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The Genomic Formation of South and Central Asia

View ORCID ProfileVagheesh M Narasimhan, Nick J Patterson, Priya Moorjani, Iosif Lazaridis, Lipson Mark, Swapan Mallick, Nadin Rohland, Rebecca Bernardos, Alexander M Kim, Nathan Nakatsuka, Inigo Olalde, Alfredo Coppa, James Mallory, Vyacheslav Moiseyev, Janet Monge, Luca M Olivieri, Nicole Adamski, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Brendan J Culleton, Matthew Ferry, Daniel Fernandes, Beatriz Gamarra, Daniel Gaudio, Mateja Hajdinjak, Eadaoin Harney, Thomas K Harper, Denise Keating, Ann-Marie Lawson, Megan Michel, Mario Novak, Jonas Oppenheimer, Niraj Rai, Kendra Sirak, Viviane Slon, Kristin Stewardson, Zhao Zhang, Gaziz Akhatov, Anatoly N Bagashev, Baurzhan Baitanayev, Gian Luca Bonora, Tatiana Chikisheva, Anatoly Derevianko, Enshin Dmitry, Katerina Douka, Nadezhda Dubova, Andrey Epimakhov, Suzanne Freilich, Dorian Fuller, Alexander Goryachev, Andrey Gromov, Bryan Hanks, Margaret Judd, Erlan Kazizov, Aleksander Khokhlov, Egor Kitov, Elena Kupriyanova, Pavel Kuznetsov, Donata Luiselli, Farhad Maksudov, Chris Meiklejohn, Deborah C Merrett, Roberto Micheli, Oleg Mochalov, Zahir Muhammed, Samridin Mustafakulov, Ayushi Nayak, Rykun M Petrovna, Davide Pettner, Richard Potts, Dmitry Razhev, Stefania Sarno, Kulyan Sikhymbaevae, Sergey M Slepchenko, Nadezhda Stepanova, Svetlana Svyatko, Sergey Vasilyev, Massimo Vidale, Dima Voyakin, Antonina Yermolayeva, Alisa Zubova, Vasant S Shinde, Carles Lalueza-Fox, Matthias Meyer, David Anthony, Nicole Boivin, Kumarasmy Thangaraj, Douglas Kennett, Michael Frachetti, Ron Pinhasi, David Reich
doi: https://doi.org/10.1101/292581
Vagheesh M Narasimhan
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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  • ORCID record for Vagheesh M Narasimhan
Nick J Patterson
Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA;
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  • For correspondence: nickp@broadinstitute.org
Priya Moorjani
Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA;
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Iosif Lazaridis
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Lipson Mark
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Swapan Mallick
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Nadin Rohland
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Rebecca Bernardos
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Alexander M Kim
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Nathan Nakatsuka
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Inigo Olalde
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Alfredo Coppa
Dipartimento di Biologia Ambientale, Sapienza Universita di Roma, Rome 00185, Italy;
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James Mallory
School of Natural and Built Environment, Queens University Belfast, Belfast BT7 1NN, N Ireland;
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Vyacheslav Moiseyev
Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Science, St. Petersburg;
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Janet Monge
University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA;
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Luca M Olivieri
ISMEO Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan;
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Nicole Adamski
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Nasreen Broomandkhoshbacht
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Francesca Candilio
University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA;
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Olivia Cheronet
Earth Institute, University College Dublin, Dublin 4, Ireland;
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Brendan J Culleton
Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA;
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Matthew Ferry
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Daniel Fernandes
Earth Institute, University College Dublin, Dublin 4, Ireland;
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Beatriz Gamarra
Earth Institute, University College Dublin, Dublin 4, Ireland;
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Daniel Gaudio
Earth Institute, University College Dublin, Dublin 4, Ireland;
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Mateja Hajdinjak
Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany;
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Eadaoin Harney
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Thomas K Harper
Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA;
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Denise Keating
Earth Institute, University College Dublin, Dublin 4, Ireland;
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Ann-Marie Lawson
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Megan Michel
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Mario Novak
Earth Institute, University College Dublin, Dublin 4, Ireland;
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Jonas Oppenheimer
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Niraj Rai
CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India;
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Kendra Sirak
Earth Institute, University College Dublin, Dublin 4, Ireland;
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Viviane Slon
Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany;
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Kristin Stewardson
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Zhao Zhang
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Gaziz Akhatov
Institute of Archaeology A.Kh. Margulan, Almaty 050010, Kazakhstan;
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Anatoly N Bagashev
Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen, Russia;
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Baurzhan Baitanayev
Institute of Archaeology A.Kh. Margulan, Almaty 050010, Kazakhstan;
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Gian Luca Bonora
Archaeology of Asia Department, ISMEO, Rome RM00186, Italy;
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Tatiana Chikisheva
Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk;
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Anatoly Derevianko
Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk;
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Enshin Dmitry
Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen, Russia;
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Katerina Douka
Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany;
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Nadezhda Dubova
Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia;
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Andrey Epimakhov
Institute of History and Archaeology, Ural Branch RAS, Yekaterinburg 620990, Russia;
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Suzanne Freilich
Department of Anthropology, University of Vienna, 1090 Vienna, Austria;
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Dorian Fuller
Institute of Archaeology, University College London, London WC1H 0PY, UK;
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Alexander Goryachev
Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen Russia;
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Andrey Gromov
Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Science, St Petersburg;
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Bryan Hanks
University of Pittsburgh, Department of Anthropology, Pittsburgh, PA 15260, USA;
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Margaret Judd
