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 wild 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 wild C. gariepinus populations from Nigeria, including an albino form found in the wild. Eleven COI haplotypes were identified, of which seven were unique to wild samples. Wild sampling sites had a slightly broader range and higher maximum values for observed heterozygosity (Ho = 0.109 - 0.165), expected heterozygosity (He = 0.111 - 0.216), and nucleotide diversity (pi = 0.125 - 0.225) compared to the farmed populations (Ho = 0.118 - 0.147, He = 0.112-0.144, pi = 0.117 - 0.151). Conversely, genetic differentiation (Fst) was higher among farmed sampling sites compared to the wild ones and there was high genetic differentiation between the farmed and wild C. gariepinus sampling sites (Fst = 0.31 - 0.47). Despite evidence for admixture for both farmed and wild fish, there was little evidence of admixture between the two groups. Nevertheless, both mtDNA and 3RAD data strongly suggested that the albino fish, collected from the wild, were in fact farm escapees. Despite overall differentiation farmed genotypes suggesting that overall genetic integrity of wild fish has been maintained, this evidence of escape provides a warning about potential risks of increasing aquaculture activities. Specifically, this indicates the need for greater regulation of fish farms to monitor and reduce the risk of escapes.