References
Dudgeon, D. Multiple threats imperil freshwater biodiversity in the Anthropocene. Curr. Biol. 29, R942–R995 (2019).
Betts, M. G. et al. Global forest loss disproportionately erodes biodiversity in intact landscapes. Nature 547, 441–444 (2017).
Arrigo, K. R. et al. Synergistic interactions among growing stressors increase risk to an Arctic ecosystem. Nat. Commun. 11, 6255 (2020).
Kopf, R. K., Finlayson, C. M., Humphries, P., Sims, N. C. & Hladyz, S. Anthropocene baselines: assessing change and managing biodiversity in human-dominated aquatic ecosystems. Bioscience 65, 798–811 (2015).
Chapin, F. S. et al. Ecosystem stewardship: sustainability strategies for a rapidly changing planet. Trends Ecol. Evol. 25, 241–249 (2010).
Seastedt, T. R., Hobbs, R. J. & Suding, K. N. Management of novel ecosystems: are novel approaches required? Front. Ecol. Environ. 6, 547–553 (2008).
Hughes, T. P. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).
Bellwood, D. R. et al. Coral reef conservation in the Anthropocene: confronting spatial mismatches and prioritizing functions. Biol. Conserv. 236, 604–615 (2019).
Graham, N. A. J., Cinner, J. E., Norström, A. V. & Nyström, M. Coral reefs as novel ecosystems: embracing new futures. Curr. Opin. Environ. Sustain. 7, 9–14 (2014).
Hughes, T. P. et al. Spatial and temporal patterns of mass bleaching of corals in the Anthropocene. Science 359, 80–83 (2018).
Sully, S., Burkepile, D. E., Donovan, M. K., Hodgson, G. & van Woesik, R. A global analysis of coral bleaching over the past two decades. Nat. Commun. 10, 1264 (2019).
Fisher, R. et al. Species richness on coral reefs and the pursuit of convergent global estimates. Curr. Biol. 25, 500–505 (2015).
Brandl, S. J. et al. Coral reef ecosystem functioning: eight core processes and the role of biodiversity. Front. Ecol. Environ. 17, 445–454 (2019).
Teh, L. S. L., Teh, L. C. L. & Sumaila, U. R. A global estimate of the number of coral reef fishers. PLoS ONE 8, e65397 (2013).
Ferrario, F. et al. The effectiveness of coral reefs for coastal hazard risk reduction and adaptation. Nat. Commun. 5, 3794 (2014).
Skirving, W. J. et al. The relentless march of mass coral bleaching: a global perspective of changing heat stress. Coral Reefs 38, 547–557 (2019).
Donovan, M. K. et al. Local conditions magnify coral loss after marine heatwaves. Science 372, 977–980 (2021).
Gilmour, J. P., Smith, L. D., Heyward, A. J., Baird, A. H. & Pratchett, M. S. Recovery of an isolated coral reef system following severe disturbance. Science 340, 69–71 (2013).
Diaz-Pulido, G. & McCook, L. J. The fate of bleached corals: patterns and dynamics of algal recruitment. Mar. Ecol. Prog. Ser. 232, 115–128 (2002).
Bellwood, D. R., Hughes, T. P., Folke, C. & Nyström, M. Confronting the coral reef crisis. Nature 429, 827–833 (2004).
Jouffray, J. B. et al. Parsing human and biophysical drivers of coral reef regimes. Proc. R. Soc. B Biol. Sci. 286, 20182544 (2019).
Reverter, M., Helber, S. B., Rohde, S., Goeij, J. M. & Schupp, P. J. Coral reef benthic community changes in the Anthropocene: biogeographic heterogeneity, overlooked configurations, and methodology. Glob. Chang. Biol. 28, 1956–1971 (2022).
Cheal, A. J., MacNeil, M. A., Emslie, M. J. & Sweatman, H. The threat to coral reefs from more intense cyclones under climate change. Glob. Chang. Biol. 23, 1511–1524 (2017).
Done, T. in Perspectives on Coral Reefs (ed. Barnes, D. J.) 107–147 (Brian Clouston, 1983).
Bruno, J. F., Côté, I. M. & Toth, L. T. Climate change, coral loss, and the curious case of the parrotfish paradigm: why don’t marine protected areas improve reef resilience? Ann. Rev. Mar. Sci. 11, 307–334 (2019).
Gardner, T. A., Cote, I. M., Gill, J. A., Grant, A. & Watkinson, A. R. Long-term region-wide declines in Caribbean corals. Science 301, 958–960 (2003).
Schutte, V. G. W., Selig, E. R. & Bruno, J. F. Regional spatio-temporal trends in Caribbean coral reef benthic communities. Mar. Ecol. Prog. Ser. 402, 115–122 (2010).
