
* I believe that “modern” African humans were present in southern Eurasia in some form and numbers between 50 and 100 thousand years ago. But, I think they left a very light genetic imprint on modern populations. I accept that modern humans were in Sumatra 65,000 years ago, but I think almost all the ancestry is from groups which expanded 50,000 years ago, from the west.