Hughes, T. et al. Coral reefs in the Anthropocene. Nature 546, 82–90 (2017).
Google Scholar
Moberg, F. & Folke, C. Ecological goods and services of coral reef ecosystems. Ecol. Econ. 29, 215–233 (1999).
Google Scholar
Brander, L. M., Van Beukering, P. & Cesar, H. S. The recreational value of coral reefs: A meta-analysis. Ecol. Econ. 63, 209–218 (2007).
Google Scholar
Jackson, J. B. et al. Historical overfishing and the recent collapse of coastal ecosystems. Science 293, 629–637 (2001).
Google Scholar
Bruno, J. F., Sweatman, H., Precht, W. F., Selig, E. R. & Schutte, V. G. Assessing evidence of phase shifts from coral to macroalgal dominance on coral reefs. Ecology 90, 1478–1484 (2009).
Google Scholar
Hughes, T. Catastrophes, phase shifts, and large-scale degradation of a Caribbean Coral Reef. Science 265, 1547–1551 (1994).
Google Scholar
Hughes, T. P., Bellwood, D. R., Folke, C. S., McCook, L. J. & Pandolfi, J. M. No-take areas, herbivory and coral reef resilience. Trends Ecol. Evol. 22, 1–3 (2007).
Google Scholar
Gardner, T. A., Côté, I. M., Gill, J. A., Grant, A. & Watkinson, A. R. Long-term region-wide declines in Caribbean corals. Science 301, 958–960 (2003).
Google Scholar
Edgar, G. J. et al. Reef Life Survey: Establishing the ecological basis for conservation of shallow marine life. Biol. Conserv. 252, 108855 (2020).
Google Scholar
Chabanet, P., Bigot, L., Garnier, R., Tessier, E. & Moyne-Picard, M. Coral reef monitoring at Reunion island (Western Indian Ocean) using the GCRMN method. Proc. 9th Int. Coral Reef Symp. 2, 873–878 (2000).
Lang, J. C., Marks, K. W., Kramer, P. A., Kramer, P. R. & Ginsburg, R. N. AGRRA Protocols Version 5.4. (2010).
Cortés, J. et al. The CARICOMP network of Caribbean Marine Laboratories (1985–2007): History, key findings, and lessons learned. Front. Mar. Sci. 5, 519 (2019).
Google Scholar
Dethier, M. N., Graham, E. S., Cohen, S. & Tear, L. M. Visual versus random-point percent cover estimations: ‘objective’ is not always better. Mar. Ecol. Prog. Ser. 96, 93–100 (1993).
Google Scholar
Beijbom, O., Edmunds, P. J., Kline, D. I., Mitchell, B. G. & Kriegman, D. Automated annotation of coral reef survey images. In 2012 IEEE Conference on Computer Vision and Pattern Recognition 1170–1177 (IEEE, 2012).
Beijbom, O. et al. Towards automated annotation of benthic survey images: Variability of human experts and operational modes of automation. PloS One 10, e0130312 (2015).
Google Scholar
Williams, I. D. et al. Leveraging automated image analysis tools to transform our capacity to assess status and trends of coral reefs. Front. Mar. Sci. 6, 222 (2019).
Google Scholar
Roelfsema, C. et al. Benthic and coral reef community field data for Heron Reef, Southern Great Barrier Reef, Australia, 2002–2018. Sci. Data 8, 1–7 (2021).
Google Scholar
Gonzalez-Rivero, M. et al. Monitoring of coral reefs using artificial intelligence: A feasible and cost-effective approach. Remote Sens. 12, 489 (2020).
Google Scholar
Cairns, S. D. Stony corals (Cnidaria: Hydrozoa, Scleractinia) of Carrie Bow Cay, Belize. Smithson. Contrib. Mar. Sci. 21, 271–302 (1982).
Rutzler, K. & Macintyre, I. G. The Atlantic Barrier Reef Ecosystem at Carrie Bow Cay, Belize, 1: Structure and Communities (Smithsonian Institution Press, 1982). https://doi.org/10.5479/si.01960768.12.539.
