Bioscience Methods 2025, Vol.16, No.4, 183-192 http://bioscipublisher.com/index.php/bm 186 Figure 2 Examples of previously described Liostrea (A, B) and Lophinae (C-G) from the Middle and early Late Triassic. A, B.Ostrea pictetiana Mortillet, 1858, SNSB BSPG AS XVI 14, right and left valve of specimen with conjoined valves. C, D.Ostrea calceoformis Broili, 1903. C. SNSB BSPG 1903 IX 200, ligament area of left valve. D. SNSB BSPG 1903 IX 1364, exterior of left valve, showing attachment scar and plicae. E-G.Ostrea montiscaprilis Klipstein, 1843. E, F. SNSB BSPG AS XVI 32, interior and exterior of left valve; note ligament area with broad resilifer and narrow, ridge-like bourrelets and plicate shell. G. SNSB BSPG AS XVI 33, interior of right valve with depressed bourrelets and relatively elevated resilifer (note that true relief may appear inverted in figure). All specimens are housed in collection of Bayerische Staatssammlung für Paläontologie und Geologie, Munich. Scale bars: A, B, E, F=10 mm; C, D, G=5 mm (Adapted from Hautmann et al., 2017) 3.3 Fossil calibration of molecular clocks Fossils are also useful for "molecular clocks". The so-called molecular clock is to estimate the time of species differentiation through the rate of genetic mutation. Fossils can provide a reference point in time, helping scientists to analyze evolutionary history more accurately (Hautmann, 2006). For example, when studying the pearl oyster (Pinctada), Bayesian analysis was used to measure that it originated around the Miocene, and this result also matches the time of the fossils (Cunha et al., 2011). By combining molecular data and fossil records, scientists can confirm the time of some major events, such as the origin of the oyster family in the early Jurassic, or the rapid differentiation in the Cretaceous and Paleogene. These changes are often related to geological movements and environmental changes (Li et al., 2021a). Fossil data can allow us to draw a more accurate timeline of oyster evolution, and also help us understand how they migrate and form different species. 4 Integration of Phylogenomics and Fossil Evidence 4.1 Concordance and conflicts between molecular and fossil evidence Phylogenomics and fossil data together can help us better understand the evolution of oysters. The two methods sometimes agree, but there are also many places where there are conflicts. For example, molecular studies using mitochondrial and nuclear DNA markers have estimated that oysters appeared in the early Jurassic period, which is consistent with the time of some important fossils. At that time, geological events such as the expansion of the Atlantic and Tethys Oceans may have driven the diversification of oysters. However, in some details, the molecular analysis and the traditional classification based on appearance are not exactly the same. Especially for shellfish like oysters, their shell morphology is very changeable and the fossil record is not very complete, so it is sometimes difficult to classify accurately (Salvi and Mariottini, 2016). Genetic data also found some lineages that had not been noticed before, which led researchers to reclassify some genera. These changes were not obvious in the previous classification system based mainly on fossils.
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