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Genomic insights into the formation of human populations in East Asia.

ABSTRACT: The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people^1,2. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during the Late Pleistocene epoch. We also follow expansions during the subsequent Holocene epoch from four regions. First, hunter-gatherers from Mongolia and the Amur River Basin have ancestry shared by individuals who speak Mongolic and Tungusic languages, but do not carry ancestry characteristic of farmers from the West Liao River region (around 3000 BC), which contradicts theories that the expansion of these farmers spread the Mongolic and Tungusic proto-languages. Second, farmers from the Yellow River Basin (around 3000 BC) probably spread Sino-Tibetan languages, as their ancestry dispersed both to Tibet-where it forms approximately 84% of the gene pool in some groups-and to the Central Plain, where it has contributed around 59-84% to modern Han Chinese groups. Third, people from Taiwan from around 1300 BC to AD 800 derived approximately 75% of their ancestry from a lineage that is widespread in modern individuals who speak Austronesian, Tai-Kadai and Austroasiatic languages, and that we hypothesize derives from farmers of the Yangtze River Valley. Ancient people from Taiwan also derived about 25% of their ancestry from a northern lineage that is related to, but different from, farmers of the Yellow River Basin, which suggests an additional north-to-south expansion. Fourth, ancestry from Yamnaya Steppe pastoralists arrived in western Mongolia after around 3000 BC but was displaced by previously established lineages even while it persisted in western China, as would be expected if this ancestry was associated with the spread of proto-Tocharian Indo-European languages. Two later gene flows affected western Mongolia: migrants after around 2000 BC with Yamnaya and European farmer ancestry, and episodic influences of later groups with ancestry from Turan.

SUBMITTER: Wang CC

PROVIDER: S-EPMC7993749 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Genomic insights into the formation of human populations in East Asia.

Wang Chuan-Chao CC Yeh Hui-Yuan HY Popov Alexander N AN Zhang Hu-Qin HQ Matsumura Hirofumi H Sirak Kendra K Cheronet Olivia O Kovalev Alexey A Rohland Nadin N Kim Alexander M AM Mallick Swapan S Bernardos Rebecca R Tumen Dashtseveg D Zhao Jing J Liu Yi-Chang YC Liu Jiun-Yu JY Mah Matthew M Wang Ke K Zhang Zhao Z Adamski Nicole N Broomandkhoshbacht Nasreen N Callan Kimberly K Candilio Francesca F Carlson Kellie Sara Duffett KSD Culleton Brendan J BJ Eccles Laurie L Freilich Suzanne S Keating Denise D Lawson Ann Marie AM Mandl Kirsten K Michel Megan M Oppenheimer Jonas J Özdoğan Kadir Toykan KT Stewardson Kristin K Wen Shaoqing S Yan Shi S Zalzala Fatma F Chuang Richard R Huang Ching-Jung CJ Looh Hana H Shiung Chung-Ching CC Nikitin Yuri G YG Tabarev Andrei V AV Tishkin Alexey A AA Lin Song S Sun Zhou-Yong ZY Wu Xiao-Ming XM Yang Tie-Lin TL Hu Xi X Chen Liang L Du Hua H Bayarsaikhan Jamsranjav J Mijiddorj Enkhbayar E Erdenebaatar Diimaajav D Iderkhangai Tumur-Ochir TO Myagmar Erdene E Kanzawa-Kiriyama Hideaki H Nishino Masato M Shinoda Ken-Ichi KI Shubina Olga A OA Guo Jianxin J Cai Wangwei W Deng Qiongying Q Kang Longli L Li Dawei D Li Dongna D Lin Rong R Nini Shrestha Rukesh R Wang Ling-Xiang LX Wei Lanhai L Xie Guangmao G Yao Hongbing H Zhang Manfei M He Guanglin G Yang Xiaomin X Hu Rong R Robbeets Martine M Schiffels Stephan S Kennett Douglas J DJ Jin Li L Li Hui H Krause Johannes J Pinhasi Ron R Reich David D

Nature 20210222 7850

The deep population history of East Asia remains poorly understood owing to a lack of ancient DNA data and sparse sampling of present-day people<sup>1,2</sup>. Here we report genome-wide data from 166 East Asian individuals dating to between 6000 BC and AD 1000 and 46 present-day groups. Hunter-gatherers from Japan, the Amur River Basin, and people of Neolithic and Iron Age Taiwan and the Tibetan Plateau are linked by a deeply splitting lineage that probably reflects a coastal migration during t ...[more]

PMID: 33618348

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Project description:As a major part of the modern Trans-Eurasian or Altaic language family, most of the Mongolic and Tungusic languages were mainly spoken in northern China, Mongolia, and southern Siberia, but some were also found in southern China. Previous genetic surveys only focused on the dissection of genetic structure of northern Altaic-speaking populations; however, the ancestral origin and genomic diversification of Mongolic and Tungusic-speaking populations from southwestern East Asia remain poorly understood because of the paucity of high-density sampling and genome-wide data. Here, we generated genome-wide data at nearly 700,000 single-nucleotide polymorphisms (SNPs) in 26 Mongolians and 55 Manchus collected from Guizhou province in southwestern China. We applied principal component analysis (PCA), ADMIXTURE, f statistics, qpWave/qpAdm analysis, qpGraph, TreeMix, Fst, and ALDER to infer the fine-scale population genetic structure and admixture history. We found significant genetic differentiation between northern and southern Mongolic and Tungusic speakers, as one specific genetic cline of Manchu and Mongolian was identified in Guizhou province. Further results from ADMIXTURE and f statistics showed that the studied Guizhou Mongolians and Manchus had a strong genetic affinity with southern East Asians, especially for inland southern East Asians. The qpAdm-based estimates of ancestry admixture proportion demonstrated that Guizhou Mongolians and Manchus people could be modeled as the admixtures of one northern ancestry related to northern Tungusic/Mongolic speakers or Yellow River farmers and one southern ancestry associated with Austronesian, Tai-Kadai, and Austroasiatic speakers. The qpGraph-based phylogeny and neighbor-joining tree further confirmed that Guizhou Manchus and Mongolians derived approximately half of the ancestry from their northern ancestors and the other half from southern Indigenous East Asians. The estimated admixture time ranged from 600 to 1,000 years ago, which further confirmed the admixture events were mediated via the Mongolians Empire expansion during the formation of the Yuan dynasty.

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Genomic insights into the formation of human populations in East Asia.

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Genomic insights into the formation of human populations in East Asia.

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