Hughes, T. P. et al. Coral reefs in the anthropocene. Nature 546, 82–90 (2017).
Intergovernmental Panel on Climate Change (IPCC). Global Warming of 1.5°C: IPCC Special Report on Impacts of Global Warming of 1.5°C above pre-industrial Levels in Context of Strengthening Response to Climate Change, Sustainable Development, and Efforts to Eradicate Poverty (Cambridge University Press, 2022). https://doi.org/10.1017/9781009157940.
Hoegh-Guldberg, O., Poloczanska, E. S., Skirving, W. & Dove, S. Coral reef ecosystems under climate change and ocean acidification. Front. Mar. Sci. 4, 158 (2017).
Hughes, T. P. et al. Global warming transforms coral reef assemblages. Nature 556, 492–496 (2018).
Zande, R. M. et al. Paradise lost: end-of‐century warming and acidification under business‐as‐usual emissions have severe consequences for symbiotic corals. Glob. Chang Biol. 26, 2203–2219 (2020).
Beyer, H. L. et al. Risk-sensitive planning for conserving coral reefs under rapid climate change. Conserv. Lett. 11 (2018).
Hoegh-Guldberg, O., Kennedy, E. V., Beyer, H. L., McClennen, C. & Possingham H. P. securing a long-term future for coral reefs. Trends Ecol. Evol. 33, 936–944 (2018).
Anthony, K. R. N. et al. Interventions to help coral reefs under global change—A complex decision challenge. PLoS One 15, e0236399 (2020).
Chauka, L. J. & Nyangoko, B. P. Climate change impacts outweigh conservation efforts in coral reefs that are highly exposed to thermal stresses in Zanzibar, Tanzania. Ocean. Coast Manag. 238, 106575 (2023).
Hilmi, N. et al. The pressures and opportunities for coral reef preservation and restoration in the Maldives. Front. Environ. Econ. 2, 1110214 (2023).
Gove, J. M. et al. Coral reefs benefit from reduced land–sea impacts under ocean warming. Nature 621, 536–542 (2023).
Battaglia, F. M. Blue planet law, the ecology of our economic and technological world. Sustain. Dev. Goals Ser. 121–130. https://doi.org/10.1007/978-3-031-24888-7_10 (2023).
Bernot, J. et al. World Register of Marine Species (WoRMS) (2024).
Veron, J. E. N. Corals of the World, 1–3 (Australian Institute of Marine Science and CRR, 2000).
Fukami, H. Short review: molecular phylogenetic analyses of reef corals. Galaxea J. Coral Reef. Stud. 10, 47–55 (2008).
Fukami, H., Tachikawa, H., Suzuki, G., Nagata, S. & Sugihara, K. Current status and problems with the identification and taxonomy of zooxanthellate scleractinian corals in Japan. J. Jpn. Coral Reef. Soc. 12, 17–31 (2010).
Kitahara, M. V., Fukami, H., Benzoni, F. & Huang, D. The Cnidaria, past, present and future, 41–59 https://doi.org/10.1007/978-3-319-31305-4_4 (2016).
Arrigoni, R. et al. An integrated morpho-molecular approach to delineate species boundaries of Millepora from the Red Sea. Coral Reefs. 37, 967–984 (2018).
Terraneo, T. I., Benzoni, F., Baird, A. H., Arrigoni, R. & Berumen, M. L. Morphology and molecules reveal two new species of Porites (Scleractinia, Poritidae) from the Red Sea and the Gulf of Aden. Syst. Biodivers. 17, 491–508 (2019).
Bridge, T. C. L. et al. A tenuis relationship: traditional taxonomy obscures systematics and biogeography of the ‘Acropora tenuis’ (Scleractinia: Acroporidae) species complex. Zoöl J. Linn. Soc. zlad062 https://doi.org/10.1093/zoolinnean/zlad062 (2023).
Furukawa, M. et al. Integrative taxonomic analyses reveal that rapid genetic divergence drives Acropora speciation. Mol. Phylogenet. Evol. 195, 108063 (2024).
Wallace, C. Staghorn corals of the world. 10.1071/9780643101388 (1999).
Veron, J. E. N., John, E. N. & Wallace, C. C. Scleractinia of eastern Australia. Part V. Family Acroporidae. Scleractinia East. Australia Part. V 6, 1–485 (1984).
Fukami, H., Niimura, A., Nakamori, T. & Iryu, Y. Species composition and mitochondrial molecular phylogeny of Acropora corals in Funakoshi, Amami-Oshima Island, Japan: a proposal for its new taxonomic grouping. Galaxea J. Coral Reef. Stud. 23, 17–35 (2021).
