In the past ten years, genomic data were obtained on hunter-gatherers from the Upper Paleolithic to the Mesolithic, from all over Europe. Although scarce and often with a poor DNA preservation, these data have led to a better understanding of the genetic substructure of the Mesolithic groups.

At the beginning of the Holocene, the Neolithic transition from foraging to farming spread as a new lifestyle towards Europe via distinct continental and Mediterranean routes, starting from 12,000 years ago in the Middle East. Both streams eventually overlapped in Western Europe. Here, a complex scenario of contact, interaction and exchange with autochthonous hunter-gatherers resulted in a mosaic pattern of the material culture between the Mesolithic and the Late Neolithic that is well-known in archaeology. 

Investigated in greater detail using genomic data, incoming farmer groups have been shown to have a clear Near Eastern/Anatolian cultural and genetic background with only limited genetic contribution from hunter-gatherers for at least two millennia from the south-east to Western Europe, despite evidence of mutual material exchange. However, so far, no genomic data was available from modern-day France, the key region where both routes converged.

Here, in the framework of the collaborative project INTERACT (ANR/DFG), we present new genome-wide data covering today's France and Germany from the Mesolithic to the Neolithic (7000-3000 BCE). Utilising the genetic substructure observed in hunter-gatherer groups across Europe, we are able to trace characteristic patterns of admixture between incoming farmers and indigenous hunter-gatherers in different regions, which are consistent with both routes of the Neolithic expansion. In particular, Western European early farmers show a higher proportion of specific Western Hunter-Gatherer ancestry compared to those linked to South-eastern or Central Europe. The proportion of Hunter-Gatherer component also varies regionally, and the highest values can be found in the French Mediterranean coast (up to 55%). Here, we were able to estimate the initial admixture date to have occurred about four generations back in time, i.e. about a century after the first Neolithic farmers settled on the coast. 

Our data shed a new light on the complexity of biological interactions between human groups during the Neolithic expansion and establishment in Western Europe, echoing the archaeological knowledge and confirming major regional variations. This increasing resolution paves the way for a finer, multi-scale approach to better document the processes implied in the mobility and evolution of prehistoric groups.