The importance of structural complexity in coral reef ecosystems - Graham, N. A. J.; Nash, K. L. (Coral Reefs, 2013)

Jones, G. P. Postrecruitment processes in the ecology of coral reef fish populations: a multifactorial perspective in The ecology of fishes on coral reefs (ed. Sale, P. F.) 294–328 (Academic Press, San Diego, 1991).

Predation, prey refuges, and the structure of coral-reef fish assemblages - Hixon, M. A.; Beets, J. P. (Ecol. Monogr., 1993)

Disturbance, habitat structure, and the dynamics of a coral-reef fish community - Syms, C.; Jones, G. P. (Ecology, 2000)

Predicting climate-driven regime shifts versus rebound potential in coral reefs - Graham, N. A. J.; Jennings, S.; MacNeil, M. A.; Mouillot, D.; Wilson, S. K. (Nature, 2015)

Confronting the coral reef crisis - Bellwood, D. R.; Hughes, T. P.; Folke, C.; Nyström, M. (Nature, 2004)

Flattening of Caribbean coral reefs: region-wide declines in architectural complexity - Alvarez-Filip, L.; Dulvy, N. K.; Gill, J. A.; Côté, I. M.; Watkinson, A. R. (Proc. R. Soc. Lond. B Biol. Sci., 2009)

Ecological extinction and evolution in the brave new ocean - Jackson, J. B. C. (Proc. Natl. Acad. Sci. USA, 2008)

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

Fish diversity on a coral reef in the Virgin Islands - Risk, M. J. (Atoll Res. Bull., 1972)

Comparison of field methods for measuring surface topography and their associations with a tropical reef fish assemblage - McCormick, M. I. (Mar. Ecol. Prog. Ser., 1994)

Quantifying habitat complexity in aquatic ecosystems - Shumway, C. A.; Hofmann, H. A.; Dobberfuhl, A. P. (Freshwater Biol., 2007)

Large-scale, long-term monitoring of Caribbean coral reefs: simple, quick, inexpensive techniques - Aronson, R. B.; Edmunds, P. J.; Precht, W. F.; Swanson, D. W.; Levitan, D. R. (Atoll Res. Bull., 1994)

Nutrient effects on coral reefs: a hypothesis on the importance of topographic and trophic complexity to reef nutrient dynamics - Szmant, A. M. (Proc. 8th Int. Coral Reef Symp., 1997)

Shifts in coral-assemblage composition do not ensure persistence of reef functionality - Alvarez-Filip, L.; Carricart-Ganivet, J. P.; Horta-Puga, G.; Iglesias-Prieto, R. (Scientific Reports, 2013)

The dynamics of architectural complexity on coral reefs under climate change - Bozec, Y. -. M.; Alvarez-Filip, L.; Mumby, P. J. (Global Change Biol., 2015)

Scleractinian corals as facilitators for other invertebrates on a Caribbean reef - Idjadi, J. A.; Edmunds, P. J. (Mar. Ecol. Prog. Ser., 2006)

The influence of coral reef benthic condition on associated fish assemblages - Chong-Seng, K. M.; Mannering, T. D.; Pratchett, M. S.; Bellwood, D. R.; Graham, N. A. (PLoS ONE, 2012)

Reef flattening effects on total richness and species responses in the Caribbean - Newman, S. P. (J. Anim. Ecol., 2015)

Rebuilding community ecology from functional traits - McGill, B. J.; Enquist, B. J.; Weiher, E.; Westoby, M. (Trends Ecol. Evol., 2006)

Relating coral species traits to environmental conditions in the Jakarta Bay/Pulau Seribu reef system, Indonesia - Rachello-Dolmen, P. G.; Cleary, D. F. R. (Estuar. Coast. Shelf Sci., 2007)

Evaluating life-history strategies of reef corals from species traits - Darling, E. S.; Alvarez-Filip, L.; Oliver, T. A.; McClanahan, T. R.; Côté, I. M. (Ecol. Lett., 2012)

Life histories predict coral community disassembly under multiple stressors - Darling, E. S.; McClanahan, T. R.; Côté, I. M. (Global Change Biol., 2013)

Recovery of an isolated coral reef system following severe disturbance - Gilmour, J. P.; Smith, L. D.; Heyward, A. J.; Baird, A. H.; Pratchett, M. S. (Science, 2013)

Enochs, I. C. & Glynn, P. W. Trophodynamics of Eastern Pacific Coral Reefs. In (eds Glynn, P. W., Manzello, D. P., Enochs, I. C.) 291–314 (Springer, Netherlands, 2017).

