The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon’ potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples’ genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.
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[FONT="]Phylogenetic analysis I. TreeMix tree with gene flows. A comparison of Sanganji Jomon, 1000 Genomes Project worldwide populations, Papuan, Karitiana, Mal’ta MA1, Ust’-Ishim and Denisovan based on 43 310 all sites. Denisovan was used as the outgroup, and three gene flow events were estimated. The tree was drawn by using MEGA6.[/FONT][FONT="]38[/FONT][FONT="] Red colored values (only those higher than 90% are shown) are bootstrap probabilities (%) for their adjacent internal branch. Arrows were manually added to this tree, and colors of migration weight (ratio of gene flow) follow TreeMix outputs. Values inside arrows are the ratio of gene flow. Bootstrap probabilities (%) of the gene flow from Sanganji Jomon to JPT, Karitiana to the root of European and Mal’ta MA1, and LWK to European, estimated out of 1000 bootstrap replicate TreeMix outputs, are 42%, 86% and 0.4%, respectively.[/FONT]
I read an article about the subject a few months ago...
https://www.nature.com/articles/jhg2016110
The conclusion is Jomon are different from anything modern, even if Japanese people are closest to them. In details, Ainu are the closest, although they are not pure Jomon. Then it's people from Okinawa, then "central islands" Japanese.
The sample are only 3000 years old, it would be interesting to do the same with a 10,000 years old Jomon sample.
Spencer Wells recently tweeted this. She certainly doesn't look East Asian to me. Not really Southeast Asian either. I'm struggling to classify it.
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Partially Australoid.
No contradiction because Jomon had archaic features very more than other East Asians ; even if the total auDNA has shifted away, these features keep them less far than the most of other pops;