Todd, P. A. Morphological plasticity in scleractinian corals. Biol. Rev. 83, 315–337 (2008).
Wallace, C., Done, B. & Muir, P. Revision and catalogue of worldwide staghorn corals Acropora and Isopora (Scleractinia: Acroporidae) in the Museum of Tropical Queensland. Mem. Qld. Mus. – Nat. 57, 1–255 (2012).
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).
Ramírez-Portilla, C. et al. Solving the coral species delimitation conundrum. Syst. Biol. 71, 461–475 (2021).
Ramírez-Portilla, C. et al. Quantitative three-dimensional morphological analysis supports species discrimination in complex-shaped and taxonomically challenging corals. Front. Mar. Sci. 9, 955582 (2022).
Odorico, D. M. & Miller, D. J. Variation in the ribosomal internal transcribed spacers and 5.8S rDNA among five species of Acropora (Cnidaria; Scleractinia): patterns of variation consistent with reticulate evolution. Mol. Biol. Evol. 14, 465–473 (1997).
van Oppen, M. J. H., McDonald, B. J., Willis, B. & Miller, D. J. The evolutionary history of the coral genus Acropora (Scleractinia, Cnidaria) based on a mitochondrial and a nuclear marker: reticulation, incomplete lineage sorting, or morphological convergence? Mol. Biol. Evol. 18, 1315–1329 (2001).
Márquez, L. M., Oppen, M. J. H. V., Willis, B. L., Reyes, A. & Miller, D. J. The highly cross-fertile coral species, Acropora hyacinthus and Acropora cytherea, constitute statistically distinguishable lineages. Mol. Ecol. 11, 1339–1349 (2002).
Richards, Z. T., Berry, O. & van Oppen, M. J. H. Cryptic genetic divergence within threatened species of Acropora coral from the Indian and pacific oceans. Conserv. Genet. 17, 577–591 (2016).
Veron, J. E. N. Corals in Space and Time: The Biogeography and Evolution of the scleractinia (Cornell University Press, 1995).
Willis, B. L., van Oppen, M. J. H., Miller, D. J., Vollmer, S. V. & Ayre, D. J. The role of hybridization in the evolution of reef corals. Ecol. Evol. Syst. 37, 489–517 (2006).
Fukami, H., Omori, M. & Hatta, M. Phylogenetic relationships in the coral family acroporidae, reassessed by inference from mitochondrial genes. Zoöl Sci. 17, 689–696 (2000).
Wolstenholme, J. K., Wallace, C. C. & Chen, C. A. Species boundaries within the Acropora humilis species group (Cnidaria; Scleractinia): a morphological and molecular interpretation of evolution. Coral Reefs 22, 155–166 (2003).
Richards, Z. T., Miller, D. J. & Wallace, C. C. Molecular phylogenetics of geographically restricted Acropora species: implications for threatened species conservation. Mol. Phylogenet. Evol. 69, 837–851 (2013).
Ladner, J. T. & Palumbi, S. R. Extensive sympatry, cryptic diversity and introgression throughout the geographic distribution of two coral species complexes. Mol. Ecol. 21, 2224–2238 (2012).
Suzuki, G. et al. Genetic evidence of peripheral isolation and low diversity in marginal populations of the Acropora hyacinthus complex. Coral Reefs. 35, 1419–1432 (2016).
Nakabayashi, A. et al. The potential role of temperate Japanese regions as refugia for the coral Acropora hyacinthus in the face of climate change. Sci. Rep. 9, 1892 (2019).
Fifer, J. E., Yasuda, N., Yamakita, T., Bove, C. B. & Davies, S. W. Genetic divergence and range expansion in a western North Pacific coral. Sci. Total Environ. 813, 152423 (2022).
Quattrini, A. M. et al. Universal target-enrichment baits for anthozoan (Cnidaria) phylogenomics: new approaches to long‐standing problems. Mol. Ecol. Resour. 18, 281–295 (2018).
Dana, J. D. Zoophytes. United States exploring expedition during the years 1838–1842 (1846).
Veron, J. E. N. (John E. N. Hermatypic Corals of Japan (Australian Institute of Marine Science, 1992).
Dai, C. & Horng, S. Scleractinia Fauna of Taiwan I. The Complex Group (National Taiwan University, 2009).
