Bioscience Methods 2025, Vol.16, No.4, 183-192 http://bioscipublisher.com/index.php/bm 187 4.2 Evolution of key traits in an integrative framework By combining molecular data with fossil records, we can more clearly see the changes in some important traits of oysters, such as their reproduction methods and shell morphology. Studies have found that the ancestors of oysters first reproduced by spreading eggs, and some species later evolved the method of raising chicks. Fossils can also provide some support for this. Genome analysis also found that there are many gene duplications and structural changes in oysters. These changes may help them better cope with stress, such as changes in salinity, high temperature, lack of oxygen and other problems (Li et al., 2020; Gundappa et al., 2022). Fossil records can also support these conclusions, such as changes in shell shape, shell thickness, and attachment methods found in different strata. These findings provide us with a timeline, telling us when these adaptive characteristics probably appeared (Wang et al., 2014). 4.3 Biogeographical patterns and historical dispersal Not all organisms rely on "running far" to spread around the world. Oysters are a typical example. They have a wide distribution range, but they are not good at long-distance diffusion-at least common species such as Crassostrea and Saccostrea are like this (Foighil and Taylor, 2000). According to current research, oysters may have originated in areas near the Arctic, around the early Jurassic. This is not a random guess, genetic data and fossil evidence are concentrated on this time point and place (Li et al., 2021a). Things later were much more complicated. Some geological events around the world-such as plate movement and climate fluctuations-seem to have paved the way for the spread of oysters. It is not that they actively spread quickly, but that the environment "carries" them away slowly. There is a point that is easily overlooked: whether the larvae can drift far is actually not that critical. On the contrary, how they adapt to the local environment and how they reproduce really determines whether they can stay and develop. Changes in the earth's crust and the transfer of habitats are the main drivers of their diffusion patterns. So, looking at molecular and fossil data together is more than just supplementary information. They can verify each other and help us better piece together the full picture of oyster spread and diversification-just like superimposing two pictures together, and only when they match up can we know that we are right. 5 Case Study: Crassostrea Genus as a Model for Evolutionary Analysis 5.1 Phylogenomic insights into Crassostrea evolution Sometimes, classification is not just a matter of “looking at it roughly”. The evolution of the oyster genus is an example. At first, many species were grouped together, such as Magallana, which was originally part of the oyster genus Crassostrea. But when the genetic data was later presented, the differences suddenly became apparent. Especially the comparison of mitochondrial and nuclear DNA-not only is there a genetic boundary, but there are also some details in appearance that can match. Of course, not all species are so different. For example, the angulata and the giant oyster (C. gigas) look very similar at first glance. But when you go deep into the chromosome-level genome, the results are a bit unexpected: their genetic structure remains quite consistent, and many positions are one-to-one (Figure 3) (Qi et al., 2022). But then again, there are differences between the two. Some gene regions still have unique variations, which may be the places that determine their respective adaptation methods and even the potential direction of species differentiation. Another interesting discovery is that some Asian oyster species have almost the same gene order in their mitochondria. From this point of view, it is likely that these species have been separated for a short time and can be considered as “relatives” who have just separated (Ren et al., 2010). 5.2 Fossil evidence supporting Crassostrea lineage history Genetic data alone is not enough, the dimension of time must be supplemented by fossils. There are actually quite a few oyster fossils, and they are widely distributed, which is quite unexpected. In other words, they have already traveled to many corners of the world. These fossils are not just "similar", many of them can also be seen from the shape of the shell, the size of the ligament and other characteristics. For example, the Hong Kong oyster (Crassostrea hongkongensis) is a typical combination. Its shell shows a unique morphology in fossils, and it can also be genetically separated from other species (Lam and Morton, 2003). And these fossils not only let us know what someone looks like, they also help a lot - they are used to calibrate the "molecular clock". In other words,
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