Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737–1742 (2007).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Carpenter, K. E. et al. One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321, 560–563 (2008).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Knowlton, N. Coral reef biodiversity-habitat size matters. Science 292, 1493–1495 (2001).

Article 
CAS 
PubMed 

Google Scholar
 

Pandolfi, J. M., Connolly, S. R., Marshall, D. J. & Cohen, A. L. Projecting coral reef futures under global warming and ocean acidification. Science 333, 418–422 (2011).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Mellin, C. et al. Cumulative risk of future bleaching for the world’s coral reefs. Sci. Adv. 10, eadn9660 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Kleypas, J. A. et al. Geochemical consequences of increased atmospheric carbon dioxide on coral reefs. Science 284, 118–120 (1999).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Gault, J. A., Bentlage, B., Huang, D. & Kerr, A. M. Lineage-specific variation in the evolutionary stability of coral photosymbiosis. Sci. Adv. 7, eabh4243 (2021).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Stolarski, J. et al. The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals. BMC Evol. Biol. 11, 316 (2011).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Arrigoni, R. et al. A new sequence data set of SSU rRNA gene for Scleractinia and its phylogenetic and ecological applications. Mol. Ecol. Resour. 17, 1054–1071 (2017).

Article 
CAS 
PubMed 

Google Scholar
 

Quattrini, A. M. et al. Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time. Nat. Ecol. Evol. 4, 1531–1538 (2020).

Article 
PubMed 

Google Scholar
 

Kiessling, W. & Simpson, C. On the potential for ocean acidification to be a general cause of ancient reef crises. Glob. Change Biol. 17, 56–67 (2011).

Article 
ADS 

Google Scholar
 

Vasseur, R. et al. Major coral extinctions during the early Toarcian global warming event. Glob. Planet. Change 207, 103647 (2021).

Article 

Google Scholar
 

Jacobs, D. K. & Lindberg, D. R. Oxygen and evolutionary patterns in the sea: onshore/offshore trends and recent recruitment of deep-sea faunas. Proc. Natl Acad. Sci. USA 95, 9396–9401 (1998).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Cairns, S. D. Deep-water corals: an overview with special reference to diversity and distribution of deep-water scleractinian corals. Bull. Mar. Sci. 81, 311–322b (2007).


Google Scholar
 

Roberts, J. M., Wheeler, A., Freiwald, A. & Cairns, S. (eds) Cold-Water Corals: The Biology and Geology of Deep-Sea Coral Habitats (Cambridge University Press, 2009).

Orejas, C. et al. Madrepora oculata forms large frameworks in hypoxic waters off Angola (SE Atlantic). Sci. Rep. 11, 15170 (2021).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Campoy, A. N. et al. The origin and correlated evolution of symbiosis and coloniality in scleractinian corals. Front. Mar. Sci. 7, 461 (2020).

Article 

Google Scholar
 

McFadden, C. S. et al. Phylogenomics, origin, and diversification of Anthozoans (phylum Cnidaria). Syst. Biol. 70, 635–647 (2021).

Article 
PubMed 

Google Scholar
 

Frankowiak, K. et al. Photosymbiosis and the expansion of shallow-water corals. Sci. Adv. 2, e1601122 (2016).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Ries, J. B. Geological and experimental evidence for secular variation in seawater Mg/Ca (calcite-aragonite seas) and its effects on marine biological calcification. Biogeosciences 7, 2795–2849 (2010).

Article 
ADS 
CAS 

Google Scholar
 

Misof, B. et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 346, 763–767 (2014).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Shao, Y. et al. Phylogenomic analyses provide insights into primate evolution. Science 380, 913–924 (2023).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Zuntini, A. R. et al. Phylogenomics and the rise of the angiosperms. Nature 629, 843–850 (2024).

Erwin, D. H., Valentine, J. W. & Sepkoski, J. J. Jr A comparative study of diversification events: the early Paleozoic versus the Mesozoic. Evolution 41, 1177–1186 (1987).

