Abstract

Neanderthal genomes have been recovered from sites across Eurasia, painting an increasingly complex picture of their populations structure, mostly indicating that late European Neanderthals belonged to a single metapopulation with no significant evidence of deep population structure. Here we report the discovery of a late Neanderthal individual, nicknamed "Thorin", from Grotte Mandrin in Mediterranean France, and his genome. These dentognathic fossils, including a rare example of distomolars, are associated with a rich archeological record of their final technological traditions in this region [~]50-42 thousand years ago. Thorins genome reveals a deep divergence with other late Neanderthals. Thorin belonged to a population with small group size that showed no genetic introgression with other known late European Neanderthals, revealing genetic isolation of his lineage despite them living in neighboring regions. These results have important implications for resolving competing hypotheses about causes of the Neanderthals disappearance. One Sentence SummaryA new French Neanderthal fossil and its genome reveal complex population dynamics during the past 100,000 years.