Genomic analysis reveals the influence of climate change and currents on adaptation in an estuarine species

Understanding the evolutionary forces driving adaptive divergence and identifying the genomic variations, especially those mediating the plastic responses are critical to evaluate the adaptive capacity of species upon rapidly changing climate. Here we report a high-quality genome assembly for an estuarine oyster (Crassostrea ariakensis) and 264 resequenced wild individuals from 11 estuaries along Chinese coastline. This estuarine oyster evolved decreased polymorphism and a clear population structure than that of marine species.

Historical glaciations, ocean currents and environmental selection play important role in shaping and maintaining their divergence patterns. We identified genes, especially for expanded genes solute carrier family, showing strong selective signals and most of them responded to temperature and salinity challenges, suggesting their significance in environmental adaptation. Higher genetic divergence of environment-responsive genes especially in upstream intergenic regions potentially regulate their higher plastic changes, providing genomic basis of plasticity upon climatic selection.

Our findings contribute to assess species’ vulnerabilities to climate-driven decline or extinction.