The nature and distribution of political power in Europe during the Neolithic era remains poorly understood 1 . During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive 2 . Although co-operative ideology has often been emphasised as a driver of megalith construction1, the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy 3 —of which the most extreme case is a small elite marshalling the labour of the masses. Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites 4 —specifically within polygynous and patrilineal royal families that are headed by god-kings 5 , 6 . We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.

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The Newferry area is situated to the north of Lough Beg which is almost a northern extension of Lough Neagh, in Co. Antrim, Northern Ireland. Newferry is not a precise geographical area; it lies on both the Antrim and Derry side of the River Bann, and is an extensive area of diatomite flats nearly one mile wide which is bounded to the east and west by the drumlins lining either side of the valley. In early post-glacial times this would have been an extension to Lough Beg and until the Bann was dredged in the 1930's it was still liable to flood during the winter months. On the northern edge on the western side of the river the diatomite is known to run under the edge of Ballymacombs More raised bog. Therefore this lacustrine basin may have extended for another two miles north to Culbane where the high ground of Ballynease would have partially separated it from the next lake basin (fig. 1).Newferry has long been known as an area where Mesolithic material could be recovered from the Quaternary deposits. Several other excavations have taken place in this area prior to the present excavations. The Harvard Archaeological Mission carried out an excavation on the Derry side of the river in the early 1930's (Movius 1936) while in the late 1950's another small investigation was carried out on the Antrim side of the River (Smith and Collins 1971). In total there are now four sites known in this area.