{"id":523696,"date":"2025-10-24T02:51:28","date_gmt":"2025-10-24T02:51:28","guid":{"rendered":"https:\/\/www.europesays.com\/uk\/523696\/"},"modified":"2025-10-24T02:51:28","modified_gmt":"2025-10-24T02:51:28","slug":"a-global-coral-phylogeny-reveals-resilience-and-vulnerability-through-deep-time","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/uk\/523696\/","title":{"rendered":"A global coral phylogeny reveals resilience and vulnerability through deep time"},"content":{"rendered":"
  • \n

    Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318<\/b>, 1737\u20131742 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Carpenter, K. E. et al. One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321<\/b>, 560\u2013563 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Knowlton, N. Coral reef biodiversity-habitat size matters. Science 292<\/b>, 1493\u20131495 (2001).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Pandolfi, J. M., Connolly, S. R., Marshall, D. J. & Cohen, A. L. Projecting coral reef futures under global warming and ocean acidification. Science 333<\/b>, 418\u2013422 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mellin, C. et al. Cumulative risk of future bleaching for the world\u2019s coral reefs. Sci. Adv. 10<\/b>, eadn9660 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kleypas, J. A. et al. Geochemical consequences of increased atmospheric carbon dioxide on coral reefs. Science 284<\/b>, 118\u2013120 (1999).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

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

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stolarski, J. et al. The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals. BMC Evol. Biol. 11<\/b>, 316 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 1054\u20131071 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Quattrini, A. M. et al. Palaeoclimate ocean conditions shaped the evolution of corals and their skeletons through deep time. Nat. Ecol. Evol. 4<\/b>, 1531\u20131538 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kiessling, W. & Simpson, C. On the potential for ocean acidification to be a general cause of ancient reef crises. Glob. Change Biol. 17<\/b>, 56\u201367 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Vasseur, R. et al. Major coral extinctions during the early Toarcian global warming event. Glob. Planet. Change 207<\/b>, 103647 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 9396\u20139401 (1998).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Cairns, S. D. Deep-water corals: an overview with special reference to diversity and distribution of deep-water scleractinian corals. Bull. Mar. Sci. 81<\/b>, 311\u2013322b (2007).<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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).<\/p>\n<\/li>\n

  • \n

    Orejas, C. et al. Madrepora oculata forms large frameworks in hypoxic waters off Angola (SE Atlantic). Sci. Rep. 11<\/b>, 15170 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Campoy, A. N. et al. The origin and correlated evolution of symbiosis and coloniality in scleractinian corals. Front. Mar. Sci. 7<\/b>, 461 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    McFadden, C. S. et al. Phylogenomics, origin, and diversification of Anthozoans (phylum Cnidaria). Syst. Biol. 70<\/b>, 635\u2013647 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Frankowiak, K. et al. Photosymbiosis and the expansion of shallow-water corals. Sci. Adv. 2<\/b>, e1601122 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 2795\u20132849 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Misof, B. et al. Phylogenomics resolves the timing and pattern of insect evolution. Science 346<\/b>, 763\u2013767 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Shao, Y. et al. Phylogenomic analyses provide insights into primate evolution. Science 380<\/b>, 913\u2013924 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zuntini, A. R. et al. Phylogenomics and the rise of the angiosperms. Nature 629<\/b>, 843\u2013850 (2024).<\/p>\n<\/li>\n

  • \n

    Erwin, D. H., Valentine, J. W. & Sepkoski, J. J. Jr A comparative study of diversification events: the early Paleozoic versus the Mesozoic. Evolution 41<\/b>, 1177\u20131186 (1987).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Scrutton, C. T. The Palaeozoic corals, I: origins and relationships. Proc. York. Geol. Soc. 51<\/b>, 177\u2013208 (1997).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Scrutton, C. T. & Clarkson, E. N. K. A new scleractinian-like coral from the Ordovician of the Southern Uplands, Scotland. Palaeontology 34<\/b>, 179\u2013194 (1991).<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ezaki, Y. The Permian coral Numidiaphyllum: new insights into anthozoan phylogeny and Triassic scleractinian origins. Palaeontology 40<\/b>, 1\u201314 (1997).<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Ezaki, Y. Paleozoic Scleractinia: progenitors or extinct experiments? Paleobiology 24<\/b>, 227\u2013234 (1998).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Barbeitos, M. S., Romano, S. L. & Lasker, H. R. Repeated loss of coloniality and symbiosis in scleractinian corals. Proc. Natl Acad. Sci. USA 107<\/b>, 11877\u201311882 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Campoy, A. N., Rivadeneira, M. M., Hern\u00e1ndez, C. E., Meade, A. & Venditti, C. Deep-sea origin and depth colonization associated with phenotypic innovations in scleractinian corals. Nat. Commun. 14<\/b>, 7458 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, e2429 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Horowitz, J. et al. Bathymetric evolution of black corals through deep time. Proc. R. Soc. B 290<\/b>, 20231107 (2023).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rocha, L. A. et al. Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 361<\/b>, 281\u2013284 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Meyer, K. M. & Kump, L. R. Oceanic euxinia in Earth history: causes and consequences. Annu. Rev. Earth Planet. Sci. 36<\/b>, 251\u2013288 (2008).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 543\u2013552 (2007).<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Veron, J. E. N. Corals in Space and Time: the Biogeography and Evolution of the Scleractinia (Cornell Univ. Press, 1995).<\/p>\n<\/li>\n