Suzuki, G. & Fukami, H. Evidence of genetic and reproductive isolation between two morphs of subtropical-dominant coral Acropora solitaryensis in the non-reef region of Japan. Zoöl Sci. 29, 134–140 (2012).
Nishihira, M. & Veron, J. E. N. Hermatypic Corals of Japan (Kaiyusha, 1995).
Veron, J. E. N., (John, E. N., Marsh, M., Museum, W. A. & Loisette Hermatypic Corals of Western Australia: Records and Annotated Species List (Western Australian Museum, 1988).
Veron, J. E. N. (John E. N. A Biogeographic Database of Hermatypic Coral Species of the Central Indo-Pacific, Genera of the WorldAustralian Institute of Marine Science, 1993).
Dai, C. & Cheng, Y. R. Corals of Taiwan: Scleractinia Fauna Vol. 1 (Owl Publishing House Co., LTD, 2020).
Furukawa, M., Ohki, S., Kitanobo, S., Fukami, H. & Morita, M. Differences in spawning time drive cryptic speciation in the coral Acropora divaricata. Mar. Biol. 167, 163 (2020).
Kuo, C. Y. et al. Coral reefs of Eastern Asia under Anthropogenic impacts. Coral Reefs World, 7–35. https://doi.org/10.1007/978-3-031-27560-9_2 (2023).
Keshavmurthy, S., Mezaki, T., Reimer, J. D., Choi, K. S. & Chen, C. A. Coral reefs of Eastern Asia under anthropogenic impacts. Coral Reefs World, 53–71. https://doi.org/10.1007/978-3-031-27560-9_4 (2023).
Hatta, M. et al. Reproductive and genetic evidence for a reticulate evolutionary history of mass-spawning corals. Mol. Biol. Evol. 16, 1607–1613 (1999).
Fukami, H., Omori, M., Shimoike, K., Hayashibara, T. & Hatta, M. Ecological and genetic aspects of reproductive isolation by different spawning times in Acropora corals. Mar. Biol. 142, 679–684 (2003).
Sukumaran, J., Holder, M. T. & Knowles, L. L. Incorporating the speciation process into species delimitation. PLoS Comput. Biol. 17, e1008924 (2021).
Pagès, J. Factorial analysis of mixed data. J. Appl. Stat. 52, 93–111 (2004).
Chong, F. et al. High-latitude marginal reefs support fewer but bigger corals than their tropical counterparts. Ecography 2023 (2023).
Sugihara, K. et al. Zooxanthellate scleractinian corals of Tanegashima Island, 1–197 (2015).
Nomura, K. The illustrated zooxanthellate scleractinian corals of Kushimoto I REFERTINA. Marine Pavilion 1–56 (2016).
Nomura, K. et al. Revision of the zooxanthellate scleractinian corals in Kushimoto, Wakayama, Japan. Mar. Pavilion (2016).
Mrquez, L. M., van Oppen, M. J. H., Willis, B. L. & J. Miller, D. Sympatric populations of the highly cross-fertile coral species Acropora hyacinthus and Acropora cytherea are genetically distinct. Proc. R Soc. Lond. Ser. B Biol. Sci. 269, 1289–1294 (2002).
Wei, N. V. et al. Reproductive isolation among Acropora species (Scleractinia: Acroporidae) in a marginal coral assemblage. Zool. Stud. 51, 85–92 (2012).
Ohki, S., Kowalski, R. K., Kitanobo, S. & Morita, M. Changes in spawning time led to the speciation of the broadcast spawning corals Acropora digitifera and the cryptic species Acropora sp. 1 with similar gamete recognition systems. Coral Reefs. 34, 1189–1198 (2015).
Kitanobo, S., Isomura, N., Fukami, H., Iwao, K. & Morita, M. The reef-building coral Acropora conditionally hybridize under sperm limitation. Biol. Lett. 12, 20160511 (2016).
Gallagher, S. J. et al. The Pliocene to recent history of the Kuroshio and Tsushima currents: a multi-proxy approach. Prog Earth Planet. Sci. 2, 17 (2015).
Ujiié, H., Tanaka, Y. & Ono, T. Late quarternary paleoceanographic record from the middle Ryukyu Trench slope, northwest Pacific. Mar. Micropaleontol. 18, 115–128 (1991).
Ujiié, Y., Ujiié, H., Taira, A., Nakamura, T. & Oguri, K. Spatial and temporal variability of surface water in the Kuroshio source region, Pacific Ocean, over the past 21,000 years: evidence from planktonic foraminifera. Mar. Micropaleontol. 49, 335–364 (2003).
