Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.

In the absence of any direct evidence, the relative importance of meat and dairy productions to Neolithic prehistoric Mediterranean communities has been extensively debated. Here, we combine lipid residue analysis of ceramic vessels with osteo-archaeological age-at-death analysis from 82 northern Mediterranean and Near Eastern sites dating from the seventh to fifth millennia BC to address this question. The findings show variable intensities in dairy and nondairy activities in the Mediterranean region with the slaughter profiles of domesticated ruminants mirroring the results of the organic residue analyses. The finding of milk residues in very early Neolithic pottery (seventh millennium BC) from both the east and west of the region contrasts with much lower intensities in sites of northern Greece, where pig bones are present in higher frequencies compared with other locations. In this region, the slaughter profiles of all domesticated ruminants suggest meat production predominated. Overall, it appears that milk or the by-products of milk was an important foodstuff, which may have contributed significantly to the spread of these cultural groups by providing a nourishing and sustainable product for early farming communities.

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The spread of early farming across Europe from its origins in Southwest Asia was a culturally transformative process which took place over millennia. Within regions, the pace of the transition was probably related to the particular climatic and environmental conditions encountered, as well as the nature of localized hunter–gatherer and farmer interactions. The establishment of farming in the interior of the Balkans represents the first movement of Southwest Asian livestock beyond their natural climatic range, and widespread evidence now exists for early pottery being used extensively for dairying. However, pottery lipid residues from sites in the Iron Gates region of the Danube in the northern Balkans show that here, Neolithic pottery was being used predominantly for processing aquatic resources. This stands out not only within the surrounding region but also contrasts markedly with Neolithic pottery use across wider Europe. These findings provide evidence for the strategic diversity within the wider cultural and economic practices during the Neolithic, with this exceptional environmental and cultural setting offering alternative opportunities despite the dominance of farming in the wider region.

Highlights d Bronze Age (BA) Helladic, Cycladic, and Minoan genomes from the Aegean were sequenced d 3,000 BCE Aegeans are homogeneous and derive ancestry mainly from Neolithic farmers d Neolithic Caucasus-like and BA Pontic-Caspian Steppe-like gene flow shaped the Aegean d Present-day Greeks are genetically similar to 2,000 BCE Aegeans from Northern Greece