Allopatric divergence contributes to the population differentiation of Coilia nasus in the upper reach of Yangtze River

Uncovering the mechanisms driving the genetic divergence of environmentally heterogeneous species is one of the biggest challenges in phylogeography. In the present study, the genetic variation and genetic structure of the Coilia nasus were examined by analyzing thirteen mitochondrial protein-coding genes (PCGs) among 60 individuals collected from 8 populations in affiliated waters of Yangtze River and their adjacent waters. Contrasted to the recently recognized multiple subdivision, our reconstructed phylogenetic tree, analysis of molecular variance (AMOVA), F_ST and haplotype networks refined only two previously recognized clades, with one clade arising from the Dongting and Poyang lakes affiliated to the upper reach of Yangtze River, and the other mainly from the remaining populations. Historical demography analysis revealed that the divergence time between the two clades could be recovered to 60.05 ka, indicating a possible role of late Pleistocene glaciers in their differentiation, possibly via isolation of diverged glaciers’ refugia. Subsequent positive selection test revealed no diverged selective pressures acting on the two clades within all 13 PCGs, suggests that the observed mitochondrial lineage divergence of C. nasus in the Yangtze River and its adjacent waters was primarily driven by neutral evolution. Our results provided new insights into the spatial patterns of genetic variation in population of C. nasus and would provide valuable implications for sustainable management and utilization of this fishery resource in the future.