Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.

1 U de Investigación en Arqueología y Patrimonio Histórico University of Alicante Sant Vicent del Raspeig Alicante Spain

Accademia dei Fisiocritici Siena Italy

Amsterdam Centre of Ancient Studies and Archaeology University of Amsterdam Amsterdam The Netherlands

Anthropologie Büro Berlin Germany

Archaeo and Palaeogenetics Institute for Archaeological Sciences Department of Geosciences University of Tübingen Tübingen Germany

ArchaeoZOOlogy in Siberia and Central Asia ZooSCAn CNRS IAET SB RAS International Research Laboratory IRL 2013 Institute of Archaeology SB RAS Novosibirsk Russia

Archäologie and Münzkabinett Universalmuseum Joanneum Graz Austria

Arpa Patrimonio S L Alicante Spain

Association APRAGE Besançon France

Biogeology Department of Geosciences University of Tübingen Tübingen Germany

Brandenburg Authorities for Heritage Management and Archaeological State Museum Zossen Germany

Center for Genomic Medicine Massachusetts General Hospital Boston MA USA

Center for Isotope Research Groningen University Groningen The Netherlands

Center of Excellence 'Archaeometry' Kazan Federal University Kazan Russia

Centre de Valorisation des Collections Scientifiques Université de Poitiers Mignaloux Beauvoir France

Centro Studi sul Quaternario ODV Sansepolcro Italy

Centro UCM ISCIII de Investigación sobre Evolución y Comportamiento Humanos Madrid Spain

Departamento de Biología de Organismos y Sistemas Universidad de Oviedo Oviedo Spain

Departamento de Geología Facultad de Ciencia y Tecnología Universidad del País Vasco Euskal Herriko Unibertsitatea Leioa Spain

Department of Anatomy Histology and Anthropology Faculty of Medicine Vilnius University Vilnius Lithuania

Department of Anthropology California State University Northridge Northridge CA USA

Department of Anthropology University of New Mexico Albuquerque NM USA

Department of Archaeogenetics Max Planck Institute for Evolutionary Anthropology Leipzig Germany

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

Department of Archeological Sciences Thuringian State Office for Monuments Preservation and Archeology Weimar Germany

Department of Biological Chemical and Pharmaceutical Sciences and Technologies University of Palermo Palermo Italy

Department of Biology University of Florence Florence Italy

Department of Biology University of Padova Padova Italy

Department of Chemistry G Ciamician Alma Mater Studiorum University of Bologna Bologna Italy

Department of Cultural Heritage University of Bologna Ravenna Italy

Department of Cultures University of Helsinki Helsinki Finland

Department of Human Evolution Max Planck Institute for Evolutionary Anthropology Leipzig Germany

Department of Human Genetics Leiden University Medical Center Leiden The Netherlands

Department of Humanities University of Ferrara Ferrara Italy

Department of Psychiatry Harvard Medical School Boston MA USA

DFG Centre for Advanced Studies 'Words Bones Genes Tools' University of Tübingen Tübingen Germany

Dipartimento di Civiltà e Forme Del Sapere Università di Pisa Pisa Italy

Dipartimento di Scienze Della Vita e Dell'Ambiente Sezione di Neuroscienze e Antropologia Università Degli Studi di Cagliari Cittadella Monserrato Cagliari Italy

Dipartimento di Scienze Fisiche della Terra e dell'Ambiente U R Preistoria e Antropologia Università degli Studi di Siena Siena Italy

Early Prehistory and Quaternary Ecology Department of Geosciences University of Tübingen Tübingen Germany

Estonian Biocentre Institute of Genomics University of Tartu Tartu Estonia

Faculty of Archaeology Leiden University Leiden The Netherlands

Foundation for Rzeszów Archaeological Centre Rzeszów Poland

GéoArchPal GéoArchÉon Viéville sous les Cotes France

German Archaeological Institute Berlin Germany

Groninger Instituut voor Archeologie Groningen University Groningen The Netherlands

Grupo de 1 D i EVOADAPTA Departamento de Ciencias Históricas Universidad de Cantabria Santander Spain

Human Ecology and Archaeology Barcelona Spain

Inrap CIF Croissy Beaubourg France

Inrap GE Metz France

INRAP UMR 8215 Trajectoires 21 Paris France

Institut National de Recherches Archéologiques Bertrange Luxembourg

Institute for Advanced Studies in Levant Culture and Civilization Bucharest Romania

Institute for Pre and Protohistory Kiel University Kiel Germany

Institute of Archaeology Academy of Sciences of the Republic of Tatarstan Kazan Russia

