Genetic Diversity and Population Structure of an Endemic Fish, Nemacheilus subfusca, in the Lower Yarlung Zangbo River Basin

Nemacheilus subfusca is an endemic fish species in the lower Yarlung Zangbo River. Its habitats are potentially threatened by geological disturbances and anthropogenic activities, but information on population status remains limited. However, existing research has been largely confined to basic biology, with limited information on its population genetic structure and connectivity. Consequently, targeted investigations are urgently needed to provide a scientific basis for the conservation of this species. In this study, genetic diversity and population structure were analyzed in 50 individuals from two geographic populations (Motuo (MT) and Chayu (CY)) in the lower Yarlung Zangbo River, using mitochondrial cytb and D-loop markers. The populations exhibited high haplotype diversity but relatively low nucleotide diversity (cytb: Hd = 0.870, Pi = 0.00281; D-loop: Hd = 0.931, Pi = 0.01655). Notably, the MT population exhibited lower diversity levels compared to the CY population (cytb: Hd = 0.757, Pi = 0.00205; D-loop: Hd = 0.633, Pi = 0.00153). Substantial genetic differentiation was observed between the two populations (cytb: FST = 0.322; D-loop: FST = 0.733); The observed mitochondrial divergence did not provide clear evidence of species-level differentiation (cytb = 0.00331; D-loop = 0.02492). The ML phylogenetic tree and haplotype network revealed geographically associated clustering of the two populations, indicating geographic structuring of mitochondrial haplotypes. Furthermore, demographic analyses were consistent with a possible historical population expansion. In conclusion, The mitochondrial data revealed high haplotype diversity but relatively low nucleotide diversity, together with substantial genetic differentiation between the two sampled populations, forming geographically associated clusters. This study elucidates the genetic background of this species’ germplasm resources, providing baseline genetic information for future conservation and management of this species.