Paleogenomic and archaeological studies show that Neolithic lifeways spread from the Fertile Crescent into Europe around 9000 BCE, reaching northwestern Europe by 4000 BCE. Starting around 4500 BCE, a new phenomenon of constructing megalithic monuments, particularly for funerary practices, emerged along the Atlantic façade. While it has been suggested that the emergence of megaliths was associated with the territories of farming communities, the origin and social structure of the groups that erected them has remained largely unknown. We generated genome sequence data from human remains, corresponding to 24 individuals from five megalithic burial sites, encompassing the widespread tradition of megalithic construction in northern and western Europe, and analyzed our results in relation to the existing European paleogenomic data. The various individuals buried in megaliths show genetic affinities with local farming groups within their different chronological contexts. Individuals buried in megaliths display (past) admixture with local hunter-gatherers, similar to that seen in other Neolithic individuals in Europe. In relation to the tomb populations, we find significantly more males than females buried in the megaliths of the British Isles. The genetic data show close kin relationships among the individuals buried within the megaliths, and for the Irish megaliths, we found a kin relation between individuals buried in different megaliths. We also see paternal continuity through time, including the same Y-chromosome haplotypes reoccurring. These observations suggest that the investigated funerary monuments were associated with patrilineal kindred groups. Our genomic investigation provides insight into the people associated with this long-standing megalith funerary tradition, including their social dynamics.

Archaeological Research Laboratory Department of Archaeology and Classical Studies Stockholm University SE 106 91 Stockholm Sweden

Centre for Anthropological Research Department of Anthropology and Development Studies University of Johannesburg 2006 Auckland Park South Africa

Department of Archaeology and Ancient History Uppsala University Campus Gotland SE 621 67 Visby Sweden

Department of Human Evolution Max Planck Institute for Evolutionary Anthropology 04103 Leipzig Germany

Department of Prehistorical Archaeology Institute of Archaeology of Czech Academy of Sciences CZ 11801 Prague Czech Republic

Department of Surgery Royal Prince Alfred Hospital Sydney NSW 2050 Australia

Human Evolution Department of Organismal Biology Uppsala University SE 752 36 Uppsala Sweden

Human Evolution Department of Organismal Biology Uppsala University SE 752 36 Uppsala Sweden;

Museums and Special Collections Sir Duncan Rice Library University of Aberdeen AB24 3AA Aberdeen Scotland

Osteoarchaeological Research Laboratory Department of Archaeology and Classical Studies Stockholm University SE 106 91 Stockholm Sweden

Osteoarchaeological Research Laboratory Department of Archaeology and Classical Studies Stockholm University SE 106 91 Stockholm Sweden;

Research Centre in Evolutionary Anthropology and Paleoecology School of Natural Sciences and Psychology Liverpool John Moores University L3 3AF Liverpool United Kingdom

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