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The genomic formation of First American ancestors in East and Northeast Asia

Chao Ning, Daniel Fernandes, Piya Changmai, Olga Flegontova, Eren Yüncü, Robert Maier, N. Ezgi Altınışık, Alexei S. Kassian, Johannes Krause, Carles Lalueza-Fox, Andrea Manica, Ben A. Potter, Martine Robbeets, Kendra Sirak, Veronika Siska, Edward J. Vajda, Leonid A. Vyazov, Ke Wang, Lixin Wang, Xiyan Wu, Xiaoming Xiao, Fan Zhang, David Reich, Stephan Schiffels, Ron Pinhasi, Yinqiu Cui, Pavel Flegontov
doi: https://doi.org/10.1101/2020.10.12.336628
Chao Ning
1Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
2School of Life Sciences, Jilin University, Changchun, China
3Department of Archaeogenetics and Eurasia3angle research group, Max Planck Institute for the Science of Human History, Jena, Germany
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Daniel Fernandes
4Department of Anthropology, University of Vienna, Vienna, Austria
5CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
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Piya Changmai
6Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
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Olga Flegontova
6Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
7Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice, Czechia
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Eren Yüncü
6Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
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Robert Maier
8Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
9Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
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N. Ezgi Altınışık
6Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
10Human-G Laboratory, Department of Anthropology, Hacettepe University, Ankara, Turkey
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Alexei S. Kassian
11Russian Presidential Academy of National Economy and Public Administration, Moscow, Russia
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Johannes Krause
3Department of Archaeogenetics and Eurasia3angle research group, Max Planck Institute for the Science of Human History, Jena, Germany
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Carles Lalueza-Fox
12Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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Andrea Manica
13Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Ben A. Potter
14Arctic Studies Centre, Liaocheng University, Liaocheng, China
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Martine Robbeets
3Department of Archaeogenetics and Eurasia3angle research group, Max Planck Institute for the Science of Human History, Jena, Germany
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Kendra Sirak
4Department of Anthropology, University of Vienna, Vienna, Austria
15Department of Anthropology, Emory University, Atlanta, United States of America
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Veronika Siska
13Department of Zoology, University of Cambridge, Cambridge, United Kingdom
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Edward J. Vajda
16Department of Modern and Classical Languages, Western Washington University, Bellingham, WA, United States of America
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Leonid A. Vyazov
17Kazan Federal University, Kazan, Tatarstan, Russia
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Ke Wang
3Department of Archaeogenetics and Eurasia3angle research group, Max Planck Institute for the Science of Human History, Jena, Germany
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Lixin Wang
2School of Life Sciences, Jilin University, Changchun, China
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Xiyan Wu
1Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
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Xiaoming Xiao
18Department of Archaeology, Liaoning University, Shenyang, China
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Fan Zhang
1Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
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David Reich
8Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
9Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
19Department of Genetics, Harvard Medical School, Boston, MA, United States of America
20Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, United States of America
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Stephan Schiffels
3Department of Archaeogenetics and Eurasia3angle research group, Max Planck Institute for the Science of Human History, Jena, Germany
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Ron Pinhasi
4Department of Anthropology, University of Vienna, Vienna, Austria
21School of Archaeology, and Earth Institute, University College Dublin, Belfield, Ireland
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  • For correspondence: pavel.flegontov@osu.cz pavel_flegontov@hms.harvard.edu cuiyq@jlu.edu.cn ron.pinhasi@univie.ac.at
Yinqiu Cui
1Research Center for Chinese Frontier Archaeology, Jilin University, Changchun, China
2School of Life Sciences, Jilin University, Changchun, China
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  • For correspondence: pavel.flegontov@osu.cz pavel_flegontov@hms.harvard.edu cuiyq@jlu.edu.cn ron.pinhasi@univie.ac.at
Pavel Flegontov
6Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
8Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, United States of America
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  • For correspondence: pavel.flegontov@osu.cz pavel_flegontov@hms.harvard.edu cuiyq@jlu.edu.cn ron.pinhasi@univie.ac.at
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Abstract

Upward Sun River 1, an individual from a unique burial of the Denali tradition in Alaska (11500 calBP), is considered a type representative of Ancient Beringians who split from other First Americans 22000–18000 calBP in Beringia. Using a new admixture graph model-comparison approach resistant to overfitting, we show that Ancient Beringians do not form the deepest American lineage, but instead harbor ancestry from a lineage more closely related to northern North Americans than to southern North Americans. Ancient Beringians also harbor substantial admixture from a lineage that did not contribute to other Native Americans: Amur River Basin populations represented by a newly reported site in northeastern China. Relying on these results, we propose a new model for the genomic formation of First American ancestors in Asia.

One Sentence Summary Ancient Beringians do not form the deepest American lineage, but harbor admixture from Amur River Basin populations.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 12, 2020.
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The genomic formation of First American ancestors in East and Northeast Asia
Chao Ning, Daniel Fernandes, Piya Changmai, Olga Flegontova, Eren Yüncü, Robert Maier, N. Ezgi Altınışık, Alexei S. Kassian, Johannes Krause, Carles Lalueza-Fox, Andrea Manica, Ben A. Potter, Martine Robbeets, Kendra Sirak, Veronika Siska, Edward J. Vajda, Leonid A. Vyazov, Ke Wang, Lixin Wang, Xiyan Wu, Xiaoming Xiao, Fan Zhang, David Reich, Stephan Schiffels, Ron Pinhasi, Yinqiu Cui, Pavel Flegontov
bioRxiv 2020.10.12.336628; doi: https://doi.org/10.1101/2020.10.12.336628
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The genomic formation of First American ancestors in East and Northeast Asia
Chao Ning, Daniel Fernandes, Piya Changmai, Olga Flegontova, Eren Yüncü, Robert Maier, N. Ezgi Altınışık, Alexei S. Kassian, Johannes Krause, Carles Lalueza-Fox, Andrea Manica, Ben A. Potter, Martine Robbeets, Kendra Sirak, Veronika Siska, Edward J. Vajda, Leonid A. Vyazov, Ke Wang, Lixin Wang, Xiyan Wu, Xiaoming Xiao, Fan Zhang, David Reich, Stephan Schiffels, Ron Pinhasi, Yinqiu Cui, Pavel Flegontov
bioRxiv 2020.10.12.336628; doi: https://doi.org/10.1101/2020.10.12.336628

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