Human genetic diversity in the Japanese Archipelago: dual structure and beyond

Abstract

The Japanese Archipelago stretches approximately 3,000 kilometers from Hokkaido in the north to the Ryukyu Islands in the south, and has seen human activity since at least 30 thousand years ago (KYA). The Jomon period from 16 to 3 KYA is associated with cord-marked pottery and the people at that time, who were hunter-gatherers, occupied a range of locations across the Japanese Archipelago. The Yayoi period from 3 to 1.7 KYA saw the introduction of migrants from the Asian Continent who brought rice agriculture to the archipelago. The dual-structure model, which is based on craniofacial measurements, proposes that admixture between the Jomon and Yayoi people resulted in current-day Japanese. Subsequent genetic studies using uniparental and autosomal markers in currentday and ancient human samples are widely in support of the dual-structure model. These genetic data have also unveiled the uniqueness of the indigenous Ainu and Ryukyuan people while further demonstrating the genetic substructure within the Mainland Japanese.

The fine-scale genetic structure and evolution of the Japanese population

“…From our widely-sampled continental Asian populations (which consist of 34 populations including the Japanese), we have successfully detected significant evidence for admixture in the Japanese population with clusters C282 (Korean), C284 and C291 (Han Chinese), and C280 (Vietnamese) used as references ( P < 0.05 for all of the instances in Table 1 ). Here, an admixture source approximated by a reference of East Asians, e.g., C282, C284 and C291, agrees with the origin of Yayoi people, who are assumed to have come through the Korean Peninsula as the second wave in the dual structure model [ 1 , 4 – 6 ]. An admixture source approximated by a reference of Southeast Asians is of interest, since the origin of Jomon people has been hypothesized to be in Southeast Asia.…”

“…The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu [ 1 ]. The Hondo people, comprising 99% of the Japanese, live in the four main islands of Japan; the Ryukyu people, comprising 1%, live in Okinawa, the southwestern archipelago; and the Ainu people are indigenous to the northernmost islands of Japan and currently comprise ~0.03% of the Japanese.…”

“…The currently accepted model for the history of Japanese populations is the ‘dual structure model’ [ 1 , 4 – 6 ]. This model assumes that there were two waves of human migrations from the Korean Peninsula or the Asian continent to the Japanese Archipelago.…”

Heterogeneous genetic make-up of Japanese house mice (Mus musculus) created by multiple independent introductions and spatio-temporally diverse hybridization processes

“…Suzuki et al, 2013) that MUS-1c was introduced to Japan in association with the historical migration of the Yayoi People via the Korean Peninsula, which is believed to have occurred 2,000-3,000 years ago (e.g. Hanihara, 1991;Jinam, Kanzawa-Kiriyama & Saitou, 2015;Nakagome et al, 2015).…”

Jomon genome sheds light on East Asian population history

“…This could be an influence of the Hokkaido Ainu who are likely to be direct descendants of the Jomon people. The ancestor of the Ainu people could have admixed with the Okhotsk people [54] who were morphologically close related to Ulchi and Nivkh currently inhabit in the the Primorye region [55][56][57] , which are supported by mtDNA [58,59] and genome-wide SNP data (Matsumae et al, unpublished data). The second explanation is that the track of the earliest-wave was erased in the inland but left over in the coastal region.…”