International Journal of Aquaculture, 2025, Vol.15, No.2, 88-98 http://www.aquapublisher.com/index.php/ija 88 Research Insight Open Access Mitochondrial Genome-Based Phylogenetic Reconstruction and Taxonomic Classification of Siluriformes Liting Wang1 , Xuelian Jiang2 1 Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China 2 Institute of Life Sciences, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China Corresponding author: 1559260335@qq.com International Journal of Aquaculture, 2025, Vol.15, No.2 doi: 10.5376/ija.2025.15.0010 Received: 08 Mar., 2025 Accepted: 20 Apr., 2025 Published: 28 Apr., 2025 Copyright © 2025 Wang and Jiang, 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: Wang L.T., and Jiang X.L., 2025, Mitochondrial genome-based phylogenetic reconstruction and taxonomic classification of siluriformes, International Journal of Aquaculture, 15(2): 88-98 (doi: 10.5376/ija.2025.15.0010) Abstract Siluriformes (commonly known as catfishes) are one of the most diverse groups of freshwater fishes in the world. Their evolutionary history and taxonomic relationships have always been a hot topic in systematic taxonomy and biogeography. In recent years, mitochondrial whole genome data have been widely used in fish phylogenetic analysis and taxonomic reconstruction studies because of their rich genetic information. This study takes Siluriformes as the object, reviews the application progress of mitochondrial genome in phylogenetic research, compares the characteristic differences of mitochondrial genomes of different major groups of Siluriformes, reconstructs the phylogenetic relationship of Siluriformes, and combines molecular clock methods to explore the origin and differentiation time and historical biogeographic pattern of Siluriformes. Specific groups (such as Silurus) are selected as cases to analyze their phylogenetic patterns and species diversity. The results show that mitochondrial genome sequences can effectively analyze the evolutionary relationships between and within Siluriformes families, discover hidden species diversity, and promote the revision of the classification system. This study looks forward to the development direction of phylogenetic research on Siluriformes fish, emphasizing that nuclear genomes and more extensive species sampling should be combined to further improve the systematic classification system of Siluriformes fish and provide a scientific basis for species protection and aquaculture resource utilization. Keywords Siluriformes; Complete mitochondrial genome; Phylogeny; Molecular clock; Taxonomic reconstruction; Species diversity 1 Introduction Siluriformes fish, commonly known as catfishes, are a highly diverse and ancient group of teleost ray-finned fishes, widely distributed in freshwater ecosystems around the world (only a few groups are distributed in coastal waters). According to the latest statistics, Siluriformes includes about 40 families, hundreds of genera, and more than 3 000 species, making it the third largest freshwater fish group after Cypriniformes and Perciformes. Siluriformes fish are diverse in morphology, ranging from small catfish of a few centimeters to giant catfish of up to several meters (such as the Amazon giant catfish) (Silvano et al., 2020; Chen et al., 2024). They play an important role in ecological function, economic value, and evolutionary research. For example, some catfish are important food and aquaculture species, while others are key species in watershed ecosystems. Catfish have a long history in evolution and are considered a typical model system for studying the biogeography of freshwater fishes and the impact of continental drift. In the past, taxonomic studies have proposed many hypotheses on the family level and inter-family relationships of the Siluriformes based on morphological characteristics, but due to the convergence and conservation of morphological evolution, traditional classification is controversial in some aspects. The rise of molecular systematics has provided a new way to solve these problems. In particular, mitochondrial DNA sequences have become a commonly used molecular marker for fish phylogenetic and taxonomic studies due to their rapid evolutionary rate, maternal monophyletic inheritance, and stable genome structure. Since the end of the 20th century, mitochondrial gene fragments (such as COI, Cyt b, 16S, etc.) have been widely used in phylogenetic analysis of taxa at all levels of the Siluridae family (Carvalho et al., 2016; Wu et al., 2021). However, due to the limited amount of single gene information, early molecular studies
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