Institute of Archaeology and Ethnology Polish Academy of Science Poznań Poland

Institute of Archaeology Russian Academy of Sciences Moscow Russia

Institute of Archaeology University of Rzeszów Rzeszów Poland

Institute of Archeology at Brno Czech Academy of Sciences Centre for Palaeolithic and Paleoanthropology Brno Czechia

Institute of Historical Research University of Girona Catalonia Spain

Institute of History Archaeology and Ethnography Dushanbe Tajikistan

Institute of Pre and Protohistory University of Tübingen Tübingen Germany

Institute of Zoology and Evolutionary Research University of Jena Jena Germany

Instituto Internacional de Investigaciones Prehistóricas de Cantabria Universidad de Cantabria Gobierno de Cantabria Banco Santander Santander Spain

Instituto Universitario de Investigación en Ciencias Ambientales de Aragón IUCA Aragosaurus Zaragoza Spain

Laboratoire de Chrono Environnement UMR 6249 du CNRS UFR des Sciences et Techniques Besançon Cedex France

Lower Saxony State Service for Cultural Heritage Hannover Germany

LVR LandesMuseum Bonn Bonn Germany

Musée National de Préhistoire Les Eyzies de Tayac France

Musées de Poitiers Ville de Poitiers Poitiers France

Musées Royaux d'Art et d'Histoire Bruxelles Belgium

Museum 'Das Dorf des Welan' Wöllersdorf Steinabrückl Austria

National Museum of Antiquities Leiden The Netherlands

Paleoanthropology Institute for Archaeological Sciences Department of Geosciences University of Tübingen Tübingen Germany

Paléotime Villard de Lans France

PALEVOPRIM Lab UMR 7262 CNRS INEE University of Poitiers Poitiers France

Peter the Great Museum of Anthropology and Ethnography Russian Academy of Sciences Saint Petersburg Russia

Pradis Cave Museum Clauzetto Italy

Quaternary Environments and Humans OD Earth and History of Life Royal Belgian Institute of Natural Sciences Brussels Belgium

Research Institute and Museum of Anthropology Moscow State University Moscow Russia

Royal Belgian Institute of Natural Sciences Brussels Belgium

Samara State University of Social Sciences and Education Samara Russia

School of Archaeology University of Oxford Oxford UK

School of Human Evolution and Social Change Arizona State University Tempe AZ USA

School of Mathematical Sciences University of Adelaide Adelaide South Australia Australia

Seminar for Pre and Protohistory Göttingen University Göttingen Germany

Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen Tübingen Germany

Service Régional de l'Archéologie de Bourgogne Franche Comté Besançon Cedex France

Skeletal Biology Research Centre School of Anthropology and Conservation University of Kent Canterbury UK

Sociedad de Ciencias Aranzadi Donostia San Sebastian Spain

St John's College University of Cambridge Cambridge UK

State Key Laboratory of Protein and Plant Gene Research School of Life Sciences Peking University Beijing China

Stralsund Museum Stralsund Germany

Ulm Germany

UMR 5140 CNRS Archéologie des Sociétés Méditerranéennes Université Paul Valéry Montpellier France

UMR 7194 Histoire Naturelle de l'Homme Préhistorique Département Homme et Environnement Muséum National d'Histoire Naturelle CNRS UPVD Paris France

UMR 7206 Éco Anthropologie Équipe ABBA CNRS MNHN Université de Paris Cité Musée de l'Homme Paris France

UMR 7209 Archéozoologie et Archéobotanique Sociétés Pratiques et Environnements Muséum National d'Histoire Naturelle Paris France

UMR 8068 CNRS TEMPS Technologie et Ethnologie des Mondes Préhistoriques Nanterre Cedex France

Unité de Recherches Art Archéologie Patrimoine Université de Liège Liège Belgium

Université de Bordeaux CNRS MC PACEA UMR 5199 Pessac France

University of Bucharest Faculty of Geology and Geophysics Department of Geology Bucharest Romania

Weyhe Germany

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Mobility and community at Mesolithic Lake Onega, Karelia, north-west Russia: insights from strontium isotope analysis

Large scale and regional demographic responses to climatic changes in Europe during the Final Palaeolithic

The genetic origin of the Indo-Europeans

Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

Earliest modern human genomes constrain timing of Neanderthal admixture

Widespread horse-based mobility arose around 2200 BCE in Eurasia

The Genetic Origin of the Indo-Europeans

A quantitative analysis of Final Palaeolithic/earliest Mesolithic cultural taxonomy and evolution in Europe

Population genomics of post-glacial western Eurasia

Modeling of African population history using f-statistics is biased when applying all previously proposed SNP ascertainment schemes