International Journal of Aquaculture, 2025, Vol.15, No.3, 99-115 http://www.aquapublisher.com/index.php/ija 104 be associated with these traits were found. For example, an amino acid substitution in the ND6 gene of Channa maculata may affect the efficiency of proton transport on the mitochondrial membrane, which is related to its metabolic rate or cold tolerance; and a unique mutation in the Cyt b gene of Channa argus may change the function of the cytochrome bc1 complex, thereby affecting its motility or growth rate (Zhang et al., 2015). 4 Phylogenetic Reconstruction 4.1 Whole-genome-based tree building strategies The phylogenetic tree of the genus Channa can be constructed using the mitochondrial whole genome sequence to obtain high-resolution species evolutionary relationships. In recent years, studies have usually used a combination of Bayesian and maximum likelihood methods to infer phylogenetic trees, and used other perciformes fishes (such as Channa or Trichopoda) as outgroups. Based on the concatenated sequences (or amino acid coding sequences) of 13 protein-coding genes in the whole genome, the phylogenetic tree obtained consistently supports the genus Channa as a monophyletic group, and the relationships between species are clear and separable. For example, Wang et al. (2023) used the mitochondrial whole genomes of five representative species of the genus Channa to construct a phylogenetic tree, and obtained three highly supported branches corresponding to different species groups: Channa andraensis + Channa rainbowi as sister groups, Channa ornate + Channa purchr as another sister group, and Channa schrenckii and Channa striata as independent groups. This result is different from the previous analysis based on fragment sequences, and some new combinations of close relationships have been found, proving the advantage of whole genome data in resolving subtle relationships. Furthermore, phylogenetic analysis with expanded species sampling included all of the approximately 20 known species of the genus Snakehead, and the results divided them into several major evolutionary lineages. For example, Rüber et al. (2020) divided Snakehead species into eight distinct lineage groups: the Argus group (including northern species such as Channa argus), the Asiatica group (including Chinese endemic species such as Channa sinensis), the Gachua group (including small species such as Channa striata), the Lucius group (southern species such as Channa stigmata), the Marulius group (South Asian species such as Channa magna), the Micropeltes group (Southeast Asian species such as Channa magna), the Punctata group (South Asian species such as Channa stigmata), and the Striata group (Southeast Asian species such as Channa striata). The phylogenetic relationships between these groups were also highly supported. For example, the Argus group first merged with the Asiatica group, and then clustered with the Lucius group in sequence, indicating that the northern Channa argus, Chinese Channa argus and southern Channa maculata are closely related, while the Marulius group in South Asia and the Micropeltes group in Southeast Asia are in another branch of the phylogenetic tree, relatively separated from the above-mentioned Asian continental populations. The topological structure of the phylogenetic tree also reveals some noteworthy details. For example, multiple analyses have shown that small species in the genus Snakehead that are small in size and live in mountain streams (such as the broad-fronted Channa group) formed an independent early branch, while large and medium-sized species differentiated into multiple later lineages. This may mean that the initial evolution of the Snakehead genus occurred in small freshwater fish, and then some lineages evolved into large-scale ones and spread to a wider area. The whole genome phylogenetic tree highly supports the sister group relationship of some species, such as the pairing of C. andrao and C. bleheri, and the pairing of C. ornatipinnis and C. pulchra. These relationships were not clear in the past, but were reliably detected by whole genome data. The construction of phylogenetic tree based on mitochondrial whole genome provides a powerful tool for clarifying the complex phylogenetic relationship of Snakehead. 4.2 Lineage resolution within the Channa genus With the help of phylogenetic tree, we can further analyze the lineage divergence (patterns of lineage divergence) within Snakehead. From the above phylogenetic tree, it can be seen that the species of Snakehead are roughly clustered along geographical and morphological characteristics, showing obvious phylogenetic geographical structure. For example, the Argus group, including Channa argus and its relatives, is mainly distributed in
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