.2019 Sep 6;365(6457):eaat7487.

doi: 10.1126/science.aat7487.

The formation of human populations in South and Central Asia

Vagheesh M Narasimhan¹, Nick Patterson^{2 3}, Priya Moorjani^{4 5}, Nadin Rohland^{6 7}, Rebecca Bernardos⁶, Swapan Mallick^{6 7 8}, Iosif Lazaridis⁶, Nathan Nakatsuka^{6 9}, Iñigo Olalde⁶, Mark Lipson⁶, Alexander M Kim^{6 10}, Luca M Olivieri¹¹, Alfredo Coppa¹², Massimo Vidale^{11 13}, James Mallory¹⁴, Vyacheslav Moiseyev¹⁵, Egor Kitov^{16 17 18}, Janet Monge¹⁹, Nicole Adamski^{6 8}, Neel Alex²⁰, Nasreen Broomandkhoshbacht^{6 8}, Francesca Candilio^{21 22}, Kimberly Callan^{6 8}, Olivia Cheronet^{21 23 24}, Brendan J Culleton²⁵, Matthew Ferry^{6 8}, Daniel Fernandes^{21 23 24 26}, Suzanne Freilich²⁴, Beatriz Gamarra^{21 23 27}, Daniel Gaudio^{21 23}, Mateja Hajdinjak²⁸, Éadaoin Harney^{6 8 29}, Thomas K Harper³⁰, Denise Keating²¹, Ann Marie Lawson^{6 8}, Matthew Mah^{6 7 8}, Kirsten Mandl²⁴, Megan Michel^{6 8}, Mario Novak^{21 31}, Jonas Oppenheimer^{6 8}, Niraj Rai^{32 33}, Kendra Sirak^{6 21 34}, Viviane Slon²⁸, Kristin Stewardson^{6 8}, Fatma Zalzala^{6 8}, Zhao Zhang⁶, Gaziz Akhatov¹⁷, Anatoly N Bagashev³⁵, Alessandra Bagnera¹¹, Bauryzhan Baitanayev¹⁷, Julio Bendezu-Sarmiento³⁶, Arman A Bissembaev^{17 37}, Gian Luca Bonora³⁸, Temirlan T Chargynov³⁹, Tatiana Chikisheva⁴⁰, Petr K Dashkovskiy⁴¹, Anatoly Derevianko⁴⁰, Miroslav Dobeš⁴², Katerina Douka^{43 44}, Nadezhda Dubova¹⁶, Meiram N Duisengali³⁷, Dmitry Enshin³⁵, Andrey Epimakhov^{45 46}, Alexey V Fribus⁴⁷, Dorian Fuller^{48 49}, Alexander Goryachev³⁵, Andrey Gromov¹⁵, Sergey P Grushin⁵⁰, Bryan Hanks⁵¹, Margaret Judd⁵¹, Erlan Kazizov¹⁷, Aleksander Khokhlov⁵², Aleksander P Krygin⁵³, Elena Kupriyanova⁵⁴, Pavel Kuznetsov⁵², Donata Luiselli⁵⁵, Farhod Maksudov⁵⁶, Aslan M Mamedov⁵⁷, Talgat B Mamirov¹⁷, Christopher Meiklejohn⁵⁸, Deborah C Merrett⁵⁹, Roberto Micheli^{11 60}, Oleg Mochalov⁵², Samariddin Mustafokulov^{56 61}, Ayushi Nayak⁴³, Davide Pettener⁶², Richard Potts⁶³, Dmitry Razhev³⁵, Marina Rykun⁶⁴, Stefania Sarno⁶², Tatyana M Savenkova⁶⁵, Kulyan Sikhymbaeva⁶⁶, Sergey M Slepchenko³⁵, Oroz A Soltobaev³⁹, Nadezhda Stepanova⁴⁰, Svetlana Svyatko^{15 67}, Kubatbek Tabaldiev⁶⁸, Maria Teschler-Nicola^{24 69}, Alexey A Tishkin⁷⁰, Vitaly V Tkachev⁷¹, Sergey Vasilyev^{16 72}, Petr Velemínský⁷³, Dmitriy Voyakin^{17 74}, Antonina Yermolayeva¹⁷, Muhammad Zahir^{43 75}, Valery S Zubkov⁷⁶, Alisa Zubova¹⁵, Vasant S Shinde⁷⁷, Carles Lalueza-Fox⁷⁸, Matthias Meyer²⁸, David Anthony⁷⁹, Nicole Boivin⁴³, Kumarasamy Thangaraj³², Douglas J Kennett^{25 30 80}, Michael Frachetti^{81 82}, Ron Pinhasi^{83 24}, David Reich^{1 7 8 84}

