International Journal of Aquaculture, 2025, Vol.15, No.5, 255-265 http://www.aquapublisher.com/index.php/ija 260 In fish phylogenetic studies, mitochondrial and nuclear gene data are often used in combination to learn from each other's strengths and weaknesses. For example, in the molecular phylogenetic research of carp, researchers not only analyze mitochondrial genome sequences to reveal the relationship between low-order taxonomies, but also combine nuclear genes (such as RAG1) to determine higher-order evolutionary branches, thus building a more comprehensive phylogenetic tree structure (Near and Keck, 2013). 5.2 Correction of traditional classification by genomic data Many past classifications based on morphology have been reassessed under genomic evidence, some have been supported and others have been overturned. Some hidden evolutionary relationships have been discovered, which has brought important changes to our understanding of fish phylogenetics. Genome data clarifies the attribution of many taxa (Wang and Chen, 2025). Former taxonomists regarded eels and cypress (Pacific eels) as members of the eels due to their similar appearance, but genomic evidence shows that cypress is actually closer to the cypress and is very different from the real eels, so they should establish a different family. Genome data found some conjunctive or multi-line problems in traditional classifications. The previous "Caraceae" covers many subfamilies such as carp, carp, whitefish, etc. in the classic classification, but the molecular phylogenetic tree shows that the old "Caraceae" is not a single family. Some subfamilies (such as the subfamily of the cleft fish) are actually far from relatives with other members of the Caraceae, and should be split out and promoted to independent families (Yang et al., 2015). Genome studies reveal new evolutionary locations in some taxa. For example, many teaching materials used the view that bone fish can be divided into two categories: radial fin fish and meat fin fish, among which radial fin fish are divided into primitive soft fin fish (such as sturgeon, multi-fin fish) and true radial fin fish. But 21st century systematic genomics confirm that sturgeons and multifin fish do not form one. 5.3 Case analysis: molecular phylogenetic reconstruction of Cyprinus fish The Cycadaceae is the most widely distributed and most species among freshwater fish. The phylogenetic relationship of the Cycadaceae has long been a hot topic and difficult issue in fish taxonomy, because the subfamilies within the Cycadaceae are highly morphologically diverse, and traditional morphological characteristics are sometimes difficult to clarify the evolution order. The introduction of molecular phylogenetics provides new ideas for clarifying the internal relationships of the Cycadae family. Yang et al. used a data set of 53 nuclear genes and 14 mitochondrial genes to phylogenetic reconstruction of the main group of Cycadaceae endemic to East Asia. The research results propose a new model of phylogenetic development of the Cyprinus family. First, confirm that the entire Cyprinus family originates from a single line, and no matter how different the morphology is, they share a common ancestor; second, the Cyprinus family is divided into several main branches, among which Cyprinus and the Cyprinus family form sister groups with the Cyprinus family, including the grass carp subfamily. The subordinate family, the Loach family, etc., which were originally regarded as independent families, may be nested in or adjacent to the Cyprinus family evolution trees (Yang et al., 2015). Molecular phylogenesis also combines with fossil records, providing clues for the geographical evolution of cycadaceae. Through molecular clock calibration, it is assumed that the origin of the Cycadaceae was approximately in the Early Cretaceous period (about 193 million years ago). Fossil evidence and biogeographic analysis show that Asia is likely to be the center of origin of the Cycadae family, and then the Cycadae family spread to Europe, Africa and other places through events such as plate drift and land bridge diffusion. 6 Key Evolutionary Events and Adaptive Radiation 6.1 Transformation and adaptation of ocean-freshwater environment During the long history of fish evolution, there have been many events that migrate from the ocean to freshwater or return to the ocean from freshwater. These environmental transformations are accompanied by physiological and morphological adaptation and evolution, and are one of the important driving forces for fish radiation and diversification. Originally vertebrates were thought to have originated from the ocean, but about 40% of today's
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