Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans

• Published in: Science (American Association for the Advancement of Science) 2024-12, Vol.386 (6727), p.eadq3010
• Main Authors: Iasi, Leonardo N M, Chintalapati, Manjusha, Skov, Laurits, Mesa, Alba Bossoms, Hajdinjak, Mateja, Peter, Benjamin M, Moorjani, Priya
• Format: Article
• Language: English
• Subjects: Animals; Chromosomes; Computer Uses in Education; Demography; Deserts; DNA, Ancient - analysis; Evolutionary genetics; Frequency variation; Gene Flow; Genealogy; Genetic analysis; Genetic diversity; Genetic drift; Genetics; Genome, Human; Genomes; Genomics; Geography; Historical structures; Hominids; Humans; Interspecific hybridization; Lower bounds; Natural selection; Neanderthals - genetics; Phenotypic variations; Population structure; Segments; Selection, Genetic; Somatic chromosomes; Time; X chromosomes
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.adq3010

Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments in more than 300 genomes spanning the past 50,000 years. We examined how Neanderthal ancestry is shared among individuals over time. Our analysis revealed that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that occurred between 50,500 to 43,500 years ago, as evidenced by ancestry correlation, colocalization of Neanderthal segments across individuals, and divergence from the sequenced Neanderthals. Most natural selection-positive and negative-on Neanderthal variants occurred rapidly after the gene flow. Our findings provide new insights into how contact with Neanderthals shaped modern human origins and adaptation.