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., We identified Neandertal introgressed segments in 59 ancient and 2118 present-day modern human individuals using an HMM approach called admixfrog., , # Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans

[https://doi.org/10.5061/dryad.zw3r228gg](https://doi.org/10.5061/dryad.zw3r228gg)

In this study, we used 59 ancient and 2118 present-day modern human genomes. We called segments in the genome that are of Neandertal and Denisovan ancestry. In this data repository are all the files used for the analysis of the study. For a detailed description of how the data was generated see the supplementary section of the study.

## Description of the data and file structure

In this data repository are 11 files in total. Most files are given or contain data for admixfrog runs. The genetic distances given in these files are from two different empirical genetic maps. Either from the Shared genetic map (these do not contain data on the X chromosome) or from the African-American map (this genetic map is specific to the African hot spot and not very precise for Eurasian populations but it contains the X chromos..., , **Changes after Nov 26, 2024:** ALL_called_ancestry_segments.csv.zip file was re-uploaded since the previous version was missing the segments for ancient and SGDP individuals called using the Shared map. Now all segments called in SGDP and ancient individuals called with both maps (African-American and Shared map) are present as well as all segments from the individuals without recent African origin from the 1000 genomes Project phase 3 (only on the Shared map).