The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.

ArchaeoBioCenter and Institute of Palaeoanatomy Domestication Research and the History of Veterinary Medicine LMU Munich 80539 Munich Germany; SNSB State Collection of Palaeoanatomy Munich 80333 Munich Germany

CMPG Institute for Ecology and Evolution University of Berne 3012 Berne Switzerland

CMPG Institute for Ecology and Evolution University of Berne 3012 Berne Switzerland; Swiss Institute of Bioinformatics 1015 Lausanne Switzerland

Department of Anthropology Natural History Museum of Vienna 1010 Vienna Austria; Department of Evolutionary Anthropology University of Vienna 1030 Vienna Austria

Department of Archaeology Laboratory for Bioarchaeology University of Belgrade 11000 Belgrade Serbia

Department of History and Archaeology Aristotle University of Thessaloniki 54124 Thessaloniki Greece

Department of Molecular and Cellular Biology University of Arizona Tucson AZ 85721 USA

Department of Prehistoric and Historical Archaeology University of Vienna 1190 Vienna Austria

Department of Prehistory İstanbul University 34434 Istanbul Turkey

Generaldirektion Kulturelles Erbe Rheinland Pfalz Dir Landesarchäologie 67346 Speyer Germany

Institute of Archaeology Innsbruck University 6020 Innsbruck Austria

Laboratory of Physical Anthropology Department of History and Ethnology Democritus University of Thrace 69100 Komotini Greece

Netherlands Institute in Turkey 34433 Istanbul Turkey; Vrije Universiteit 1081 HV Amsterdam the Netherlands

Palaeogenetics Group Institute of Organismic and Molecular Evolution Johannes Gutenberg University Mainz 55099 Mainz Germany

Palaeogenetics Group Institute of Organismic and Molecular Evolution Johannes Gutenberg University Mainz 55099 Mainz Germany; Research Department of Genetics Evolution and Environment University College London Gower Street London WC1E 6BT UK

Swiss Institute of Bioinformatics 1015 Lausanne Switzerland; Department of Biology University of Fribourg 1700 Fribourg Switzerland

Swiss Institute of Bioinformatics 1015 Lausanne Switzerland; Department of Biology University of Fribourg 1700 Fribourg Switzerland; Max Planck Institute for Evolutionary Anthropology 04103 Leipzig Germany; Department of Archaeology and Museology Faculty of Arts Masaryk University 60200 Brno Czech Republic

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