Genomic analysis refines timing of Neandertal admixture – and its impact on modern humans

A genomic study encompassing more than 300 genomes spanning the last 50,000 years has revealed how a single wave of Neandertal gene flow into early modern humans left an indelible mark on human evolution. Among other findings, the study reports that modern humans acquired several Neanderthal genes that ended up being advantageous to our lineage, including those involved in skin pigmentation, immune response, and metabolism. To date, sequencing of Neanderthal and Denisovan genomes has revealed substantial gene flow between these archaic hominins and modern human ancestors, even as scientists have also reported that Neanderthal ancestry is unevenly distributed across the genome. Moreover, certain regions of the genome – known as archaic deserts – completely lack Neandertal ancestry, while others exhibit high frequencies of Neanderthal variants, potentially due to beneficial adaptive mutations. However, much about the nature of this ancient admixture, including the role evolutionary forces like genetic drift or natural selection played in shaping these patterns, remains unclear. Using genomic data from 334 modern humans, including 59 ancient individuals ranging from 45,000 to 2,200 years old, and 275 present-day individuals from diverse global populations, Leonardo Iasi et al. performed a comprehensive evaluation of Neanderthal ancestry variation in modern humans over the last ~50,000 years. Iasi et al. discovered that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that likely occurred 50,500 to 43,500 years ago, which is consistent with archeological evidence for the overlap of modern humans and Neandertals in Europe. Additionally, the findings demonstrate that Neanderthal ancestry underwent rapid natural selection – both positive and negative – within 100 generations after gene flow, especially on the X chromosome.

Nature is publishing a related paper, “Earliest modern human genomes constrain timing of Neanderthal admixture,” embargoed for the same time (Thursday, 12 December at 2pm US ET). To obtain a copy of this paper, please email press@nature.com or visit the Springer Nature press site. An online press briefing for the two papers will take place UNDER STRICT EMBARGO on Wednesday at 3pm London time (GMT) / 10 am US Eastern Time. To attend this briefing please pre-register here.