Fisher, R. et al. Species richness on coral reefs and the pursuit of convergent global estimates. Curr. Biol. 25, 500–505 (2015).
Reaka-Kudla, M. L. The Global biodiversity of coral reefs: A comparison with Rain Forests. In: Biodiversity II Understanding and Protecting Our Natural Resources (eds. Reaka-Kudla, M. L., Wilson, D. E. & Wilson, E. O.) 83–108 (Joseph Henry/National Academy Press, 1997).
WoRMS. Scleractinia. https://www.marinespecies.org/aphia.php?p=taxdetails&id=1363 (2024).
Baker, A. C., Glynn, P. W. & Riegl, B. Climate change and coral reef bleaching: An ecological assessment of long-term impacts, recovery trends and future outlook. Estuar. Coast. Shelf Sci. 80, 435–471 (2008).
Eddy, T. D., Cheung, W. W. L. & Bruno, J. F. Historical baselines of coral cover on tropical reefs as estimated by expert opinion. PeerJ 6, e4308 (2018).
Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science. 359, 80–83 (2018).
Ceballos, G. et al. Accelerated modern human-induced species losses: Entering the sixth mass extinction. Sci. Adv. 1, e1400253 (2015).
Hoeksema, B. W. & Cairns, S. D. World List of Scleractinia. Stylophora pistillata (Esper, 1792). World Register of Marine Species, https://www.marinespecies.org/aphia.php?p=taxdetails&id=206982 on 2024-01-31 (2023).
Scheer, G. & Pillai, C. S. G. Report on the stony corals from the Red Sea. Zoologica 131, 1–198 (1983).
Keshavmurthy, S. et al. DNA barcoding reveals the coral ‘laboratory-rat’, Stylophora pistillata encompasses multiple identities. Sci. Rep. 3, 1520 (2013).
Flot, J.-F. et al. Incongruence between morphotypes and genetically delimited species in the coral genus Stylophora: phenotypic plasticity, morphological convergence, morphological stasis or interspecific hybridization? BMC Ecol. 11, 22 (2011).
Stefani, F. et al. Comparison of morphological and genetic analyses reveals cryptic divergence and morphological plasticity in Stylophora (Cnidaria, Scleractinia). Coral Reefs 30, 1033–1049 (2011).
Arrigoni, R., Benzoni, F., Terraneo, T. I., Caragnano, A. & Berumen, M. L. Recent origin and semi-permeable species boundaries in the scleractinian coral genus Stylophora from the Red Sea. Sci. Rep. 6, 34612 (2016).
Todd, P. a. Morphological plasticity in scleractinian corals. Biol. Rev. 83, 315–337 (2008).
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).
Schmidt-Roach, S. et al. Assessing hidden species diversity in the coral Pocillopora damicornis from Eastern Australia. Coral Reefs 32, 161–172 (2013).
Warner, P. A., Van Oppen, M. J. H. & Willis, B. L. Unexpected cryptic species diversity in the widespread coral Seriatopora hystrix masks spatial-genetic patterns of connectivity. Mol. Ecol. 24, 2993–3008 (2015).
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 (Cornell University Press, 1995). https://doi.org/10.1017/S0016756800008050.
Richards, Z. T. & Hobbs, J. P. A. Hybridisation on coral reefs and the conservation of evolutionary novelty. Curr. Zool. 61, 132–145 (2015).
Hobbs, J. P. A. et al. Hybridisation and the evolution of coral reef biodiversity. Coral Reefs 41, 535–549 (2022).
Chen, C. A., Odorico, D. M., Tenlohuis, M., Veron, J. E. N. & Miller, D. J. Systematic Relationships within the Anthozoa (Cnidaria, Anthozoa) Using the 5′-End of the 28s rDNA. Mol. Phylogenet. Evol. 4, 175–183 (1995).
Romano, S. L. & Palumbi, S. R. Molecular evolution of a portion of the mitochondrial 16S ribosomal gene region in scleractinian corals. J. Mol. Evol. 45, 397–411 (1997).
Romano, S. L. & Cairns, S. Molecular phylogenetic hypothesis for the evolution of scleractinian corals. Bull. Mar. Sci. 67, 1043–1068 (2000).
Fukami, H. et al. Conventional taxonomy obscures deep divergence between Pacific and Atlantic corals. Microb. Ecol. 427, 0–3 (2004).
