International Journal of Aquaculture, 2025, Vol.15, No.2, 88-98 http://www.aquapublisher.com/index.php/ija 89 were still insufficient in distinguishing some deeper branch relationships. In the past five years, with the development of sequencing technology and the accumulation of data, the complete mitochondrial genome (about 16 Kb in size, containing 13 protein-coding genes and 37 RNA genes in total) has become an important data source for phylogenetic studies. Large-scale phylogenetic analyses based on the whole mitochondrial genome continue to emerge, greatly advancing our understanding of the evolutionary relationships of Siluriformes fish. For example, a study assembled almost all the publicly available mitochondrial genome data of Siluriformes species, reconstructed a time-corrected Siluriformes phylogenetic tree, and provided many new insights (Prosdocimi et al., 2017). Therefore, it is of great significance to summarize the progress of mitochondrial genomes in the phylogenetic and taxonomic research of catfishes, which not only helps to clarify the evolutionary history and biogeographic pattern of this group, but also provides a scientific basis for the classification and protection of related species. This study took fishes of the order Siluriformes as the research object. Based on the large-scale data of mitochondrial genome, it systematically explored the phylogenetic relationships and classification system within the order Siluriformes, including comparative analysis of the mitochondrial genome characteristics of the Catfish family and related groups, reconstruction of the phylogenetic tree using complete mitochondrial genome data, analysis of the kinship structure and topological characteristics among the main families and genera, identification of deep phylogenetic divergence and estimation of differentiation time, and inference of the origin and global diffusion history of the order Siluriformes using molecular clock methods. Taking typical groups such as the genus Silurus as cases, it explored the processes of species formation, diversification and geographical diffusion, in order to provide a scientific basis for practical issues such as protecting genetic diversity, optimizing fishery management, improving aquaculture varieties and preventing the invasion of alien species, and promoting the sustainable utilization and ecological protection of Catfish species resources in the future. 2 Application of Mitochondrial Genomes in Phylogenetic Studies 2.1 Basic structure and features of mitochondrial genomes Due to its compact structure, moderate evolution rate and no recombination, the mitochondrial genome has unique advantages in animal systematic research. The whole mitochondrial genome is usually about 16 kb~17 kb, containing 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a control region. This structure is highly conserved, and the base composition shows a certain degree of A+T enrichment, providing stable and rich genetic information for phylogenetic research. 2.2 Advantages of mtDNA in fish phylogenetics For fish, mitochondrial whole genome data has been widely used in species identification, phylogenetic relationship reconstruction, and evolutionary history inference. Compared with a single or a few mitochondrial genes, the complete mitochondrial genome provides an exponentially increased amount of base information, greatly improving the resolution and credibility of the phylogenetic tree (Lv et al., 2020). For example, in the past, when using COI barcodes to classify catfishes, the monophyly of some genera could not be strongly supported, while the use of mitochondrial whole genome data can clearly distinguish these evolutionary lineages. For another example, in terms of species identification, mitochondrial genome sequences can improve the accuracy of identification and help discover cryptic species or misclassified populations (Wen et al., 2017; Wang and Zhao, 2024). Another important application of mitochondrial genomes in fish phylogeny is to infer the branch lengths of phylogenetic trees and then perform molecular clock analysis. Since mitochondrial DNA evolution is relatively uniform, it can be used as an approximate molecular clock and performs well in estimating divergence time after combining fossil calibration. Mitochondrial genomes can also be used in phylogeographic studies to infer the historical diffusion paths of species by analyzing the genetic structure between populations. 2.3 Molecular markers suitable for Siluriformes analysis Of course, mitochondrial genomes also have limitations, such as only representing maternal genetic history and being easily affected by hybridization and incomplete pedigree sorting. Therefore, many studies have begun to
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