Article 
CAS 
PubMed 

Google Scholar
 

Scrutton, C. T. The Palaeozoic corals, I: origins and relationships. Proc. York. Geol. Soc. 51, 177–208 (1997).

Article 

Google Scholar
 

Scrutton, C. T. & Clarkson, E. N. K. A new scleractinian-like coral from the Ordovician of the Southern Uplands, Scotland. Palaeontology 34, 179–194 (1991).


Google Scholar
 

Ezaki, Y. The Permian coral Numidiaphyllum: new insights into anthozoan phylogeny and Triassic scleractinian origins. Palaeontology 40, 1–14 (1997).


Google Scholar
 

Ezaki, Y. Paleozoic Scleractinia: progenitors or extinct experiments? Paleobiology 24, 227–234 (1998).

Article 

Google Scholar
 

Barbeitos, M. S., Romano, S. L. & Lasker, H. R. Repeated loss of coloniality and symbiosis in scleractinian corals. Proc. Natl Acad. Sci. USA 107, 11877–11882 (2010).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Campoy, A. N., Rivadeneira, M. M., Hernández, C. E., Meade, A. & Venditti, C. Deep-sea origin and depth colonization associated with phenotypic innovations in scleractinian corals. Nat. Commun. 14, 7458 (2023).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Lindner, A., Cairns, S. D. & Cunningham, C. W. From offshore to onshore: multiple origins of shallow-water corals from deep-sea ancestors. PLoS ONE 3, e2429 (2008).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Horowitz, J. et al. Bathymetric evolution of black corals through deep time. Proc. R. Soc. B 290, 20231107 (2023).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Rocha, L. A. et al. Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 361, 281–284 (2018).

Article 
ADS 
CAS 
PubMed 

Google Scholar
 

Meyer, K. M. & Kump, L. R. Oceanic euxinia in Earth history: causes and consequences. Annu. Rev. Earth Planet. Sci. 36, 251–288 (2008).

Article 
ADS 
CAS 

Google Scholar
 

Buhl-Mortensen, L., Mortensen, P. B., Armsworthy, S. & Jackson, D. Field observations of Flabellum spp. and laboratory study of the behavior and respiration of Flabellum alabastrum. Bull. Mar. Sci. 81, 543–552 (2007).


Google Scholar
 

Veron, J. E. N. Corals in Space and Time: the Biogeography and Evolution of the Scleractinia (Cornell Univ. Press, 1995).

Ying, H. et al. Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biol. 19, 175 (2018).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Stanley, Jr. G. D. & Fautin, D. G. The origins of modern corals. Science 291, 1913–1914 (2001).

Article 
CAS 
PubMed 

Google Scholar
 

Chadwick, N. E. & Adams, C. in Coelenterate Biology: Recent Research on Cnidaria and Ctenophora (eds Williams, R. B. et al.) 263–269 (Springer, 1991).

Daly, M. et al. The phylum Cnidaria: a review of phylogenetic patterns and diversity 300 years after Linnaeus. Zootaxa 1668, 127–182 (2007).

Minter, N. J. et al. Early bursts of diversification defined the faunal colonization of land. Nat. Ecol. Evol. 1, 0175 (2017).

Article 

Google Scholar
 

Judd, E. J. et al. A 485-million-year history of Earth’s surface temperature. Science 385, eadk3705 (2024).

Article 
CAS 
PubMed 

Google Scholar
 

Hongzhen, W. & Jianqiang, C. Late Ordovician and early Silurian rugose coral biogeography and world reconstruction of palaeocontinents. Palaeogeogr. Palaeoclimatol. Palaeoecol. 86, 3–21 (1991).

Article 

Google Scholar
 

Fedorowski, J. Extinction of Rugosa and Tabulata near the Permian Triassic boundary. Acta Palaeont. Polonica. 34, 47–70 (1989).


Google Scholar
 

Stanley, G. D. Jr. The evolution of modern corals and their early history. Earth Sci. Rev. 60, 195–225 (2003).

Article 
ADS 

Google Scholar
 

Roniewicz, E. & Morycowa, E. Evolution of the Scleractinia in the light of microstructural data. Cour. Forsch. Senckenberg 164, 233–240 (1993).


