International Journal of Aquaculture, 2025, Vol.15, No.5, 255-265 http://www.aquapublisher.com/index.php/ija 259 4.2 Molecular evidence revealing the evolutionary relationships of ray-finned fishes Although ray-finned fishes are highly diverse and morphologically varied, molecular phylogenetics has helped clarify their evolutionary relationships. Since the late 20th century, comparisons of mitochondrial DNA and nuclear gene sequences have continually refined the phylogenetic tree of ray-finned fishes. In particular, over the past five years, large-scale genome sequencing and transcriptome sequencing projects of fishes have greatly advanced this field. Molecular evidence has revealed that some traditional taxonomic units require adjustment. For example, groups that were previously classified together based on morphology, such as Cypriniformes and Acipenseriformes, are in fact distantly related on molecular trees. Similarly, some morphologically highly specialized deep-sea fishes (e.g., spiny-rayed scales fishes) have been found to belong to the evolutionary lineage of Osteoglossiformes rather than being independent orders as traditionally assumed (Near and Thacker, 2024). These findings suggest that morphological similarities among different groups may be the result of convergent evolution, and that molecular data are essential for clarifying true phylogenetic relationships. The establishment of molecular phylogenies has also reshaped our understanding of the evolutionary sequence of ray-finned fishes. For a long time, bichirs, sturgeons, and gars were regarded as primitive ray-finned fish groups, but genomic studies in the late 2010s showed that these ancient fishes are not each other’s closest relatives; rather, they diverged from the main ray-finned fish lineage at very early stages (Sallan, 2014). Beyond evolutionary relationships, molecular evidence has also provided estimates of divergence times among ray-finned fish lineages. Molecular clock analyses, calibrated with fossils, have been used to infer the origin periods of major clades. Results indicate that most modern order-level groups of ray-finned fishes had already emerged during the Mesozoic, with groups such as Salmoniformes beginning to diversify in the Jurassic. Moreover, during the mass extinction at the end of the Cretaceous, many teleost lineages survived and subsequently radiated further in the Cenozoic. This resilience is closely tied to the strong adaptive capacity and broad ecological diversity of teleost fishes. 4.3 The impact of diversification of radial fin fish on the pattern of modern aquatic ecosystems In marine ecosystems, from shallow sea coral reefs to deep sea dark areas, there are radiant fin fish. Colorful damselfish, clownfish, and thorntail fish on the coral reefs form a complex food web, which together with invertebrates and algae maintain the ecological balance of the coral reef. In the oceanic seas, clustered middle and upper-level fish such as mackerel and herring are important food chain mediators. They filter out plankton and are preyed by large predators. Specialized radiated fin fishes in the deep-sea environment, such as squid fish with luminescent organs, lion fish that can withstand high pressure and low temperatures, etc., filling the ecological niche that other vertebrates cannot access. This distribution breadth from the surface to the deep sea can be achieved in vertebrates only by radial fin fish (Bak et al., 2023). In freshwater ecosystems, radiated fin fish are the absolute rulers. The fish in the world's big rivers and lakes are all radiant fin fish. They conquered various inland water bodies with amazing adaptability; crucian carp and carp in the still water of lakes can survive under hypoxia (Alfaro, 2018) and gain energy through omnivorousness. These various fish work together to maintain the material flow and energy circulation of freshwater ecology. 5 Reconstruction of Fish Evolution Pathways by Molecular Phylogenetics 5.1 Application of nuclear genes and mitochondrial genes in phylogenetic development Molecular phylogenetics uses genetic information from different sources to reconstruct relationships between species. Among them, nuclear genes and mitochondrial genes are the two main sources of data, each with its characteristics and complement each other. Mitochondrial DNA (mtDNA) is widely used in species or genus-level phylogenetic analysis because it is present in cellular mitochondria, with relatively simple structure, has a faster evolution rate in animals and is mostly maternal. For example, mitochondrial sequences such as cytochrome b (cyt b) gene and 16S rRNA gene have a long history of application in fish taxonomy research (Parhi et al., 2019). The advantages of mtDNA are haplotype structure, no recombination, and easy to analyze, but the disadvantages are that they represent a single genetic lineage, are susceptible to maternal history, and different genes may have the problem of evolutionary rate saturation.
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