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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Afrosiab Museum Samarkand 140151 Uzbekistan

Aktobe Regional Historical Museum Aktobe 030006 Kazakhstan

Al Farabi Kazakh National University Almaty 050040 Kazakhstan

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CHRONO Centre for Climate the Environment and Chronology Queen's University of Belfast Belfast BT7 1NN Northern Ireland UK

CIAS Department of Life Sciences University of Coimbra Coimbra 3000 456 Portugal

CNRS EXT500 Directeur de la Delegation Archaologique Francaise en Afghanistan Embassy of France in Kabul Afghanistan

CSIR Centre for Cellular and Molecular Biology Hyderabad 500 007 India

Department of Anthropology Emory University Atlanta GA 30322 USA

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Department of Anthropology National Museum Prague 115 79 Czech Republic

Department of Anthropology Natural History Museum Vienna 1010 Vienna Austria

Department of Anthropology Pennsylvania State University University Park PA 16802 USA

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Department of Anthropology University of Pittsburgh Pittsburgh PA 15260 USA

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Department of Archaeology Ethnography and Museology Altai State University Barnaul 656049 Russia

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Department of Archaeology Hazara University Mansehra 21300 Pakistan

Department of Archaeology Kemerovo State University Kemerovo 650043 Russia

Department of Archaeology Max Planck Institute for the Science of Human History Jena 07745 Germany

Department of Archaeology Simon Fraser University Burnaby BC V5A 1S6 Canada

Department of Biological Geological and Environmental Sciences Alma Mater Studiorum University of Bologna Bologna 40126 Italy

Department of Cultural Heritage Archaeology and History of Art Cinema and Music University of Padua Padua 35139 Italy

Department of Cultural Heritage University of Bologna 48121 Ravenna Italy

Department of Electrical Engineering and Computer Science University of California Berkeley CA 94720 USA

Department of Environmental Biology Sapienza University Rome 00185 Italy

Department of Evolutionary Anthropology University of Vienna 1090 Vienna Austria

Department of Genetics Harvard Medical School Boston MA 02115 USA

Department of Molecular and Cell Biology University of California Berkeley CA 94720 USA

Department of Organismic and Evolutionary Biology Harvard University Cambridge MA 02138 USA

Department of Political History National and State Confessional Relations Altai State University Barnaul 656049 Russia

Earth Institute University College Dublin Dublin 4 Ireland

F Voino Yasenetsky Krasnoyarsk State Medical University Krasnoyarsk 660022 Russia

Harvard MIT Division of Health Sciences and Technology Harvard Medical School Boston MA 02115 USA

Howard Hughes Medical Institute Harvard Medical School Boston MA 02115 USA

Human Origins Program National Museum of Natural History Smithsonian Institution Washington DC 20013 USA

Institute for Anthropological Research Zagreb 10000 Croatia

Institute for Archaeological Research Uzbekistan Academy of Sciences Samarkand 140151 Uzbekistan

Institute of Archaeology and Ethnography Siberian Branch Russian Academy of Sciences Novosibirsk 630090 Russia

Institute of Archaeology Czech Academy of Sciences Prague 118 01 Czech Republic

Institute of Archaeology University College London London WC1H 0PY UK

Institute of Evolutionary Biology CSIC Universitat Pompeu Fabra Barcelona 08003 Spain

Institute of History and Archaeology Ural Branch RAS Yekaterinburg 620990 Russia

Institute of Steppe Ural Branch RAS Orenburg 460000 Russia

Institutes of Energy and the Environment Pennsylvania State University University Park PA 16802 USA

ISMEO International Association of Mediterranean and Oriental Studies Italian Archaeological Mission in Pakistan 19200 Saidu Sharif Pakistan

Kyrgyz National University 720033 Bishkek Kyrgyzstan

Kyrgyz Turkish Manas University Bishkek Kyrgyzstan

Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean Cambridge MA 02138 USA

Max Planck Institute for Evolutionary Anthropology Leipzig 04103 Germany

MiBAC Ministero per i Beni e le Attività Culturali Soprintendenza Archeologia belle arti e paesaggio del Friuli Venezia Giulia 34135 Trieste Italy

N F Katanov Khakassia State University Abakan 655017 Russia

National Research Tomsk State University Tomsk 634050 Russia

Oxford Radiocarbon Accelerator Unit Research Laboratory for Archaeology and the History of Art University of Oxford Oxford OX1 3QY UK

Peter the Great Museum of Anthropology and Ethnography Russian Academy of Science St Petersburg 199034 Russia

Radcliffe Institute for Advanced Study Harvard University Cambridge MA 02138 USA

Samara State University of Social Sciences and Education Samara 443099 Russia

School of Archaeology University College Dublin Dublin 4 Ireland

School of Cultural Heritage Northwest University Shanxi 710069 China

School of Natural and Built Environment Queen's University Belfast Belfast BT7 1NN Northern Ireland UK

Scientific and Educational Center of Study on the Problem of Nature and Man Chelyabinsk State University Chelyabinsk 454021 Russia

Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Cagliari e le Province di Oristano e Sud Sardegna Cagliari 09124 Italy

South Ural State University Chelyabinsk 454080 Russia

Spatial Analysis Interpretation and Exploration Laboratory Washington University in St Louis St Louis MO 63112 USA

Tyumen Scientific Centre SB RAS Institute of the Problems of Northern Development Tyumen 625003 Russia

University of Pennsylvania Museum of Archaeology and Anthropology Philadelphia PA 19104 USA

West Kazakhstan Regional Center for History and Archaeology Uralsk 090000 Kazakhstan

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