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SAI: A Python Package for Statistics for Adaptive Introgression.

Xin Huang1,2, Simon Chen1, Josef Hackl1,2

  • 1Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.

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|November 19, 2025
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Summary
This summary is machine-generated.

We developed SAI, a Python package for analyzing adaptive introgression using genetic data. It computes key statistics, aiding evolutionary studies and identifying introgressed regions in humans and primates.

Keywords:
Pythonadaptive introgressionpopulation geneticsreproducibilitystatistical inference

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Area of Science:

  • Evolutionary biology
  • Population genetics
  • Bioinformatics

Background:

  • Adaptive introgression is a key evolutionary mechanism driving genetic adaptation.
  • Existing summary statistics for identifying adaptive introgression lack accessible software implementations.
  • Novel statistics like D+ and Danc require user-friendly tools for broader application.

Purpose of the Study:

  • To introduce SAI, a Python package for computing statistics related to adaptive introgression.
  • To provide accessible implementations for established and novel statistics (DD).
  • To demonstrate the utility of SAI in identifying introgressed genomic regions.

Main Methods:

  • Development of the SAI Python package for statistical analysis.
  • Application of SAI to the 1000 Genomes Project dataset.
  • Analysis of bonobo introgression into central chimpanzees.

Main Results:

  • SAI successfully replicated known introgressed regions in the 1000 Genomes data and identified novel candidate regions.
  • One identified region showed overlap with areas detected by deep learning methods.
  • Investigation of chimpanzee-bonobo introgression revealed candidate genes, including a region overlapping Denisovan-introgressed haplotypes in Papuans.

Conclusions:

  • The SAI package offers accessible tools for evolutionary geneticists studying adaptive introgression.
  • SAI facilitates the discovery of introgressed regions across diverse species and datasets.
  • Findings highlight the significance of adaptive introgression across divergent evolutionary lineages.