Ancient genome-wide DNA from France highlights the complexity of interactions between Mesolithic hunter-gatherers and Neolithic farmers

Starting from 12,000 years ago in the Middle East, the Neolithic lifestyle spread across Europe via separate continental and Mediterranean routes, which eventually overlapped in western Europe. Genomes from early European farmers have shown a clear Near Eastern/Anatolian genetic affinity with limited contribution from hunter-gatherers. However, no genomic data is available from modern-day France, where both routes converged, as evidenced by a mosaic cultural pattern. Here we present new genome-wide data from 101 individuals from 12 sites covering today's France and Germany from the Mesolithic (N=3) to the Neolithic (N=98) (7000-3000 BCE). Using the genetic substructure observed in European hunter-gatherers, we characterise diverse patterns of admixture in different regions, consistent with both routes of expansion. Western early European farmers show a higher proportion of distinctly western hunter-gatherer ancestry compared to central/south-eastern farmers. Our data highlight the complexity of the biological interactions during the Neolithic expansion by revealing major regional variations.