International Journal of Marine Science, 2025, Vol.15, No.3, 144-153 http://www.aquapublisher.com/index.php/ijms 151 that traditional methods may miss, molecular evidence helps confirm species identity and reveal new species clues. We found that some fish that were previously recorded as a single species actually contained multiple lineages with significant genetic divergence, suggesting that species diversity was underestimated. Once these lineages are confirmed as new species by further study, the actual number of species in offshore fish in Hainan will increase. Even for taxa that have not been found, molecular classification has established an "identity card" for each fish species to ensure the accuracy and reliability of the species list. Secondly, the clarification of phylogenetic relations allows us to have a deeper understanding of the evolutionary background of Hainan's fish diversity. Now, through the phylogenetic tree, we have clarified which species are close to each other and which groups are derived from common ancestors. This revelation of lineage diversity is an important aspect of diversity perception-focusing not only on species counts, but also on evolutionary differences and uniqueness among species. Third, molecular analysis also provides information on fish diversity function and genetic diversity. For example, species with high genetic diversity tend to be more ecologically adaptable, while species with unique lineages are of great value to maintaining evolutionary potential. Sustainable use of fishery resources and marine ecological conservation need to be based on scientific species and population boundaries. The new classification and kinship information provided by the Institute of Molecular Systems has direct guiding significance for fishery management and species protection. By clarifying the true identity and distribution of species, we can more accurately assess the status of fishery resources and develop management measures. With the results of molecular identification, management departments can formulate differentiated quotas and protection strategies for different lineages. Second, understanding the population structure and gene flow characteristics of fish can help demarcate the snap-in. Molecular markers reveal that certain populations of Hainan offshore fish are geographically independent of each other (the FST is obvious), so these populations should be regarded as independent management units, avoiding simply distributing resources or seedlings from one area to another. For example, if the populations in the closed bay and offshore populations around Hainan Island are significantly differentiated, they should not be combined and evaluated, otherwise the local recession trend may be concealed. Furthermore, the study of phylogenetic relationships can point to evolutionary unique species that need special protection. Some species that are isolated on the phylogenetic tree (such as endemic species of a family that is only one genus) represent an irreplaceable evolutionary heritage and deserve priority protection. This consideration has been adopted in the international EDGE species protection index, and we can also identify and pay attention to the "evolutionary treasure" species in the Hainan sea area. The research progress summarized in this study not only provides current understanding, but also reveals many issues that need to be explored in depth, and points out the direction of future research. In terms of data depth and breadth, genomic level research will be a future trend. Most of the current analysis is still based on mitochondria and a few nuclear genes, but the whole genome and high-throughput SNP data will provide richer information and higher resolution. Using ddRAD, whole genome sequencing and other means, more refined genetic structures and adaptive variants can be analyzed at the population level. As sequencing costs decrease, these technologies should be introduced into the study of important species offshore Hainan to make up for the shortcomings of traditional markers. Secondly, the research on interdisciplinary integration is worth strengthening. The conclusions of molecular systems need to be comprehensively explained in combination with morphological, biogeography and ecological evidence. The identification of some hidden species depends on morphological reexamination, and the driving forces of some lineage differentiation require ecological experiments and modeling verification. Future research should strengthen cooperation between taxonomic experts and molecular biologists, carry out integrated taxonomic research, combine morphological, DNA and ecological data, and make authoritative classification revisions to controversial groups. In terms of macro-structure, it is recommended to conduct regional comparative research. Comparative analysis of the molecular phylogenetic results of fish offshore in Hainan with adjacent areas (such as Beibu Gulf, Taiwan Strait, Nansha Islands, etc.) can test which models are universal and which are unique to Hainan. This helps deepen our understanding of the mechanisms of biogeographic pattern formation in the South China Sea.
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