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
² Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
³ Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA.
⁴ Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
⁵ Center for Computational Biology, University of California, Berkeley, CA 94720, USA.
⁶ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁷ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁸ Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
⁹ Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.
¹⁰ Department of Anthropology, Harvard University, Cambridge, MA 02138, USA.
¹¹ ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan.
¹² Department of Environmental Biology, Sapienza University, Rome 00185, Italy.
¹³ Department of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padua, Padua 35139, Italy.
¹⁴ School of Natural and Built Environment, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, UK.
¹⁵ Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia.
¹⁶ Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia.
¹⁷ A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.
¹⁸ Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan.
¹⁹ University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA.
²⁰ Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA.
²¹ Earth Institute, University College Dublin, Dublin 4, Ireland.
²² Soprintendenza Archeologia, Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e le Province di Oristano e Sud Sardegna, Cagliari 09124, Italy.
²³ School of Archaeology, University College Dublin, Dublin 4, Ireland.
²⁴ Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.
²⁵ Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA.
²⁶ CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal.
²⁷ Catalan Institute of Human Paleoecology and Social Evolution (IPHES), Tarragona 43007, Spain.
²⁸ Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
²⁹ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
³⁰ Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
³¹ Institute for Anthropological Research, Zagreb 10000, Croatia.
³² CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
³³ Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India.
³⁴ Department of Anthropology, Emory University, Atlanta, GA 30322, USA.
³⁵ Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia.
³⁶ CNRS-EXT500, Directeur de la Delegation Archaologique Francaise en Afghanistan (DAFA), Embassy of France in Kabul, Afghanistan.
³⁷ Aktobe Regional Historical Museum, Aktobe 030006, Kazakhstan.
³⁸ Archaeology of Asia Department, ISMEO - International Association of Mediterranean and Oriental Studies, Rome RM00186, Italy.
³⁹ Kyrgyz National University, 720033 Bishkek, Kyrgyzstan.
⁴⁰ Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia.
⁴¹ Department of Political History, National and State-Confessional Relations, Altai State University, Barnaul 656049, Russia.
⁴² Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic.
⁴³ Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany.
⁴⁴ Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK.
⁴⁵ Institute of History and Archaeology, Ural Branch RAS, Yekaterinburg 620990, Russia.
⁴⁶ South Ural State University, Chelyabinsk 454080, Russia.
⁴⁷ Department of Archaeology, Kemerovo State University, Kemerovo 650043, Russia.
⁴⁸ Institute of Archaeology, University College London, London WC1H 0PY, UK.
⁴⁹ School of Cultural Heritage, Northwest University, Shanxi, 710069, China.
⁵⁰ Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul 656049, Russia.
⁵¹ Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
⁵² Samara State University of Social Sciences and Education, Samara 443099, Russia.
⁵³ West Kazakhstan Regional Center for History and Archaeology, Uralsk 090000, Kazakhstan.
⁵⁴ Scientific and Educational Center of Study on the Problem of Nature and Man, Chelyabinsk State University, Chelyabinsk 454021, Russia.
⁵⁵ Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy.
⁵⁶ Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan.
⁵⁷ Center for Research, Restoration and Protection of Historical and Cultural Heritage of Aktobe Region, Aktobe 030007, Kazakhstan.
⁵⁸ Department of Anthropology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada.
⁵⁹ Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
⁶⁰ MiBAC - Ministero per i Beni e le Attività Culturali - Soprintendenza Archeologia, belle arti e paesaggio del Friuli Venezia Giulia, 34135 Trieste, Italy.
⁶¹ Afrosiab Museum, Samarkand 140151, Uzbekistan.
⁶² Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna 40126, Italy.
⁶³ Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
⁶⁴ National Research Tomsk State University, Tomsk 634050, Russia.
⁶⁵ F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.
⁶⁶ Central State Museum Republic of Kazakhstan, Samal-1 Microdistrict, Almaty 050010, Kazakhstan.
⁶⁷ CHRONO Centre for Climate, the Environment, and Chronology, Queen's University of Belfast, Belfast BT7 1NN, Northern Ireland, UK.
⁶⁸ Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan.
⁶⁹ Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria.
⁷⁰ Department of Archaeology, Ethnography and Museology, The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Altai State University, Barnaul 656049, Russia.
⁷¹ Institute of Steppe, Ural Branch RAS, Orenburg 460000, Russia.
⁷² Center for Egyptological Studies RAS, Moscow 119991, Russia.
⁷³ Department of Anthropology, National Museum, Prague 115 79, Czech Republic.
⁷⁴ Archaeological Expertise LLP, Almaty 050060, Kazakhstan.
⁷⁵ Department of Archaeology, Hazara University, Mansehra 21300, Pakistan.
⁷⁶ N.F. Katanov Khakassia State University, Abakan 655017, Russia.
⁷⁷ Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India.
⁷⁸ Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain.
⁷⁹ Anthropology Department, Hartwick College, Oneonta, NY 13820, USA.
⁸⁰ Department of Anthropology, University of California, Santa Barbara, CA 93106, USA.
⁸¹ Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63112, USA. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
⁸² Spatial Analysis, Interpretation, and Exploration Laboratory, Washington University in St. Louis, St. Louis, MO 63112, USA.
⁸³ Earth Institute, University College Dublin, Dublin 4, Ireland. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
⁸⁴ Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA.

