Genetic Diversity, Population Structure and Differentiation of Farmed and Wild African Catfish ( Clarias gariepinus ) in Nigeria

ABSTRACT The African catfish ( Clarias gariepinus ) is a commercially important species, for both fisheries and aquaculture, and is now the most commonly farmed fish in sub‐Saharan Africa. However, knowledge about the genetic diversity and population structure of natural and farmed populations, which is crucial for effective conservation and sustainable aquaculture management, is scarce. Using mitochondrial DNA (mtDNA) cytochrome c oxidase 1 gene (COI) sequencing and genomic analysis using triple restriction site‐associated DNA sequencing (3RAD), we investigated the genetic diversity and population structure of farmed and natural C. gariepinus populations from Nigeria including an albino form found in the natural environment. Eleven COI haplotypes were identified, of which seven were unique to natural samples. From the 3RAD results, natural sampling sites had a slightly broader range and higher maximum values for observed heterozygosity ( H o = 0.150–0.178), expected heterozygosity ( H e = 0.173–0.213) and nucleotide diversity ( pi = 0.181–0.228) compared to the farmed populations ( H o = 0.133–0.161, H e = 0.116–0.149, pi = 0.121–0.156). Conversely, genetic differentiation ( F st ) was higher among farmed sampling sites compared to the natural ones and there was high genetic differentiation between the farmed and natural C. gariepinus sampling sites ( F st = 0.29–0.44). Admixture patterns suggested occasional mixing, possibly driven by hydrological connectivity and fish transport practices. Notably, five albino individuals sampled from the wild supported evidence of farm escapees. Outlier analyses and GO enrichment revealed loci potentially under selection related to lipid metabolism, immune signalling and apoptotic processes, indicating metabolic and immune‐related adaptations to environmental stress. Our finding of potential farm escapees highlights the potential risks associated with increasing aquaculture activities and the need for greater regulation of fish farms, which could aid monitoring and reduce the risk of escapes.