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It is now widely accepted that agriculture and settled village life arrived in Europe as a cultural package, carried by people migrating from Anatolia and the Aegean Basin. The putative fisher-forager site of Lepenski Vir in Serbia has long been acknowledged as an exception to this model. Here, the Mesolithic–Neolithic transition—possibly inspired by interaction with the new arrivals—was thought to have taken place autochthonously on site. Our reinterpretation, based on ancient genomes, as well as archaeological and isotopic evidence, indicates that here, too, house construction, early village society and agriculture were primarily associated with Europe's first farmers, thus challenging the long-held view of Lepenski Vir as a Mesolithic community that adopted Neolithic practices. Although aspects of the site's occupation, such as the trapezoidal houses, were inspired by local Mesolithic traditions, it is far from certain that the village was founded by Iron Gates foragers. A detailed timeline of population changes at the site suggests that Aegean incomers did not simply integrate into an established Mesolithic society, but rather founded new lineages and households. Iron Gates foragers and their admixed descendants largely appear to have been buried separately, on the fringes of the settlement. The diet of those buried outside in pits shows no major shift from aquatic to terrestrial food resources. [ABSTRACT FROM AUTHOR]

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.