PMID:31488661
PMCID: PMC6822619
DOI: 10.1126/science.aat7487

The formation of human populations in South and Central Asia

Vagheesh M Narasimhan et al. Science.2019.

.2019 Sep 6;365(6457):eaat7487.

doi: 10.1126/science.aat7487.

Authors

Affiliations

¹ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
² Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
³ Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA.
⁴ Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.
⁵ Center for Computational Biology, University of California, Berkeley, CA 94720, USA.
⁶ Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁷ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁸ Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
⁹ Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115, USA.
¹⁰ Department of Anthropology, Harvard University, Cambridge, MA 02138, USA.
¹¹ ISMEO - International Association of Mediterranean and Oriental Studies, Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), Pakistan.
¹² Department of Environmental Biology, Sapienza University, Rome 00185, Italy.
¹³ Department of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padua, Padua 35139, Italy.
¹⁴ School of Natural and Built Environment, Queen's University Belfast, Belfast BT7 1NN, Northern Ireland, UK.
¹⁵ Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, Russia.
¹⁶ Center of Physical Anthropology, Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia.
¹⁷ A.Kh. Margulan Institute of Archaeology, Almaty 050010, Kazakhstan.
¹⁸ Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan.
¹⁹ University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA.
²⁰ Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA 94720, USA.
²¹ Earth Institute, University College Dublin, Dublin 4, Ireland.
²² Soprintendenza Archeologia, Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e le Province di Oristano e Sud Sardegna, Cagliari 09124, Italy.
²³ School of Archaeology, University College Dublin, Dublin 4, Ireland.
²⁴ Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.
²⁵ Institutes of Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA.
²⁶ CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal.
²⁷ Catalan Institute of Human Paleoecology and Social Evolution (IPHES), Tarragona 43007, Spain.
²⁸ Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.
²⁹ Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
³⁰ Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
³¹ Institute for Anthropological Research, Zagreb 10000, Croatia.
³² CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, India.
³³ Birbal Sahni Institute of Palaeosciences, Lucknow 226007, India.
³⁴ Department of Anthropology, Emory University, Atlanta, GA 30322, USA.
³⁵ Tyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, Russia.
³⁶ CNRS-EXT500, Directeur de la Delegation Archaologique Francaise en Afghanistan (DAFA), Embassy of France in Kabul, Afghanistan.
³⁷ Aktobe Regional Historical Museum, Aktobe 030006, Kazakhstan.
³⁸ Archaeology of Asia Department, ISMEO - International Association of Mediterranean and Oriental Studies, Rome RM00186, Italy.
³⁹ Kyrgyz National University, 720033 Bishkek, Kyrgyzstan.
⁴⁰ Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia.
⁴¹ Department of Political History, National and State-Confessional Relations, Altai State University, Barnaul 656049, Russia.
⁴² Institute of Archaeology, Czech Academy of Sciences, Prague 118 01, Czech Republic.
⁴³ Department of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, Germany.
⁴⁴ Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK.
