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Paleo-Eskimo genetic legacy across North America

Pavel Flegontov, N. Ezgi Altinişik, Piya Changmai, Nadin Rohland, Swapan Mallick, Deborah A. Bolnick, Francesca Candilio, Olga Flegontova, Choongwon Jeong, Thomas K. Harper, Denise Keating, Douglas J. Kennett, Alexander M. Kim, Thiseas C. Lamnidis, Iñigo Olalde, Jennifer Raff, Robert A. Sattler, Pontus Skoglund, Edward J. Vajda, Sergey Vasilyev, Elizaveta Veselovskaya, M. Geoffrey Hayes, Dennis H. O’Rourke, Ron Pinhasi, Johannes Krause, David Reich, Stephan Schiffels
doi: https://doi.org/10.1101/203018
Pavel Flegontov
1Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 71000, Czech Republic
2A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia
3Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice 37005, Czech Republic
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N. Ezgi Altinişik
1Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 71000, Czech Republic
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Piya Changmai
1Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava 71000, Czech Republic
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Nadin Rohland
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Swapan Mallick
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
5Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
6Broad Institute of MIT and Harvard, Cambridge, MA 02412, USA
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Deborah A. Bolnick
7Department of Anthropology and Population Research Center, University of Texas at Austin, Austin, TX 78712, USA
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Francesca Candilio
8Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
9Soprintendenza Archeologia belle arti e paesaggio per la città metropolitana di Cagliari e per le province di Oristano e Sud Sardegna, Cagliari 9124, Italy
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Olga Flegontova
3Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budĕjovice 37005, Czech Republic
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Choongwon Jeong
10Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
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Thomas K. Harper
11Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
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Denise Keating
8Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
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Douglas J. Kennett
11Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
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Alexander M. Kim
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Thiseas C. Lamnidis
10Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
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Iñigo Olalde
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Jennifer Raff
12Department of Anthropology, University of Kansas, Lawrence, KS 66045, USA
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Robert A. Sattler
13Tanana Chiefs Conference, Fairbanks, AK 99701, USA
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Pontus Skoglund
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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Edward J. Vajda
14Department of Modern and Classical Languages, Western Washington University, Bellingham, WA 98225, USA
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Sergey Vasilyev
15Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119017, Russia
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Elizaveta Veselovskaya
15Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119017, Russia
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M. Geoffrey Hayes
16Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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Dennis H. O’Rourke
12Department of Anthropology, University of Kansas, Lawrence, KS 66045, USA
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Ron Pinhasi
8Earth Institute and School of Archaeology, University College Dublin, Dublin 4, Ireland
17Department of Anthropology, University of Vienna, Vienna 1090, Austria
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Johannes Krause
10Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
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David Reich
4Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
5Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
6Broad Institute of MIT and Harvard, Cambridge, MA 02412, USA
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Stephan Schiffels
10Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
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Abstract

Paleo-Eskimos were the first people to settle vast regions of the American Arctic around 5,000 years ago, and were subsequently joined and largely displaced around 1,000 years ago by ancestors of the present-day Inuit and Yupik. The genetic relationship between Paleo-Eskimos and Native American populations remains uncertain. We analyze ancient and present-day genome-wide data from the Americas and Siberia, including new data from Alaskan Iñupiat and West Siberian populations, and the first genome-wide DNA from ancient Aleutian Islanders, ancient northern Athabaskans, and a 4,250-year-old individual of the Chukotkan Ust'-Belaya culture. Employing new methods based on rare allele and haplotype sharing as well as established methods based on allele frequency correlations, we show that Paleo-Eskimo ancestry is widespread among populations who speak Na-Dene and Eskimo-Aleut languages. Using phylogenetic modelling with allele frequency correlations and rare variation, we present a comprehensive model for the complex peopling of North America.

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Posted October 13, 2017.
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Paleo-Eskimo genetic legacy across North America
Pavel Flegontov, N. Ezgi Altinişik, Piya Changmai, Nadin Rohland, Swapan Mallick, Deborah A. Bolnick, Francesca Candilio, Olga Flegontova, Choongwon Jeong, Thomas K. Harper, Denise Keating, Douglas J. Kennett, Alexander M. Kim, Thiseas C. Lamnidis, Iñigo Olalde, Jennifer Raff, Robert A. Sattler, Pontus Skoglund, Edward J. Vajda, Sergey Vasilyev, Elizaveta Veselovskaya, M. Geoffrey Hayes, Dennis H. O’Rourke, Ron Pinhasi, Johannes Krause, David Reich, Stephan Schiffels
bioRxiv 203018; doi: https://doi.org/10.1101/203018
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Paleo-Eskimo genetic legacy across North America
Pavel Flegontov, N. Ezgi Altinişik, Piya Changmai, Nadin Rohland, Swapan Mallick, Deborah A. Bolnick, Francesca Candilio, Olga Flegontova, Choongwon Jeong, Thomas K. Harper, Denise Keating, Douglas J. Kennett, Alexander M. Kim, Thiseas C. Lamnidis, Iñigo Olalde, Jennifer Raff, Robert A. Sattler, Pontus Skoglund, Edward J. Vajda, Sergey Vasilyev, Elizaveta Veselovskaya, M. Geoffrey Hayes, Dennis H. O’Rourke, Ron Pinhasi, Johannes Krause, David Reich, Stephan Schiffels
bioRxiv 203018; doi: https://doi.org/10.1101/203018

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