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

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.