Genome-wide SNP data of Izumo and Makurazaki populations support inner-dual structure model for origin of Yamato people

Abstract

The “Dual Structure” model on the formation of the modern Japanese population assumes that the indigenous hunter-gathering population (symbolized as Jomon people) admixed with rice-farming population (symbolized as Yayoi people) who migrated from the Asian continent after the Yayoi period started. The Jomon component remained high both in Ainu and Okinawa people who mainly reside in northern and southern Japan, respectively, while the Yayoi component is higher in the mainland Japanese (Yamato people). The model has been well supported by genetic data, but the Yamato population was mostly represented by people from Tokyo area. We generated new genome-wide SNP data using Japonica Array for 45 individuals in Izumo City of Shimane Prefecture and for 72 individuals in Makurazaki City of Kagoshima Prefecture in Southern Kyushu, and compared these data with those of other human populations in East Asia, including BioBank Japan data. Using principal component analysis, phylogenetic network, and f4 tests, we found that Izumo, Makurazaki, and Tohoku populations are slightly differentiated from Kanto (including Tokyo), Tokai, and Kinki regions. These results suggest the substructure within Mainland Japanese maybe caused by multiple migration events from the Asian continent following the Jomon period, and we propose a modified version of “Dual Structure” model called the “Inner-Dual Structure” model.

Modern Japanese ancestry-derived variants revealed the formation process of the current Japanese regional gradations

“…The JAS was especially high in Aomori (0.0192), Iwate (0.0195), Fukushima (0.0187), and Akita (0.0186) prefectures of the Tohoku region, as well as Kagoshima Prefecture (0.0186) in Kyushu. Interestingly, the JAS in Shimane Prefecture (0.0184) was on the same level as the prefectures in Tohoku and Kagoshima in Kyushu, being consistent with the genetic affinity in the Izumo individuals to Okinawa and Kyushu individuals in Jinam et al 23 . Japanese individuals in these prefectures are considered to possess more Jomon-derived genomic components than those in other prefectures.…”

“…Interestingly, the JAS in Shimane Prefecture (0.0184) was on the same level as the prefectures in Tohoku and Kagoshima in Kyushu, being consistent with the genetic affinity in the Izumo individuals to Okinawa and Kyushu individuals in Jinam et al 23 .…”

Phylogeographic study using nuclear genome sequences of <i>Asip</i> to infer the origins of ventral fur color variation in the house mouse <i>Mus musculus</i>

“…Given the already widespread distribution of CAS-related sequences from Hokkaido to Okinawa, it is conceivable that human activity related to this event substantially affected the Japanese archipelago. These results are useful for understanding prehistoric human migration to and through the Japanese archipelago, and our findings strengthen archaeological and human genomic knowledge related to pre-and post-Yayoi period migration events (Leipe et al, 2020;Jinam et al, 2021).…”

Preface to the special issue on the Yaponesia Genome Project

“…,Saitou and Jinam (2017), andJinam et al (2021a) is compatible with these datasets Adachi et al (2021). reported the first Jomon genome data from the Higashimyo shell midden site, Kyushu, dated c. 8000 years ago.…”