International Journal of Marine Science, 2025, Vol.15, No.3, 130-143 http://www.aquapublisher.com/index.php/ijms 138 lower than those of the wild population, and the FST values of both reached statistically significant levels. It can be inferred that if a whole-genome SNP analysis is conducted on the Japanese Spanish mackerel population released along the coast of China in recent years, subtle but existing signals of population differences may be found, which deserves further study. In addition to genetic diversity, phylogenetic analysis can also compare population adaptive genetic variation. For example, it can be screened whether some key gene variants related to disease resistance and migratory behavior are missing in farmed populations. These variants may be retained by natural selection in wild populations, but lost under artificial conditions due to different selection pressures. The phylogenetic tree cannot directly reflect the differences in specific genes, but it can be combined with methods such as GWAS to locate sites with functional significance, and then look at their degree of differentiation between populations. For example, if it is found that the farmed population has a single allele on immune-related genes, while the wild population is diverse, it needs to be taken seriously. Existing literature has pointed out that artificial continuous breeding may cause hidden inbreeding depression and domestication selection effects, which may reduce the competitiveness of released fish in the wild (Yáñez et al., 2023). 5.3 Phylogenetic-based population optimization recommendations First, enrich the breeding germplasm and maintain genetic diversity. Phylogenetic analysis emphasizes the importance of genetic diversity for population health. Therefore, in the selection of artificial breeding broodstock, a sufficient number of wild individuals should be caught from the target sea area, covering different subpopulations and families, to avoid over-reliance on a few populations or close relatives as parents. The more broodstock there are, the richer the genetic variation of the offspring population, and the lower the risk of inbreeding degeneration in the future release or breeding population. In particular, if phylogenetic studies have revealed that the target species has genetic branches (for example, there are two lineages in leopard mackerel), the lineage homologous to the local wild population should be used as the parent to avoid problems such as foreign gene invasion or hybrid sterility caused by mixed breeding of different lineages (Zeng et al., 2022). Secondly, strengthen pre-release domestication and selection to improve the survival rate of release. Phylogenetic relationships can tell us the differences between farmed fish and wild fish, but how to bridge this gap requires efforts in breeding management. Some studies have pointed out that by conducting "survival skills training" before release, such as simulating predation and escape scenarios in the wild, the survival rate of released fish in the wild can be significantly improved (Gao et al., 2024). Third, regular genetic monitoring and feedback improvement. It is recommended to establish a genetic monitoring archive for the Spanish mackerel release project, and sample and analyze the genetic structure of the population before and after each batch of release, including allele frequency, heterozygosity, and phylogenetic clustering relationship with historical samples. Once it is found that the seedlings of a certain breeding are too genetically deviated from the wild population (for example, obvious grouping appears in cluster analysis), the parental composition or breeding method should be adjusted in time (Da Cunha et al., 2020). Finally, for farms with fully artificial closed breeding (such as the development of Spanish mackerel factory breeding in the future), phylogenetic and genomic selection technologies can also be used to accelerate strain breeding. With the help of genomic data, whole genome selection for growth, disease resistance and other traits can be carried out to quickly select dominant individuals from many families for breeding. At the same time, molecular markers can be used to avoid inbreeding, maintain a certain effective population size, and maintain genetic diversity. Gene editing technologies (such as CRISPR) have been successfully used to improve growth and disease resistance traits in some aquatic animals, and may also be used in mackerel in the future (Wang, 2024). 6 Implications for Aquaculture Research 6.1 Genetic resource protection and genetic improvement The first implication of whole genome phylogenetic research for aquaculture is the re-recognition of the
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