Hughes, T. P. Catastrophes, phase shifts and large-scale degradation of a Caribbean coral reef. Science 265, 1547–1551 (1994).
Souter, D. et al. Status of Coral Reefs of the World: 2020 (Global Coral Reef Monitoring Network, 2021).
Bruno, J. F. & Selig, E. R. Regional decline of coral cover in the Indo-Pacific: timing, extent, and subregional comparisons. PLoS One 2, e711 (2007).
Ateweberhan, M., McClanahan, T. R., Graham, N. A. J. & Sheppard, C. R. C. Episodic heterogeneous decline and recovery of coral cover in the Indian Ocean. Coral Reefs 30, 739–752 (2011).
Bellwood, D. R., Hemingson, C. R. & Tebbett, S. B. Subconscious biases in coral reef fish studies. Bioscience 70, 621–627 (2020).
Kench, P. S. et al. Sustained coral reef growth in the critical wave dissipation zone of a Maldivian atoll. Commun. Earth Environ. 3, 9 (2022).
Eddy, T. D. et al. Global decline in capacity of coral reefs to provide ecosystem services. One Earth 4, 1278–1285 (2021).
Mumby, P. J., Hastings, A. & Edwards, H. J. Thresholds and the resilience of Caribbean coral reefs. Nature 450, 98–101 (2007).
Roff, G. & Mumby, P. J. Global disparity in the resilience of coral reefs. Trends Ecol. Evol. 27, 404–413 (2012).
Bruno, J. F., Sweatman, H., Precht, W. F., Selig, E. R. & Schutte, V. G. W. Assessing evidence of phase shifts from coral to macroalgal dominance on coral reefs. Ecology 90, 1478–1484 (2009).
Renema, W. et al. Hopping hotspots: global shifts in marine biodiversity. Science 321, 654–657 (2008).
Bellwood, D. R., Goatley, C. H. R. & Bellwood, O. The evolution of fishes and corals on reefs: form, function and interdependence. Biol. Rev. 92, 878–901 (2017).
Roff, G. Evolutionary history drives biogeographic patterns of coral reef resilience. Bioscience 71, 26–39 (2021).
Siqueira, A. C., Bellwood, D. R. & Cowman, P. F. The evolution of traits and functions in herbivorous coral reef fishes through space and time. Proc. R. Soc. B Biol. Sci. 286, 20182672 (2019).
Birrell, C. L., McCook, L. J., Willis, B. L. & Diaz-Pulido, G. A. Effects of benthic algae on the replenishment of corals and the implications for the resilience of coral reefs. Oceanogr. Mar. Biol. Annu. Rev. 46, 25–63 (2008).
Speare, K. E., Duran, A., Miller, M. W. & Burkepile, D. E. Sediment associated with algal turfs inhibits the settlement of two endangered coral species. Mar. Pollut. Bull. 144, 189–195 (2019).
Diaz-Pulido, G., Harii, S., McCook, L. J. & Hoegh-Guldberg, O. The impact of benthic algae on the settlement of a reef-building coral. Coral Reefs 29, 203–208 (2010).
Johns, K. A. et al. Macroalgal feedbacks and substrate properties maintain a coral reef regime shift. Ecosphere 9, e02349 (2018).
Houk, P. et al. Commercial coral-reef fisheries across Micronesia: a need for improving management. Coral Reefs 31, 13–26 (2012).
Edwards, C. B. et al. Global assessment of the status of coral reef herbivorous fishes: evidence for fishing effects. Proc. R. Soc. B Biol. Sci. 281, 20131835 (2014).
Choat, J. H. & Clements, K. D. Vertebrate herbivores in marine and terrestrial environments: a nutritional ecology perspective. Annu. Rev. Ecol. Syst. 29, 375–403 (1998).
Tebbett, S. B., Morais, R. A., Goatley, C. H. R. & Bellwood, D. R. Collapsing ecosystem functions on an inshore coral reef. J. Environ. Manag. 289, 112471 (2021).
Cornwall, C. E. et al. Global declines in coral reef calcium carbonate production under ocean acidification and warming. Proc. Natl Acad. Sci. USA. 118, e2015265118 (2021).
Diaz-Pulido, G. et al. Greenhouse conditions induce mineralogical changes and dolomite accumulation in coralline algae on tropical reefs. Nat. Commun. 5, 3310 (2014).
Nash, M. C. et al. Dolomite-rich coralline algae in reefs resist dissolution in acidified conditions. Nat. Clim. Chang. 3, 268–272 (2013).
