Genetic Pattern and Demographic History of Orange‐Spotted Grouper ( <i>Epinephelus coioides</i> ) in the South China Sea by the Influence of Pleistocene Climatic Oscillations

Orange-spotted groupers (<i>Epinephelus coioides</i>) are commercially important fish species that inhabit coral reef areas and are distributed across tropical coastal regions throughout the Indo-West Pacific Oceans. This study aims to assess the phylogeographic structure of <i>E. coioides</i> by analyzing 180 individuals collected from six locations along the coast of mainland China and Hainan Island, using the mitochondrial Cyt <i>b</i> gene and 17 microsatellite DNA markers. The mitochondrial DNA analysis revealed high haplotype diversity (0.882), while the microsatellite DNA data showed an average of 8.677 alleles among the six populations, indicating that all populations exhibit a high level of genetic diversity. The presence of two distinct evolutionary lineages of <i>E. coioides</i>, along with the lack of significant genealogical structures corresponding to sampling localities, suggests that isolation in marginal seas during glaciation with lower sea levels shaped their phylogeographic distribution patterns. The results from STRUCTURE, PCoA, and pairwise <i>F</i> _ST revealed significant genetic differentiation in the Lingshui region (LS population) compared to other populations, suggesting that the Lingshui region, adjacent to deep-sea areas, remained isolated during glacial periods as it was not connected to the continental shelf of mainland China. Analysis of demographic history using ABC revealed that <i>E. coioides</i> experienced historical lineage diversification and admixture due to secondary contact.