Genetic studies pinpoint Neanderthal-modern human interbreeding to 45,000-49,000 years ago
New analyses of ancient genomes show that interbreeding between Neanderthals and early modern humans began around 47,000 years ago and continued for several millennia, leaving 1-2% Neanderthal DNA in most non-African populations today.
Genetic research published in December 2024 narrows the timing of Neanderthal-modern human interbreeding to a single episode between 45,000 and 49,000 years ago. A study in Science that compared 58 ancient Eurasian genomes with 275 modern ones estimated the average admixture event at about 47,000 years ago, with gene flow persisting for roughly 7,000 years. A companion paper in Nature examined 45,000-year-old remains from Germany and the Czech Republic and traced the same admixture window, which appears to be shared by every sequenced non-African individual.
The findings build on earlier work that first identified Neanderthal DNA in modern Eurasians after the 2010 draft Neanderthal genome. Current estimates place Neanderthal ancestry at about one to two percent of the genome in present-day non-Africans, with East Asian populations carrying a slightly higher proportion.
"These deserts may have formed very rapidly after the gene flow," said Leonardo Iasi, a co-author of the Nature paper, referring to genomic regions where no Neanderthal DNA is detected. He explained that such "Neanderthal deserts" suggest certain archaic variants were disadvantageous and were eliminated from the modern human gene pool within a few thousand years.
The Oase individual from a Romanian cave, dated to roughly 40,000 years ago, carried an unusually high 6-9% Neanderthal ancestry, indicating a recent Neanderthal ancestor within four to six generations. However, his lineage left little trace in later European populations.
Research continues to map the functional impact of the surviving Neanderthal fragments. Studies have linked some inherited variants to immune response, skin pigmentation and metabolism, while others, such as a segment on chromosome three associated with severe COVID-19 risk, illustrate potential health liabilities.
Overall, the genetic evidence reshapes the narrative of Neanderthal extinction, showing that the species was not simply replaced but was gradually absorbed into the expanding modern human gene pool.