International Journal of Marine Science, 2025, Vol.15, No.3, 130-143 http://www.aquapublisher.com/index.php/ijms 136 During the Miocene (23 million to 5.3 million years ago), the genus S. regalis ushered in the second peak of diversification. The ancestral lineages of many living species originated from this period. For example, the time calibration results show that in the Eastern population, the common ancestor of Japanese and Montenegrin mackerels appeared about 42 million years ago (late Eocene), and then the differentiation of S. niphonius and S. munroi occurred about 15 million to 10 million years ago (middle Miocene). In the Indo-West Pacific group, the differentiation of the multi-lined mackerel and the leopard mackerel-Korean mackerel-true mackerel complex was concentrated in the late Oligocene to the early Miocene (roughly 30 million to 20 million years ago) (Gao et al., 2024. 5 Case analysis: Phylogenetic Relationships of Aquaculture-Related Populations 5.1 Genetic structure of common aquaculture populations in Asia InAsia, Scomberomorus niphonius (also known as blue-spotted Spanish mackerel) in the Spanish mackerel genus is an important target for aquaculture and stocking, especially in coastal areas of China. Every year, a large number of artificially bred juveniles are released into natural waters, making it a typical representative for studying the genetic interaction between aquaculture populations and wild populations. Understanding its genetic structure is of great significance for evaluating the effect of stocking, optimizing parent selection and maintaining genetic diversity (Pan et al., 2024). Studies have analyzed Spanish mackerel populations along the Yellow Sea and East China Sea coasts of China using mitochondrial DNA and microsatellite markers. The results showed that the genetic differences between populations in these areas were low, the gene mobility was strong, and the overall structural differentiation between populations was low. This shows that a large amount of genetic variation is shared between different geographical populations, and no obvious local branches or subspecies divisions have been found. Therefore, if wild broodstock are collected from adjacent waters for reproduction, their offspring will have a high genetic compatibility with the local wild population, and it is not easy to introduce foreign genes after release, which is conducive to maintaining ecological stability (Jeena et al., 2022). However, high migration does not mean that there is no population structure at all. Higher-resolution genetic tools, such as SNP whole-genome scanning, may reveal subtle genetic differentiation between different spawning populations of Japanese Spanish mackerel. This refined analysis is expected to reveal genetic heterogeneity that cannot be detected by mitochondrial markers, especially regional adaptive variation formed under different habitats or ecological pressures. Figure 2 shows the phylogenetic relationships of several representative species and cryptic lineages of Spanish mackerel, clearly showing that the Indo-Pacific Spanish mackerel (S. guttatus sensu lato) includes multiple different genetic branches, such as true Spanish mackerel (S. guttatus), leopard Spanish mackerel (S. leopardus) and other subtypes (aff. guttatus 1/2). This result reinforces the view of this article: individuals with similar phenotypes may come from lineages with significant genetic differences (Figure 2). If these differences are not identified during parent selection or release, problems such as genetic mixing and reduced adaptability may occur. Therefore, phylogenetic information should be used as an important reference for population management to improve the genetic adaptability and ecological safety of farmed populations (Jeena et al., 2022). In addition, there is inevitably selection pressure in the process of artificial breeding, such as high-density environment and artificial feed conditions, which may cause the allele frequency associated with certain traits to shift. Although there is no whole-genome study on the released Japanese mackerel, there is evidence in marine fish such as large yellow croaker that artificially released individuals often have low genetic diversity and are enriched in certain genes related to adaptation to artificial environments. Therefore, it is recommended to strengthen genome monitoring of farmed and released populations in the future to prevent genetic erosion of wild populations caused by long-term release (Yáñez et al., 2023).
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