The population genetic structure and genetic diversity of Neolissochilus hexagonolepis were studied using three mitochondrial genes (CoxI, Cytb, ATPase 6/8). A total of 120 individuals representing nine populations from different drainages of Northeast India were used for the study. Thirty-three distinct haplotypes were identified from concatenated gene analysis. The total haplotype and nucleotide diversities are 0.8880 and 0.0280, respectively. The analysis of molecular variance (AMOVA) reveals that the main variation (89.33%) was among populations. Most of the populations showed high polymorphisms, parsimony and haplotype diversity which indicate genetically healthy stocks in the wild. The genetic differentiation patterns were consistent with geographical distributions. Pairwise FST comparison of populations showed significant genetic differentiation (0.9088, p < .05). The pattern of haplotype network and phylogenetic tree revealed six major groups. Results suggested that chocolate mahseer populations in Northeast India having high haplotype diversity and genetic differentiation can be utilized in breeding programs to maintain genetic diversity in the descendant populations. The present study would be beneficial for sustainable management, stock-specific strategies for breeding and conservation of the wild population of N. hexagonolepis in future.
Keywords: Population expansion; bottleneck; conservation; geographic diversity; phylogeography.