⁴⁵ Institute of History and Archaeology, Ural Branch RAS, Yekaterinburg 620990, Russia.
⁴⁶ South Ural State University, Chelyabinsk 454080, Russia.
⁴⁷ Department of Archaeology, Kemerovo State University, Kemerovo 650043, Russia.
⁴⁸ Institute of Archaeology, University College London, London WC1H 0PY, UK.
⁴⁹ School of Cultural Heritage, Northwest University, Shanxi, 710069, China.
⁵⁰ Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul 656049, Russia.
⁵¹ Department of Anthropology, University of Pittsburgh, Pittsburgh, PA 15260, USA.
⁵² Samara State University of Social Sciences and Education, Samara 443099, Russia.
⁵³ West Kazakhstan Regional Center for History and Archaeology, Uralsk 090000, Kazakhstan.
⁵⁴ Scientific and Educational Center of Study on the Problem of Nature and Man, Chelyabinsk State University, Chelyabinsk 454021, Russia.
⁵⁵ Department of Cultural Heritage, University of Bologna, 48121 Ravenna, Italy.
⁵⁶ Institute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, Uzbekistan.
⁵⁷ Center for Research, Restoration and Protection of Historical and Cultural Heritage of Aktobe Region, Aktobe 030007, Kazakhstan.
⁵⁸ Department of Anthropology, University of Winnipeg, Winnipeg, MB R3B 2E9, Canada.
⁵⁹ Department of Archaeology, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
⁶⁰ MiBAC - Ministero per i Beni e le Attività Culturali - Soprintendenza Archeologia, belle arti e paesaggio del Friuli Venezia Giulia, 34135 Trieste, Italy.
⁶¹ Afrosiab Museum, Samarkand 140151, Uzbekistan.
⁶² Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum - University of Bologna, Bologna 40126, Italy.
⁶³ Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA.
⁶⁴ National Research Tomsk State University, Tomsk 634050, Russia.
⁶⁵ F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk 660022, Russia.
⁶⁶ Central State Museum Republic of Kazakhstan, Samal-1 Microdistrict, Almaty 050010, Kazakhstan.
⁶⁷ CHRONO Centre for Climate, the Environment, and Chronology, Queen's University of Belfast, Belfast BT7 1NN, Northern Ireland, UK.
⁶⁸ Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan.
⁶⁹ Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria.
⁷⁰ Department of Archaeology, Ethnography and Museology, The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Altai State University, Barnaul 656049, Russia.
⁷¹ Institute of Steppe, Ural Branch RAS, Orenburg 460000, Russia.
⁷² Center for Egyptological Studies RAS, Moscow 119991, Russia.
⁷³ Department of Anthropology, National Museum, Prague 115 79, Czech Republic.
⁷⁴ Archaeological Expertise LLP, Almaty 050060, Kazakhstan.
⁷⁵ Department of Archaeology, Hazara University, Mansehra 21300, Pakistan.
⁷⁶ N.F. Katanov Khakassia State University, Abakan 655017, Russia.
⁷⁷ Department of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, India.
⁷⁸ Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, Spain.
⁷⁹ Anthropology Department, Hartwick College, Oneonta, NY 13820, USA.
⁸⁰ Department of Anthropology, University of California, Santa Barbara, CA 93106, USA.
⁸¹ Department of Anthropology, Washington University in St. Louis, St. Louis, MO 63112, USA. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
⁸² Spatial Analysis, Interpretation, and Exploration Laboratory, Washington University in St. Louis, St. Louis, MO 63112, USA.
⁸³ Earth Institute, University College Dublin, Dublin 4, Ireland. vagheesh@mail.harvard.edu nickp@broadinstitute.org frachetti@wustl.edu ron.pinhasi@univie.ac.at reich@genetics.med.harvard.edu.
⁸⁴ Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA.

