This project will quantify runs of homozygosity (ROH) and genomic inbreeding (FROH) across three fish species (Atlantic salmon, rainbow trout and Nile tilapia) using whole-genome sequencing (WGS) and high-density SNP array data. ROH provide a direct identity-by-descent (IBD)–based measure of inbreeding, and their length and distribution inform both recent and historical autozygosity. We will perform genome-wide ROH detection, classify ROH length categories, and identify ROH islands (ROHi) that represent putative selection footprints associated with domestication and breeding. The workflow requires computationally intensive steps, including WGS alignment, joint variant calling, large-scale VCF filtering, phasing, and ROH inference under multiple parameter settings. In addition, evolutionary modelling using SLiMwill be used to simulate population evolution under complex demographic and life-history scenarios, incorporating empirical genomic patterns and species-specific traits (e.g., fecundity and lifespan, particularly for Wels catfish). Comparative analyses across species and strains will assess how breeding and management practices shape genomic diversity, haplotype structure, and selection signatures. Dardel’s HPC resources are essential for processing multi-terabyte WGS datasets, parallelizing variant calling and ROH scans, running large-scale SLiM simulations, and ensuring reproducible, high-throughput genomic analyses for aquaculture and conservation applications.