Modern human DNA analyses with special reference to the inner dual-structure model of Yaponesian

Abstract

Previous studies suggested two major migration events during the Jomon and Yayoi periods that affected the genetic diversity of modern Japanese (Yaponesians). We explored the possibility of a three-wave migration model by examining three datasets of modern human DNA: (1) whole mitochondrial (mt) DNA genomes of 1642 Yaponesians; (2) mtDNA haplogroup frequencies of 59105 Yaponesians from 47 prefectures; and (3) genome-wide SNP data of two Yaponesians (Ainu, Okinawa) and whole-genome sequence data of Yamato individuals, the Funadomari Jomon F23 individual, and three East Asian populations (Korean, northern Chinese, and southern Chinese). Past population size change was estimated based on dataset 1, and we clearly observed a steep population increase after the Yayoi period. Principal-component analysis and phylogenetic network analysis were applied to dataset 2, and we confirmed the pattern consistent with our model. An admixture program was used on dataset 3, and we found that the two-and three-layer migration models are both compatible with these SNP data. Taken together, these three datasets provide support for our three-wave, 'inner dual-structure' model.

Ancient genomics reveals tripartite origins of Japanese populations

“…This hypothesis was originally proposed on the basis of morphological data but has been widely tested and evaluated across disciplines [see a recent review in (6)]. Genetic studies have identified population stratifications within present-day Japanese populations, supporting at least two waves of migrations to the Japanese archipelago (7)(8)(9)(10). Previous ancient DNA studies have also illustrated the genetic affinity of Jomon and Yayoi individuals to Japanese populations today (11)(12)(13)(14)(15).…”

Germline PRDM1 Variant rs2185379 in Long-Term Recurrence-Free Survivors of Advanced Ovarian Cancer

“…We used the DNA specimens to perform a whole-genome SNV analysis (Asian Screening Array assay; 6 Genesis Healthcare, Tokyo, Japan) specified to East Asian populations, with the iScan System (Illumina, San Diego, CA, USA). Briefly, this analysis can comprehensively analyze approximately 660,000 SNVs.…”

Genetic variation of olfactory receptor gene family in a Japanese population

“…Building on this previous research, we focus on the Japanese population as a case study of OR gene family variation. The Japanese population is a hybrid between the Yayoi people, farmers who migrated from the East Eurasian Continent ~3000 years ago, and the Jomon people, indigenous huntergatherers who were likely to be the descendants of late-Paleolithic people in the Japanese archipelago (Hanihara, 1991;Adachi et al, 2021;Jinam et al, 2021;Koganebuchi and Oota, 2021;Osada and Kawai, 2021). Ancient DNA analyses inferred that the Jomon people diverged from the current East Asians earlier than 26000 years ago (McColl et al, 2018;Gakuhari et al, 2020).…”