The Late Pleistocene-Holocene climate fluctuations have had a major impact on phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. Lagocephalus spadiceus is a high-nutritional and economic-value species in the Southeast China Sea. The study was to assess the population genetic diversity and demography of L. spadiceus in the South China Sea (SCS). A sample of 300 specimens from eight geographic locations along the coast of mainland China and Hainan Island were obtained for this study. The mitochondrial cytochrome oxidase I (COI) and cytochrome b (Cyt b) gene datasets had high haplotype diversity but low nucleotide diversity. The genetic structure and phylogenetic analyses indicated that there was no significant population structure among the eight geographic locations. The low genetic diversity of L. spadiceus was associated with population expansion in the Late Pleistocene-Holocene period. This was supported by star haplotype networks, neutrality tests, unimodal mismatch distributions and Bayesian skyline plots. These findings have important reference value for the protection of genetic resources. Furthermore, the study illuminates the complex relationship between Pleistocene-Holocene temperature variability and phylogeography.

Forward and reverse splicing of all sequences using SeqMan in Larsergene v7.1.0 , and then compare and edit the sequences using the Clustal W method in MEGA v7.0 . The COI and Cyt b sequences were matched one by one for Multi-locus Sequence Analysis (MLSA) using PhyloSuite v1.2.2.

Required software: MEGA v7.0 and DnaSP v6.0