Genetic characterization of Clupisoma garua (Hamilton 1822) from six Indian populations using mtDNA cytochrome b gene

Clupisoma garua (Hamilton, 1822) is a commercially important freshwater fish and a potential candidate species for aquaculture. This study investigates the genetic diversity and population structure of six Indian populations of C. garua using cytochrome b (cyt b) sequences of mitochondrial DNA (mtDNA). We sequenced cyt b gene of 64 individuals collected from five distant rivers: Ganga, Gomti, Betwa, Gandak and Brahmaputra. Sequencing of 1054 bp cyt b mtDNA fragment revealed the presence of 19 haplotypes with a haplotype diversity value of 1.000 and a nucleotide diversity value of 0.0258 ± 0.00164. The Gandak river fish population showed highest nucleotide diversity. The fixation index analysis indicated significant genetic divergence among populations from different geographical areas. Both the neighbor-joining tree and median-joining network analysis of the haplotype data showed distinct patterns of phylo-geographic structure. The hierarchical analysis of molecular variance revealed that intra-group variation among populations was highly significant. The results of this study suggest that C. garua populations, especially geographically isolated groups, have developed significant genetic structures within the population. In addition, tests of neutrality suggest that C. garua may have experienced a population expansion. The study results establish cyt b as polymorphic and a potential marker to determine the population structure of C. garua. Information of genetic variation and population structure generated from this study would be useful for planning effective strategies for the conservation and rehabilitation of Schilibid cat fishes.