Preprint

The Genomic Formation of South and Central Asia

Vagheesh M. NarasimhanDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USANick PattersonBroad Institute of Harvard and MIT, Cambridge, MA 02142, USAPriya MoorjaniCenter for Computational Biology, University of California, Berkeley, CA 94720, USAIosif LazaridisDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAMark LipsonDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USASwapan MallickBroad Institute of Harvard and MIT, Cambridge, MA 02142, USANadin RohlandBroad Institute of Harvard and MIT, Cambridge, MA 02142, USARebecca BernardosDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAAlexander M. KimDepartment of Anthropology, Harvard University, Cambridge, MA 02138, USANathan NakatsukaDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAÍñigo OlaldeDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAAlfredo CoppaDipartimento di Biologia Ambientale, Sapienza Università di Roma, Rome 00185, ItalyJ. P. MallorySchool of Natural and Built Environment, Queen’s University Belfast, Belfast BT7 1NN, Northern Ireland, UKVyacheslav MoiseyevPeter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, RussiaJanet MongeUniversity of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USALuca M. OlivieriNicole AdamskiDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USANasreen BroomandkhoshbachtDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAFrancesca CandilioEarth Institute, University College Dublin, Dublin 4, IrelandOlivia CheronetDepartment of Anthropology, University of Vienna, 1090 Vienna, AustriaBrendan J. CulletonDepartment of Anthropology, Pennsylvania State University, University Park, PA 16802, USAMatthew FerryDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USADaniel FernandesCIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, PortugalBeatriz GamarraEarth Institute, University College Dublin, Dublin 4, IrelandDaniel GaudioEarth Institute, University College Dublin, Dublin 4, IrelandMateja HajdinjakMax Planck Institute for Evolutionary Anthropology, Leipzig 04103, GermanyÉadaoin HarneyDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAThomas K. HarperDepartment of Anthropology, Pennsylvania State University, University Park, PA 16802, USADenise KeatingEarth Institute, University College Dublin, Dublin 4, IrelandAnn Marie LawsonDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAMegan MichelDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAMario NovakEarth Institute, University College Dublin, Dublin 4, IrelandJonas OppenheimerDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USANiraj RaiBirbal Sahni Institute of Palaeosciences, Lucknow 226007, IndiaKendra SirakDepartment of Anthropology, Emory University, Atlanta, GA 30322, USAViviane SlonMax Planck Institute for Evolutionary Anthropology, Leipzig 04103, GermanyKristin StewardsonDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAZhao ZhangDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAGaziz AkhatovInstitute of Archaeology A.Kh. Margulan, Almaty 050010, KazakhstanA.N. BagashevTyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, RussiaBauryzhan BaitanayevInstitute of Archaeology A.Kh. Margulan, Almaty 050010, KazakhstanGian Luca BonoraArchaeology of Asia Department, ISMEO - International Association of Mediterranean and Oriental Studies, Rome RM00186, ItalyТ. А. ЧикишеваInstitute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, RussiaА. П. ДеревянкоInstitute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, RussiaEnshin DmitryTyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, RussiaKaterina DoukaDepartment of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, GermanyНадежда ДубоваInstitute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, RussiaAndrey EpimakhovInstitute of History and Archaeology, Ural Branch RAS, Yekaterinburg 620990, RussiaSuzanne FreilichDepartment of Anthropology, University of Vienna, 1090 Vienna, AustriaDorian Q. FullerInstitute of Archaeology, University College London, London WC1H 0PY, UKAlexander GoryachevTyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, RussiaAndrey GromovPeter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St. Petersburg 199034, RussiaBryan HanksUniversity of Pittsburgh, Department of Anthropology, Pittsburgh, PA 15260, USAMargaret A. JuddUniversity of