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.

Researchers agree that domesticated plants were introduced into southeast Europe from southwest Asia as a part of a Neolithic "package," which included domesticated animals and artifacts typical of farming communities. It is commonly believed that this package reached inland areas of the Balkans by ∼6200 calibrated (cal.) BC or later. Our analysis of the starch record entrapped in dental calculus of Mesolithic human teeth at the site of Vlasac in the Danube Gorges of the central Balkans provides direct evidence that already by ∼6600 cal. BC, if not earlier, Late Mesolithic foragers of this region consumed domestic cereals, such as Triticum monococcum, Triticum dicoccum, and Hordeum distichon, which were also the main crops found among Early Neolithic communities of southeast Europe. We infer that "exotic" Neolithic domesticated plants were introduced to southern Europe independently almost half a millennium earlier than previously thought, through networks that enabled exchanges between inland Mesolithic foragers and early farming groups found along the Aegean coast of Turkey.Mesolithic foragers | starch analysis | domesticated cereals | forager/farmer interaction | human dental calculus

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Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe—the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.

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