Genetic diversity and population structure of the near threatened fish Harpadon nehereus in the Northwest Pacific: implications for conservation

Genetic diversity studies not only improve the understanding of the wild genetic resources of species but also provide a theoretical basis for the protection, development, and utilization of species and formulation of reasonable protection measures. Fishing pressure on the near threatened fish Harpadon nehereus has recently increased, leading to the aging and miniaturization of its population. We determined the gene sequences of mitochondrial cytochrome b (Cytb) and nuclear recombination-activating 1 (RAG1) in eight populations of H. nehereus in the Northwest Pacific, analyzed their genetic diversity levels, and compared the effectiveness of these two markers for analyzing genetic diversity and population structure. Sequence analysis of Cytb revealed that the eight populations showed low haplotype diversity (H_d = 0.110–0.356) and low nucleotide diversity (pi = 0.00015–0.00053). No significant genetic differentiation was observed among the populations (F_st = − 0.0197–0.000, P > 0.05). The haplotype network diagram did not exhibit evident geographical clustering or a pedigree structure. Molecular variance analysis revealed that variation primarily occurred within populations. Further comparative analysis of the RAG1 and Cytb sequences revealed two differences. RAG1 showed high haplotype diversity (H_d = 0.780–0.900) and low nucleotide diversity (pi = 0.00355–0.00463). The genetic differentiation index value revealed a significantly low level of genetic differentiation among some populations.