O’Leary, B. C. et al. Effective coverage targets for ocean protection. Conserv. Lett. 9, 398–404 (2016).
Edgar, G. J. et al. Global conservation outcomes depend on marine protected areas with five key features. Nature 506, 216–220 (2014).
Google Scholar
Lester, S. E. et al. Biological effects within no-take marine reserves: A global synthesis. Mar. Ecol. Prog. Ser. 384, 33–46 (2009).
Google Scholar
Brandl, S. J., Emslie, M. J. & Ceccarelli, D. M. Habitat degradation increases functional originality in highly diverse coral reef fish assemblages. Ecosphere 7, e01557 (2016).
Ramírez-Ortiz, G. et al. Reduced fish diversity despite increased fish biomass in a Gulf of California Marine Protected Area. PeerJ 2020, e8885 (2020).
Miatta, M., Bates, A. E. & Snelgrove, P. V. R. Incorporating biological traits into conservation. Strategies https://doi.org/10.1146/annurev-marine-032320 (2021).
Google Scholar
Coleman, M. A. et al. Functional traits reveal early responses in marine reserves following protection from fishing. Divers. Distrib. 21, 876–887 (2015).
Google Scholar
Bellwood, D. R., Streit, R. P., Brandl, S. J. & Tebbett, S. B. The meaning of the term ‘function’ in ecology: A coral reef perspective. Funct. Ecol. 33, 1365–2435. https://doi.org/10.1111/1365-2435.13265 (2019).
Google Scholar
Brandl, S. J. et al. Coral reef ecosystem functioning: Eight core processes and the role of biodiversity. Front. Ecol. Environ. https://doi.org/10.1002/fee.2088 (2019).
Google Scholar
McLean, M., Mouillot, D., Villéger, S., Graham, N. A. J. & Auber, A. Interspecific differences in environmental response blur trait dynamics in classic statistical analyses. Mar. Biol. 166, 1–10 (2019).
Hadj-Hammou, J., Mouillot, D. & Graham, N. A. J. Response and effect traits of coral reef fish. Front. Mar. Sci. 8, 640619 (2021).
Griffin-Nolan, R. J. et al. Trait selection and community weighting are key to understanding ecosystem responses to changing precipitation regimes. Funct. Ecol. 32, 1746–1756 (2018).
Lefcheck, J. S. et al. Tropical fish diversity enhances coral reef functioning across multiple scales. Sci. Adv. 5, eaav6420 (2019).
Google Scholar
McLean, M. et al. A climate-driven functional inversion of connected marine ecosystems. Curr. Biol. 28, 3654-3660.e3 (2018).
Google Scholar
Mouillot, D., Graham, N. A. J., Villéger, S., Mason, N. W. H. & Bellwood, D. R. A functional approach reveals community responses to disturbances. Trends Ecol. Evol. 28, 167–177 (2013).
Google Scholar
Harborne, A. R. & Mumby, P. J. Novel ecosystems: Altering fish assemblages in warming waters. Curr. Biol. 21, R822–R824 (2011).
Google Scholar
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).
Woodhead, A. J., Hicks, C. C., Norström, A. V., Williams, G. J. & Graham, N. A. J. Coral reef ecosystem services in the Anthropocene. Funct. Ecol. 33, 1023–1034 (2019).
Munday, P. L. & Jones, G. P. The ecological implications of small body size among coral-reef fishes. Oceanogr. Mar. Biol. Annu. Rev. 36, 373–411 (1998).
Babcock, R. C. et al. Decadal trends in marine reserves reveal differential rates of change in direct and indirect effects. Proc. Natl. Acad. Sci. 107, 18256–18261 (2010).
Google Scholar
Robinson, J. P. W. et al. Fishing degrades size structure of coral reef fish communities. Glob. Change Biol. 23, 1009–1022 (2017).
Google Scholar
Villéger, S., Brosse, S., Mouchet, M., Mouillot, D. & Vanni, M. J. Functional ecology of fish: Current approaches and future challenges. Aquat. Sci. 79, 783–801 (2017).
Cinner, J. E. et al. Meeting fisheries, ecosystem function, and biodiversity goals in a human-dominated world. Science (80-.) 368, 307–311 (2020).
