Bioscience Methods 2025, Vol.16, No.4, 183-192 http://bioscipublisher.com/index.php/bm 188 they can tell us when these species began to differentiate and spread. Without these reference points, the timing of many evolutionary events is actually "uncertain". 5.3 Synthesis of molecular and fossil data inCrassostrea When we look at genetic data and fossil evidence together, we have a more complete understanding of the evolution of oysters. The results of molecular phylogeny are roughly consistent with the fossil timeline. This also supports the claim that Asian oyster species have recently diversified, and it also shows the overall evolutionary history of the oyster genus (Salvi and Mariottini, 2016). Putting genetic and morphological data together can not only help us distinguish some species that are originally difficult to classify, but also find hidden species that have not been discovered before. For example, research on Hong Kong oysters shows that its distribution range may have expanded northward (Liu et al., 2022). Combining genomic research with fossil data is a good way to understand the evolution and adaptive diversity of oysters. It allows us to see farther and see more clearly. 6 Future Directions and Methodological Advances 6.1 Advances in sequencing and analytical tools In recent years, sequencing technology and analytical tools used in oyster research have advanced rapidly. We now have high-quality reference genomes, such as the genomes of the American oyster (Crassostrea virginica) and the ball oyster (Saccostrea glomerata). These data allow us to carefully study their genetic structure, which gene families have become more abundant, and which genes are related to environmental adaptation (Powell et al., 2018). In addition, transcriptome and proteome analysis also allows us to better understand how oysters cope with stress, how they grow shells, and how they determine sex. Whole-genome studies have found that the genetic structure has changed in many places, and even the number of genes has changed. These changes may be the reason for the different appearances and differences in adaptability (Modak et al., 2021). These new technologies can not only be used to compare different types of oysters, but also provide a lot of useful tools for evolution, living environment research and aquaculture (Zhang et al., 2012). 6.2 Challenges in data integration It's easier said than done. Although gene sequencing and analysis technology are becoming more and more advanced, once these data are put together with fossil data, problems begin to emerge. Especially in some oyster genera (such as Ostrea), which have many changes, the situation is even more complicated. Sometimes, genetic analysis gives a relationship map, but when you look at the fossil classification, it doesn't match at all (Li et al., 2021a). At this time, you will find that the existing classification system may not be enough, and there are far from enough new fossil samples. Let's talk about morphology. The appearance of oysters is very "changeable". The shape of the shell is greatly affected by the environment. Sometimes even the same species can look different in different places. Therefore, it is often easy to misjudge based on appearance alone. Moreover, unfortunately, the fossil record we have is not complete, and there are many gaps, which has a great impact on the use of molecular clocks to push time (Anzai et al., 2024). Of course, it doesn't mean that these problems cannot be solved. It's just that to connect genes, environment and evolutionary trends in series, we need to rely on more solid experimental design and analysis methods. Which ones are caused by the genes themselves? Which ones are forced by the external environment? These need to be separated step by step (Sirovy et al., 2021). 6.3 Opportunities for multidisciplinary research Now, more and more studies are combining genetics, paleontology, ecology and environmental science (Jin, 2024). This approach gives us the opportunity to gain a deeper understanding of the origin, distribution changes and adaptability of oysters. For example, some studies have used the Mg/Ca ratio in oyster shells to estimate ancient seawater temperatures. This can link past climate change with the evolution of oyster populations (Bougeois et al., 2016). Genome sequencing and data analysis tools continue to improve, which can drive us to discover more new things. Collaboration between different disciplines will also help us more fully understand how oysters adapt to the environment and whether they have the ability to recover in the face of environmental changes (Zhang et al., 2016).
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