Google Scholar
Rutzler, K. Caribbean coral reef ecosystems: Thirty-five years of smithsonian marine science in Belize. In Proceedings of the Smithsonian Marine Science Symposium (2009).
McField, M. et al. Mesoamerican Reef Report Card. (2020).
Cox, C. E. et al. Genetic testing reveals some mislabeling but general compliance with a ban on herbivorous fish harvesting in Belize. Conserv. Lett. 6, 132–140 (2013).
Google Scholar
Pebesma, E. J. & Bivand, R. S. Classes and methods for spatial data in R. R News 5, 9–13 (2005).
Pebesma, E. Simple features for R: Standardized support for spatial vector data. R J. 10, 439–446 (2018).
Google Scholar
R Core Team. A language and environment for statistical computing. (2020).
Althaus, F. et al. A standardised vocabulary for identifying benthic biota and substrata from underwater imagery: The CATAMI classification scheme. PLoS One 10, e0141039 (2015).
Google Scholar
Goatley, C. H., Bonaldo, R. M., Fox, R. J. & Bellwood, D. R. Sediments and herbivory as sensitive indicators of coral reef degradation. Ecol. Soc. 21(1), 29 (2016).
Google Scholar
Connell, S., Foster, M. & Airoldi, L. What are algal turfs? Towards a better description of turfs. Mar. Ecol. Prog. Ser. 495, 299–307 (2014).
Google Scholar
Lozada-Misa, P., Schumacher, B. D. & Vargas-Angel, B. Analysis of benthic survey images via CoralNet: A summary of standard operating procedures and guidelines. Pacific
Islands Fish. Sci. Cent. Natl. Mar. Fish. Serv. https://doi.org/10.7289/V5%2FAR-PIFSC-H-17-02 (2017).
Google Scholar
Obura, D. & Grimsditch, G. Resilience Assessment of Coral Reefs: Assessment Protocol for Coral Reefs, Focusing on Coral Bleaching and Thermal Stress (Citeseer, 2009).
Broeke, J., Pérez, J. M. M., & Pascau, J. Image processing with ImageJ. (Packt Publishing Ltd, 2015).
Wood, S. N. Generalized Additive Models: An Introduction with R (CRC Press, 2017).
Google Scholar
Fasiolo, M., Nedellec, R., Goude, Y. & Wood, S. N. Scalable visualization methods for modern generalized additive models. J. Comput. Graph. Stat. 29, 78–86 (2020).
Google Scholar
Oksanen, J. et al. Community ecology package. R Package Version 2, (2013).
Arnold, S. N. & Steneck, R. S. Settling into an increasingly hostile world: The rapidly closing ‘“Recruitment Window”’ for corals. PLoS One. https://doi.org/10.1371/journal.pone.0028681 (2011).
Google Scholar
Mumby, P. J. & Harborne, A. R. Marine reserves enhance the recovery of corals on Caribbean reefs. PLoS One 5, e8657 (2010).
Google Scholar
Adam, T. C., Burkepile, D. E., Ruttenberg, B. I. & Paddack, M. J. Herbivory and the resilience of Caribbean coral reefs: Knowledge gaps and implications for management. Mar. Ecol. Prog. Ser. 520, 1–20 (2015).
Google Scholar
Suchley, A., McField, M. D. & Alvarez-Filip, L. Rapidly increasing macroalgal cover not related to herbivorous fishes on Mesoamerican reefs. PeerJ 4, e2084 (2016).
Google Scholar
Arnold, S. N., Steneck, R. S. & Mumby, P. J. Running the gauntlet: Inhibitory effects of algal turfs on the processes of coral recruitment. Mar. Ecol. Prog. Ser. 414, 91–105 (2010).
Google Scholar
Box, S. J. & Mumby, P. J. Effect of macroalgal competition on growth and survival of juvenile Caribbean corals. Mar. Ecol. Prog. Ser. 342, 139–149 (2007).