Google Scholar
McClanahan, T. R. Kenyan coral reef lagoon fish: Effects of fishing, substrate complexity, and sea urchins. Coral Reefs 13, 231–241 (1994).
Google Scholar
McClanahan, T. R. & Graham, N. A. J. Recovery trajectories of coral reef fish assemblages within Kenyan marine protected areas. Mar. Ecol. Prog. Ser. 294, 241–248 (2005).
Google Scholar
Graham, N. A. J. et al. Changing role of coral reef marine reserves in a warming climate. Nat. Commun. 111(11), 1–8 (2020).
Greene, L. E. The use of discrete group censusing for assessment and monitoring of reef fish assemblages. PhD diss., Florida Institute of Technology, Melbourne (1990).
McClanahan, T. R., Graham, N. A. J., Calnan, J. M. & MacNeil, M. A. Toward pristine biomass: Reef fish recovery in coral reef marine protected areas in Kenya. Ecol. Appl. 17, 1055–1067 (2007).
Google Scholar
McClanahan, T. R. & Humphries, A. T. Differential and slow life-history responses of fishes to coral reef closures. Mar. Ecol. Prog. Ser. 469, 121–131 (2012).
Google Scholar
Kublicki, M. GASPAR general approach to species-abundance relationships in a context of global change, reef fish species as a model (2010).
Froese, R. & Pauly, D. FishBase. World Wide Web Electronic Publication. (2019). Available at: http://www.fishbase.org. Accessed 23 May 2019.
Thorson, J. T., Munch, S. B., Cope, J. M. & Gao, J. Predicting life history parameters for all fishes worldwide. Ecol. Appl. 27, 2262–2276 (2017).
Google Scholar
Rousseeuw, P. et al. Finding Groups in Data: Cluster Analysis Extended Rousseeuw et al. CRAN (Comprehensive R Archive Network (CRAN), 2018).
Paradis, E. et al. Package ‘ape’: Analyses of Phylogenetics and Evolution Depends R. (2019).
Laliberté, E., Legendre, P. & Maintainer, B. S. Package ‘FD’ Type Package Title Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology (2015).
Lavorel, S. et al. Assessing functional diversity in the field—Methodology matters!. Funct. Ecol. 22, 134–147 (2007).
Fontoura, L. et al. Climate-driven shift in coral morphological structure predicts decline of juvenile reef fishes. Glob. Change Biol. 26, 557–567 (2020).
Google Scholar
McClanahan, T. Coral reef fish communities, diversity, and their fisheries and biodiversity status in East Africa. Mar. Ecol. Prog. Ser. 632, 175–191 (2019).
Google Scholar
Selig, E. R., Casey, K. S. & Bruno, J. F. New insights into global patterns of ocean temperature anomalies: Implications for coral reef health and management. Glob. Ecol. Biogeogr. 19, 397–411 (2010).
Ye, H., Deyle, E. R., Gilarranz, L. J. & Sugihara, G. Distinguishing time-delayed causal interactions using convergent cross mapping. Sci. Rep. 5, 14750 (2015).
Google Scholar
Wilson, S. K. et al. Influence of nursery microhabitats on the future abundance of a coral reef fish. Proc. R. Soc. B Biol. Sci. 283, 1–7 (2016).
McClanahan, T. R. Decadal turnover of thermally stressed coral taxa support a risk-spreading approach to marine reserve design. Coral Reefs https://doi.org/10.1007/s00338-020-01984-w (2020).
Google Scholar
Yeager, L. A., Marchand, P., Gill, D. A., Baum, J. K. & McPherson, J. M. Marine socio-environmental covariates: Queryable global layers of environmental and anthropogenic variables for marine ecosystem studies. Ecology 98, 1976 (2017).
Google Scholar
Zuur, A. F., Ieno, E. N., Walker, N. J., Saveliev, A. A. & Smith, G. M. Mixed Effects Models and Extensions in Ecology with R (2009).
Wood, S. N. Generalized Additive Models: An Introduction with R 2nd edn. (CRC Press, 2017).
Google Scholar
Simpson, G. L. Modelling palaeoecological time series using generalised additive models. Front. Ecol. Evol. 6, 149 (2018).
