Modern humans arrived in Europe more than 45,000 years ago, overlapping at least 5,000 years with Neanderthals1-4. Limited genomic data from these early modern humans have shown that at least two genetically distinct groups inhabited Europe, represented by Zlatý kůň, Czechia3 and Bacho Kiro, Bulgaria2. Here we deepen our understanding of early modern humans by analysing one high-coverage genome and five low-coverage genomes from approximately 45,000-year-old remains from Ilsenhöhle in Ranis, Germany4, and a further high-coverage genome from Zlatý kůň. We show that distant familial relationships link the Ranis and Zlatý kůň individuals and that they were part of the same small, isolated population that represents the deepest known split from the Out-of-Africa lineage. Ranis genomes harbour Neanderthal segments that originate from a single admixture event shared with all non-Africans that we date to approximately 45,000-49,000 years ago. This implies that ancestors of all non-Africans sequenced so far resided in a common population at this time, and further suggests that modern human remains older than 50,000 years from outside Africa represent different non-African populations.

California State University Northridge Northridge CA USA

Chaire de Paléoanthropologie CIRB Collège de France Paris France

Charles University Prague Czechia

Department of Archaeology University of Reading Reading UK

Francis Crick Institute London UK

Friedrich Alexander Universität Erlangen Nürnberg Institut für Ur und Frühgeschichte Erlangen Germany

Friedrich Schiller University Jena Institute of Zoology and Evolutionary Research Jena Germany

Globe Institute University of Copenhagen Copenhagen Denmark

Institute of Computer Science Universität Leipzig Leipzig Germany

Institute of Evolutionary Biology CSIC Universitat Pompeu Fabra Barcelona Spain

Karolinska Institutet Stockholm Sweden

Landesamt für Denkmalpflege und Archäologie Sachsen Anhalt Landesmuseum für Vorgeschichte Halle Germany

Max Planck Institute for Evolutionary Anthropology Leipzig Germany

National Museum Prague Czechia

Prähistorische Archäologie Freie Universität Berlin Germany

School of Biological Sciences University of Adelaide Adelaide South Australia Australia

Thuringian State Office for the Preservation of Historical Monuments and Archaeology Weimar Germany

Tübingen University Tübingen Germany

University of Bordeaux CNRS Bordeaux INP CBMN UMR 5248 and Bordeaux Proteome Platform Bordeaux France

University of Bordeaux CNRS Ministère de la Culture PACEA Pessac France

University of Bristol Bristol UK

University of California Berkeley CA USA

University of Rochester Rochester NY USA

Weizmann Institute of Science Tel Aviv Israel

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