Ampou, EE, Johan, O, Menkes, CE, Niño, F, Birol, F, Ouillon, S and Andréfouët, S (2017) Coral mortality induced by the 2015–2016 El-Niño in Indonesia: the effect of rapid sea level fall. Biogeosciences (Online) 14, 817–826.
Arnold, SN, Steneck, RS and Mumby, PJ (2010) Running the gauntlet: inhibitory effects of algal turfs on the processes of coral recruitment. Marine Ecology Progress Series 414, 91–105.
Baird, AH, Pratchett, MS, Hoey, A, Herdiana, Y and Campbell, SJ (2013) Acanthaster planci is a major cause of coral mortality in Indonesia. Coral Reefs 32, 803–812.
Bell, JJ and Smith, D (2004) Ecology of sponge assemblages (Porifera) in the Wakatobi region, south-east Sulawesi, Indonesia: richness and abundance. Journal of the Marine Biological Association of the United Kingdom 84, 581–591.
Bell, JJ, Davy, SK, Jones, T, Taylor, MW and Webster, NS (2013) Could some coral reefs become sponge reefs as our climate changes? Global Change Biology 19, 2613–2624.
Biggerstaff, A, Smith, DJ, Jompa, J and Bell, JJ (2015) Photoacclimation supports environmental tolerance of a sponge to turbid low-light conditions. Coral Reefs 34, 1049–1061.
Biggerstaff, A, Smith, DJ, Jompa, J and Bell, JJ (2017 a) Metabolic responses of a phototrophic sponge to sedimentation supports transitions to sponge-dominated reefs. Scientific Reports 7, 2725.
Biggerstaff, A, Jompa, J and Bell, J (2017 b) Increasing benthic dominance of the phototrophic sponge Lamellodysidea herbacea on a sedimented reef within the coral triangle. Marine Biology 164, 220.
Briggs, JC (2005) The marine East Indies: diversity and speciation. Journal of Biogeography 32, 1517–1522.
Bruno, JF and Selig, ER (2007) Regional decline of coral cover in the Indo-Pacific: timing, extent, and subregional comparisons. PLoS ONE 2, e711.
Bruno, JF, Sweatman, H, Precht, WF, Selig, ER and Schutte, VG (2009) Assessing evidence of phase shifts from coral to macroalgal dominance on coral reefs. Ecology 90, 1478–1484.
Bruno, JF, Precht, WF, Vroom, PS and Aronson, RB (2014) Coral reef baselines: how much macroalgae is natural? Marine Pollution Bulletin 80, 24–29.
Burke, LM, Reytar, K, Spalding, M and Perry, A (2011) Reefs at Risk Revisited. Washington, DC: World Resources Institute.
Cleary, DF, Polónia, AR, Renema, W, Hoeksema, BW, Wolstenholme, J, Tuti, Y and de Voogd, NJ (2014) Coral reefs next to a major conurbation: a study of temporal change (1985–2011) in coral cover and composition in the reefs of Jakarta, Indonesia. Marine Ecology Progress Series 501, 89–98.
Connell, S, Foster, M and Airoldi, L (2014) What are algal turfs? Towards a better description of turfs. Marine Ecology Progress Series 495, 299–307.
Côté, IM, Gill, JA, Gardner, TA and Watkinson, AR (2005) Measuring coral reef decline through meta-analyses. Philosophical Transactions of the Royal Society of London B: Biological Sciences 360, 385–395.
Crabbe, MJC and Smith, DJ (2005) Sediment impacts on growth rates of Acropora and Porites corals from fringing reefs of Sulawesi, Indonesia. Coral Reefs 24, 437–441.
Curtis-Quick, JA (2013) Drivers of change of reef fish assemblages within the Coral Triangle (PhD thesis). University of Essex, Colchester, UK.
Diaz-Pulido, G and McCook, LJ (2002) The fate of bleached corals: patterns and dynamics of algal recruitment. Marine Ecology Progress Series 232, 115–128.
Edinger, EN, Jompa, J, Limmon, GV, Widjatmoko, W and Risk, MJ (1998) Reef degradation and coral biodiversity in Indonesia: effects of land-based pollution, destructive fishing practices and changes over time. Marine Pollution Bulletin 36, 617–630.
