Farming was first introduced to Europe in the mid-7th millennium BCE–associated with migrants from Anatolia who settled in the Southeast before spreading throughout Europe. To understand the dynamics of this process, we analyzed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document a West-East cline of ancestry in indigenous hunter-gatherers and–in far-eastern Europe–early stages in the formation of Bronze Age Steppe ancestry. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited hunter-gatherer admixture, but that some groups that remained mixed extensively, without the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West, with intermittent genetic contact with the Steppe up to 2000 years before the migrations that replaced much of northern Europe’s population.

Farming was first introduced to southeastern Europe in the mid-7th millennium BCE – brought by migrants from Anatolia who settled in the region before spreading throughout Europe. To clarify the dynamics of the interaction between the first farmers and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient DNA data from 223 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document previously uncharacterized genetic structure, showing a West-East cline of ancestry in hunter-gatherers, and show that some Aegean farmers had ancestry from a different lineage than the northwestern Anatolian lineage that formed the overwhelming ancestry of other European farmers. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited admixture with local hunter-gatherers, but that some groups mixed extensively, with relatively sex-balanced admixture compared to the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West after farming arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the migration that replaced much of northern Europe’s population.

By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra–West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.

Since their domestication in the Mediterranean zone of Southwest Asia in the eighth millennium BC, sheep, goats, pigs and cattle have been remarkably successful in colonizing a broad variety of environments. The initial steps in this process can be traced back to the dispersal of farming groups into the interior of the Balkans in the early sixth millennium BC, who were the first to introduce Mediterranean livestock beyond its natural climatic range. Here, we combine analysis of biomolecular and isotopic compositions of lipids preserved in prehistoric pottery with faunal analyses of taxonomic composition from the earliest farming sites in southeast Europe to reconstruct this pivotal event in the early history of animal husbandry. We observe a marked divergence between the (sub)Mediterranean and temperate regions of Southeast Europe, and in particular a significant increase of dairying in the biochemical record coupled with a shift to cattle and wild fauna at most sites north of the Balkan mountain range. The findings strongly suggest that dairying was crucial for the expansion of the earliest farming system beyond its native bioclimatic zone.

During the course of the diffusion of Neolithic agropastoral societies across Europe, animal husbandry was adapted to local constraints and resources, involving changes in practices, as well as in animal physiology. As a result, the timing of animal breeding was impacted, with consequences on the organization of agro-pastoral tasks and the seasonal availability of animal productions. Past sheep birth seasonality can be investigated through the reconstruction of the seasonal cycle recorded in molars, based on the sequential analysis of stable oxygen isotope ratios (δ 18 O) in enamel. Modern sheep serve as comparative material to define the season of birth. In the present study, we provide new reference values for winter births in the sheep third molar (M3) using data from the modern Kemenez sheep herd. The dataset also includes paired upper and lower M3s in order to test the comparability of results obtained from both teeth. Results show a moderate shift in the isotopic record between upper and lower M3s. The consecutive difference in the assessment of the timing of birth is one month, on average. Additionally, we provide a new set of results for sheep from Nova Nadezhda (Bulgaria, early sixth millennium BC), combining upper and lower molars, in order to expand data relating to the earliest stages of the introduction of sheep to Europe. At Nova Nadezhda, sheep were born in late winter and spring, and the pattern of birth distribution does not indicate the control of sheep reproduction by separating males from females. When compared to previously published results at other Neolithic and Chalcolithic sites in the Balkans, corrected for the shift between upper and lower M3s, no latitudinal and chronological trend is observed between the Southern Balkans, Northern Balkans and Hungarian plains over the early sixth to the second half of the fifth millennia BC. This apparent uniformity for the length (3-4 months) and timing of the birth period could be challenged in the future by enlarged datasets.