Kitahara, M. V., Cairns, S. D., Stolarski, J., Blair, D. & Miller, D. J. A comprehensive phylogenetic analysis of the Scleractinia (Cnidaria, Anthozoa) based on mitochondrial CO1 sequence data. PLoS One 5, e11490 (2010).
Stolarski, J. et al. The ancient evolutionary origins of Scleractinia revealed by azooxanthellate corals. BMC Evol. Biol. 11, 316 (2011).
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).
Benzoni, F., Arrigoni, R., Waheed, Z., Stefani, F. & Hoeksema, B. W. Phylogenetic relationships and revision of the genus Blastomussa (Cnidaria: Anthozoa: Scleractinia) with description of a new species. Raffles Bull. Zool. 62, 358–378 (2014).
Arrigoni, R. et al. Species delimitation in the reef coral genera Echinophyllia and Oxypora (Scleractinia, Lobophylliidae) with a description of two new species. Mol. Phylogenet. Evol. 105, 146–159 (2016).
Seiblitz, I. G. L. et al. Caryophylliids (Anthozoa, Scleractinia) and mitochondrial gene order: Insights from mitochondrial and nuclear phylogenomics. Mol. Phylogenet. Evol. 175, 107565 (2022).
McFadden, C. S. et al. Phylogenomics, origin, and diversification of Anthozoans (Phylum Cnidaria). Syst. Biol. 70, 635–647 (2021).
Fukami, H. et al. Mitochondrial and nuclear genes suggest that stony corals are monophyletic but most families of stony corals are not (Order Scleractinia, Class Anthozoa, Phylum Cnidaria). PLoS One 3, e3222 (2008).
Loya, Y. Settlement, mortality and recruitment of a Red Sea Scleractinian coral population. In: Coelenterate Ecology and Behavior (ed. Mackie, G. O.) 89–100 (Springer, Boston, MA, 1976). https://doi.org/10.1007/978-1-4757-9724-4.
Harrison, P. L. & Wallace, C. Reproduction, dispersal and recruitment of scleractinian corals. In: Ecosystems of the World 25: Coral Reefs (ed. Dubinsky, Z.) 133–207 (Elsevier Science Publisher, 1990).
Shefy, D. & Rinkevich, B. Stylophora pistillata – A model colonial species in basic and applied studies. In: Handbook of Marine Model Organisms in Experimental Biology: Established and Emerging (eds. Boutet, A. & Schierwater, B.) 195–216 (CRC Press, 2021). https://doi.org/10.1201/9781003217503-11.
Veron, J. E. N. Corals of the World (Australian Institute of Marine Science, 2000).
Fadlallah, Y. H. Sexual reproduction, development and larval biology in Scleractinian corals: a review. Coral Reefs 2, 129–150 (1983).
Rundle, H. D. & Nosil, P. Ecological speciation. Ecol. Lett. 8, 336–352 (2005).
Underwood, J. N., Smith, L. D., Van Oppen, M. J. H. & Gilmour, J. P. Multiple scales of genetic connectivity in a brooding coral on isolated reefs following catastrophic bleaching. Mol. Ecol. 16, 771–784 (2007).
Underwood, J. N., Smith, L. D., Van Oppen, M. J. H. & Gilmour, J. P. Ecologically relevant dispersal of corals on isolated reefs: Implications for managing resilience. Ecol. Appl. 19, 18–29 (2009).
Nunes, F. L. D., Norris, R. D. & Knowlton, N. Long Distance Dispersal and Connectivity in Amphi-Atlantic Corals at Regional and Basin Scales. PLoS One 6, e22298 (2011).
Thomas, L. et al. Contrasting patterns of genetic connectivity in brooding and spawning corals across a remote atoll system in northwest Australia. Coral Reefs 39, 55–60 (2020).
van der Ven, R. M., Heynderickx, H. & Kochzius, M. Differences in genetic diversity and divergence between brooding and broadcast spawning corals across two spatial scales in the Coral Triangle region. Mar. Biol. 168, 17 (2021).
Ayre, D. J., Hughes, T. P. & Standish, R. J. Genetic differentiation, reproductive mode, and gene flow in the brooding coral Pocillopora damicornis along the Great Barrier Reef, Australia. Mar. Ecol. Prog. Ser. 159, 175–187 (1997).
Serrano, X. M. et al. Long distance dispersal and vertical gene flow in the Caribbean brooding coral Porites astreoides. Sci. Rep. 6, 21619 (2016).
Buitrago-López, C. et al. Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories. Mol. Ecol. 32, 2151–2173 (2023).