Endean, R, Cameron, A and DeVantier, L (1988) Acanthaster planci predation on massive corals: the myth of rapid recovery of devastated reefs. Proceedings of the 6th International Coral Reef Symposium, Townsville, Australia, 8–12 August 1988, Volume 2, pp. 143–148.
Exton, D (2010) Nearshore fisheries of the Wakatobi. In Clifton, J, Unsworth, RKF and Smith, DJ (eds), Marine Research and Conservation in the Coral Triangle: The Wakatobi National Park. New York, NY: Nova Publishers, pp. 193–207.
Fabricius, K and De'Ath, G (2001) Environmental factors associated with the spatial distribution of crustose coralline algae on the Great Barrier Reef. Coral Reefs 19, 303–309.
Fox, HE, Pet, JS, Dahuri, R and Caldwell, RL (2003) Recovery in rubble fields: long-term impacts of blast fishing. Marine Pollution Bulletin 46, 1024–1031.
Fox, HE, Mous, PJ, Pet, JS, Muljadi, AH and Caldwell, RL (2005) Experimental assessment of coral reef rehabilitation following blast fishing. Conservation Biology 19, 98–107.
Halford, A (2003) In Pet-Soede, L and Erdmann, MV (eds), Rapid Ecological Assessment Wakatobi National Park. WWF/TNC Joint Publication. Denpasar, Bali: WWF/TNC, pp. 53–64.
Hay, ME (1981) The functional morphology of turf-forming seaweeds: persistence in stressful marine habitats. Ecology 62, 739–750.
Heyward, A and Negri, A (1999) Natural inducers for coral larval metamorphosis. Coral Reefs 18, 273–279.
Hughes, TP (1994) Catastrophes, phase shifts, and large-scale degradation of a Caribbean coral reef. Science 265, 1547–1551.
Littler, MM, Littler, DS and Brooks, BL (2006) Harmful algae on tropical coral reefs: bottom-up eutrophication and top-down herbivory. Harmful Algae 5, 565–585.
Marlow, J, Davy, SK, Haris, A and Bell, JJ (2018) Photoacclimation to light-limitation in a clionaid sponge; implications for understanding sponge bioerosion on turbid reefs. Marine Pollution Bulletin 135, 466–474.
Marlow, J, Schönberg, CH, Davy, SK, Haris, A, Jompa, J and Bell, JJ (2019) Bioeroding sponge assemblages: the importance of substrate availability and sediment. Journal of the Marine Biological Association of the United Kingdom 99, 343–358.
McMellor, S and Smith, DJ (2010) Coral reefs of the Wakatobi. In Clifton, J, Unsworth, RKF and Smith, DJ (eds), Marine Research and Conservation in the Coral Triangle: The Wakatobi National Park. New York, NY: Nova Publishers, pp. 18–32.
Mumby, PJ (2009) Phase shifts and the stability of macroalgal communities on Caribbean coral reefs. Coral Reefs 28, 761–773.
Norström, AV, Nyström, M, Lokrantz, J and Folke, C (2009) Alternative states on coral reefs: beyond coral-macroalgal phase shifts. Marine Ecology Progress Series 376, 295–306.
Pandolfi, JM, Jackson, JB, Baron, N, Bradbury, RH, Guzman, HM, Hughes, TP, Kappel, CV, Micheli, F, Ogden, JC, Possingham, HP and Sala, E (2005) Are U.S. coral reefs on the slippery slope to slime? Science 307, 1725–1726.
Plass-Johnson, JG, Ferse, SC, Jompa, J, Wild, C and Teichberg, M (2015) Fish herbivory as key ecological function in a heavily degraded coral reef system. Limnology and Oceanography 60, 1382–1391.
Powell, A, Smith, DJ, Hepburn, LJ, Jones, T, Berman, J, Jompa, J and Bell, JJ (2014) Reduced diversity and high sponge abundance on a sedimented Indo-Pacific reef system: implications for future changes in environmental quality. PLoS ONE 9, e85253.
