Bioscience Methods 2025, Vol.16, No.4, 183-192 http://bioscipublisher.com/index.php/bm 183 Feature Review Open Access Origin and Evolutionary History of Oysters Based on Comparative Phylogenomics and Fossil Evidence Chengmin Sun1, RudiMai 2 1 Tropical Marine Fisheries Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China 2 Tropical Biological Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: rudi.mai@hitar.org Bioscience Methods, 2025, Vol.16, No.4 doi: 10.5376/bm.2025.16.0017 Received: 12 May, 2025 Accepted: 23 Jun., 2025 Published: 15 Jul., 2025 Copyright © 2025 Sun and Mai., This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Sun C.M., and Mai R.D., 2025, Origin and evolutionary history of oysters based on comparative phylogenomics and fossil evidence, Bioscience Methods, 16(4): 183-191 (doi: 10.5376/bm.2025.16.0017) Abstract Oysters represent a biologically and ecologically significant group of marine bivalves with a complex evolutionary history. This study integrates comparative phylogenomics and fossil evidence to explore the origin, diversification, and morphological evolution of oysters. We examined recent advances in phylogenomic methodologies, including high-throughput sequencing and ortholog identification, to resolve oyster lineages and their adaptive traits. In parallel, we assessed the rich fossil record of oysters to trace evolutionary trends and provide calibration points for molecular clocks. Through synthesis of these two complementary datasets, we addressed consistencies and discrepancies in evolutionary timelines, reconstructed key trait evolution, and analyzed biogeographical dispersal patterns. A focused case study on the genus Crassostrea highlights the power of integrated approaches in uncovering lineage-specific evolutionary events. This study underscores the importance of combining genomic and paleontological data to achieve a more comprehensive understanding of oyster evolution and provides a framework for future research leveraging multidisciplinary approaches and advanced analytical tools. Keywords Oyster evolution; Phylogenomics; Fossil record; Crassostrea; Comparative genomics 1 Introduction Walking along the beach, you can often see rows of oysters attached to the reefs. This bivalve is basically found along the coasts of the world, active in intertidal zones or not too deep waters (Zhang et al., 2024). People may not pay much attention to their existence, but they are actually a key part of coastal ecology - they purify water quality, provide hiding places for other marine life, and are also important targets for aquaculture. In fact, oysters rely on more than just "toughness" to survive well and widely in such a complex and changeable marine environment. They have strong adaptability and rich genetic background. Some can float, while others stay in one place for their entire lives. Different species have their own set of shell shapes and reproduction methods, and their appearance changes quickly and they adapt to the environment quickly (Li et al., 2021; Li et al., 2022). However, when it comes to their "origin"-that is, where they came from and how they became what they are today, things are not so clear. Many people think that they can judge their species by looking at their shells, but the shells change all the time, and their appearance is not reliable. Previous classification methods often leave people confused (Hautmann, 2006; Guo et al., 2018). Now scientists no longer rely solely on appearance. They begin to pull out genomic data and study them together with clues from fossils. Genes tell us about their genetic changes and ways of adaptation, while fossils allow us to look back at the traces they left in ancient strata (Márquez-Aliaga et al., 2005; Liu et al., 2024). Together, the two are expected to give us a more complete understanding of the evolution of oysters. So this study intends to start from two perspectives: genomics and fossils. We want to figure out how different types of oysters are divided and whether there are any regularities in their geographical distribution. We also want to know which genes have changed and which morphologies have changed in the process of adapting to the environment, and how they interact with environmental changes. We hope that in this way, we can provide some more reliable references for future research on the classification, evolutionary mechanism, and protection strategies of oysters.
RkJQdWJsaXNoZXIy MjQ4ODYzNA==