ddRAD-seq reveals conservation units and signatures of local adaptation in wild Nile tilapia populations of Ethiopia

As native genetic resources of Nile tilapia populations face numerous anthropogenic and natural disturbances, we aimed to identify populations worthy of conservation management to facilitate the natural evolutionary trajectory of this species. Here, we used the ddRAD-seq approach for population genomic analysis and delineation of conservation units (CUs). In total, 209 fin-clip samples from nine wild populations in Ethiopia were subjected to ddRAD-seq, producing 121,149 high-quality SNPs that were used for downstream analyses. Genetic diversity metrics revealed low-to-moderate levels of within-population genetic variation, with population pairwise F_ST analysis indicating significant genetic differentiation between populations from the Nile River Basin and those from the Ethiopian Rift Valley lakes. Genetic clustering analyses suggested the presence of 3–4 genetic groups. A combined outlier loci detection approach identified thousands of putative SNPs under selection, with enrichment analysis revealing genes and pathways associated with environmental response, metabolism, growth, and reproduction. Moreover, recently outlined workflows for CU delineation have identified three CUs that are of interest for conservation and aquaculture applications.