Google Scholar
 

Anagnostou, E., Huang, K. F., You, C. F., Sikes, E. L. & Sherrell, R. M. Evaluation of boron isotope ratio as a pH proxy in the deep sea coral Desmophyllum dianthus: evidence of physiological pH adjustment. Earth Planet. Sci. Lett. 349, 251–260 (2012).

Article 
ADS 

Google Scholar
 

McCulloch, M. et al. Resilience of cold-water scleractinian corals to ocean acidification: boron isotopic systematics of pH and saturation state up-regulation. Geochim. Cosmochim. Acta 87, 21–34 (2012).

Article 
ADS 
CAS 

Google Scholar
 

Plusquellec, Y., Webb, G. E. & Hoeksema, B. W. Automobility in Tabulata, Rugosa, and extant scleractinian analogues: stratigraphic and paleogeographic distribution of Paleozoic mobile corals. J. Paleontol. 73, 985–1001 (1999).

Article 
ADS 

Google Scholar
 

Hoeksema, B. W. & Bongaerts, P. Mobility and self-righting by a free-living mushroom coral through pulsed inflation. Mar. Biodivers. 46, 521–524 (2016).

Article 

Google Scholar
 

Sentoku, A., Tokuda, Y. & Ezaki, Y. Burrowing hard corals occurring on the sea floor since 80 million years ago. Sci. Rep. 6, 24355 (2016).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Peijnenburg, K. T. et al. The origin and diversification of pteropods precede past perturbations in the Earth’s carbon cycle. Proc. Natl Acad. Sci. USA 117, 25609–25617 (2020).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Kitahara, M. V. Species richness and distribution of azooxanthellate Scleractinia in Brazil. Bull. Mar. Sci. 81, 497–518 (2007).


Google Scholar
 

Capel, K. C. et al. Atlantia, a new genus of Dendrophylliidae (Cnidaria, Anthozoa, Scleractinia) from the eastern Atlantic. PeerJ 8, e8633 (2020).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Kitahara, M. & Cairns, S. Tropical Deep-Sea Benthos Vol. 32 (Publications Scientifiques du Muséum, 2021).

Cairns, S. D. The Marine Fauna of New Zealand: Scleractinia (Cnidaria: Anthozoa) (NIWA, 1995).

Wong, J. S. Y. et al. Comparing patterns of taxonomic, functional and phylogenetic diversity in reef coral communities. Coral Reefs 37, 737–750 (2018).

Article 
ADS 

Google Scholar
 

Seiblitz, I. G. et al. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics. Mol. Phylogenet. Evol. 175, 107565 (2022).

Article 
CAS 
PubMed 

Google Scholar
 

Quattrini, A. M. et al. Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to longstanding problems. Mol. Ecol. Resour. 18, 281–295 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Cowman, P. F. et al. An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives. Mol. Phylogenet. Evol. 153, 106944 (2020).

Article 
PubMed 

Google Scholar
 

Quek, Z. B. R., Jain, S. S., Neo, M. L., Rouse, G. W. & Huang, D. Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia). Mol. Ecol. Resour. 20, 807–818 (2020).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).

Article 
MathSciNet 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Faircloth, B. C. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32, 786–788 (2016).

Article 
CAS 
PubMed 

Google Scholar
 

Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17, 540–552 (2000).

Article 
CAS 
PubMed 

Google Scholar
 

Duchêne, D. A., Mather, N., van der Wal, C. & Ho, S. Y. W. Excluding loci with substitution saturation improves inferences from phylogenomic data. Syst. Biol. 71, 676–689 (2021).

Article 
PubMed Central 

Google Scholar
 

Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).

Article 
CAS 
PubMed 

Google Scholar
 

Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).

Article 
CAS 
PubMed 

Google Scholar
 

Anisimova, M., Gil, M., Dufayard, J.-F., Dessimoz, C. & Gascuel, O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst. Biol. 60, 685–699 (2011).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19, 15–30 (2018).