The impact of exploiting grazers (Scaridae) on the dynamics of Caribbean coral reefs - Mumby, P. J. (Ecol. Appl., 2006)

Adaptive strategies of coral-reef invertebrates - Jackson, J. B. C.; Hughes, T. P. (Am. Sci., 1985)

Mechanical vulnerability explains size-dependant mortality of reef corals - Madin, J. S.; Baird, A. H.; Dornelas, M.; Connoly, S. R. (Ecol. Lett., 2014)

Darling, E. S. et al. Relationships between structural complexity, coral traits, and reef fish assemblages. Coral Reefs, doi:10.1007/s00338-017-1539-z (2017).

Fecundity and the demographic strategies of coral morphologies - Álvarez‐Noriega, M. (Ecology, 2016)

Allometric growth in reef-building corals - Dornelas, M.; Madin, J. S.; Baird, A. H.; Connolly, S. R. (Proc. R. Soc. B, 2017)

A trait-based approach to advance coral reef science - Madin, J. S. (Trends Ecol. Evol., 2016)

Coverage, diversity, and functionality of a high-latitude coral community (Tatsukushi, Shikoku Island, Japan) - Denis, V. (PLoS ONE, 2013)

Typhoon damage on a shallow mesophotic reef in Okinawa, Japan - White, K. N. (PeerJ, 2013)

Functional diversity: back to basics and looking forward - Petchey, O. L.; Gatson, K. J. (Ecol. Lett., 2006)

A statistical analysis of coral community response to the 1982-83 El Niño in the Thousand Islands, Indonesia - Warwick, R. M.; Clarke, K. R.; Suharsono (Coral Reefs, 1990)

Navigating the multiple meanings of β diversity: a roadmap for the practicing ecologist - Anderson, M. J. (Ecol. Lett., 2011)

& Suharsono. Damage and recovery of coral reefs affected by El Niño related seawater warming in the Thousand Islands, Indonesia - Brown, B. E. (Coral Reefs, 1990)

Wang, Y., Naumann, U., Wright, S., Eddelbuettel, D. & Warton, D. mvabund: statistical methods for analysing multivariate abundance data. R package version 3.12 https://CRAN.R-project.org/package=mvabund (2017).

A general coefficient of similarity and some of its properties - Gower, J. C. (Biometrics, 1971)

Numerical Ecology with R - Borcard, D.; Gillet, F.; Legendre, P. (Springer, 2011)

A functional approach reveals community response to disturbance - Mouillot, D.; Graham, N. A. J.; Villéger, S.; Mason, N. W. H.; Bellwood, D. R. (Trends Ecol. Evol., 2013)

Controlling the false discovery rate: a practical and powerful approach to multiple testing - Benjamini, Y.; Hochberg, Y. (J. R. Stat. Soc. Series B Stat. Methodol., 1995)

Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs - Mouillot, D. (Proc. Natl. Acad. Sci. USA, 2014)

R Core Team. R: A language and environment for statistical computing. R Foundation for Statistical Computing http://www.R-project.org (2014).

Maechler, M. et al. cluster: cluster analysis basics and extensions. R package version 1.15.2 https://CRAN.R-project.org/package=cluster (2014).

Hennig, C. fpc: flexible procedures for clustering. R package version2, 1–7 https://CRAN.R-project.org/package=fpc (2014)

Plotrix: a package in the red light district of R - Lemon, J. (R-News, 2006)

A distance-based framework for measuring functional diversity from multiple traits - Laliberté, E.; Legendre, P. (Ecology, 2010)

Laliberté, E. & Shipley, B. FD: measuring functional diversity from multiple traits, and other tools for functional ecology. R package version 1.0-11 https://CRAN.R-project.org/package=FD (2011).

New multidimensional functional diversity indices for a multifaceted framework in functional ecology - Villéger, S.; Mason, N. W. H.; Mouillot, D. (Ecology, 2008)

Functional diversity responses to changing species richness in reef fish communities - Halpern, B. S.; Floeter, S. R. (Mar. Ecol. Prog. Ser., 2008)

Sleeping functional group drives coral-reef recovery - Bellwood, D. R.; Hughes, T. P.; Hoey, A. S. (Curr. Biol., 2006)

Functional versatility supports coral reef biodiversity - Bellwood, D. R.; Wainwright, P. C.; Fulton, C. J.; Hoey, A. S. (Proc. R. Soc. Lond. B Biol. Sci., 2006)