University of Pittsburgh, Department of Anthropology, Pittsburgh, PA 15260, USA;
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Erlan Kazizov
Institute of Archaeology A.Kh. Margulan, Almaty 050010, Kazakhstan;
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Aleksander Khokhlov
Samara State University of Social Sciences and Education, Samara 443099, Russia;
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Egor Kitov
Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia;
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Elena Kupriyanova
Scientific and Educational Center of Study on the Problem of Nature and Man, Chelyabinsk, Russia;
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Pavel Kuznetsov
Samara State University of Social Sciences and Education, Samara 443099, Russia;
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Donata Luiselli
Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy;
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Farhad Maksudov
Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan;
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Chris Meiklejohn
Department of Anthropology, University of Winnipeg, Winnipeg, MB, R3B 2E9, Canada;
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Deborah C Merrett
Department of Archaeology, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada;
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Roberto Micheli
ISMEO Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan;
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Oleg Mochalov
Samara State University of Social Sciences and Education, Samara 443099, Russia;
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Zahir Muhammed
Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany;
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Samridin Mustafakulov
Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan;
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Ayushi Nayak
Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany;
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Rykun M Petrovna
Tomsk State National Research University, Tomsk 634050, Russia;
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Davide Pettner
Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy;
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Richard Potts
Human Origins Program, National Museum of Natural History, Smithsonian Institution, Wash. DC., USA;
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Dmitry Razhev
Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen, Russia;
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Stefania Sarno
Department of Biological, Geological and Environmental Sciences, University of Bologna, Italy;
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Kulyan Sikhymbaevae
Central State Museum Republic of Kazakhstan, Samal-1 Microdistrict, Almaty 050010, Kazakhstan;
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Sergey M Slepchenko
Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen, Russia;
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Nadezhda Stepanova
Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk;
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Svetlana Svyatko
School of Natural and Built Environment, Queens University Belfast, Belfast BT7 1NN, N Ireland;
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Sergey Vasilyev
Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia;
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Massimo Vidale
ISMEO Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan;
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Dima Voyakin
Institute of Archaeology A.Kh. Margulan, Almaty 050010, Kazakhstan;
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Antonina Yermolayeva
Institute of Archaeology A.Kh. Margulan, Almaty 050010, Kazakhstan;
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Alisa Zubova
Peter the Great Museum of Anthropology and Ethnography, Russian Academy of Science, St. Petersburg;
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Vasant S Shinde
Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India;
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Carles Lalueza-Fox
Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain;
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Matthias Meyer
Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany;
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David Anthony
Anthropology Department, Hartwick College, Oneonta, New York 13820, USA;
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Nicole Boivin
Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany;
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Kumarasmy Thangaraj
CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India;
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Douglas Kennett
Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA;
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Michael Frachetti
Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63112, USA
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Ron Pinhasi
Earth Institute, University College Dublin, Dublin 4, Ireland;
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David Reich
Department of Genetics, Harvard Medical School, Boston, MA 02115, USA;
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Abstract

The genetic formation of Central and South Asian populations has been unclear because of an absence of ancient DNA. To address this gap, we generated genome-wide data from 362 ancient individuals, including the first from eastern Iran, Turan (Uzbekistan, Turkmenistan, and Tajikistan), Bronze Age Kazakhstan, and South Asia. Our data reveal a complex set of genetic sources that ultimately combined to form the ancestry of South Asians today. We document a southward spread of genetic ancestry from the Eurasian Steppe, correlating with the archaeologically known expansion of pastoralist sites from the Steppe to Turan in the Middle Bronze Age (2300-1500 BCE). These Steppe communities mixed genetically with peoples of the Bactria Margiana Archaeological Complex (BMAC) whom they encountered in Turan (primarily descendants of earlier agriculturalists of Iran), but there is no evidence that the main BMAC population contributed genetically to later South Asians. Instead, Steppe communities integrated farther south throughout the 2nd millennium BCE, and we show that they mixed with a more southern population that we document at multiple sites as outlier individuals exhibiting a distinctive mixture of ancestry related to Iranian agriculturalists and South Asian hunter-gathers. We call this group Indus Periphery because they were found at sites in cultural contact with the Indus Valley Civilization (IVC) and along its northern fringe, and also because they were genetically similar to post-IVC groups in the Swat Valley of Pakistan. By co-analyzing ancient DNA and genomic data from diverse present-day South Asians, we show that Indus Periphery-related people are the single most important source of ancestry in South Asia — consistent with the idea that the Indus Periphery individuals are providing us with the first direct look at the ancestry of peoples of the IVC — and we develop a model for the formation of present-day South Asians in terms of the temporally and geographically proximate sources of Indus Periphery-related, Steppe, and local South Asian hunter-gatherer-related ancestry. Our results show how ancestry from the Steppe genetically linked Europe and South Asia in the Bronze Age, and identifies the populations that almost certainly were responsible for spreading Indo-European languages across much of Eurasia.

