International Journal of Marine Science, 2025, Vol.15, No.3, 154-166 http://www.aquapublisher.com/index.php/ijms 159 5 Analysis of the Evolutionary Trajectory and Selection Pressure of Key Genes 5.1 Construction and comparison of phylogenetic tree of growth/reproduction genes To explore the evolutionary history of growth and reproduction-related genes, researchers often compare homologous gene relationships in different species by constructing phylogenetic trees. Such analysis can reveal gene origin and differentiation and species specificity. Taking the insulin-like growth factor binding protein (IGFBP) as an example, Pang et al. (2021) compared the phylogenetic relationship between three IGFBPgenes in vannerbine shrimp and other invertebrates and vertebrates IGFBP. The results show that shrimp IGFBP and insects and other invertebrates are clustered into one branch, which is obviously different from the IGFBP subfamily of mammals. This suggests that shrimp IGFBP is evolutionarily unique to invertebrates and may also differ in function. For males to decide to switch the IAGgene, the phylogenetic tree constructed by Lü et al. (2023) shows that the IAG of small freshwater shrimps (such as the genus Cypress) gathers into one branch, while the IAG of marine shrimps gathers into another branch, and the two separate in the tree. This suggests that IAGgenes may have lineage-specific differentiation in different ecological groups, and their functional regulation may be different. Through phylogenetic tree comparisons, we can also speculate on gene replication and loss events. For example, if a shrimp species has two sequences on a tree that corresponds to one gene of another species, it means that a gene duplication has occurred; conversely, if it is missing, it may be a gene loss or pseudogeneization. 5.2 Analysis of positive selection, negative selection and neutral evolutionary events The selection pressures that genes are subject to during evolution can be inferred by molecular evolution rate analysis. Researchers have discovered some interesting selection patterns for growth and reproduction-related genes in the shrimp genome. Positive selection (adaptive evolution) often acts on genes that are functionally important and require rapid adaptation to the environment. At the same time, artificial breeding is also driving selective changes in some genes. By resequencing the genome of 6 Vannebine shrimp breeding lines, approximately 370 000 significantly differentiated SNP sites and a batch of selected genes were identified. Some of these genes are related to growth and immune function and are considered to be artificially selected during breeding and domestication. These genes exhibit high frequency enrichment of specific alleles in breeding line populations, reflecting the directed selection pressure of breeding on fast growth and disease-resistant traits (Ma et al., 2024). In contrast to positive selection, negative selection (purification selection) keeps functionally critical reproductive genes highly evolutionarily conserved. In addition, a large number of structural and metabolic-related genes are also maintained by purification selection, and their amino acid sequences are almost unchanged in shrimp evolution. As for neutral evolution, it mainly involves those non-functional regions or redundant genes in the shrimp genome. A high degree of polymorphism in simple repeat sequences (SSRs) is an example: many of the newly expanded SSRs in the shrimp genome vary in length between different strains, but do not affect survival adaptation. This suggests that these SSR variants may be neutral evolutionary products and are not subject to obvious choice constraints. After some duplicate genes are functionally replaced or redundant, their mutations accumulate in a neutral way, gradually turning into pseudogenes present in the genome. 5.3 Convergence and differentiation and evolutionary characteristics of functional genes among different shrimps Shrimps differentiate into diverse ecological groups during the long evolution process, and different species show evolutionary characteristics of convergence or divergence in functional genes. Convergent evolution refers to the fact that species without kinship evolve similar genetic characteristics when facing similar environmental pressures. Among shrimps, low-salt environmental adaptation is an example. Vannebane prawns and Chinese prawns live in low salinity waters of the estuary. Although their phylogenetic distance is far away, their genomes have experienced a large expansion of simple repeat sequences (SSRs), which is believed to confer adaptability to low salt stress (Zhang et al., 2023). Multiomic analysis showed that these SSR enrichment near osmotic regulation-related genes, affecting gene expression, thereby improving survival under low-salt conditions. This suggests that the two shrimps achieve convergent environmental adaptation through similar genomic mechanisms in independent evolution.
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