International Journal of Aquaculture, 2024, Vol.14, No.4, 184-194 http://www.aquapublisher.com/index.php/ija 190 sustaining their survival and diversification across various habitats. The frequent transitions of diatoms between marine and freshwater environments not only drive their species diversification but also provide important insights into the adaptive evolution of aquatic organisms. Freshwater environments present unique opportunities and challenges for diversification. The "freshwater fish paradox" describes the high concentration of vertebrate diversity in continental freshwaters, with over 15 000 fish species representing more than 20% of all vertebrate species in a tiny fraction of the Earth's surface area (Val et al., 2022). Landscape evolution, particularly river capture events, has been proposed as a significant driver of this diversity. River captures can accelerate biotic diversification by affecting dispersal, speciation, and extinction rates. Large, lowland river basins in tropical regions, such as South America, Africa, and Southeast Asia, exhibit the highest fish species richness, likely due to their stable tectonic conditions and high habitat volume. Figure 2 The temporal sequence of marine–freshwater transitions (Adopted from Roberts et al., 2023) Image caption: (a) Divergence times and ancestral state reconstruction of marine and freshwater habitat in Thalassiosirales; (b) Summary of the difference between the number of parsimony optimized marine-freshwater transitions on rooted orthologs with the estimated gene tree topology (GT) versus the topology constrained to match the species tree (ST); (c) Summary of the percentage of aligned amino acid sites that have greater (purple), equal (green), or fewer (yellow) numbers of state transitions on the GT versus ST (Adopted from Roberts et al., 2023) 7 Technological Advances in Studying Molecular Diversification 7.1 Genomics and transcriptomics Recent advancements in genomics and transcriptomics have significantly enhanced our understanding of molecular diversification in aquatic life forms. The integration of these technologies has allowed researchers to delve into the genetic and transcriptomic underpinnings of species adaptation and diversification. For instance, large-scale projects such as the Marine Mammal Genome Project and the Fish10K have provided extensive genomic data that facilitate the study of evolutionary biology in aquatic organisms (Ovchinnikova and Shi, 2023). These projects have enabled the identification of novel bioactive macromolecules and the exploration of differential gene expression and evolutionary selection mechanisms. Additionally, the genomic analysis of
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