Pittsburgh, Department of Anthropology, Pittsburgh, PA 15260, USAErlan KazizovInstitute of Archaeology A.Kh. Margulan, Almaty 050010, KazakhstanAleksandr KhokhlovSamara State University of Social Sciences and Education, Samara 443099, RussiaЕgor KitovInstitute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, RussiaElena KupriyanovaScientific and Educational Center of Study on the Problem of Nature and Man, Chelyabinsk State University, Chelyabinsk 454021, RussiaPavel KuznetsovSamara State University of Social Sciences and Education, Samara 443099, RussiaDonata LuiselliDepartment of Biological, Geological and Environmental Sciences, Alma Mater Studiorum – University of Bologna, Bologna 40126, ItalyFarhod MaksudovInstitute for Archaeological Research, Uzbekistan Academy of Sciences, Samarkand 140151, UzbekistanChristopher MeiklejohnDepartment of Anthropology, University of Winnipeg, Winnipeg, MB, R3B 2E9, CanadaDeborah C. MerrettDepartment of Archaeology, Simon Fraser University, Burnaby, BC, V5A 1S6, CanadaRoberto MicheliISMEO Italian Archaeological Mission in Pakistan, 19200 Saidu Sharif (Swat), PakistanOleg Dmitrievich MochalovSamara State University of Social Sciences and Education, Samara 443099, RussiaZahir MuhammedDepartment of Archaeology, Hazara University, Mansehra 21300, PakistanSamariddin MustafokulovAfrosiab Museum, Samarkand 140151, UzbekistanAyushi NayakDepartment of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, GermanyRykun M. PetrovnaTomsk State National Research University, Tomsk 634050, RussiaDavide PettenerDepartment of Biological, Geological and Environmental Sciences, Alma Mater Studiorum – University of Bologna, Bologna 40126, ItalyRichard PottsHuman Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USADmitry RazhevTyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, RussiaStefania SarnoDepartment of Biological, Geological and Environmental Sciences, Alma Mater Studiorum – University of Bologna, Bologna 40126, ItalyKulyan SikhymbaevaSergey SlepchenkoTyumen Scientific Centre SB RAS, Institute of the Problems of Northern Development, Tyumen 625003, RussiaN. StepanovaInstitute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, RussiaSvetlana V SvyatkoCHRONO Centre for Climate, the Environment, and Chronology, Queen’s University of Belfast, Belfast BT7 1NN, Northern Ireland, UKSergey VasilyevInstitute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, RussiaMassimo VidaleDepartment of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padua, Padua 35139, ItalyDmitriy VoyakinArchaeological Expertise LLP, Almaty 050060, KazakhstanAntonina YermolayevaInstitute of Archaeology A.Kh. Margulan, Almaty 050010, KazakhstanА. В. ЗубоваInstitute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, RussiaVasant ShindeDepartment of Archaeology, Deccan College Post-Graduate and Research Institute, Pune 411006, IndiaCarles Lalueza‐FoxInstitute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona 08003, SpainMatthias MeyerMax Planck Institute for Evolutionary Anthropology, Leipzig 04103, GermanyDavid W. AnthonyAnthropology Department, Hartwick College, Oneonta, New York 13820, USANicole BoivinDepartment of Archaeology, Max Planck Institute for the Science of Human History, Jena 07745, GermanyKumarasamy ThangarajCSIR-Centre for Cellular and Molecular Biology, Hyderabad 500 007, IndiaDouglas J. KennettDepartment of Anthropology, Pennsylvania State University, University Park, PA 16802, USAMichael D. FrachettiDepartment of Anthropology, Washington University in St. Louis, St. Louis, MO 63112, USARon PinhasiDepartment of Anthropology, University of Vienna, 1090 Vienna, AustriaDavid ReichBroad Institute of Harvard and MIT, Cambridge, MA 02142, USA

bioRxiv (Cold Spring Harbor Laboratory)repository2018en

ABI

Annotatsiya

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. One Sentence Summary Genome wide ancient DNA from 357 individuals from Central and South Asia sheds new light on the spread of Indo-European languages and parallels between the genetic history of two sub-continents, Europe and South Asia.

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Forensic and Genetic Research Race, Genetics, and Society Forensic Anthropology and Bioarchaeology Studies

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DOI: 10.1101/292581

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