Global climate change and its consequences for the symbiosis between corals and microalgae are impacting coral reefs worldwide—ecosystems that support more than one-quarter of marine species and sustain nearly one billion people1–3. Understanding how stony corals, the primary architects of both shallow and deep reef ecosystems, responded to past environmental challenges is key to predicting their future4. Here we describe a time-calibrated molecular phylogenetic analysis that includes hundreds of newly sequenced coral taxa, and sheds light on the deep-time evolution of scleractinian corals. We date the emergence of the most recent common ancestor of Scleractinia to about 460 million years ago and infer that it was probably a solitary, heterotrophic and free-living organism—or one that could reproduce through transverse division—thriving in both shallow and deep waters. Our analyses suggest that symbiosis with photosynthetic dinoflagellates was established around 300 million years ago and spurred coral diversification. However, only a few photosymbiotic lineages survived major environmental disruptions in the Mesozoic era. By contrast, solitary, heterotrophic corals with flexible depth and substrate preferences appear to have thrived in the deep sea despite these environmental disturbance events. Even though ongoing environmental changes are expected to severely affect shallow reefs5, our finding that stony corals have shown resilience throughout geological history offers hope for the persistence of some lineages in the face of climate and other environmental changes.
