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A Rarefaction Approach to Identify Local Introgression in a Three Population Tree
T Quinn Smith1, Zachary A Szpiech1
1Department of Biology, The Pennsylvania State University, University Park, PA 16802.
Biorxiv : the Preprint Server for Biology
|May 25, 2026
Summary
Patterson's D statistic detects archaic introgression but has limitations. A new method, D* (D Statistic with Allelic Rarefaction), improves detection accuracy for introgressed DNA segments using multiple lineages and without an outgroup.
Area of Science:
- Population Genetics
- Ancient DNA Analysis
- Genomic Introgression
Background:
- Patterson's D statistic (ABBA-BABA) is a standard tool for detecting archaic genome-wide introgression.
- This method relies on a single lineage per taxon and an outgroup, limiting its application and leading to false positives in smaller genomic regions.
Purpose of the Study:
- To introduce a novel method, D* (D Statistic with Allelic Rarefaction), to overcome the limitations of Patterson's D.
- To enhance the detection of introgressed DNA segments with improved precision and recall.
Main Methods:
- D* utilizes multiple lineages and does not require an outgroup for introgression analysis.
- Employs allelic rarefaction to manage unequal sample sizes and accommodate multiallelic sites.
- Validated through simulations across diverse model parameters and technical artifacts.
Main Results:
- D* demonstrates superior precision and recall in identifying introgressed DNA segments compared to existing methods.
- The method effectively handles challenges posed by ancient DNA data, including technical artifacts.
- Successfully applied to analyze Denisovan DNA introgression in modern Papuan populations.
Conclusions:
- D* offers a more robust and accurate approach for detecting archaic introgression, especially in smaller genomic segments.
- The method advances the analysis of complex population histories and ancient DNA.
- Provides a valuable tool for population geneticists studying gene flow and introgression.
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