Lyons, M., Larsen K. & Skone, M. Allen Coral Atlas. Imagery, maps and monitoring of the world’s tropical coral reefs. Zenodo https://doi.org/10.5281/zenodo.3833242 (2020).
Tebbett, S. B. & Bellwood, D. R. Algal turf sediments on coral reefs: what’s known and what’s next. Mar. Pollut. Bull. 149, 110542 (2019).
Nugues, M. M. & Bak, R. P. M. Long-term dynamics of the brown macroalga Lobophora variegata on deep reefs in Curaçao. Coral Reefs 27, 389–393 (2008).
Tsounis, G. & Edmunds, P. J. Three decades of coral reef community dynamics in St. John, USVI: a contrast of scleractinians and octocorals. Ecosphere 8, e01646 (2017).
Toth, L. T. et al. Do no-take reserves benefit Florida’s corals? 14 years of change and stasis in the Florida Keys National Marine Sanctuary. Coral Reefs 33, 565–577 (2014).
Smith, J. E. et al. Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific. Proc. R. Soc. B Biol. Sci. 283, 20151985 (2016).
Wolfe, K., Kenyon, T. M. & Mumby, P. J. The biology and ecology of coral rubble and implications for the future of coral reefs. Coral Reefs 40, 1769–1806 (2021).
Harris, J. L., Lewis, L. S. & Smith, J. E. Quantifying scales of spatial variability in algal turf assemblages on coral reefs. Mar. Ecol. Prog. Ser. 532, 41–57 (2015).
Moher, D., Liberati, A., Tetzlaff, J., Altman, D. G. & Group, T. P. Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med. 6, e1000097 (2009).
Crisp, S. K., Tebbett, S. B. & Bellwood, D. R. A critical evaluation of benthic phase shift studies on coral reefs. Mar. Environ. Res. 178, 105667 (2022).
WebPlotDigitizer v. 4.3 (A. Rohatgi, 2020); https://automeris.io/WebPlotDigitizer
Kulbicki, M. et al. Global biogeography of reef fishes: a hierarchical quantitative delineation of regions. PLoS ONE 8, e81847 (2013).
Spalding, M. D. et al. Marine ecoregions of the world: a bioregionalization of coastal and shelf areas. Bioscience 57, 573–583 (2007).
R Core Team: R: A Language and Environment for Statistical Computing. (R Foundation for Statistical Computing, 2020).
Zychaluk, K., Bruno, J. F., Clancy, D., McClanahan, T. R. & Spencer, M. Data-driven models for regional coral-reef dynamics. Ecol. Lett. 15, 151–158 (2012).
Dudgeon, S. R., Aronson, R. B., Bruno, J. F. & Precht, W. F. Phase shifts and stable states on coral reefs. Mar. Ecol. Prog. Ser. 413, 201–216 (2010).
Jost, L., Chao, A. & Chazdon, R. L. in Biological Diversity: Frontiers in Measurement and Assessment (eds Magurran, A. E. & McGill, B. J.) 66–84 (Oxford Univ. Press, 2011).
Oksanen, J. F. et al. Vegan: Community ecology package. R package version 2.5-6 (2019).
Calenge, C. The package “adehabitat” for the R software: a tool for the analysis of space and habitat use by animals. Ecol. Modell. 197, 516–519 (2006).
Worton, B. J. Kernel methods for estimating the utilization distribution in home‐range studies. Ecology 70, 164–168 (1989).
Blonder, B. Hypervolume concepts in niche- and trait-based ecology. Ecography 41, 1441–1455 (2018).
Wood, S. N. Generalized Additive Models: an Introduction with R 2nd edn (Chapman & Hall/CRC, 2017).
Gräler, B., Pebesma, E. & Heuvelink, G. Spatio-temporal interpolation using gstat. R. J. 8, 204–218 (2016).
Hartig, F. DHARMa: Residual diagnostics for hierarchical (multi-level/mixed) regression models. R package version 0.3.3.0 (2020).
Lenth, R. emmeans: Estimated marginal means, aka least-squares means. R package version 1.5.1 (2020).
Wickham, H. et al. tidyverse: easily install and load the ‘tidyverse’. J. Open Source Softw. 4, 1686 (2019).
Pebesma, E. Simple features for R: standardized support for spatial vector data. R. J. 10, 439–446 (2018).
South, A. rnaturalearth: World map data from natural earth. R package version 0.1.0 (2017).
Hamilton, N. E. & Ferry, M. ggtern: ternary diagrams using ggplot2. J. Stat. Softw., Code Snippets 87, 1–17 (2018).
Pedersen, T. L. patchwork: The composer of plots. R package version 1.1.1 (2020).
