International Journal of Marine Science, 2025, Vol.15, No.1, 35-44 http://www.aquapublisher.com/index.php/ijms 41 6.4 Pathogen resistance and immune adaptation In the process of adapting to the environment, shrimps are not only faced with physical and chemical conditions such as temperature and salinity, but also biological pressure, especially the threat of pathogens and viruses, which also forces them to constantly adjust themselves. Along the way of evolution, shrimps have launched an endless arms race with various viruses and bacteria, and many immune-related genomic features are the product of this confrontation. From the perspective of comparative genomics, the changes in immune genes of different shrimps are quite obvious. For example, compared with wild species, those selected and disease-resistant Vannamei shrimp strains have more duplications in pattern recognition receptor and lectin genes (Fu et al., 2024). It may be this amplification that gives them stronger broad-spectrum immunity. However, the situation is not the same for all shrimp populations. Comparisons between shrimp populations found that shrimp living in densely populated waters have higher polymorphisms and evolution rates of immune-related genes, after all, there are many types of pathogens and high pressure; while small populations in isolated waters have relatively low immune gene diversity. It can be seen that genome comparison can not only help us understand how shrimps resist diseases, but also provide a lot of references in disease-resistant breeding. 7 Case Study: Comparative Genomic Analysis of Alpheidae The Alpheidae, commonly known as pistol shrimp or pistol shrimp family, is a striking group of decapod shrimps. Species in this family are known for their ability to close their claws at high speed to make a popping sound, and are peculiar in behavior and ecology: some species of the genus Synalpheus have evolved an insect-like eusocial group structure, that is, a breeding "queen" and many infertile workers form a group to raise the larvae together. This sociality is quite rare in invertebrates. The uniqueness of the Alpheidae provides a good example for comparative genomics studies to explore the association between behavioral evolution and genomic changes. 7.1 Genome size and social evolution Pistol shrimps have a wide range of lifestyles, from solitary to eusocial, and there are quite a few species. Chak et al. (2021) did a very interesting study, measuring the genome size of 33 species of pistol shrimps in the family Pleurotus eryngii to see if there is any relationship between their genomes and social behavior (Figure 2). The results were quite unexpected: the pistol shrimps that developed eusociality generally had larger genomes than solitary species, about 1.5 times larger on average. However, it was not the number of coding genes that expanded, but the number of copies of transposable elements, such as LINE and ERV, that increased sharply. After further reconstruction of the ancestral state, the study found that once a lineage evolved sociality, the genome size and transposon content continued to rise; while those that lived alone did not change much. This trend makes people begin to wonder whether highly socialized life reduces the natural selection pressure at the individual level, thereby giving "selfish" transposons an opportunity to take advantage. This discovery not only reveals the possible linkage between social behavior and genome evolution, but also allows us to see the potential of comparative genomics in studying non-model species. 7.2 Comparison of social-related genes Of course, social evolution is not just about genome expansion. From the molecular details, the genome comparison of the family of shrimp has also found many interesting changes. Because eusociality is accompanied by complex reproductive division of labor and cooperative care, researchers speculate that genes in the fields of neural development, hormone regulation, and immune defense should also be somewhat special. After comparing eusocial species with solitary species, some candidate genes were indeed found. For example, genes that control neurotransmitter receptors showed traces of positive selection in eusocial pistol shrimps, suggesting that they may have been adjusted to adapt to group life. In addition, pattern recognition receptors related to immune recognition have also expanded or specialized in function, perhaps to avoid treating individuals in the same group as enemies. A more special point is that some studies have reported that some antimicrobial peptide genes in eusocial pistol shrimps are downregulated (Guryanova et al., 2023), which is speculated to be because group life reduces the chance of individuals being exposed to pathogens. Although these results are still preliminary, they at least provide some molecular clues to explain the evolution of sociality.
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