Bioscience Methods 2025, Vol.16, No.4, 183-192 http://bioscipublisher.com/index.php/bm 185 2.2 Insights into oyster lineage diversification Phylogenomic analysis has found that oysters have great genetic differences at the species, population and even genome levels. These differences can sometimes reveal some hidden species that cannot be seen from the outside, and can also show some species differentiation processes that are taking place. For example, the evolution of different oyster species (such as Pacific oysters and European oysters) coincides with some geological changes, such as the expansion of the Atlantic Ocean, changes in the Paleo-Tethys Ocean, and major climate fluctuations in the past (Guo et al., 2018). The diversification of oysters is mainly not based on larval dispersal, but on their local adaptability and different reproduction methods (Li et al., 2021a). Some groups are very different, and some seem to be one species, but actually contain multiple genetically different groups, all of which indicate that they may be differentiating into new species. 2.3 Comparative genomics and adaptive traits Studies have also found that oysters have many genes related to stress response, immune defense, and environmental adaptation. These genes have been significantly expanded in their gene families (Takeuchi et al., 2016). For example, some solute carrier families and genes involved in energy metabolism and shell formation are very numerous. These expansions help oysters adapt to different salinities, temperatures, and other pressures. Studies have also found that oysters are very flexible in phenotype, especially gene expression can change according to the environment. This flexibility is related to their evolutionary direction, indicating that in a changing environment, this variability in gene expression is actually an advantage (Li et al., 2018a; Li et al., 2018b). However, this adaptation also has a price. For example, in order to have stronger stress resistance, oysters may have to sacrifice growth rate or metabolic efficiency (Li et al., 2017; Li et al., 2020). In addition, some special genomic features, such as the positional changes of Hox genes and gene expansion caused by transposable elements, have also helped different oyster species to form their own unique characteristics and adaptability during evolution. 3 Fossil Record and Morphological Evolution of Oysters 3.1 Overview of the oyster fossil record Oysters have a very rich fossil record. They first appeared in the early Triassic, shortly after the Permian extinction (Figure 2) (Hautmann et al., 2017). Early oysters, such as the species called Liostrea, had some special features, such as the left shell being fixed to a hard object and a unique ligament structure. The fossils of these early oysters are generally found in open marine environments, sometimes wrapped in ammonites. Judging from the fossils, oysters are distributed in many places and at many times. Especially in the Jurassic and Cretaceous periods, their species became very diverse. Scientists have discovered many different oyster populations in Central Europe, the Tethys Sea, and the Americas (Anzai et al., 2024). 3.2 Evolutionary trends inferred from fossils Looking at fossils is not always about finding the oldest one. Often, what is really interesting is to see the changes, such as oysters. Their evolutionary pace is quite fast in some periods, especially in the way they cope with different environments. For example, the ribs of the shell are sometimes obvious and sometimes almost invisible. This is not entirely accidental, but has something to do with the conditions of the seabed at the time. When the seawater flows slowly and there is fine sand underneath, the shells of oysters often have more obvious patterns (Rantuch, 2023). But once the water flow becomes faster and the environmental energy is high, their shells become thicker and larger, and look more "hardcore" (Moneer et al., 2024). Of course, not all fossils are so regular, and there are occasional exceptions. The morphology changes, and the lifestyle also changes. Some species used to lie directly on the seabed, but later they became able to "live" close to the rocks. This change from "lying to attaching" actually left traces in the stratigraphic record, and it is quite obvious (Márquez-Aliaga et al., 2005). Not only did the depth change, some even moved from shallow seas to deeper places, and also changed their body shape (Hook et al., 2012). So sometimes, a fossil is not an isolated piece of information. Behind it, there may be a story of environmental change and adjustment of survival strategies.
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