The Genomic Formation of Human Populations in East Asia
Authors: Wang Chuan-Chao , Yeh Hui-Yuan , Popov Alexander N , Zhang Hu-Qin , Matsumura Hirofumi , Sirak Kendra , Cheronet Olivia , Kovalev Alexey , Rohland Nadin , Kim Alexander M. , Bernardos Rebecca , Tumen Dashtseveg , Zhao Jing , Liu Yi-Chang , Liu Jiun-Yu , Mah Matthew , Mallick Swapan , Wang Ke , Zhang Zhao , Adamski Nicole , Broomandkhoshbacht Nasreen , Callan Kimberly , Culleton Brendan J. , Eccles Laurie , Lawson Ann Marie , Michel Megan , Oppenheimer Jonas , Stewardson Kristin , Wen Shaoqing , Yan Shi , Zalzala Fatma , Chuang Richard , Huang Ching-Jung , Shiung Chung-Ching , Nikitin Yuri G. , Tabarev Andrei V. , Tishkin Alexey A. , Lin Song , Sun Zhou-Yong , Wu Xiao-Ming , Yang Tie-Lin , Hu Xi , Chen Liang , Du Hua , Bayarsaikhan Jamsranjav , Mijiddorj Enkhbayar , Erdenebaatar Diimaajav , Iderkhangai Tumur-Ochir , Myagmar Erdene , Kanzawa-Kiriyama Hideaki , Nishino Msato , Shinoda Ken-ichi , Shubina Olga A. , Guo Jianxin , Deng Qiongying , Kang Longli , Li Dawei , Li Dongna , Lin Rong , Cai Wangwei , Shrestha Rukesh , Wang Ling-Xiang , Wei Lanhai , Xie Guangmao , Yao Hongbing , Zhang Manfei , He Guanglin , Yang Xiaomin , Hu Rong , Robbeets Martine , Schiffels Stephan , Kennett Douglas J. , Jin Li , Li Hui , Krause Johannes , Pinhasi Ron , Reich David 
Published: March 2020

The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people. We report genome-wide data from 191 individuals from Mongolia, northern China, Taiwan, the Amur River Basin and Japan dating to 6000 BCE – 1000 CE, many from contexts never previously analyzed with ancient DNA. We also report 383 present-day individuals from 46 groups mostly from the Tibetan Plateau and southern China. We document how 6000-3600 BCE people of Mongolia and the Amur River Basin were from populations that expanded over Northeast Asia, likely dispersing the ancestors of Mongolic and Tungusic languages. In a time transect of 89 Mongolians, we reveal how Yamnaya steppe pastoralist spread from the west by 3300-2900 BCE in association with the Afanasievo culture, although we also document a boy buried in an Afanasievo barrow with ancestry entirely from local Mongolian hunter-gatherers, representing a unique case of someone of entirely non-Yamnaya ancestry interred in this way. The second spread of Yamnaya-derived ancestry came via groups that harbored about a third of their ancestry from European farmers, which nearly completely displaced unmixed Yamnaya-related lineages in Mongolia in the second millennium BCE, but did not replace Afanasievo lineages in western China where Afanasievo ancestry persisted, plausibly acting as the source of the early-splitting Tocharian branch of Indo-European languages. Analyzing 20 Yellow River Basin farmers dating to ∼3000 BCE, we document a population that was a plausible vector for the spread of Sino-Tibetan languages both to the Tibetan Plateau and to the central plain where they mixed with southern agriculturalists to form the ancestors of Han Chinese. We show that the individuals in a time transect of 52 ancient Taiwan individuals spanning at least 1400 BCE to 600 CE were consistent with being nearly direct descendants of Yangtze Valley first farmers who likely spread Austronesian, Tai-Kadai and Austroasiatic languages across Southeast and South Asia and mixing with the people they encountered, contributing to a four-fold reduction of genetic differentiation during the emergence of complex societies. We finally report data from Jomon hunter-gatherers from Japan who harbored one of the earliest splitting branches of East Eurasian variation, and show an affinity among Jomon, Amur River Basin, ancient Taiwan, and Austronesian-speakers, as expected for ancestry if they all had contributions from a Late Pleistocene coastal route migration to East Asia.