An Original Investigation of the Population Genetics and Phylogeography of Nile Tilapia across Nigerian Water Bodies: Implications for Broodstock Management

Nile tilapia populations have been widely introduced and translocated across Nigerian water bodies over six decades of aquaculture development, creating a complex genetic landscape that confounds the identification of genetically distinct wild populations suitable for conservation and domesticated strains suitable for selective breeding. This study conducts an original population genetics and phylogeographic investigation of Oreochromis niloticus across 18 water bodies distributed across Nigeria's six geopolitical zones, representing wild riverine populations, reservoir populations, and farm escapees. A total of 720 fish were genotyped using 18 microsatellite loci and a 7,000 single nucleotide polymorphism panel generated by restriction-site associated DNA sequencing. Population structure analysis using STRUCTURE, FINERADSTRUCTURE, and discriminant analysis of principal components identified six genetically distinct population clusters corresponding broadly to the Upper Niger, Lower Niger, Cross River, Chad Basin, Benue, and coastal lagoon origins. Significant genetic admixture between wild and farmed strains was detected in reservoir populations close to fish farm infrastructure, with admixture proportions ranging from 11% to 68%. Phylogeographic analysis revealed that the Chad Basin and Upper Niger populations represent genetically distinct lineages warranting separate conservation status. Selective sweep analysis on the single nucleotide polymorphism dataset identified candidate genes under artificial selection in commercially farmed strains, primarily in growth hormone receptor and thyroid hormone pathway genes. The study provides the first comprehensive population genetic map of Oreochromis niloticus across Nigeria and delivers evidence-based broodstock management recommendations for the national tilapia selective breeding programme.

Keywords: population genetics, phylogeography, Oreochromis niloticus, broodstock management, RADseq