International Journal of Aquaculture, 2025, Vol.15, No.2, 88-98 http://www.aquapublisher.com/index.php/ija 92 5 Case Studies of Phylogenetic Patterns 5.1 Pangasiidae: divergence history and taxonomic revision Fishes of the genus Silurus are mainly distributed in Eurasia, including several economically and ecologically important species, such as the common yellow catfish (Silurus asotus) in East Asia and one of the largest freshwater fish in Europe, Silurus glanis. The classification and evolutionary relationships of species in this genus have long been controversial. On the one hand, the morphological variation of populations in different regions makes the species definition complicated; on the other hand, Silurus is widely distributed in Eurasia, and its origin and diffusion history involve the influence of multiple geological and climatic events (Kishimoto et al., 2022). Recently, Chen et al. (2024) used mitochondrial whole genomes to conduct a comprehensive study of the phylogeny and biogeography of Silurus, providing new insights. In the study, 109 mitochondrial whole genome sequences of 13 morphological species of Silurus (89 of which were newly sequenced) were collected, and a phylogenetic tree was constructed using maximum likelihood and Bayesian methods. The results showed that Silurus can be divided into 8 highly supported main branches. These eight phylogenetic lineages do not completely correspond to species in traditional morphological classification. For example, Silurus asotus (catfish), which is widely distributed in East Asia, is not of a single origin, but contains four clearly differentiated branches (MOTUs), indicating that multiple species may be implied under the current nomenclature. For another example, the Chinese endemic species Silurus microdorsalis is also divided into two genetic branches, suggesting the existence of subspecific differentiation or hidden new species. These findings show that the species diversity of the genus Silurus has been underestimated in the past, and mitochondrial genome data help reveal hidden lineages. 5.2 Clariidae: evolution of hypoxia tolerance Molecular clock analysis based on time calibration further reveals the evolutionary time frame of the genus Silurus: the last common ancestor of the genus Silurus lived in the early Oligocene about 37.6 million years ago. In the subsequent long evolution, the main branches successively differentiated between about 29.4~11.6 Ma; and within several recognized species, the differentiation time of different hidden branches is roughly between 11.6~3.7 Ma, roughly corresponding to the geological period from the middle and late Miocene to the Pliocene. This means that the species differentiation of the genus Silurus mainly occurred in the middle Cenozoic, when East Asia experienced significant geological and climatic changes (Chen et al., 2024). 5.3 Loricariidae: lineage radiation in south America In order to reconstruct the origin and diffusion path of Silurus, the study further conducted an ancestral distribution area reconstruction analysis. The results support that the ancestors of the genus Silurus are likely to originate in East Asia, that is, the area centered on today's China and the Korean Peninsula. From the end of the Oligocene to the middle Miocene (about 26.7~21.8 Ma), some branches of the genus Silurus spread westward from East Asia many times, reaching Central Asia, West Asia and even Europe. This period coincided with the complete closure of the Tethys Sea and the uplift of the Pamir Plateau, and the inland rivers of East Asia were connected with the Eurasian water system, providing a corridor for the cross-regional diffusion of freshwater fish. Subsequently, from the late Miocene to the Pliocene (about 18.4~2.5 Ma), some branches of the ancestors of the genus Silurus migrated eastward to the Japanese Islands. It is worth noting that climate events in different periods had a profound impact on these diffusion and differentiation activities. The study pointed out that the Paleocene-Eocene extinction event at the turn of the Eocene-Oligocene, the establishment and strengthening of the East Asian monsoon in the Neogene, and the repeated glacial sea level rise and fall in the Pleistocene may all be key driving factors in shaping the evolutionary history of the genus Catfish. For example, the East China Sea shelf was exposed during the glacial retreat, forming a land bridge between the continent and Japan, which facilitated the spread of catfish to Japan; and the rise in sea levels during the interglacial period isolated its population on the island, leading to genetic differentiation (Figure 1) (Chen et al., 2024). For another example, the strengthening of the East Asian monsoon has brought about periodic climate fluctuations, which may lead to the fragmentation of catfish habitats and accelerate the geographical isolation of populations and the formation of lineages. Through the above-mentioned Catfish case, it can be seen that the mitochondrial genome combined with molecular clock and biogeographic analysis can finely depict the phylogenetic pattern and historical distribution dynamics at the
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