Genetic structure and historical demography of the Pacific rudderfish Psenopsis anomala in the Northwestern Pacific Ocean

Current genetic patterns of marine organisms are the result of various historical and environmental factors working together on different spatial scales. As a unique economic fish species in the Northwestern Pacific Ocean, Psenopsis anomala is ideal for studying the molecular phylogenetic geography of the Northwestern Pacific Ocean. To understand the genetic background of P. anomala, we analyzed a total of 98 samples from the East and South China Seas and found a total of 18 haplotypes. The overall haplotype diversity (0.3991 ± 0.0641) and nucleotide diversity (0.0005 ± 0.0005) were low. An analysis of molecular variance, haplotype network analysis, interpopulation Fst values, and maximum likelihood phylogenetic trees indicated that there was no significant difference between P. anomala populations, which could be due to frequent gene exchange (spawning migration and ocean circulation) and recent population expansion events. Overall Tajima’s D and Fu’s Fs values of P. anomala were significantly negative. The mismatch analysis diagram showed an obvious single peak, and the haplotype network diagram had a star-shaped structure, indicating that the P. anomala population has experienced population expansion. It is estimated that the expansion occurred approximately 17,377–13,901 years ago and might have been caused by the alternating rise and fall of the sea level during the Pleistocene. In addition, the haplotype diversity (0.1000) and nucleotide diversity (0.0001) of the Zhoushan population were significantly lower than those of the other geographic populations, and thus, this population urgently needs to be protected.