International Journal of Marine Science, 2025, Vol.15, No.3, 144-153 http://www.aquapublisher.com/index.php/ijms 144 Research Report Open Access Molecular Systematics and Phylogenetic Relationships of Wild Fish in Coastal Waters of Hainan Island RudiMai , Chengmin Sun Center for Tropical Marine Fisheries Research, Hainan Institute of Tropical Agricultural Resouces, Sanya, 572025, Hainan, China Corresponding author: rudi.mai@hibio.org International Journal of Marine Science, 2025, Vol.15, No.3, doi: 10.5376/ijms.2025.15.0013 Received: 10 Apr., 2025 Accepted: 28 May, 2025 Published: 10 Jun, 2025 Copyright © 2025 Mai and Sun, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Mai R.D., and Sun C.M., 2025, Molecular systematics and phylogenetic relationships of wild fish in coastal waters of Hainan Island, International Journal of Marine Science, 15(3): 144-153 (doi: 10.5376/ijms.2025.15.0013) Abstract The offshore waters of Hainan Island are a hot spot for tropical marine biodiversity in China. Wild fish resources are abundant but there is insufficient classification awareness. Traditional fish classification mainly relies on morphological characteristics and appears to be limited in the face of species diversity and hidden species problems. This study reviews the development history and main methods of molecular systems, sorts out the progress of fish molecular classification research at home and abroad, and its application cases in the tropical waters of the South China Sea. Focus on summarizing the current status of fish classification in Hainan offshore, comparing the applicability and polymorphic differences of commonly used molecular markers (such as COI, 16S, Cytb), and discussing the practice of building phylogenetic trees based on NJ, ML, and BI methods and evaluating reliability. Based on recent research results, the kinship pattern and population genetic structural characteristics of fish in Hainan near-shore areas are analyzed, and the discovery and significance of potential hidden species are revealed. From the perspective of geological evolution, the impact of environmental changes in Hainan Island and surrounding sea areas on fish lineage differentiation is discussed, and the ecological significance of the research results in marine biodiversity conservation and fishery resource management is expounded, and the research direction is expected to be carried out in the future. This study provides scientific reference for further in-depth research on molecular systems of fish in Hainan offshore fish and improving species classification system and protection strategies. Keywords Offshore of Hainan Island; Fish classification; Phylogenetic; Kinship; Geographical evolution 1 Introduction Hainan Island is located in the tropical shelf waters of the northern South China Sea and is an important hot spot for marine fish biodiversity. There are many species of tropical and subtropical fish in this area, however, there is still a big gap between traditional classification research based on morphological characteristics and actual fish diversity. The complex ecological environment offshore Hainan (such as the Qiongzhou Strait in the north, the deep water and land slope in the south, the semi-closed Beibu Gulf in the west, etc.) has nurtured a variety of fish communities (Chen et al., 2025). For a long time, Chinese fish classification has mainly relied on morphological diagnostic characteristics. However, since fish have a high degree of diversity in body shape, color, pattern, scales, fin strips, etc., the morphology varies significantly in different development stages, and simple morphology identification has limitations on accuracy and efficiency. Especially in tropical waters where species classification is complex, many close species have subtle morphological differences, and even hidden species (species with extremely similar morphology but genetically independent). These factors make it difficult to fully identify species and reveal true kinship by traditional methods alone (Wang et al., 2012). With the development of molecular biology technology, DNA sequencing has become a powerful tool for fish classification and phylogenetic research. Molecular phylogenetics provides an objective basis for species identification and lineage reconstruction by analyzing the sequence differences of specific gene fragments. A large number of studies have shown that molecular means such as DNA barcode can efficiently discover unidentified species and accelerate the identification of sister species or hidden species (Xu et al., 2021). Therefore, introducing molecular systems into the classification of fish offshore fish in Hainan is of great significance to improving the regional species list and clarifying the evolutionary relationship of fish lineages.
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