Google Scholar
Williams, I. & Polunin, N. Large-scale associations between macroalgal cover and grazer biomass on mid-depth reefs in the Caribbean. Coral Reefs 19, 358–366 (2001).
Google Scholar
Newman, M. J., Paredes, G. A., Sala, E. & Jackson, J. B. Structure of Caribbean coral reef communities across a large gradient of fish biomass. Ecol. Lett. 9, 1216–1227 (2006).
Google Scholar
Mumby, P. J., Steneck, R. S., Roff, G. & Paul, V. J. Marine reserves, fisheries ban, and 20 years of positive change in a coral reef ecosystem. Conserv. Biol. https://doi.org/10.1111/cobi.13738 (2021).
Google Scholar
Aronson, R., Precht, W., Toscano, M. & Koltes, K. The 1998 bleaching event and its aftermath on a coral reef in Belize. Mar. Biol. 141, 435–447 (2002).
Google Scholar
Green, D. H., Edmunds, P. J. & Carpenter, R. C. Increasing relative abundance of Porites astreoides on Caribbean reefs mediated by an overall decline in coral cover. Mar. Ecol. Prog. Ser. 359, 1–10 (2008).
Google Scholar
Roff, G., Joseph, J. & Mumby, P. J. Multi-decadal changes in structural complexity following mass coral mortality on a Caribbean reef. Biogeosciences 17, 5909–5918 (2020).
Google Scholar
Graham, N. & Nash, K. The importance of structural complexity in coral reef ecosystems. Coral Reefs 32, 315–326 (2013).
Google Scholar
Aronson, R. B. & Precht, W. F. White-band disease and the changing face of Caribbean coral reefs. Ecol. Etiol. New. Emerg. Mar. Dis. 159, 25–38 (2001).
Aronson, R. B., Macintyre, I. G., Precht, W. F., Murdoch, T. J. & Wapnick, C. M. The expanding scale of species turnover events on coral reefs in Belize. Ecol. Monogr. 72, 233–249 (2002).
Google Scholar
McField, M. et al. Status of the Mesoamerican Reef after the 2005 coral bleaching event. Status Caribb. Coral Reefs Bleach. Hurric. In 45–60 (2005).
Arias-González, J. E. et al. A coral-algal phase shift in Mesoamerica not driven by changes in herbivorous fish abundance. PLoS One 12, e0174855 (2017).
Google Scholar
Miller, S. Automatically Annotating 175,000+ Images with the CoralNet API. CoralNet (Accessed 23 August 2021); https://coralnet.ucsd.edu/blog/automatically-annotating-175000-images-with-the-coralnet-api/ (2020).
Muller, E. M., Sartor, C., Alcaraz, N. I. & van Woesik, R. Spatial epidemiology of the stony-coral-tissue-loss disease in Florida. Front. Mar. Sci. 7, 163 (2020).
Google Scholar
Alvarez-Filip, L., Estrada-Saldívar, N., Pérez-Cervantes, E., Molina-Hernández, A. & González-Barrios, F. J. A rapid spread of the stony coral tissue loss disease outbreak in the Mexican Caribbean. PeerJ 7, e8069 (2019).
Google Scholar
Weil, E. et al. Spread of the new coral disease “SCTLD” into the Caribbean: implications for Puerto Rico. Reef Encount. 34, 38–43 (2019).
Heres, M. M., Farmer, B. H., Elmer, F. & Hertler, H. Ecological consequences of Stony Coral Tissue Loss Disease in the Turks and Caicos Islands. Coral Reefs 40, 609–624 (2021).
Google Scholar
Walton, C. J., Hayes, N. K. & Gilliam, D. S. Impacts of a regional, multi-year, multi-species coral disease outbreak in Southeast Florida. Front. Mar. Sci. 5, 323 (2018).
Google Scholar
Source: Ecology - nature.com
