The Linearbandkeramik (LBK) Neolithic communities were the first to spread farming across large parts of Europe. We report genome-wide data for 250 individuals: 178 individuals from whole-cemetery surveys of the Alföld Linearbankeramik Culture eastern LBK site of Polgár-Ferenci-hát, the western LBK site of Nitra Horné Krškany and the western LBK settlement and massacre site of Asparn-Schletz, as well as 48 LBK individuals from 16 other sites and 24 earlier Körös and Starčevo individuals from 17 more sites. Here we show a systematically higher percentage of western hunter-gatherer ancestry in eastern than in western LBK sites, showing that these two distinct LBK groups had different genetic trajectories. We find evidence for patrilocality, with more structure across sites in the male than in the female lines and a higher rate of within-site relatives for males. At Asparn-Schletz we find almost no relatives, showing that the massacred individuals were from a large population, not a small community.

AHKR University of Bergen Bergen Norway

Anthropological Center Croatian Academy of Sciences and Arts Zagreb Croatia

Anthropos Institute Moravian Museum Brno Czechia

BIOMICs Research Group University of the Basque Country UPV EHU Vitoria Gasteiz Spain

Broad Institute of MIT and Harvard Cambridge MA USA

Centre for Applied Bioanthropology Institute for Anthropological Research Zagreb Croatia

Centre for Human Genetics University of Oxford Oxford UK

CIAS Department of Life Sciences University of Coimbra Coimbra Portugal

Collection of Prehistory and Historical Archaeology State Collections of Lower Austria Asparn an der Zaya Austria

Department for Prehistory and Migration Period Budapest History Museum Budapest Hungary

Department of Anthropology Natural History Museum Vienna Vienna Austria

Department of Anthropology New York University New York NY USA

Department of Anthropology Slovak National Museum Natural History Museum Bratislava Slovak Republic

Department of Antiquities and Museum Ras al Khaimah United Arab Emirates

Department of Archaeogenetics Max Planck Institute for Evolutionary Anthropology Leipzig Germany

Department of Archaeology Faculty of Arts and Social Sciences University of Szeged Szeged Hungary

Department of Archaeology University of York York UK

Department of Biological Anthropology Faculty of Science and Informatics University of Szeged Szeged Hungary

Department of Biological Anthropology Institute of Biology Faculty of Science Eötvös Loránd University Budapest Hungary

Department of Environmental Biology Sapienza University of Rome Rome Italy

Department of Evolutionary Anthropology University of Vienna Vienna Austria

Department of Genetics Harvard Medical School Boston MA USA

Department of Human Evolutionary Biology Harvard University Cambridge MA USA

Department of Statistics University of Oxford Oxford UK

Déri Museum Debrecen Hungary

Dornyay Béla Museum Salgótarján Hungary

Eger Hungary

Ex Voto Régészeti Kft Budapest Hungary

Faculty of Medicine Center of Bone Biology University of Belgrade Belgrade Serbia

Ferenczy Museum Center Szentendre Hungary

Göcseji Museum Zalaegerszeg Hungary

Herman Ottó Museum Miskolc Hungary

Howard Hughes Medical Institute Boston MA USA

Human Evolution and Archaeological Sciences University of Vienna Vienna Austria

HUN REN Research Centre for the Humanities Institute of Archaeology Budapest Hungary

Hungarian National Museum Budapest Hungary

Ikerbasque Basque Foundation of Science Bilbao Spain

Institute of Archaeological Sciences Eötvös Loránd University Budapest Hungary

Institute of Archaeology Slovak Academy of Sciences Nitra Slovakia

Municipal Museum of Subotica Subotica Serbia

Museo delle Civiltà Italian Ministry for Culture Rome Italy

Museum Unit of Public Library 'Branko Radičević' Odžaci Serbia

National Museum of Serbia Belgrade Serbia

Research Institute of the University of Bucharest University of Bucharest Bucharest Romania

Salisbury Kft Budapest Hungary

Székely National Museum Sfântu Gheorghe Romania

Teleorman County Museum Alexandria Romania

Town Museum of Sombor Sombor Serbia

Vinkovci Municipal Museum Vinkovci Croatia

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