International Journal of Marine Science, 2025, Vol.15, No.3, 144-153 http://www.aquapublisher.com/index.php/ijms 145 This study first introduces the development history and core technical methods of molecular systems, summarizes the main progress of fish molecular classification research at home and abroad, and the application of these methods in tropical waters including the South China Sea; explains the current classification research status of fish offshore in Hainan, analyzes the limitations of traditional morphological classification and the results of existing molecular classification work, and introduces the target fish targeted by this research and its preliminary classification situation; compares the characteristics and polymorphic differences of several commonly used molecular markers, and explains the scientific basis for selecting molecular markers in this study. On this basis, the common methods of phylogenetic tree construction (NJ, ML, BI) and evaluation indicators of phylogenetic tree reliability (Bootstrap value, posterior probability) are introduced, and the correction suggestions for the current classification are proposed based on the research results. This study aims to systematically summarize and analyze the research progress on the system classification and evolutionary relationship between fish molecular system in Hainan Island in the past five years, explore the rules and shortcomings in existing research results, and provide reference for subsequent in-depth research. 2 Summary of Molecular Systems Research 2.1 Development history and core methods of molecular systems Molecular systems originated in the mid-20th century and are a discipline that applies molecular biology technology to biological classification and evolutionary research. Early molecular classification studies used protein electrophoresis and isoenzyme analysis to compare differences between species. DNA sequencing technology emerged in the 1970s, first making breakthroughs in the development of viruses and microbial phylogenetics, and then quickly promoted to the field of animals and plants. Entering the 21st century, the development of high-throughput sequencing and genomics has promoted molecular phylogenetics into the era of "metagenome" and "transcriptionome", which can analyze hundreds or even thousands of genes at the same time, thereby building a more refined and reliable phylogenetic tree (Oliveira et al., 2018). The core methods of molecular phylogenetics include DNA/RNA extraction and purification, PCR amplification and sequencing of specific gene fragments, bioinformatics comparison, and phylogenetic tree construction. Commonly used phylogenetic reconstruction algorithms include distance-based adjacency method (NJ), maximum likelihood method (ML) based on optimal model, and Bayesian method (BI) based on Bayesian inference. 2.2 Research progress on fish molecular classification at home and abroad Internationally, a lot of work has been carried out in the study of molecular classification and phylogenetic fish. DNA barcoding technology has been rapidly applied to global fish diversity surveys since Hebert proposed the standard mitochondrial COI gene as a species recognition tool. Fish DNA barcode databases in various major sea areas have been successively established. In addition to mitochondrial sequences, fish genome data have also begun to be used in phylogenetic analysis in recent years, allowing the traditional morphological classification framework to obtain a strong test of molecular evidence. In China, fish molecular classification research started relatively late but progressed rapidly. Chinese scholars have conducted DNA molecular identification and phylogenetic research on many fish in the Yangtze River, Pearl River and other river basins and near the sea. Through DNA classification methods, Chinese scientific researchers discovered some undistinguished population differences under traditional classification, such as the relative species with genetic differentiation between the Taiwan Strait and the South China Sea (Shen et al., 2016; Wang et al., 2022). 2.3 Application cases of related research in the South China Sea and tropical regions Molecular systems have broad application prospects in fish research in the South China Sea and other tropical waters. As the center of biodiversity in the Western Pacific, the South China Sea has unique and complex fish species, which has attracted many scholars to conduct molecular analysis. For example, DNA barcode technology is used to investigate the fish diversity in the northern and southern seas of Hainan Island: Xu et al. (2023) collected fish samples from the northern and southern seas of Hainan Island, and identified 56 species of fish through COI barcodes, belonging to 17 orders and 34 families. The study found that the composition of fish populations in the northern and southern Hainan Island was significantly different, and only 5 species were shared
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