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 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 the contact with Neandertals shaped human origins and adaptation.

In summary, the majority of positive and negative selection on Neandertal ancestry happened very quickly, and left clear signals in the genetic diversity of the first modern humans outside Africa. Only a smaller proportion of variants became adaptive later on.