International Journal of Marine Science, 2025, Vol.15, No.3, 144-153 http://www.aquapublisher.com/index.php/ijms 148 experience in fish species identification globally. Previous environmental DNA studies on Hainan fish have proved that COI sequences have the highest coverage in public databases and the accuracy of species annotation is significantly better than the 12S and 16S sequences (Ahmad et al., 2024). The Cytb gene has been widely proven to be effective in fish system geography and population studies. Its higher nucleotide polymorphism is conducive to distinguishing recent differentiation events and is very suitable for exploring the genetic structure and lineage differentiation of populations near Hainan Island. Again, we consider that a single mitochondrial gene may have maternal bias and other limitations, so we also introduced another mitochondrial marker 16S for cross-validation. On the one hand, 16S has rich reference data in some taxa, and on the other hand, its conservatism helps to test the robustness of the relationship constructed by COI and Cytb. 5 Progress in Research on the Kinship and Genetic Structure of Fish in Hainan Offshore 5.1 Phylogenetic relationship of fish in Hainan based on molecular data Molecular systems research provides a new perspective for understanding the kinship of fish offshore in Hainan. Overall, Hainan offshore fish belong to part of the Western Pacific tropical-subtropical system, and its phylogenetic relationship reflects the historical evolution of regional biogeography. Based on the preliminary molecular phylogenetic tree, it can be seen that many fish in Hainan waters are closely related to populations in the South China Sea and other regions of the Indo-Western Pacific, showing the characteristics of the pan-Indian-Pacific system (Luo et al., 2025). For example, coral reef fish such as Dambesaidae and Floycephala, mixed branches with corresponding groups in the South China Sea and Southeast Asia adjacent waters on the systemic trees, indicating that these species have experienced frequent regional diffusion and genetic exchange in geological history, and Hainan is not an isolated evolutionary unit (Xu et al., 2023). However, molecular phylogenetic trees also reveal some previously unnoticed details of kinship. Some Hainan offshore fish were previously thought to be closer to southern China coastal populations based on geographical sources, but genetic data suggest that they are more closely related to populations in the further south (such as Southeast Asia or the South Pacific). This suggests that we should have a more open understanding of the genealogical relationships of Hainan fish, and we cannot infer the systematic relationship based on geographical proximity. For some small fish that are locally distributed near Hainan, molecular evidence suggests that they may represent unique evolutionary branches, alienated from other known species, and have a unique evolutionary status. Such discoveries are very important for understanding the uniqueness of Hainan's marine biodiversity. 5.2 Population structure, gene flow and genetic diversity characteristics In addition to analyzing systematic relationships among species, molecular data can also be used to study population genetic structures and gene flow dynamics within Hainan offshore fish species. Research in recent years has shown that there is significant genetic differentiation among different geographical populations of some offshore fish in Hainan. Mitochondrial DNA analysis of freshwater fish Hainan phlegm showed that the FST differentiation index between groups in Hainan Island and Pearl River water system population was as high as 0.511, and showed obvious isolation and distance-related patterns. This means that although Hainan saphenous morphology is similar, groups on and off the island have long been isolated, with extremely limited genetic communication, and have formed an independent lineage (Lin et al., 2022). Similarly, among marine fish, some nearshore settled fish (such as local reef species) may form their respective genetic groups in different sea areas of Hainan Island (Beibu Gulf, Xisha Sea, etc.). On the other hand, for marine fish with strong migration ability or larvae in the plankton period, their population genetic structure is often more diffuse. Some distant migratory fish species do not show significant genetic differentiation between Hainan and surrounding waters, and molecular mutations mainly exist between individuals rather than between regions. This suggests that these species may conduct extensive gene flows through ocean currents, etc., thereby maintaining the genetic continuity and homogeneity of the population. In this group of fish, the level of genetic diversity is usually high, often with abundant haplotype types and larger effective population sizes. A study on a variety of freshwater fishes in South China pointed out that freshwater fishes in the southern continent and Hainan Island generally have high haplotype diversity, which is believed to be related to the warm climate and diverse environment in the region (Lin et al., 2023).
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