Roberts, CM, McClean, CJ, Veron, JE, Hawkins, JP, Allen, GR, McAllister, DE, Mittermeier, CG, Schueler, FW, Spalding, M, Wells, F, Vynne, C and Werner, TB (2002) Marine biodiversity hotspots and conservation priorities for tropical reefs. Science 295, 1280–1284.
Robinson, D (1971) Observations on Fijian coral reefs and the crown of thorns starfish. Journal of the Royal Society of New Zealand 1, 99–112.
Salinas-de-León, P, Dryden, C, Smith, D and Bell, J (2013) Temporal and spatial variability in coral recruitment on two Indonesian coral reefs: consistently lower recruitment to a degraded reef. Marine Biology 160, 97–105.
Sandin, SA, Smith, JE, DeMartini, EE, Dinsdale, EA, Donner, SD, Friedlander, AM, Konotchick, T, Malay, M, Maragos, JE, Obura, D and Pantos, O (2008) Baselines and degradation of coral reefs in the Northern Line Islands. PLoS ONE 3, e1548.
Schutte, VG, Selig, ER and Bruno, JF (2010) Regional spatio-temporal trends in Caribbean coral reef benthic communities. Marine Ecology Progress Series 402, 115–122.
Spalding, M, Ravilious, C and Green, EP (2001) World Atlas of Coral Reefs. Los Angeles, CA: University of California Press.
Stanley, GD Jr (2003) The evolution of modern corals and their early history. Earth-Science Reviews 60, 195–225.
Steneck, RS and Sala, EA (2005) Large marine carnivores: trophic cascades and top-down controls in coastal ecosystems past and present. In Ray, JC, Redford, KH, Steneck, R and Berger, J (eds), Large Carnivores and the Conservation of Biodiversity. Washington, DC: Island Press, pp. 110–137.
Stobart, B, Teleki, K, Buckley, R, Downing, N and Callow, M (2005) Coral recovery at Aldabra atoll, Seychelles: five years after the 1998 bleaching event. Philosophical Transactions of the Royal Society of London A: Mathematical, Physical and Engineering Sciences 363, 251–255.
Swierts, T and Vermeij, MJ (2016) Competitive interactions between corals and turf algae depend on coral colony form. PeerJ 4, e1984.
Szmant, AM (2002) Nutrient enrichment on coral reefs: is it a major cause of coral reef decline? Estuaries 25, 743–766.
Turak, E (2003) In Pet-Soede, L and Erdmann, MV (eds), Rapid Ecological Assessment Wakatobi National Park. WWF/TNC Joint Publication. Denpasar, Bali: WWF/TNC, pp. 33–52.
Unsworth, RK, Clifton, J and Smith, DJ (2010) Marine Research and Conservation in the Coral Triangle: The Wakatobi National Park. New York: Nova Publishers.
Veron, J, Devantier, LM, Turak, E, Green, AL, Kininmonth, S, Stafford-Smith, M and Peterson, N (2009) Delineating the coral triangle. Galaxea 11, 91–100.
Vroom, PS, Page, KN, Kenyon, JC and Brainard, RE (2006) Algae-dominated reefs. American Scientist 94, 430–437.
Webster, NS, Smith, LD, Heyward, AJ, Watts, JE, Webb, RI, Blackall, LL and Negri, AP (2004) Metamorphosis of a scleractinian coral in response to microbial biofilms. Applied and Environmental Microbiology 70, 1213–1221.
Wilkinson, CR and Evans, E (1989) Sponge distribution across Davies Reef, Great Barrier Reef, relative to location, depth, and water movement. Coral Reefs 8, 1–7.
Williams, GJ, Smith, JE, Conklin, EJ, Gove, JM, Sala, E and Sandin, SA (2013) Benthic communities at two remote Pacific coral reefs: effects of reef habitat, depth, and wave energy gradients on spatial patterns. PeerJ 1, e81.
Williams, GJ, Sandin, SA, Zgliczynski, BJ, Fox, MD, Gove, JM, Rogers, JS, Furby, KA, Hartmann, AC, Caldwell, ZR and Price, NN (2018) Biophysical drivers of coral trophic depth zonation. Marine Biology 165, 60.