sstar:A Python package for detecting archaic introgression from population genetic data with S*
More On Article
- At the onset of the Late Gravettian: An updated chronology and stratigraphy for the multi-layered Gravettian open-air site Grub-Kranawetberg I (Austria).
- New Chronology Sheds Light on Human Occupation just before the onset of the Last Glacial Maximum
- Fire, temperature control, and silcrete heat treatment at Diepkloof and Mertenhof Rock Shelters, West Coast, South Africa
- Gerhard Weber and Harald Wilfing Retire
- HEAS Workshop in New Methodologies and Perspectives in Palaeolithic Archaeofauna takes place in Vienna.
Huang, X., Kuhlwilm, M., 2022. sstar: A Python package for detecting archaic introgression from population genetic data with S*. Molecular Biology and Evolution
Abstract
S* is a widely used statistic for detecting archaic admixture from population genetic data. Previous studies used freezing-archer to apply S*, which is only directly applicable to the specific case of Neanderthal and Denisovan introgression in Papuans. Here, we implemented sstar for a more general purpose. Compared with several tools, including SPrime, SkovHMM, and ArchaicSeeker2.0, for detecting introgressed fragments with simulations, our results suggest that sstar is robust to differences in demographic models, including ghost introgression and two-source introgression. We believe sstar will be a useful tool for detecting introgressed fragments in various scenarios and in non-human species.