Meziere, Z. et al. Exploring coral speciation: Multiple sympatric Stylophora pistillata taxa along a divergence continuum on the Great Barrier Reef. Evol. Appl. 17, 1–17 (2024).
Bongaerts, P. et al. Genetic divergence across habitats in the widespread coral Seriatopora hystrix and its associated Symbiodinium. PLoS One 5, e10871 (2010).
Sturm, A. B. et al. Does depth divide? Variable genetic connectivity patterns among shallow and mesophotic Montastraea cavernosa coral populations across the Gulf of Mexico and western Caribbean. Ecol. Evol. 13, e10622 (2023).
Serrano, X. M. et al. Geographic differences in vertical connectivity in the Caribbean coral Montastraea cavernosa despite high levels of horizontal connectivity at shallow depths. Mol. Ecol. 23, 4226–4240 (2014).
Rocha, L. A. et al. Mesophotic coral ecosystems are threatened and ecologically distinct from shallow water reefs. Science 361, 281–284 (2018).
Bell, J. J. et al. Global status, impacts, and management of rocky temperate mesophotic ecosystems. Conserv. Biol. 38, 1–17 (2022).
Hinderstein, L. M. et al. Theme section on ‘Mesophotic Coral Ecosystems: Characterization, Ecology, and Management. Coral Reefs 29, 247–251 (2010).
Pyle, R. L. & Copus, J. M. Mesophotic Coral Ecosystems: Introduction and Overview. Coral Reefs World 12, 3–27 (2019).
Glynn, P. W. Coral reef bleaching: Facts, hypotheses and implications. Glob. Chang. Biol. 2, 495–509 (1996).
Bongaerts, P. et al. Deep reefs are not universal refuges: Reseeding potential varies among coral species. Sci. Adv. 3, e1602373 (2017).
Loya, Y. Community structure and species diversity of hermatypic corals at Eilat, Red Sea. Mar. Biol. 13, 100–123 (1972).
Kramer, N., Eyal, G., Tamir, R. & Loya, Y. Upper mesophotic depths in the coral reefs of Eilat, Red Sea, offer suitable refuge grounds for coral settlement. Sci. Rep. 9, 1–12 (2019).
Eyal, G., Tamir, R., Kramer, N., Eyal-Shaham, L. & Loya, Y. The Red Sea: Israel. in Mesophotic Coral Ecosystems. Coral Reefs of the World (eds. Loya, Y., Puglise, K. & Bridge, T.) 12 199–214 (Springer, 2019).
Kleinhaus, K. et al. Science, Diplomacy, and the Red Sea’s Unique Coral Reef: It’s Time for Action. Front. Mar. Sci. 7, 1–9 (2020).
Ayalon, I., de Barros Marangoni, L. F., Benichou, J. I. C., Avisar, D. & Levy, O. Red Sea corals under Artificial Light Pollution at Night (ALAN) undergo oxidative stress and photosynthetic impairment. Glob. Chang. Biol. 25, 4194–4207 (2019).
Rosenberg, Y. et al. Urbanization comprehensively impairs biological rhythms in coral holobionts. Glob. Chang. Biol. 28, 3349–3364 (2022).
Levy, O. et al. Complex diel cycles of gene expression in coral-algal symbiosis. Science 331, 175 (2011).
Levy, O. et al. Light-Responsive Cryptochromes from a Simple Multicellular Animal, the Coral Acropora millepora. Science 318, 467–470 (2007).
Ayalon, I. et al. Coral gametogenesis collapse under artificial light pollution. Curr. Biol. 31, 413–419 (2021).
Tamir, R., Eyal, G., Cohen, I. & Loya, Y. Effects of Light Pollution on the Early Life Stages of the Most Abundant Northern Red Sea Coral. Microorganisms 8, 193 (2020).
Quek, Z. B. R. et al. A hybrid-capture approach to reconstruct the phylogeny of Scleractinia (Cnidaria: Hexacorallia). Mol. Phylogenet. Evol. 186, 107867 (2023).
Shaish, L., Abelson, A. & Rinkevich, B. How plastic can phenotypic plasticity be? The branching coral Stylophora pistillata as a model system. PLoS One 2, e644 (2007).
Kramer, N., Guan, J., Chen, S., Wangpraseurt, D. & Loya, Y. Morpho-functional traits of the coral Stylophora pistillata enhance light capture for photosynthesis at mesophotic depths. Commun. Biol. 5, 861 (2022).
Roberty, S. et al. Shallow and mesophotic colonies of the coral Stylophora pistillata share similar regulatory strategies of photosynthetic electron transport but differ in their sensitivity to light. Coral Reefs 42, 645–659 (2023).
