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

Gene flow from Neandertals has shaped the landscape of genetic and
phenotypic variation in modern humans. We identify the location and size
of introgressed Neandertal ancestry segments in more than 300 genomes
spanning the last 50,000 years. We study how Neandertal ancestry is shared
among individuals to infer the time and duration of the Neandertal gene
flow. We find the correlation of Neandertal segment locations across
individuals and their divergence to sequenced Neandertals, both support a
model of a single major Neandertal gene flow. Our catalog of introgressed
segments through time confirms that most natural selection–positive and
negative–on Neandertal ancestry variants occurred immediately after the
gene flow, and provides new insights into how contact with Neandertals
shaped human origins and adaptation.