PMID:31488661
PMCID: PMC6822619
DOI: 10.1126/science.aat7487

Abstract

By sequencing 523 ancient humans, we show that the primary source of ancestry in modern South Asians is a prehistoric genetic gradient between people related to early hunter-gatherers of Iran and Southeast Asia. After the Indus Valley Civilization's decline, its people mixed with individuals in the southeast to form one of the two main ancestral populations of South Asia, whose direct descendants live in southern India. Simultaneously, they mixed with descendants of Steppe pastoralists who, starting around 4000 years ago, spread via Central Asia to form the other main ancestral population. The Steppe ancestry in South Asia has the same profile as that in Bronze Age Eastern Europe, tracking a movement of people that affected both regions and that likely spread the distinctive features shared between Indo-Iranian and Balto-Slavic languages.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

Figures

**Fig. 1. Overview of ancient DNA data.**
(A) Distribution of sites and associated archeological or radiocarbon dates along with the number of individuals meeting our analysis thresholds from each site. (B) Locations of ancient individuals for whom we generated ancient DNA that passed our analysis thresholds along with the locations of individuals from 140 groups from present-day South Asia that we analyzed as forming theModern Indian Cline. Shapes distinguish the individuals from different sites. Data from 106 South Asian groups that do not fit along theModern Indian Cline as well asAHG are not shown.(C) PCA analysis of ancient and modern individuals projected onto a basis formed by 1,340 present day Eurasians reflects clustering of individuals that mirrors their geographical relationships. An interactive version of this figure is presented in the Online Data Visualizer.

**Fig. 2.. Outlier analysis reveals ancient contacts between sites.**
We plot the average of Principal Component 1 (x-axis) and Principal Component 2 (y-axis) for the West Eurasian and All Eurasian PCA plots, as we found that this aids visual separation of the ancestry profiles. (A) In the Middle to Late Bronze Age Steppe, we observe in addition to theWestern_Steppe_MLBA andCentral_Steppe_MLBA clusters (indistinguishable in this projection), outliers admixed with other ancestries. TheBMAC-related admixture in Kazakhstan documents northward gene flow onto the Steppe and confirms the Inner Asian Mountain Corridor as a conduit for movement of people.(B) At Shahr-i-Sokhta in eastern Iran, there are two primary groupings: one with ~20% Anatolian farmer-related ancestry and no detectableAHG-related ancestry, and the other with ~0% Anatolian farmer-related ancestry and substantialAHG-related ancestry (*Indus Periphery Cline*). (C) In individuals of the BMAC and successor sites, we observe a main cluster as well as numerous outliers: outliers >2000 BCE with admixture related toWSHG, outliers >2000 BCE on theIndus Periphery Cline (with an ancestral similar similar to the outliers at Shahr-i-Sokhta), and outliers after 2000 BCE that reveal howCentral_Steppe_MLBA ancestry had arrived.(D) In the Late Bronze Age and Iron Age of northernmost South Asia, we observe a main cluster consistent with admixture between peoples of theIndus Periphery Cline andCentral_Steppe_MLBA, and variable Steppe pastoralist-related admixture.

**Fig. 3.. Ancestry Transformations in Holocene Eurasia.**
**(A)** Ancestry clines before and after the advent of farming. We document aSouth Eurasian Early Holocene Cline of increasing Iranian farmer- and West Siberian hunter-gatherer related ancestry moving west-to-east from Anatolia to Iran, and aNorth Eurasian Early Holocene Cline of increasing relatedness to East Asians moving west-to-east from Europe to Siberia. Mixtures of peoples along these two clines following the spread of farming formed five later gradients (shaded): moving west-to-east: theEuropean Cline, theCaucasus Cline from which the Yamnaya formed, theCentral Asian Cline which characterized much of Central Asia in the Copper and Bronze Ages, theSouthwest Asian Cline established by spreads of farmers in multiple directions from several loci of domestication, and theIndus Periphery Cline.(B) Following the appearance of the Yamnaya Steppe pastoralists,*Western_Steppe_EMBA* (*Yamnaya*-like) ancestry then spread across this vast region. We use arrows to show plausible directions of spread of increasingly diluted ancestry (the arrows are not meant as exact routes which we do not have enough sampling to determine at present). Rough estimates of the timing of the arrival of this ancestry and estimated ancestry proportions are shown.

