Neolithic genomes from Southern France showcase intensified interactions with hunter-gatherer communities

The onset of agriculture in Western Europe was accompanied by major demographic changes that shaped the genetic structure of human populations. The expansion of early farmers from Anatolia and the Near East is now well documented, but the complexity of interactions with local hunter-gatherers is less clear. Studies on the local scale can elucidate the regional variability during this transition phase and add nuance to the broader pan-European picture. Furthermore, some regions are still understudied, in particular those associated with the Neolithic expansion along the Mediterranean coastline. To address this, we report new data from Occitanie, a key geographical region in southern France, located between culturally-distinct Neolithic groups of the Iberian Peninsula, southeastern France, and northern Italy. We sequenced 28 ancient human genomes from six sites in Southern France covering a wide range of archaeological contexts and funerary practices, and report new 14C dates for 23 individuals. Spanning from c. 5,500 to c. 2,500 BCE, this dataset allowed us to characterize regional patterns of ancestries in farmer groups throughout the Neolithic in southern France. We find differences between the Mediterranean and Continental waves of the Neolithic expansion regarding the processes and modes of migration and interaction. We detect high proportions of hunter-gatherer ancestry in early Neolithic groups in the South of France, as opposed to other French and West European regions. Our results also highlight the persistence of a high level of hunter-gatherer ancestry in some late Neolithic individuals. The presence of this pattern of ancestry in multiple Western European regions in Late Neolithic communities suggests multiple pulses of inter-group gene flow throughout time and space pointing to complex demographic phenomena.