International Journal of Marine Science, 2025, Vol.15, No.1, 1-14 http://www.aquapublisher.com/index.php/ijms 6 et al., 2023). Phylogenetic studies based on the whole genome provide more solid evidence support for abalone taxonomy. This study suggests that future revisions of abalone classification should fully refer to genomic data and reasonably divide species and subspecies boundaries. For example, the abalone genus can be divided into the North Pacific subgenus, the Southern Hemisphere subgenus, etc. according to genetic distance, thereby reflecting its systematic evolutionary pattern. 4 Adaptive Evolutionary Mechanisms 4.1 Identification of positively selected genes related to temperature, salinity, and immunity Abalone can live in a variety of waters, from cold high-latitude waters to warm tropical waters. Different species of abalone have very different adaptability to the environment. Some are more tolerant to high temperatures, while others are more adaptable to low temperatures or salinity changes. In this study, we compared the whole genome of abalone and found some key genes related to temperature and salinity adaptation. This study also used positive selection analysis and found signs of accelerated evolution in some genes related to stress response. For example, genes encoding heat shock proteins (HSPs) and molecular chaperones showed positive selection signals in tropical abalone. This may indicate that changes in these genes help proteins become more stable and more heat-resistant. In the cold-adapted Japanese abalone, some antifreeze protein genes may have played a role. These genes may have become more numerous or their functions have been enhanced, but this needs further verification. Regarding salinity adaptation, some genes that regulate water and salt inside and outside the cell, such as Na+/K+-ATPase and organic matter transport proteins, have also changed at certain sites. Some gene families may also become larger. This may help abalone maintain homeostasis in environments with large salinity changes (Creencia and Noro, 2018). In addition to temperature and salinity, abalone's defense against pathogens is also an important aspect of their adaptation to the environment. We found sequence differences in some immune-related genes in different abalone species. For example, the Toll-like receptor (TLR) genes related to innate immunity are more numerous in temperate abalone, while in some tropical abalone, some TLR genes have become pseudogenes or even completely disappeared. All abalone lack a gene called MAVS. This gene is critical in many vertebrates, mainly to help fight viruses. Although abalone does not have MAVS, their RIG-I-like receptor (RLR) genes have undergone significant changes, which may initiate antiviral responses in other ways (Agius et al., 2024). This shows that abalone has formed its own defense method in long-term evolution, perhaps by adjusting the pathway of signal transmission to compensate for the lack of MAVS. Some immune genes related to colistin response and phagocytosis, such as TRAF, also showed adaptive changes at specific sites, indicating that these genes may have also undergone positive selection. 4.2 Gene family expansions in shell formation and metabolic pathways The precious value of abalone is not only reflected in the quality of the meat, but also in its strong and beautiful shells. The abalone shell is composed of aragonite calcium carbonate and organic matrix, which has evolved into a complex biomineralization mechanism. Genome analysis found that the gene family involved in shell formation has expanded and diversified significantly in abalone. For example, genes encoding nacre organic matrix proteins (such as velvet snail protein, gelatin protein, etc.) have multiple copies and variant forms in the abalone genome. These genes are usually highly expressed by the mantle, and their products are secreted into the shell to regulate crystal growth (Mann et al., 2018; Sharker et al., 2021). Comparison of the mantle "secretome" of different abalone species shows that even closely related species have very different sets of shell matrix proteins. Shell proteins of a large number of gene families were independently innovated in each lineage. For example, the proline-rich shell protein family found only in the wrinkled abalone was replaced by another set of serine-rich proteins in the green abalone. This phenomenon of "same function, different sequence" indicates that the shell formation-related gene family has undergone rapid divergent evolution in different lineages of abalone. Gene family expansion is not limited to structural proteins. This study also noted that some metabolism and detoxification-related genes are particularly abundant in abalone. For example, the multifunctional oxidase gene
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