**Fig. 4.. The Genomic Formation of South Asia.**
**(A)** The degree of allele sharing with southern Asian hunter-gatherers (*AASI*) measured byf₄*(Ethiopia_4500BP, X; Ganj_Dareh_N*,*AHG*) and with Steppe pastoralists measured byf₄*(Ethiopia_4500BP, X; Central_Steppe_MLBA, Ganj_Dareh_N*) reveals three ancestry clines that succeeded each other in time: theIndus Periphery Cline prior to ~2000 BCE, theSteppe Cline represented by northern South Asian individuals after ~2000 BCE, and theModern Indian Cline.(B) Modeling South Asians as a mixture ofCentral_Steppe_MLBA, AHG (as a proxy forAASI), andIndus_Periphery_West (the individual from theIndus Periphery Cline with the leastAASI ancestry). Groups along the edges of the triangle fit a two-way model, and in the interior only fit a three-way model. The 140 present-day South Asian groups on theModern Indian Cline are shown as small dots. (C) Groups that traditionally view themselves as being of priestly status in this and the preceding panel are shown in red (“Brahmin,” “Pandit,” and “Bhumihar” but excluding “Catholic Brahmins”), and tend to have a significantly higher ratio ofCentral_Steppe_MLBA toIndus_Periphery_Cline ancestry than other groups. (D) Plot of the proportion ofCentral_Steppe_MLBA ancestry on the autosomes (x-axis) and the Y chromosome (y-axis) shows that the source of this ancestry is primarily from females in Late Bronze Age and Iron Age individuals from the Swat District of northernmost South Asia, and primarily from males in most present-day South Asians.

**Fig. 5.. Admixture Graph Model.**
The largest deviation between empirical and theoreticalf-statistics is |Z|=2.9, indicating a good fit considering the large number off-statistics analyzed. Admixture events are shown as dotted lines labeled by proportions, with the minor ancestry in gray. The present-day groups are shown in orange ovals, the ancient ones in blue, and unsampled groups in white. (The ovals and admixture events are positioned according to guesses about their relative dates to help in visualization, although the dates are in no way meant to be exact.) In this graph we do not attempt to model the contribution ofWSHG and Anatolian farmer-related ancestry, and thus cannot modelCentral_Steppe_EMBA, the proximal source of Steppe ancestry in South Asia (instead we model the Steppe ancestry in South Asia through the more distally relatedYamnaya). However, the admixture graph does highlight several key findings of the study, including the deep separation of theAASI from other Eurasian lineages, and the fact that some Austroasiatic-speaking groups in South Asia (e.g. Juang) harbor ancestry from a South Asian group with a higher ratio ofAASI-related to Iranian farmer-related ancestry than any groups on theModern Indian Cline, thus revealing that groups with substantial Iranian farmer-related ancestry were not ubiquitous in peninsular South Asia in the 3^rd millennium BCE when Austroasiatic languages likely spread across the subcontinent.

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Comment in

New middle chapter in the story of human evolution.
Schaefer NK, Shapiro B.Schaefer NK, et al.Science. 2019 Sep 6;365(6457):981-982. doi: 10.1126/science.aay3550.Science. 2019.PMID:31488673No abstract available.

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References

1. Online Data Visualizer, (available athttps://public.tableau.com/views/TheGenomicFormationofSouthandCentralAsi...).
1. Fuller DQ, Lucas L, in Human Dispersal and Species Movement, Boivin N, Petraglia M, Crassard R, Eds. (Cambridge University Press, Cambridge, 2017), pp. 304–331.
1. Stevens CJ et al., Between China and South Asia: A Middle Asian corridor of crop dispersal and agricultural innovation in the Bronze Age. The Holocene. 26, 1541–1555 (2016). - PMC - PubMed
1. Allaby RG, Stevens C, Lucas L, Maeda O, Fuller DQ, Geographic mosaics and changing rates of cereal domestication. Philos. Trans. R. Soc. B Biol. Sci 372, 20160429 (2017). - PMC - PubMed
1. Dani AH et al., History of Civilizations of Central Asia: The Development of Sedentary and Nomadic Civilizations, 700 B. C. to A (UNESCO Publishing, 1994).

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The formation of human populations in South and Central Asia

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The formation of human populations in South and Central Asia

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