International Journal of Molecular Ecology and Conservation, 2025, Vol.15, No.3, 111-122 http://ecoevopublisher.com/index.php/ijmec 118 case comes from the Indo-Pacific Spanish mackerel (S. guttatus). This species often appears in mixed salt waters in estuaries, and the salinity of its environment is lower and fluctuates more than that of a completely marine environment. This suggests that the Indo-Pacific Spanish mackerel has a certain ability to tolerate low salt (Noegroho, 2020). Although there is no direct report on the salinity adaptation genomics of Spanish mackerel, data from other fish can be used as a reference. For example, in the study of spotted sea bass, it was found that its HSP gene evolved rapidly and was co-expressed under high alkalinity and high salt stress. HSP genes are not only sensitive to temperature stress, but also to salinity stress, and participate in protecting the normal folding function of cell proteins. This shows that fish may partially adapt to salinity changes through the evolution of molecular chaperone systems. Spanish mackerel may also have a similar mechanism: when salinity drops sharply, stress proteins such as HSP are rapidly expressed to protect cell functions; in the long run, the number of genotypes that are more tolerant to salinity fluctuations in Spanish mackerel populations is relatively increasing. 6.3 Cases of genomic adaptation related to migratory behavior Spanish mackerel are famous for their long-distance migration and seasonal migration. Migratory behavior involves complex physiological and behavioral adaptations, including navigation orientation, long-distance swimming endurance, and gonad development timing. At the genomic level, migration-related traits may be controlled by multiple genes, and current research is beginning to reveal some clues. The differences between the northern and southern populations of Japanese Spanish mackerel provide an interesting case. As mentioned above, the Japanese mackerel along the coast of China can be divided into two groups, the northern and southern groups, which differ in their migration routes and spawning times: the northern group mainly spawns in the Bohai Sea and the Yellow Sea and migrates south to the East China Sea for wintering, while the southern group may reside in the East China Sea and the South China Sea (Yang et al., 2022) (Figure 2). Whole-genome methylation analysis showed that the two groups had different DNA methylation patterns in several genes related to movement and behavior. These genes include genes involved in skeletal muscle development, limb movement (corresponding to the fin and swimming muscle function of fish), and adult individual movement behavior. Differential methylation usually reflects differences in gene expression regulation. This suggests that the northern and southern groups may have phenotypic differences in muscle development, swimming endurance, etc. to adapt to different migration distances and water temperature conditions. 7 Technical Challenges and Future Directions in the Study of Adaptive Evolution of Spanish mackerel 7.1 Technical challenges in the study Although the study of Spanish mackerel genome and adaptive evolution has made great progress, it still faces many challenges. The first is the acquisition of high-quality samples and data. Spanish mackerels are mostly oceanic migratory fish, and field sampling and live experiments are difficult, resulting in limited sample size and representativeness of population genomics research. The problem of signal weakening caused by high gene mobility is still prominent. Local adaptation signals of marine fish are often diluted by large-scale gene exchanges. Weak functional verification is also one of the challenges. Although the population genome can indicate which sites are selected, it is difficult to confirm the specific effects of these variations on the phenotype without in-depth functional research. In the context of Spanish mackerel as a non-model species, it is particularly difficult to conduct gene function experiments. Environmental and ecological data acquisition is also a bottleneck. Adaptive evolution research needs to be combined with detailed environmental factor data. However, for highly mobile species such as Spanish mackerel, it is very difficult to track the environmental combinations experienced by individuals. Solving these problems requires multidisciplinary collaboration and technological innovation. 7.2 Future research directions and technology development trends Currently, there are only a few reference genomes and limited population data for Spanish mackerel species. In the future, it is possible to consider conducting population genome sequencing projects for multiple species of Spanish mackerel, covering representative populations from different geographical regions. Epigenomics will play
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