International Journal of Aquaculture, 2025, Vol.15, No.2, 88-98 http://www.aquapublisher.com/index.php/ija 93 species level. On the one hand, it clarifies the relationship and hidden diversity between species, providing a basis for taxonomic revision (for example, suggesting that the Silurus asotus complex should be split); on the other hand, it links species evolution with geological and climatic events, revealing the spatiotemporal background of species differentiation (such as the changes in the inland water system of East Asia in the Miocene that led to the differentiation of eastern and western populations). This comprehensive case fully demonstrates the ideas and value of conducting phylogenetic and taxonomic reconstruction research based on mitochondrial genome data (Yang et al., 2019; Li and You, 2024). Figure 1 Dispersal routes of Silurus inferred from biogeographic analyses at different time scales (Adopted from Chen et al., 2024) Image caption: A: 25-20 Ma. B: 20-15 Ma. C: 15-10 Ma. D: 4-0 Ma. A, B, and C on each map represent three recognized biogeographical regions, i.e., China and Korean Peninsula, Europe and Central and Western Asia, and Japan, respectively (Adopted from Chen et al., 2024) 6 Molecular Clock Analysis and Historical Biogeography 6.1 Methods for divergence time estimation using mtDNA The phylogenetic tree itself can only reflect kinship, but the molecular clock model combined with the node time estimation can add time scale information to the system evolution, thereby inferring the age and rate of species differentiation. In the study of Siluriformes fish, the use of mitochondrial genomes for molecular clock analysis has achieved many important results. For example, the study by Kappas et al. (2016) provided the first quantitative estimate of the origin and divergence time of Siluriformes: the results showed that Siluriformes can be traced back to the Early Cretaceous (about 120 million years ago), and its origin and early evolution are consistent with the time frame of the breakup of the supercontinent Gondwana. This time is slightly earlier than the origin time of other freshwater fish such as cold-water fish, suggesting that catfish may be a fairly ancient branch of freshwater fish (Yang et al., 2019). Recent further analysis also supports similar conclusions. Brito et al. (2024) used the mitochondrial genomes of 138 Siluriformes species to construct a time correction tree and estimated that Siluriformes originated in the middle Cretaceous about 118 million years ago. The study also found that the oldest branch, the armored catfish (South America), first differentiated about 100 million years ago, followed by the South American catfish Diplomystidae slightly later, and the Siluriformes, which accounted for
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