A few months ago there was a preprint with an ancient Japanese genome, Jomon genome sheds light on East Asian population history. I read it but didn’t say anything at the time. I read it again, partly because I’m reading a history of Korea where the Wa, the early Japanese, show up to intervene in mainland affairs. This cameo made me think more deeply about what happened in Japan several thousand years ago.
The above genome comes from Honshu, and dates to 2,500 years before the present. And yet it’s quite different from modern Japanese! Here is the abstract:
Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.
Let me be frank: the term basal probably is somewhat misleading. Ancient DNA in East Asia is in its infancy. We don’t really know what’s going on, and what went down. But I can offer a guess.
I think in the next few years we will realize that there was a massive demographic expansion out of a few agricultural hearths in the eastern regions of what we now call China during the early Holocene. The Sino-Tibetan peoples, Austro-Asiatic, and Austronesian are derived from this series of expansions. But with hindsight, I think we will see that the peoples to the north and east of China proper, are also downstream of this agricultural revolution.
Within China proper a secondary expansion occurred, dating to the rise of the Chinese civilization. This ‘erased’ a lot of the variation in southern China, and a quasi-panmixia was enforced through the Chinese dynastic cycles, as northerners moved south and vice versa.
In the first figure, the Treemix panel shows that only ~3% of the modern Japanese ancestry needs to be accounted for by an edge from this Jomon genome. This implies that there was massive population replacement of the Jomon by the Yayoi people, from southern proto-Korea. I say “proto-Korea,” because the origins of the ancestors of the modern Korean culture seem to be located much further north, in what is the border region of Manchuria and North Korea today. The Yayoi is quite possibly derived from one of the indigenous peoples of the southern Korean peninsula, who were assimilated by the expanding Koreans as they moved southward around 0 A.D.
Within the preprint, the authors seem to converge on two facts. First, the Ancestral North Eurasian (ANE) admixture into much of East and Southeast Asia was minimal but much more substantial in Siberia. This is entirely plausible, though I think there needs to be more ancient East Asians besides Tianyun to conclude there isn’t some basal fraction The authors suggest that shared drift between Hoabinhian hunter-gatherers in ancient Southeast Asia and the Jomon individual confirm the likely southward origin of modern-day East Asians. I suspect the inference is correct, though I don’t know the shared drift tells us that much without more samples.
In the preprint, the authors observe that this is a much stronger affinity among coastal East Asians to the Jomon sample than from interior peoples. I don’t know what to say about this, except that it seems likely to me that coastal pre-agricultural populations would have greater numbers than interior peoples.