The Jomon genome preprint: biorxiv.org/content/biorxi…
Enormously important for understanding the origin of the people of Japan: The AIT equivalent of those regions. A few comments below
Enormously important for understanding the origin of the people of Japan: The AIT equivalent of those regions. A few comments below
It clearly establishes that the earlier peoples of Japan, the Jomon, were ancestors of the Ainu some of whom even today retain that Jomon ancestry in an unadulterated form. This Jomon-type ancestry is also seen elsewhere in east Asia like: 1. The Ulchi who live in eastern Russia& 
speak a Tungusic language. 2) They show relationship to the ancient Devils Gate people of Sikhote-Alin mountains of Russia who also show a similar admixture with the Jomon-like component as the Ulchi; 3) the ancient Hòabìnhian hunter gatherers of Vietnam also show some of this
Jomon-Ainu like ancestry. 4) The ~40KY old Tianyuan man from China also shows some of this Jomon-like Ancestry. This is seen clearly in the below PCA analysis they have done. Note the Koreans are shifted towards the Japanese wrt to the northern Hans.
They also find evidence that a lineage related to the Jomon contributed to the ancestry of the Taiwan aborigines like the Ami & the Atayal. All together it appears that the Jomon were remnants of an old basal Asian branch that branched off from the rest of east-moving Homo after
the Onge but before the common ancestor of the First Americans and East Asians had split into those two branches. Their presence in coastal East Asia like Taiwan, Malaysia, Japan suggests that they spread along the coast to eventually go deeper into what's now eastern Russia.
Eventually by the Neolithic they were wiped out in most of Asia except for remnants like those noted above. Using ALDER they estimate the admixture between the Jomon and an invading East Asian group related to Hans happening around 42-57 generations back in Japan. The suggest a
lower bound date for this as ~200-300 CE. That can be taken to be the point of ethnogenesis of the modern Japanese. The Ulchi appear to have arisen from the absorption of a Jomon-like group on a more recent time scale of 8-33 gens.The Koreans might have mixed with them around the
same time as the J or acquired their Jomon ancestry due to reverse gene flow from J or there was some of both. This does have some implications for culture and Linguistics. The time-frame from the admixture evidence points to the ethnogenesis of J in the Kofun rather than Yayoi
period. The Kofun period was when there was a dramatic change in Japanese archaeological horizon with shared developments seen in Korea. This is also the period when chIna-s like the descendants of the Chin Shi Huang & several clansmen of Han warlords and K reached Japan. Some
Korean lords also reached Japan. However, it is notable that despite the big influence of these chIna warlords Japanese is not a Sino-Burman language and while sharing some typological commonalities with Korean is at best very distantly related to it. Moreover, the Kofun period
marks the emergence of horse-borne elite that had distinctive role in the development of the unique aspects of Japanese culture and religion. These had similarities in a cultural sense to the Iranic steppe peoples. However, the genetic evidence does not point to any role of those
people in directly contributing to J ancestry. Hence, it might be suggested that an East Asian steppe group with genetic links to Mongolic peoples and speaking a language with those "Altaic" features that developed on the Mongol and eastern steppes were the invaders of Japan who
conquered it from the Ainu-like people and mixed with that substratum. This was probably followed by even more Hanization by the rise of chIna-s from warlord clans to high positions in Japan.
