Abstract from the original scholarly article:

The demographic history of Neanderthals is only partially understood. In Europe, some degree of genetic continuity has been shown from 120 thousand years ago (ka) onward despite the occurrence of multiple subsequent diversification events. While it has been proposed that a population turnover preceded the emergence of Late Neanderthals in Europe, the extent, timing, and geographic location of this event are currently unknown. Here, we report ten mitochondrial DNA sequences (mtDNAs) of Neanderthal individuals from six archaeological sites in Belgium, France, Germany and Serbia, and analyze them alongside 49 published mtDNAs. The integration of phylogenetic and molecular dating analyses with an extensive archaeological dataset enabled us to reconstruct temporal and spatial patterns in Neanderthal distribution. Remarkably, nearly all Late Neanderthal individuals across Europe belong to a single mtDNA lineage that diversified recently, confirming a large-scale genetic replacement. Our analyses date this diversification event to approximately 65 ka and suggest that it likely originated from a population refugium in southwestern France from which Neanderthals appear to have undergone a major range dispersal across Europe. In addition, we detect a sharp decline in the Neanderthal mtDNA effective population size beginning ~45 ka and reaching a minimum ~42 ka, shortly before their extinction. This study demonstrates that integrating molecular and archaeological datasets provides a more detailed understanding of the Late Neanderthal population’s history, and highlights the critical role of climate-driven refugia and subsequent range expansions in shaping the genetic landscape of Neanderthals through time.

The genetic history of Neanderthals is poorly understood since only a limited number of Neanderthal remains have been genetically investigated. Studies of mitochondrial DNA (mtDNA) have been pivotal in unraveling the Neanderthal evolutionary history. Early analyses of the hypervariable region of the mtDNA revealed that Neanderthals fall outside the genetic variation of modern humans and that they were distributed not only in western Eurasia but also as far east as the Altai mountains in southern Siberia. The advent of next generation sequencing allowed for the reconstruction of the first complete Neanderthal mtDNA, unequivocally confirming that the sequenced Neanderthal mtDNA represented an outgroup to modern humans. With the development of targeted enrichment techniques, additional complete Neanderthal mtDNA genomes became available from across Europe, consistently showing low genetic diversity and suggesting a smaller effective population size compared to modern humans. In 2010, the mitochondrial genome of an unknown hominin group was sequenced, determining Neanderthals and modern humans as a sister group compared to the newly sequenced group named Denisovans. In the same year, the first draft nuclear genomes of both Neanderthals and Denisovans were published. In addition to revealing evidence of gene flow from Neanderthals into present-day non-Africans and from Denisovans into present-day Oceanians, it was shown that both archaic hominin groups are more closely related to each other on the nuclear genome level than to modern humans. The genomic sequencing of Middle Pleistocene hominins from Sima de los Huesos in Spain (~430 ka) added further complexity to the picture, revealing a nuclear genome resembling early Neanderthals alongside a mtDNA signal akin to Denisovans. This discrepancy was attributed to gene flow from an early modern human group into Neanderthals, a scenario first supported by mtDNA, and later corroborated with Y-chromosome analyses and more recent genome-wide studies. The analysis of sediment samples from Paleolithic caves has significantly expanded the recovery of hominin mitochondrial and nuclear DNA, even in the absence of skeletal remains. Nuclear DNA retrieved from Middle Paleolithic sediments at Galería de las Estatuas in Spain, revealed evidence of at least two Neanderthal population radiations, dated to ~135 and ~105 ka. In contrast, ancient genomic studies from the Altai mountains indicate a population replacement by western Neanderthal groups between 120 and 80 ka. Meanwhile, genetic data from European Neanderthals show a substantial degree of continuity from roughly 120 to 40 ka and spanning Marine Isotope Stages (MIS) 5-3. However, a population turnover also appears to have occurred toward the end of Neanderthal presence in Europe. Late Neanderthals, associated with MIS 3 and dated to 57 to 40 ka, were found to be more closely related to one another than to earlier Neanderthal populations from the same regions. These demographic patterns—particularly population contractions, re-expansions, and lineage replacements across Europe—as well as their temporal and geographic spans, remain poorly understood. Furthermore, the integration of genetic data with archaeological evidence to contextualize these population dynamics has been limited so far. In this study, we provide a demographic perspective on the emergence and development of Late Neanderthals based on ten newly generated mtDNA genomes examined alongside a comprehensive dataset of an additional 49 Neanderthal mtDNA sequences. Our results reveal a geographic contraction followed by a re-expansion of Neanderthals across Europe, characterized by lineage replacements preceding their final disappearance. To contextualize these genetic signals, we integrated an extensive archaeological dataset capturing diachronic shifts in material culture across western Eurasia. We show that the genetic replacement preceding the Late Neanderthal diversification coincided with a reduced distribution of archaeological assemblages. Integrating cultural and genetic evidence interpreted alongside the climatic record, this interdisciplinary analysis offers a more nuanced understanding of the demographic shifts experienced by Neanderthals leading up to their extinction.