  • \n

    Ying, H. et al. Comparative genomics reveals the distinct evolutionary trajectories of the robust and complex coral lineages. Genome Biol. 19<\/b>, 175 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stanley, Jr. G. D. & Fautin, D. G. The origins of modern corals. Science 291<\/b>, 1913\u20131914 (2001).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Chadwick, N. E. & Adams, C. in Coelenterate Biology: Recent Research on Cnidaria and Ctenophora (eds Williams, R. B. et al.) 263\u2013269 (Springer, 1991).<\/p>\n<\/li>\n

  • \n

    Daly, M. et al. The phylum Cnidaria: a review of phylogenetic patterns and diversity 300 years after Linnaeus. Zootaxa 1668<\/b>, 127\u2013182 (2007).<\/p>\n<\/li>\n

  • \n

    Minter, N. J. et al. Early bursts of diversification defined the faunal colonization of land. Nat. Ecol. Evol. 1<\/b>, 0175 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Judd, E. J. et al. A 485-million-year history of Earth\u2019s surface temperature. Science 385<\/b>, eadk3705 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hongzhen, W. & Jianqiang, C. Late Ordovician and early Silurian rugose coral biogeography and world reconstruction of palaeocontinents. Palaeogeogr. Palaeoclimatol. Palaeoecol. 86<\/b>, 3\u201321 (1991).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Fedorowski, J. Extinction of Rugosa and Tabulata near the Permian Triassic boundary. Acta Palaeont. Polonica. 34<\/b>, 47\u201370 (1989).<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stanley, G. D. Jr. The evolution of modern corals and their early history. Earth Sci. Rev. 60<\/b>, 195\u2013225 (2003).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Roniewicz, E. & Morycowa, E. Evolution of the Scleractinia in the light of microstructural data. Cour. Forsch. Senckenberg 164<\/b>, 233\u2013240 (1993).<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 251\u2013260 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 21\u201334 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 985\u20131001 (1999).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hoeksema, B. W. & Bongaerts, P. Mobility and self-righting by a free-living mushroom coral through pulsed inflation. Mar. Biodivers. 46<\/b>, 521\u2013524 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

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

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Peijnenburg, K. T. et al. The origin and diversification of pteropods precede past perturbations in the Earth\u2019s carbon cycle. Proc. Natl Acad. Sci. USA 117<\/b>, 25609\u201325617 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kitahara, M. V. Species richness and distribution of azooxanthellate Scleractinia in Brazil. Bull. Mar. Sci. 81<\/b>, 497\u2013518 (2007).<\/p>\n


    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Capel, K. C. et al. Atlantia, a new genus of Dendrophylliidae (Cnidaria, Anthozoa, Scleractinia) from the eastern Atlantic. PeerJ 8<\/b>, e8633 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Kitahara, M. & Cairns, S. Tropical Deep-Sea Benthos Vol. 32 (Publications Scientifiques du Mus\u00e9um, 2021).<\/p>\n<\/li>\n

  • \n

    Cairns, S. D. The Marine Fauna of New Zealand: Scleractinia (Cnidaria: Anthozoa) (NIWA, 1995).<\/p>\n<\/li>\n

  • \n

    Wong, J. S. Y. et al. Comparing patterns of taxonomic, functional and phylogenetic diversity in reef coral communities. Coral Reefs 37<\/b>, 737\u2013750 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Seiblitz, I. G. et al. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: insights from mitochondrial and nuclear phylogenomics. Mol. Phylogenet. Evol. 175<\/b>, 107565 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Quattrini, A. M. et al. Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to longstanding problems. Mol. Ecol. Resour. 18<\/b>, 281\u2013295 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 106944 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 807\u2013818 (2020).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30<\/b>, 2114\u20132120 (2014).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19<\/b>, 455\u2013477 (2012).<\/p>\n

    Article<\/a>\u00a0
    \n     MathSciNet<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Faircloth, B. C. PHYLUCE is a software package for the analysis of conserved genomic loci. Bioinformatics 32<\/b>, 786\u2013788 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 3059\u20133066 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17<\/b>, 540\u2013552 (2000).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Duch\u00eane, 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<\/b>, 676\u2013689 (2021).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 268\u2013274 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 587\u2013589 (2017).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35<\/b>, 518\u2013522 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 685\u2013699 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19<\/b>, 15\u201330 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Junier, T. & Zdobnov, E. M. The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell. Bioinformatics 26<\/b>, 1669\u20131670 (2010).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Mai, U. & Mirarab, S. TreeShrink: fast and accurate detection of outlier long branches in collections of phylogenetic trees. BMC Genom. 19<\/b>, 23\u201340 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Wells, J. W. in Treatise on Invertebrate Paleontology, Part F. Coelenterata (ed. Moore, R. C.) F328\u2013F444 (Geological Society of America, 1956).<\/p>\n<\/li>\n