Article 

Google Scholar
 

Junier, T. & Zdobnov, E. M. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26, 1669–1670 (2010).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Mai, U. & Mirarab, S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genom. 19, 23–40 (2018).

Article 

Google Scholar
 

Wells, J. W. in Treatise on Invertebrate Paleontology, Part F. Coelenterata (ed. Moore, R. C.) F328–F444 (Geological Society of America, 1956).

Romano, S. L. & Palumbi, S. R. Evolution of scleractinian corals inferred from molecular systematics. Science 271, 640–642 (1996).

Article 
ADS 
CAS 

Google Scholar
 

Kitahara, M. V. et al. A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS ONE 5, e11490 (2010).

Article 
ADS 
PubMed 
PubMed Central 

Google Scholar
 

Huang, D., Licuanan, W. Y., Baird, A. H. & Fukami, H. Cleaning up the ‘Bigmessidae’: molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evol. Biol. 11, 37 (2011).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Stolarski, J. et al. A unique coral biomineralization pattern has resisted 40 million years of major ocean chemistry change. Sci. Rep. 6, 27579 (2016).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Janiszewska, K. et al. Microstructural disparity between basal micrabaciids and other scleractinia: new evidence from Neogene Stephanophyllia. Lethaia 48, 417–428 (2015).

Article 

Google Scholar
 

Carbone, F., Matteucci, R., Rosen, B. R. & Russo, A. Recent coral facies of the Indian Ocean coast of Somalia with an interim check list of corals. Facies 30, 1–13 (1994).

Article 

Google Scholar
 

Vecsei, A. & Moussavian, E. Paleocene reefs on the Maiella platform margin, Italy: an example of the effects of the Cretaceous/Tertiary boundary events on reefs and carbonate platforms. Facies 36, 123–139 (1997).

Article 

Google Scholar
 

Stolarski, J. & Vertino, A. First Mesozoic record of the scleractinian Madrepora from the Maastrichtian siliceous limestones of Poland. Facies 53, 67–78 (2007).

Article 

Google Scholar
 

Squires, D. F. The Cretaceous and Tertiary Corals of New Zealand Paleontological Bulletin 29 (New Zealand Geological Survey, 1958).

Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15, e1006650 (2019).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Oliveros, C. H. et al. Earth history and the passerine superradiation. Proc. Natl Acad. Sci. USA 116, 7916–7925 (2019).

Article 
ADS 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Sanderson, M. J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19, 101–109 (2002).

Article 
CAS 
PubMed 

Google Scholar
 

Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67, 901–904 (2018).

Article 
CAS 
PubMed 
PubMed Central 

Google Scholar
 

Brown, J. W. & Smith, S. A. The past sure is tense: on interpreting phylogenetic divergence time estimates. Syst. Biol. 67, 340–353 (2018).

Article 
PubMed 

Google Scholar
 

Revell, L. J. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 12, e16505 (2024).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Höhna, S. et al. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Syst. Biol. 65, 726–736 (2016).

Article 
PubMed 
PubMed Central 

Google Scholar
 

Tribble, C. M. et al. RevGadgets: an R package for visualizing Bayesian phylogenetic analyses from RevBayes. Methods Ecol. Evol. 13, 314–323 (2022).

Article 

Google Scholar
 

Höhna, S. et al. A Bayesian approach for estimating branch-specific speciation and extinction rates. Preprint at BioRxiv https://doi.org/10.1101/555805 (2019).

Vaga, C. F. et al. Data for ‘A global coral phylogeny reveals resilience and vulnerability through deep time’. Figshare https://doi.org/10.6084/m9.figshare.29242487 (2025).

Bosellini, F. R., Papazzoni, C., A. & Vescogni, A. Exceptional development of dissepimental coenosteum in the new Eocene scleractinian coral genus Nancygyra (Ypresian, Monte Postale, NE Italy). Boll. Soc. Paleontol. Ital. 59, 291–298 (2020).

Stolarski, J. On Cretaceous Stephanocyathus (Scleractinia) from the Tatra Mts. Acta Palaeontol. Pol. 35, 31–39 (1990).