English: (a) A neighbor-joining tree for the three Japanese populations and other Asian populations listed in Supplementary Table S2.

(b) A maximum-likelihood tree for the three Japanese populations with Northeast Asians (Hezhen, Daur, Oroqen, Mongolian), Koreans, Han Chinese and populations from central China (Tu, Naxi, Yi). All bootstrap values shown with arrows were obtained from 5000 replications.

Hezhen, Daur, Oroqen and Mongolians as the northeast Asian population, and three populations in southern China (Tu, Naxi and Yi) were also merged. The Ainu and the Ryukyuan were clustered with 100% bootstrap probability, followed by the Mainland Japanese. The three populations in the Japanese Archipelago clustered with the Korean with 100% bootstrap probability. The Ainu population has a long branch and is clearly different from the other populations in this figure, confirming the unique phylogenetic position of this population in East Asia. The very short, almost nonexistent branch leading to the Mainland Japanese, as well as its intermediate position between the Ainu-Ryukyu and the cluster for the remaining populations suggest that the Mainland Japanese was formed by the result of admixture between these two ancestral population sources, symbolized as the Jomon and the Yayoi. The northeast Asian population was phylogenetically closest to the Korean–Japanese Archipelago population cluster, followed by the populations in southern China. The three Han Chinese populations in Beijing, Taiwan and Shanghai clustered together with 92% bootstrap probability.

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