  • \n

    Romano, S. L. & Palumbi, S. R. Evolution of scleractinian corals inferred from molecular systematics. Science 271<\/b>, 640\u2013642 (1996).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

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

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Huang, D., Licuanan, W. Y., Baird, A. H. & Fukami, H. Cleaning up the \u2018Bigmessidae\u2019: molecular phylogeny of scleractinian corals from Faviidae, Merulinidae, Pectiniidae and Trachyphylliidae. BMC Evol. Biol. 11<\/b>, 37 (2011).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

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

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Janiszewska, K. et al. Microstructural disparity between basal micrabaciids and other scleractinia: new evidence from Neogene Stephanophyllia. Lethaia 48<\/b>, 417\u2013428 (2015).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 1\u201313 (1994).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    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<\/b>, 123\u2013139 (1997).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Stolarski, J. & Vertino, A. First Mesozoic record of the scleractinian Madrepora from the Maastrichtian siliceous limestones of Poland. Facies 53<\/b>, 67\u201378 (2007).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Squires, D. F. The Cretaceous and Tertiary Corals of New Zealand Paleontological Bulletin 29 (New Zealand Geological Survey, 1958).<\/p>\n<\/li>\n

  • \n

    Bouckaert, R. et al. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput. Biol. 15<\/b>, e1006650 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Oliveros, C. H. et al. Earth history and the passerine superradiation. Proc. Natl Acad. Sci. USA 116<\/b>, 7916\u20137925 (2019).<\/p>\n

    Article<\/a>\u00a0
    \n     ADS<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Sanderson, M. J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19<\/b>, 101\u2013109 (2002).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Rambaut, A., Drummond, A. J., Xie, D., Baele, G. & Suchard, M. A. Posterior summarization in Bayesian phylogenetics using Tracer 1.7. Syst. Biol. 67<\/b>, 901\u2013904 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     CAS<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Brown, J. W. & Smith, S. A. The past sure is tense: on interpreting phylogenetic divergence time estimates. Syst. Biol. 67<\/b>, 340\u2013353 (2018).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Revell, L. J. phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ 12<\/b>, e16505 (2024).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    H\u00f6hna, S. et al. RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language. Syst. Biol. 65<\/b>, 726\u2013736 (2016).<\/p>\n

    Article<\/a>\u00a0
    \n     PubMed<\/a>\u00a0
    \n     PubMed Central<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    Tribble, C. M. et al. RevGadgets: an R package for visualizing Bayesian phylogenetic analyses from RevBayes. Methods Ecol. Evol. 13<\/b>, 314\u2013323 (2022).<\/p>\n

    Article<\/a>\u00a0
    \n
    \n Google Scholar<\/a>\u00a0\n <\/p>\n<\/li>\n

  • \n

    H\u00f6hna, S. et al. A Bayesian approach for estimating branch-specific speciation and extinction rates. Preprint at BioRxiv https:\/\/doi.org\/10.1101\/555805<\/a> (2019).<\/p>\n<\/li>\n

  • \n

    Vaga, C. F. et al. Data for \u2018A global coral phylogeny reveals resilience and vulnerability through deep time\u2019. Figshare https:\/\/doi.org\/10.6084\/m9.figshare.29242487<\/a> (2025).<\/p>\n<\/li>\n

  • \n

    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<\/b>, 291\u2013298 (2020).<\/p>\n<\/li>\n

  • \n

    Stolarski, J. On Cretaceous Stephanocyathus (Scleractinia) from the Tatra Mts. Acta Palaeontol. Pol. 35<\/b>, 31\u201339 (1990).<\/p>\n<\/li>\n","protected":false},"excerpt":{"rendered":"Hoegh-Guldberg, O. et al. Coral reefs under rapid climate change and ocean acidification. Science 318, 1737\u20131742 (2007). Article\u00a0…\n","protected":false},"author":2,"featured_media":523697,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[8],"tags":[39036,3965,10809,99991,3966,37581,12517,70,16,15],"class_list":{"0":"post-523696","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-science","8":"tag-climate-change-impacts","9":"tag-humanities-and-social-sciences","10":"tag-marine-biology","11":"tag-molecular-evolution","12":"tag-multidisciplinary","13":"tag-phylogenetics","14":"tag-population-genetics","15":"tag-science","16":"tag-uk","17":"tag-united-kingdom"},"share_on_mastodon":{"url":"https:\/\/pubeurope.com\/@uk\/115426878111137347","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/523696","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/comments?post=523696"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/posts\/523696\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media\/523697"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/media?parent=523696"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/categories?post=523696"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/uk\/wp-json\/wp\/v2\/tags?post=523696"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}