sstar: A Python Package for Detecting Archaic Introgression from Population Genetic Data with <i>S</i> *
Xin Huang, Patricia Kruisz, Martin Kuhlwilm
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.
Topics & Concepts
BiologyPython (programming language)IntrogressionEvolutionary biologyGenetic dataPopulationR packageGeneticsProgramming languageComputer scienceDemographyGeneSociologyGenetic Mapping and Diversity in Plants and AnimalsGenetic and phenotypic traits in livestockGenetic diversity and population structure