A new genetic study of Neanderthal remains found that nearly all Late Neanderthals in Europe descended from one lineage that diversified around 65,000 years ago, most likely in what is now southwestern France, following a major population contraction driven by glacial conditions.
Neanderthals occupied Europe for roughly 360,000 years before disappearing around 40,000 years ago. Despite sustained research effort, the population history leading up to that disappearance has remained poorly understood. Prior studies established that some degree of genetic continuity existed among European Neanderthals from at least 120,000 years ago and that multiple diversification events occurred over that span. It had also been proposed that a population turnover preceded the emergence of what researchers call Late Neanderthals those living roughly between 60,000 and 40,000 years ago but the timing, extent, and geographic location of that event were not established. As Professor Cosimo Posth of the Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, who led the research, noted: “We have evidence that Neanderthals inhabited Europe continuously between 400,000 and 40,000 years ago. However, we have only fragmentary details of their population history.”
Earlier ancient DNA work had established that Neanderthals were genetically distinct from anatomically modern humans, that limited interbreeding occurred between the two groups, and that regional genetic diversity existed among Neanderthal populations across Europe and western Asia. What had not been characterized in detail was the specific demographic structure of the final 20,000 years of Neanderthal existence in Europe.
The team sequenced mitochondrial DNA (mtDNA) from ten Neanderthal individuals across six archaeological sites in Belgium, France, Germany, and Serbia, and analyzed these alongside 49 previously published Neanderthal mtDNA sequences. Mitochondrial DNA is inherited through the maternal line and captures only one lineage of an individual’s ancestry. As first author Charoula M. Fotiadou, a researcher in Posth’s group at the University of Tübingen, explained: “Mitochondrial DNA does not contain nearly as much genetic information as the entire genome of a human being, but it usually survives longer and is easier to obtain.”
The genetic data were integrated with archaeological site records from the ROAD database, a large-scale dataset documenting Neanderthal presence across western Eurasia, compiled by the ROCEEH project (The Role of Culture in Early Expansions of Humans). Phylogenetic analysis and molecular dating were applied to establish the timing and branching structure of the mtDNA lineages. Co-author Jesper Borre Pedersen, also part of the ROCEEH project, described the value of this approach: “This allowed us to combine the two lines of evidence and reconstruct the demographic history of Neanderthals in terms of space and time.”
Remarkably, nearly all Late Neanderthal individuals across Europe belong to a single mtDNA lineage that diversified recently, confirming a large-scale genetic replacement. The analyses placed the origin of this lineage at approximately 65,000 years ago in southwestern France. During the harsh climatic conditions of the Ice Age around 75,000 years ago, archaeological sites declined in number and became increasingly concentrated in southwestern Europe, consistent with a population retreating to a glacial refugium in that region. Professor Posth stated: “Our data enabled us to reconstruct geographically that Neanderthals retreated to what is now southwestern France. There, around 65,000 years ago, a new population emerged and later spread across the whole of Europe.”
The researchers also found that these Neanderthals later suffered a sharp decline in population around 45,000 years ago, reaching a minimum around 42,000 years ago shortly before Neanderthals became extinct altogether.
The authors concluded that the high genetic homogeneity observed among Late Neanderthals was the result of this contraction-and-expansion sequence, with climate as a likely contributing driver. The study does not identify a cause for the final extinction, nor does it address the role of contact with modern humans in the population’s decline.
The primary limitation the researchers noted is the use of mitochondrial DNA alone. Because mtDNA is maternally inherited and represents only a fraction of an individual’s total genetic history, it cannot capture the full complexity of population structure or admixture events. The study is also geographically bounded to western Eurasia, and the sample, while the largest mtDNA dataset yet assembled for this analysis, remains small relative to the span of time and territory involved. The geographic placement of the refugium in southwestern France is a reconstruction based on the convergence of genetic and archaeological signals, not a direct observation.
Reference:
Charoula M. Fotiadou, Jesper Borre Pedersen, Hélène Rougier, Mirjana Roksandic, Maria A. Spyrou, Kathrin Nägele, Ella Reiter, Hervé Bocherens, Andrew W. Kandel, Miriam N. Haidle, Timo P. Streicher, Nicholas J. Conard, Flora Schilt, Ricardo Miguel Godinho, Thorsten Uthmeier, Luc Doyon, Patrick Semal, Johannes Krause, Alvise Barbieri, Dušan Mihailović, Isabelle Crevecoeur, and Cosimo Posth. “Archaeogenetic insights into the demographic history of Late Neanderthals.” Proceedings of the National Academy of Sciences, Vol. 123, No. 13, e2520565123 (2026).
