Eppie R. Jones, Gloria M. González-Fortes, Sarah Connell, Veronika Siska, Anders Eriksson, Rui Martiniano, Russell L. McLaughlin, Marcos Gallego Llorente, Lara M. Cassidy, Cristina Gamba, Tengiz Meshveliani, Ofer Bar-Yosef, Werner Müller, Anna Belfer-Cohen, Zinovi Matskevich, Nino Jakeli, Thomas F. G. Higham, Mathias Currat, David Lordkipanidze, Michael Hofreiter, Andrea Manica, Ron Pinhasi, Daniel G. Bradley

• We extend the scope of European palaeogenomics by sequencing the genomes of Late Upper Palaeolithic (13,300 years old, 1.4-fold coverage) and Mesolithic (9,700 years old, 15.4-fold) males from western Georgia in the Caucasus and a Late Upper Palaeolithic (13,700 years old, 9.5-fold) male from Switzerland. While we detect Late Palaeolithic–Mesolithic genomic continuity in both regions, we find that Caucasus hunter-gatherers (CHG) belong to a distinct ancient clade that split from western hunter-gatherers ∼45 kya, shortly after the expansion of anatomically modern humans into Europe and from the ancestors of Neolithic farmers ∼25 kya, around the Last Glacial Maximum. CHG genomes significantly contributed to the Yamnaya steppe herders who migrated into Europe ∼3,000 BC, supporting a formative Caucasus influence on this important Early Bronze age culture. CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.