Rare species support vulnerable functions in high-diversity ecosystems - Mouillot, D. (PLoS Biology, 2013)

Coral bleaching: the winners and the losers - Loya, Y. (Ecol. Lett., 2001)

Differential thermal bleaching susceptibilities among coral taxa: re-posing the role of the host - Wooldridge, S. C. (Coral Reefs, 2014)

Porites and the Phoenix effect: unprecedented recovery after a mass coral bleaching event at Rangiroa Atoll, French Polynesia - Roff, G. (Mar. Biol., 2014)

Doom and boom on a resilient reef: climate change, algal overgrowth and coral recovery - Diaz-Pulido, G. (PLoS ONE, 2009)

Assessing the ‘deep reef refugia’ hypothesis: focus on Caribbean reefs - Bongaert, P.; Ridgway, T.; Sampayo, E. M.; Hoegh-Guldberg, O. (Coral Reefs, 2010)

Connectivity and management of Caribbean coral reefs - Roberts, C. M. (Science, 1997)

Harrison, P. L. & Wallace, C. C. Reproduction, dispersal and recruitment of scleractinian corals in Ecosystem of the world, Vol 25: coral reefs (ed. Dubinsky, Z.) 133–207 (Elsevier Science Publications, Amsterdam, 1990).

Van Oppen, J. H., Bongaerts, P., Underwood, J. N., Peplow, L. M. & Cooper, T. F. The role of deep reefs in shallow reef recovery: an assessment of vertical connectivity in a brooding coral from west and east Australia. Mol. Ecol.20, 1647–1660 (2011).

Linking demographic processes of juvenile corals to benthic recovery trajectories in two common reef habitats - Doropoulos, C.; Ward, S.; Roff, G.; González-Rivero, M.; Mumby, P. J. (PLoS ONE, 2015)

Revisiting the winners and the losers a decade after coral bleaching - Woesik, R.; Sakai, K.; Ganase, A.; Loya, Y. (Mar. Ecol. Prog. Ser., 2011)

The distribution and abundance of black band disease and white syndrome in Kepuluan Seribu, Indonesia - Johan, O.; Bengen, D. G.; Zamani, N. P.; Suharsono; Sweet, M. J. (HAYATI J. Biosci., 2015)

Prevalence and incidence of black band disease of scleratinian corals in the Kepulauan Seribu region of Indonesia - Johan, O.; Zamany, N. P.; Smith, D.; Sweet, M. J. (Divers., 2016)

Variation in the composition of corals, fishes, sponges, echinoderms, ascidians, molluscs, foraminifera and macroalgae across a pronounced in-to-offshore environmental gradient in the Jakarta Bay-Thousand Islands coral reef complex - Cleary, D. F. R. (Mar. Poll. Bull., 2016)

Contrasting patterns of coral bleaching susceptibility in 2010 suggest an adaptive response to thermal stress - Guest, J. R. (PLoS ONE, 2012)

Rao’s quadratic entropy as a measure of functional diversity based on multiple traits - Botta-Dukát, Z. (J. Veg. Sci., 2005)

Towards a unifying approach to diversity measures: bridging the gap between the Shannon entropy and Rao’s quadratic index - Ricotta, C.; Szeidl, L. (Theor. Popul. Biol., 2006)

Diversity partitioning of Rao’s quadratic entropy - Ricotta, C.; Szeidl, L. (Theor. Popul. Biol., 2009)

Distance-based functional diversity measures and their decomposition: a framework based on Hill numbers - Chiu, C. -. H.; Chao, A. (PLoS ONE, 2014)

Coral mortality induced by the 2015–2016 El-Niño in Indonesia: the effect of rapid sea level fall - Ampou, E. E.; Johan, O.; Menkès, C. E. (Biogeosciences, 2017)

DeVantier, L. et al. Status of coral communities of Pulau Seribu, 1985-1995 in Proceedings: coral reef evaluation workshop Pulau Seribu, Jakarta, Indonesia (ed. Soemodihardjo, S.) 1–24 (UNESCO, Jakarta, 1998).

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 - Cleary, D. F. R. (Mar. Ecol. Prog. Ser., 2014)

Long-term changes in coral assemblages under natural and anthropogenic stress in Jakarta Bay (1920–2005) - Meij, S. E. T.; Suharsono; Hoeksema, B. W. (Mar. Poll. Bull., 2010)

Rethinking ecosystem resilience in the face of climate change - Côté, I. M.; Darling, E. S. (PLoS Biol., 2010)