Dai, C., Wang, S. & Chang, J. Handbook for Ecological Tours of Guanyin Algae Reef (Liquefied Natural Gas Engineering Office, CPC Corporation, 2009).
Schöne, B. R. et al. Holocene seasonal environmental trends at Tokyo Bay, Japan, reconstructed from bivalve mollusk shells—implications for changes in the east Asian monsoon and latitudinal shifts of the Polar Front. Quat Sci. Rev. 23, 1137–1150 (2004).
Hoshino, M. The absolute age of the Numa Coral reef, Chiba prefecture. 14 C-Age Quaternary Deposits Japan XXXVI. 21, 38–39 (1967).
Matsushima, Y. Shallow marine molluscan assemblages of postglacial period in the Japan islands-its historical and geographical changes induced by the environmental changes. Bull. Kanagawa Prefectural Museum. 15, 37–109 (1984).
Liou, C. Y., Yang, S. Y. & Chen, C. A. Unprecedented calcareous algal reefs in northern Taiwan merit high conservation priority. Coral Reefs 36, 1253–1253 (2017).
Chen, M. et al. Enhanced monsoon-driven upwelling in southeast asia during the little ice age. Paleoceanogr. Paleoclimatol. 38 (2023).
Kuo, C. Y. et al. Lonely giant on the sand: unexpected massive Taiwanese coral, Polycyathus chaishanensis in the Datan algal reef demands a conservation focus. Galaxea J. Coral Reef. Stud. 21, 11–12 (2019).
Kuo, C. Y. et al. Demographic census confirms a stable population of the critically-endangered caryophyllid coral Polycyathus chaishanensis (Scleractinia; Caryophyllidae) in the Datan Algal Reef, Taiwan. Sci. Rep. 10, 10585 (2020).
Serisawa, Y., Imoto, Z., Ishikawa, T. & Ohno, M. Decline of the Ecklonia cava population associated with increased seawater temperatures in Tosa Bay, southern Japan. Fish. Sci. 70, 189–191 (2004).
Yamano, H., Sugihara, K. & Nomura, K. Rapid poleward range expansion of tropical reef corals in response to rising sea surface temperatures. Geophys. Res. Lett. 38 (2011).
Tkachenko, K. S., Soong, K. & Dongsha Atoll A potential thermal refuge for reef-building corals in the South China Sea. Mar. Environ. Res. 127, 112–125 (2017).
Wang, W. et al. Isolation and characterization of a mini-collagen gene encoding a nematocyst capsule protein from a reef-building coral, Acropora donei. Gene 152, 195–200 (1995).
Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539–539 (2011).
Darriba, D. et al. ModelTest-NG: a new and scalable tool for the selection of DNA and protein evolutionary models. Mol. Biol. Evol. 37, 291–294 (2020).
Edler, D., Klein, J., Antonelli, A. & Silvestro, D. raxmlGUI 2.0: a graphical interface and toolkit for phylogenetic analyses using RAxML. Methods Ecol. Evol. 12, 373–377 (2021).
Bouckaert, R. et al. BEAST 2: a software platform for bayesian evolutionary analysis. PLoS Comput. Biol. 10, e1003537 (2014).
Yang, Z. & Rannala, B. Unguided species delimitation using DNA sequence data from multiple loci. Mol. Biol. Evol. 31, 3125–3135 (2014).
Flouri, T., Jiao, X., Rannala, B. & Yang, Z. Species tree inference with BPP using genomic sequences and the multispecies coalescent. Mol. Biol. Evol. 35, 2585–2593 (2018).
Barido-Sottani, J. et al. Taming the BEAST—A community teaching material resource for BEAST 2. Syst. Biol. 67, 170–174 (2018).
Wallace, C. C. & Dai, C. F. Scleractinia of Taiwan (IV): review of the coral genus Acropora from Taiwan. Zool. Stud. Taipei 36, 288–324 (1997).
Royston, P. Approximating the Shapiro-Wilk W-test for non-normality. Stat. Comput. 2, 117–119 (1992).
Tukey, J. Multiple comparisons. J. Am. Stat. Assoc. 48, 624–625 (1953).
Trawiński, B., Smętek, M., Telec, Z. & Lasota, T. Nonparametric statistical analysis for multiple comparison of machine learning regression algorithms. Int. J. Appl. Math. Comput. Sci. 22, 867–881 (2012).
Lê, S., Josse, J., Husson, F. & FactoMineR An R package for multivariate analysis. J. Stat. Softw. 25 (2008).