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The Genomic Formation of South and Central Asia
Vagheesh M Narasimhan, Nick J Patterson, Priya Moorjani, Iosif Lazaridis, Lipson Mark, Swapan Mallick, Nadin Rohland, Rebecca Bernardos, Alexander M Kim, Nathan Nakatsuka, Inigo Olalde, Alfredo Coppa, James Mallory, Vyacheslav Moiseyev, Janet Monge, Luca M Olivieri, Nicole Adamski, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Brendan J Culleton, Matthew Ferry, Daniel Fernandes, Beatriz Gamarra, Daniel Gaudio, Mateja Hajdinjak, Eadaoin Harney, Thomas K Harper, Denise Keating, Ann-Marie Lawson, Megan Michel, Mario Novak, Jonas Oppenheimer, Niraj Rai, Kendra Sirak, Viviane Slon, Kristin Stewardson, Zhao Zhang, Gaziz Akhatov, Anatoly N Bagashev, Baurzhan Baitanayev, Gian Luca Bonora, Tatiana Chikisheva, Anatoly Derevianko, Enshin Dmitry, Katerina Douka, Nadezhda Dubova, Andrey Epimakhov, Suzanne Freilich, Dorian Fuller, Alexander Goryachev, Andrey Gromov, Bryan Hanks, Margaret Judd, Erlan Kazizov, Aleksander Khokhlov, Egor Kitov, Elena Kupriyanova, Pavel Kuznetsov, Donata Luiselli, Farhad Maksudov, Chris Meiklejohn, Deborah C Merrett, Roberto Micheli, Oleg Mochalov, Zahir Muhammed, Samridin Mustafakulov, Ayushi Nayak, Rykun M Petrovna, Davide Pettner, Richard Potts, Dmitry Razhev, Stefania Sarno, Kulyan Sikhymbaevae, Sergey M Slepchenko, Nadezhda Stepanova, Svetlana Svyatko, Sergey Vasilyev, Massimo Vidale, Dima Voyakin, Antonina Yermolayeva, Alisa Zubova, Vasant S Shinde, Carles Lalueza-Fox, Matthias Meyer, David Anthony, Nicole Boivin, Kumarasmy Thangaraj, Douglas Kennett, Michael Frachetti, Ron Pinhasi, David Reich
bioRxiv 292581; doi: https://doi.org/10.1101/292581
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The Genomic Formation of South and Central Asia
Vagheesh M Narasimhan, Nick J Patterson, Priya Moorjani, Iosif Lazaridis, Lipson Mark, Swapan Mallick, Nadin Rohland, Rebecca Bernardos, Alexander M Kim, Nathan Nakatsuka, Inigo Olalde, Alfredo Coppa, James Mallory, Vyacheslav Moiseyev, Janet Monge, Luca M Olivieri, Nicole Adamski, Nasreen Broomandkhoshbacht, Francesca Candilio, Olivia Cheronet, Brendan J Culleton, Matthew Ferry, Daniel Fernandes, Beatriz Gamarra, Daniel Gaudio, Mateja Hajdinjak, Eadaoin Harney, Thomas K Harper, Denise Keating, Ann-Marie Lawson, Megan Michel, Mario Novak, Jonas Oppenheimer, Niraj Rai, Kendra Sirak, Viviane Slon, Kristin Stewardson, Zhao Zhang, Gaziz Akhatov, Anatoly N Bagashev, Baurzhan Baitanayev, Gian Luca Bonora, Tatiana Chikisheva, Anatoly Derevianko, Enshin Dmitry, Katerina Douka, Nadezhda Dubova, Andrey Epimakhov, Suzanne Freilich, Dorian Fuller, Alexander Goryachev, Andrey Gromov, Bryan Hanks, Margaret Judd, Erlan Kazizov, Aleksander Khokhlov, Egor Kitov, Elena Kupriyanova, Pavel Kuznetsov, Donata Luiselli, Farhad Maksudov, Chris Meiklejohn, Deborah C Merrett, Roberto Micheli, Oleg Mochalov, Zahir Muhammed, Samridin Mustafakulov, Ayushi Nayak, Rykun M Petrovna, Davide Pettner, Richard Potts, Dmitry Razhev, Stefania Sarno, Kulyan Sikhymbaevae, Sergey M Slepchenko, Nadezhda Stepanova, Svetlana Svyatko, Sergey Vasilyev, Massimo Vidale, Dima Voyakin, Antonina Yermolayeva, Alisa Zubova, Vasant S Shinde, Carles Lalueza-Fox, Matthias Meyer, David Anthony, Nicole Boivin, Kumarasmy Thangaraj, Douglas Kennett, Michael Frachetti, Ron Pinhasi, David Reich
bioRxiv 292581; doi: https://doi.org/10.1101/292581

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