Population Genetic Structure and Regional Divergence of the Endangered Freshwater Fish Black Shinner Pseudopungtungia nigra Based on Mitochondrial DNA

Assessing genetic structure is important for conserving endangered freshwater fishes inhabiting fragmented river systems. Pseudopungtungia nigra, a Korean endemic species, occurs in several isolated drainages, but its mitochondrial population structure has not been fully evaluated. In this study, we analyzed mitochondrial cytochrome b (cytb) sequences from 80 individuals across eight populations to examine genetic diversity, haplotype composition, and population differentiation. A total of 25 haplotypes were detected, indicating relatively high diversity at the species level. However, diversity was uneven among populations: the Mangyeonggang (MG) population contained only two haplotypes, both of which were not found in the other populations, and showed the lowest haplotype and nucleotide diversity among the sampled populations. Multiple analyses, including pairwise differentiation, haplotype network reconstruction, principal coordinates analysis, and AMOVA, consistently identified MG as the most divergent population. The mitochondrial pattern was also concordant with previously reported microsatellite-based structure, supporting a major division between MG and the remaining populations. These findings indicate that P. nigra preserves substantial diversity overall, whereas the MG population showed a restricted and population-specific cytb haplotype composition. This study provides a genetic basis for defining conservation units and for guiding restoration and management strategies in this endangered species.