Wood, S. N. Low-rank scale-invariant tensor product smooths for generalized additive mixed models. Biometrics 62, 1025–1036 (2006).
Google Scholar
Pedersen, E. J., Miller, D. L., Simpson, G. L. & Ross, N. Hierarchical generalized additive models in ecology: An introduction with mgcv. PeerJ 2019, e6876 (2019).
Pecuchet, L. et al. From traits to life-history strategies: Deconstructing fish community composition across European seas. Glob. Ecol. Biogeogr. 26, 812–822 (2017).
Dormann, F. et al. Methods to account for spatial autocorrelation in the analysis of species distributional data: A review. Ecography 30, 609–628 (2007).
Schulp, C. J. E., Lautenbach, S. & Verburg, P. H. Quantifying and mapping ecosystem services: Demand and supply of pollination in the European Union. Ecol. Indic. 36, 131–141 (2014).
Warton, D. I. & Hui, F. K. C. The arcsine is asinine: The analysis of proportions in ecology. Ecology 92, 3–10 (2011).
Google Scholar
R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).
MacNeil, M. A. et al. Recovery potential of the world’s coral reef fishes. Nature 520, 341–344 (2015).
Google Scholar
McClanahan, T. R., Ateweberhan, M., Muhando, C. A., Maina, J. & Mohammed, M. S. Effects of climate and seawater temperature variation on coral bleaching and mortality. Ecol. Monogr. 77, 503–525 (2007).
Chirico, A. A. D., McClanahan, T. R. & Eklöf, J. S. Community- and government-managed marine protected areas increase fish size, biomass and potential value. PLoS ONE 12, e0182342 (2017).
Google Scholar
McClanahan, T. R., Friedlander, A. M., Graham, N. A. J., Chabanet, P. & Bruggemann, J. H. Variability in coral reef fish baseline and benchmark biomass in the central and western Indian Ocean provinces. Aquat. Conserv. Mar. Freshw. Ecosyst. https://doi.org/10.1002/aqc.3448 (2020).
Google Scholar
Mbaru, E. K., Graham, N. A. J., McClanahan, T. R. & Cinner, J. E. Functional traits illuminate the selective impacts of different fishing gears on coral reefs. J. Appl. Ecol. https://doi.org/10.1111/1365-2664.13547 (2019).
Google Scholar
Dulvy, N. K., Polunin, N. V. C., Mill, A. C. & Graham, N. A. J. Size structural change in lightly exploited coral reef fish communities: Evidence for weak indirect effects. Can. J. Fish. Aquat. Sci. 61, 466–475 (2004).
D’Agata, S. et al. Marine reserves lag behind wilderness in the conservation of key functional roles. Nat. Commun. 7, 12000 (2016).
Google Scholar
Mbaru, E. K. & McClanahan, T. R. Escape gaps in African basket traps reduce bycatch while increasing body sizes and incomes in a heavily fished reef lagoon. Fish. Res. 148, 90–99 (2013).
Grime, J. P. Benefits of plant diversity to ecosystems: Immediate, filter and founder effects. J. Ecol. 86, 902–910 (1998).
Campbell, S. J. et al. Fishing restrictions and remoteness deliver conservation outcomes for Indonesia’s coral reef fisheries. Conserv. Lett. https://doi.org/10.1111/conl.12698 (2020).
Google Scholar
Heenan, A., Williams, G. J. & Williams, I. D. Natural variation in coral reef trophic structure across environmental gradients. Front. Ecol. Environ. 18, 69–75 (2020).
Morais, R. A. & Bellwood, D. R. Pelagic subsidies underpin fish productivity on a degraded coral reef. Curr. Biol. 29, 1521-1527.e6 (2019).
Google Scholar
González-Rivero, M. et al. Linking fishes to multiple metrics of coral reef structural complexity using three-dimensional technology. Sci. Rep. 7, 1–15 (2017).
Coker, D. J., Graham, N. A. J. & Pratchett, M. S. Interactive effects of live coral and structural complexity on the recruitment of reef fishes. Coral Reefs 31, 919–927 (2012).
