The Genomic History of Southeastern Europe 1

116 Farming was first introduced to southeastern Europe in the mid-7 millennium BCE – 117 brought by migrants from Anatolia who settled in the region before spreading 118 throughout Europe. To clarify the dynamics of the interaction between the first farmers 119 and indigenous hunter-gatherers where they first met, we analyze genome-wide ancient 120 DNA data from 223 individuals who lived in southeastern Europe and surrounding 121 regions between 12000 and 500 BCE. We document previously uncharacterized genetic 122 structure, showing a West-East cline of ancestry in hunter-gatherers, and show that 123 some Aegean farmers had ancestry from a different lineage than the northwestern 124 Anatolian lineage that formed the overwhelming ancestry of other European farmers. 125 We show that the first farmers of northern and western Europe passed through 126 southeastern Europe with limited admixture with local hunter-gatherers, but that some 127 groups mixed extensively, with relatively sex-balanced admixture compared to the male128 biased hunter-gatherer admixture that prevailed later in the North and West. 129 Southeastern Europe continued to be a nexus between East and West after farming 130 arrived, with intermittent genetic contact from the Steppe up to 2,000 years before the 131 migration that replaced much of northern Europe’s population. 132 133