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Thread: 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[

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


    Abstract
    The deep population history of East Asia remains poorly understood due to a lack of ancient DNA data and sparse sampling of present-day people1,2. We report genome-wide data from 166 East Asians dating to 6000 BCE – 1000 CE 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 likely reflecting a Late Pleistocene coastal migration. We follow Holocene expansions from four regions. First, hunter-gatherers of Mongolia and the Amur River Basin have ancestry shared by Mongolic and Tungusic language speakers but do not carry West Liao River farmer ancestry contradicting theories that their expansion spread these proto-languages. Second, Yellow River Basin farmers at ~3000 BCE likely spread Sino-Tibetan languages as their ancestry dispersed both to Tibet where it forms up ~84% to some groups and to the Central Plain where it contributed ~59-84% to Han Chinese. Third, people from Taiwan ~1300 BCE to 800 CE derived ~75% ancestry from a lineage also common in modern Austronesian, Tai-Kadai and Austroasiatic speakers likely deriving from Yangtze River Valley farmers; ancient Taiwan people also derived ~25% ancestry from a northern lineage related to but different from Yellow River farmers implying an additional north-to-south expansion. Fourth, Yamnaya Steppe pastoralist ancestry arrived in western Mongolia after ~3000 BCE but was displaced by previously established lineages even while it persisted in western China as expected if it spread the ancestor of Tocharian Indo-European languages. Two later gene flows affected western Mongolia: after ~2000 BCE migrants with Yamnaya and European farmer ancestry, and episodic impacts of later groups with ancestry from Turan.



    Genomic insights into the origin of pre-historic populations in East Asia
    Integrating evidence from genetics and archaeology resarchers shed light on East Asia's population history

    FEBRUARY 22, 2021
    East Asia today harbours more than a fifth of the world’s population and some of the most deeply branching modern human lineages outside of Africa. The archaeological record attests that this region was also one of the earliest centers of animal and plant domestication. However, its genetic diversity and deep population history remain poorly understood relative to many other parts of the world. In a new study, a team of international researchers analyzes genome-wide data for 166 ancient individuals spanning 8,000 years and 46 present-day groups, and provides insights into the formation of East Asian populations.
    YFull: YF14620 (Dante Labs 2018)

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  3. #2
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    At the moment I'm unable to download the main paper. However the supplements are available.
    In particular, haplogroups are found in "Online Table 1 Newly reported ancient individuals.xlsx" of this zip file download.
    Supplementary Tables
    Last edited by pmokeefe; 02-22-2021 at 05:52 PM.
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    Quote Originally Posted by pmokeefe View Post
    At the moment I'm unable to download the main paper. However the supplements are available.
    In particular, haplogroups are found in "Online Table 1 Newly reported ancient individuals.xlsx" of this zip file download.
    Supplementary Tables
    It's not very different from the March 2020 preprint from what I've read with a rewritten focus on aDNA-language family links and a focus on the viability of the Transeurasian hypothesis with a couple populations renamed.

    The Japanese Jomon percentage was revised to ~8% and 92% West Liao with no Yellow River ancestry needed. And surprisingly,
    A surprising finding is our observation that ancient North Chinese individuals are more closely related to ancient individuals of our Taiwan time transect than to early Holocene hunter-gatherers on the mainland side of the Straits of Taiwan (Online Table 23). This suggests gene flow from Neolithic northern China into Taiwan, which we estimate at ~25% if we model it as derived from one of the two source lineages of Yellow River farmers (Figure 2). This ancestry does not fit as coming from Yellow River farmers themselves, suggesting a north-to-south migration not associated with expansions of these farmers. A speculative possibility is that this ancestry was carried by cultivators of foxtail millet which was domesticated in the north by ~8000 BCE42, and which in the south appears relatively early in the Taiwan Neolithic Tapenkeng culture (~3000-2500 BCE)
    Last edited by traject; 02-22-2021 at 06:01 PM.
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    It looks like there are no new samples since the preprint; actually I think there are a few less (low quality ones).

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    Quote Originally Posted by traject View Post
    It's not very different from the March 2020 preprint from what I've read with a rewritten focus on aDNA-language family links and a focus on the viability of the Transeurasian hypothesis with a couple populations renamed.

    The Japanese Jomon percentage was revised to ~8% and 92% West Liao with no Yellow River ancestry needed. And surprisingly,
    Sorry I can't seem to find the March 2020 preprint, link?
    EDIT:
    The Genomic Formation of Human Populations in East Asia

    I hate it when they change the title!
    Last edited by pmokeefe; 02-22-2021 at 06:09 PM.
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    Quote Originally Posted by pmokeefe View Post
    Sorry I can't seem to find the March 2020 preprint, link?
    This should be the preprint.
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    Target: RUS_Trans-Baikal_N:brn003
    Distance: 3.5436% / 0.03543608
    84.2 CHN_Amur_River_EN
    6.2 CHN_Yumin_N
    4.8 CHN_HMMH_MN
    4.8 RUS_Ust_Kyakhta

    Target: RUS_Trans-Baikal_N:brn008
    Distance: 3.3291% / 0.03329095
    91.6 CHN_Amur_River_EN
    8.4 RUS_Ust_Kyakhta

    Target: CHN_Amur_River_EN
    Distance: 5.8543% / 0.05854263
    100.0 CHN_HMMH_MN

    Target: RUS_Trans-Baikal_N:brn003
    Distance: 5.9875% / 0.05987545
    95.4 CHN_HMMH_MN
    4.6 RUS_Ust_Kyakhta

    Target: RUS_Trans-Baikal_N:brn008
    Distance: 6.7354% / 0.06735360
    91.4 CHN_HMMH_MN
    8.6 RUS_Ust_Kyakhta

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    Quote Originally Posted by VladimirTaraskin View Post
    Target: RUS_Trans-Baikal_N:brn003
    Distance: 3.5436% / 0.03543608
    84.2 CHN_Amur_River_EN
    6.2 CHN_Yumin_N
    4.8 CHN_HMMH_MN
    4.8 RUS_Ust_Kyakhta

    Target: RUS_Trans-Baikal_N:brn008
    Distance: 3.3291% / 0.03329095
    91.6 CHN_Amur_River_EN
    8.4 RUS_Ust_Kyakhta

    Target: CHN_Amur_River_EN
    Distance: 5.8543% / 0.05854263
    100.0 CHN_HMMH_MN

    Target: RUS_Trans-Baikal_N:brn003
    Distance: 5.9875% / 0.05987545
    95.4 CHN_HMMH_MN
    4.6 RUS_Ust_Kyakhta

    Target: RUS_Trans-Baikal_N:brn008
    Distance: 6.7354% / 0.06735360
    91.4 CHN_HMMH_MN
    8.6 RUS_Ust_Kyakhta
    What's this sample: 100.0 CHN_HMMH_MN?

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