Google Scholar
Benkwitt, C. E., Wilson, S. K. & Graham, N. A. J. Seabird nutrient subsidies alter patterns of algal abundance and fish biomass on coral reefs following a bleaching event. Glob. Change Biol. 25, 2619–2632 (2019).
Google Scholar
Russ, G. R., Aller-Rojas, O. D., Rizzari, J. R. & Alcala, A. C. Off-reef planktivorous reef fishes respond positively to decadal-scale no-take marine reserve protection and negatively to benthic habitat change. Mar. Ecol. 38, e12442 (2017).
Google Scholar
Darling, E. S., McClanahan, T. R. & Côté, I. M. Life histories predict coral community disassembly under multiple stressors. Glob. Change Biol. 19, 1930–1940 (2013).
Google Scholar
Strain, E. M. A. et al. A global assessment of the direct and indirect benefits of marine protected areas for coral reef conservation. Divers. Distrib. 25, 9–20 (2019).
Floeter, S. R., Bender, M. G., Siqueira, A. C. & Cowman, P. F. Phylogenetic perspectives on reef fish functional traits. Biol. Rev. 93, 131–151 (2018).
Google Scholar
Michael, P. J., Hyndes, G. A., Vanderklift, M. A. & Vergés, A. Identity and behaviour of herbivorous fish influence large-scale spatial patterns of macroalgal herbivory in a coral reef. Mar. Ecol. Prog. Ser. 482, 227–240 (2013).
Google Scholar
Paijmans, K. C., Booth, D. J. & Wong, M. Y. L. Predation avoidance and foraging efficiency contribute to mixed-species shoaling by tropical and temperate fishes. J. Fish Biol. 96, 806–814 (2020).
Google Scholar
White, J. W. & Warner, R. R. Behavioral and energetic costs of group membership in a coral reef fish. Oecologia 154, 423–433 (2007).
Google Scholar
van Kooten, T., Persson, L. & de Roos, A. M. Population dynamical consequences of gregariousness in a size-structured consumer-resource interaction. J. Theor. Biol. 245, 763–774 (2007).
Google Scholar
Kelley, J. L., Grierson, P. F., Collin, S. P. & Davies, P. M. Habitat disruption and the identification and management of functional trait changes. Fish Fish. 19, 716–728 (2018).
Rochet, M. Short-term effects of fishing on life history traits of fishes. ICES J. Mar. Sci. 55, 371–391 (1998).
McClanahan, T. R. et al. Global baselines and benchmarks for fish biomass: Comparing remote reefs and fisheries closures. Mar. Ecol. Prog. Ser. https://doi.org/10.3354/meps12874 (2019).
Google Scholar
Jacob, U. et al. The role of body size in complex food webs: A cold case. Adv. Ecol. Res. 45, 181–223 (2011).
McClanahan, T. R. & Graham, N. A. J. Marine reserve recovery rates towards a baseline are slower for reef fish community life histories than biomass. Proc. Biol. Sci. 282, 20151938 (2015).
Google Scholar
Humphries, A. T. Algal turf consumption by sea urchins and fishes is mediated by fisheries management on coral reefs in Kenya. Coral Reefs https://doi.org/10.1007/s00338-020-01943-5 (2020).
Google Scholar
Ward, T. J., Heinemann, D. & Evans, N. The role of marine reserves as fisheries management tools. A review of concepts, evidence and international experience. Bur. Rural Sci. Aust. 192, 105 (2001).
Bergseth, B. J., Williamson, D. H., Russ, G. R., Sutton, S. G. & Cinner, J. E. A social-ecological approach to assessing and managing poaching by recreational fishers. Front. Ecol. Environ. 15, 67–73 (2017).
McClanahan, T. R. Recovery of functional groups and trophic relationships in tropical fisheries closures. Mar. Ecol. Prog. Ser. 497, 13–23 (2014).
Google Scholar
Mcclanahan, T. R. & Omukoto, J. O. Comparison of modern and historical fish catches (AD 750–1400) to inform goals for marine protected areas and sustainable fisheries. Conserv. Biol. 25, 945–955 (2011).
Google Scholar
Williams, G. J. & Graham, N. A. J. Rethinking coral reef functional futures. Funct. Ecol. 33, 942–947 (2019).
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