Martinez, S. et al. Energy sources of the depth-generalist mixotrophic coral Stylophora pistillata. Front. Mar. Sci. 7, 1–16 (2020).
Osman, E. O. et al. Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities. Microbiome 8, 8 (2020).
Rossbach, S. et al. Flexibility in Red Sea Tridacna maxima-Symbiodiniaceae associations supports environmental niche adaptation. Ecol. Evol. 11, 3393–3406 (2021).
LaJeunesse, T. C. et al. Systematic revision of Symbiodiniaceae highlights the antiquity and diversity of coral endosymbionts. Curr. Biol. 28, 2570–2580 (2018).
Cohen, I. & Dubinsky, Z. Long term photoacclimation responses of the coral Stylophora pistillata to reciprocal deep to shallow transplantation: photosynthesis and calcification. Front. Mar. Sci. 2, 45 (2015).
Einbinder, S. et al. Novel Adaptive Photosynthetic Characteristics of Mesophotic Symbiotic Microalgae within the Reef-Building Coral, Stylophora pistillata. Front. Mar. Sci. 3, 195 (2016).
Scucchia, F., Nativ, H., Neder, M., Goodbody-Gringley, G. & Mass, T. Physiological Characteristics of Stylophora pistillata Larvae Across a Depth Gradient. Front. Mar. Sci. 7, 13 (2020).
Prada, C. & Hellberg, M. E. Long prereproductive selection and divergence by depth in a Caribbean candelabrum coral. Proc. Natl. Acad. Sci. 110, 3961–3966 (2013).
Eckert, R. J., Studivan, M. S. & Voss, J. D. Populations of the coral species Montastraea cavernosa on the Belize Barrier Reef lack vertical connectivity. Sci. Rep. 9, 7200 (2019).
Bongaerts, P. et al. Morphological stasis masks ecologically divergent coral species on tropical reefs. Curr. Biol. 31, 2286–2298.e8 (2021).
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).
Davies, T. W. & Smyth, T. Why artificial light at night should be a focus for global change research in the 21st century. Glob. Chang. Biol. 24, 872–882 (2018).
Marangoni, L. F. B. et al. Impacts of artificial light at night in marine ecosystems—A review. Glob. Chang. Biol. 28, 5346–5367 (2022).
Meziere, Z. et al. Stylophora under stress: A review of research trends and impacts of stressors on a model coral species. Sci. Total Environ. 816, 151639 (2022).
Levy, O. et al. Artificial light at night (ALAN) alters the physiology and biochemistry of symbiotic reef building corals. Environ. Pollut. 266, 114987 (2020).
Cresswell, A. K. et al. Structure-from-motion reveals coral growth is influenced by colony size and wave energy on the reef slope at Ningaloo Reef, Western Australia. J. Exp. Mar. Bio. Ecol. 530–531, 151438 (2020).
Tamir, R., Lerner, A., Haspel, C., Dubinsky, Z. & Iluz, D. The spectral and spatial distribution of light pollution in the waters of the northern Gulf of Aqaba (Eilat). Sci. Rep. 7, 42329 (2017).
Walsh, P. S., Metzger, D. A. & Higuchi, R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10, 506–513 (1991).
Feine, I., Shpitzen, M., Roth, J. & Gafny, R. A novel cell culture model as a tool for forensic biology experiments and validations. Forensic Sci. Int. Genet. 24, 114–119 (2016).
Russello, M. A., Waterhouse, M. D., Etter, P. D. & Johnson, E. A. From promise to practice: pairing non-invasive sampling with genomics in conservation. PeerJ 3, e1106 (2015).
Voolstra, C. R. et al. Comparative analysis of the genomes of Stylophora pistillata and Acropora digitifera provides evidence for extensive differences between species of corals. Sci. Rep. 7, 17583 (2017).
Jombart, T. adegenet: a R package for the multivariate analysis of genetic markers. Bioinformatics 24, 1403–1405 (2008).
Jombart, T. & Ahmed, I. adegenet 1.3-1: New tools for the analysis of genome-wide SNP data. Bioinformatics 27, 3070–3071 (2011).
Beugin, M., Gayet, T., Pontier, D., Devillard, S. & Jombart, T. A fast likelihood solution to the genetic clustering problem. Methods Ecol. Evol. 9, 1006–1016 (2018).
Nei, M. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89, 583–590 (1978).
Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655–1664 (2009).