AdmixLD: Fast genome-scale inference of ancestry disequilibrium in hybrid zones

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ID: 326655
2026
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Abstract
SUMMARY: Hybrid zones represent powerful natural systems for studying reproductive isolation and speciation. One key genomic signature of genetic incompatibilities and epistatic interactions is linkage disequilibrium (LD) - non-random associations between loci from different lineage backgrounds, generated by selection against maladaptive allele combinations. However, admixture alone induces strong genome-wide LD in hybrid populations, obscuring selection-driven signals. Here, we present AdmixLD, a fast, scalable C ++ tool for genome-wide LD scanning in hybrid zones that estimates LD using partial correlation to control for individual hybrid index. By removing admixture-driven covariance, AdmixLD enhances detection of locus-specific associations and enables genome-scale identification of candidate barrier loci and interacting genomic regions. AVAILABILITY: The software and its code source are available at https://github.com/yzfranci/AdmixLD, and scripts for the data analysis are available at https://github.com/yzfranci/AdmixLDAnalysis. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Authors Yannick Francioli, Richard H. Adams, Kaas Ballard, Zachariah Gompert, Todd A. Castoe
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Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag633
URL
https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btag633/70818935/btag633.pdf
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