Jomon genome sheds light on East Asian population history

Abstract

Anatomical modern humans reached East Asia by >40,000 years ago (kya). However, key questions still remain elusive with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of East Eurasia may shed light on the detail picture of peopling to East Eurasia. Here, we analyze the whole-genome sequence of a 2.5 kya individual (IK002) characterized with a typical Jomon culture that started in the Japanese archipelago >16 kya. The phylogenetic analyses support multiple waves of migration, with IK002 forming a lineage basal to the rest of the ancient/present-day East Eurasians examined, likely to represent some of the earliest-wave migrants who went north toward East Asia from Southeast Asia. Furthermore, IK002 has the extra genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration from Southeast Asia to the Japanese archipelago. This study highlight the power of ancient genomics with the isolated population to provide new insights into complex history in East Eurasia.

Fine‐scale genetic structure of Tujia and central Han Chinese revealing massive genetic admixture under language borrowing

“…Four Neolithic hunter–gatherer genomes from Devil's Gate (Siska et al, 2017) (~7.7 kybp) in northeastern China revealed large‐scale ancestry sharing with the modern Tungusic‐speaking populations, which suggested a genetic continuity in this region (Siska et al, 2017; Sikora et al, 2019). One 2.5‐kya‐Jomon ancient genome at the edge of East Asia further shed light on the shared ancestral component among indigenous Taiwan Ami and Atayal, Jomon ancients, DevilsGate, and other Tungusic people (McColl et al, 2018; Gakuhari et al, 2019). However, the population genetic history of the heartland of China is underrepresented.…”

Munda languages are father tongues, but Japanese and Korean are not

“…Much later, at the far shallower time depth of the Qín dynasty in the third century BC, this ethnicity spread southward from the Yellow River basin into southern China (Wen et al 2004), where this martial and male-biased historical spread during the cultural sinification of the region south of the Yangtze involved both the spread of language and the introduction of paternal lineages, as historically documented in the Chinese chronicles. The peopling of Japan Our original reconstruction of the peopling of Japan (van Driem 2014), based on earlier genetic research (Kivisild et al 2002;Tajima et al 2004;Tanaka et al 2004;Hammer et al 2006;Jin et al 2009;Karafet et al 2009), has been borne outand can now also be fleshed outby additional work on modern Japanese DNA (Mabuchi et al 2007;Nonaka et al 2007;Yamaguchi-Kabata et al 2008;Nohira et al 2008;Pen and Zhang 2012;Poznik et al 2016) and on ancient Japanese and East Asian DNA (Shinoda 2004;Xue et al 2006;Shinoda and Doi 2008;Adachi et al 2009Adachi et al , 2011Adachi et al , 2013Igawa et al 2009;Kim et al 2011;Jinam et al 2012Jinam et al , 2015Kanzawa-Kiriyama et al 2013;Trejaut et al 2014;Nakagome et al 2015;Yao et al 2017a, c;Adachi et al 2018;Watanabe et al 2019;Gakuhari et al 2019). The synoptic reconstruction presented here and in Figure 5 embodies a number of hypotheses, which may be corroborated or refuted by future ancient DNA findings, or perhaps just require minor reformulation.…”

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

“…To examine the detection accuracy of Jomon-derived SNPs, we calculated the Jomon allele score (JAS, see Methods section for details) for the Ikawazu (Mccoll et al 2018;Gakuhari et al 2020)/Funadomari(Kanzawa-Kiriyama et al 2019) Jomon individuals and mainland Japanese. If Jomonderived SNPs were properly detected by the AMI, the JAS of the Ikawazu or Funadomari Jomon were expected to be higher than those of mainland Japanese.…”

“…Most existing methods (Price et al 2009; Baran et al 2012;Churchhouse and Marchini 2013;Guan 2014;Hui et al 2017) for estimating the local ancestry of genomes using the LD state require genome information of ancestral populations or of modern populations as proxies of ancestral populations. In the Japanese population, only a few Jomon individuals (Kanzawa-Kiriyama et al 2017;Mccoll et al 2018;Kanzawa-Kiriyama et al 2019;Gakuhari et al 2020) have been sequenced so far. Furthermore, the sequence depths of these samples are low, except for the Funadomari Jomon(Kanzawa-Kiriyama et al 2019) people excavated from Rebun Island in Hokkaido, making it difficult to obtain sufficient genome information to accurately estimate the local ancestry of modern Japanese (i.e., the genomes of many Jomon individuals are required to perform highly accurate studies).…”

“…For the verification of Jomon-derived SNPs based on the whole genome sequence data, the "Jomon allele score" (JAS) was calculated for the Ikawazu (Mccoll et al 2018;Gakuhari et al 2020) and Funadomari(Kanzawa-Kiriyama et al 2019) Jomon, as well as for 104 individuals from the 1KG JPT.…”