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Mapping Coral Reef Resilience Indicators Using Field and Remotely Sensed Data

DOI: 10.3390/rs5031311

Keywords: coral reefs, resilience, spatial prediction, mapping, random forest, universal kriging, Fiji

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In the face of increasing climate-related impacts on coral reefs, the integration of ecosystem resilience into marine conservation planning has become a priority. One strategy, including resilient areas in marine protected area (MPA) networks, relies on information on the spatial distribution of resilience. We assess the ability to model and map six indicators of coral reef resilience—stress-tolerant coral taxa, coral generic diversity, fish herbivore biomass, fish herbivore functional group richness, density of juvenile corals and the cover of live coral and crustose coralline algae. We use high spatial resolution satellite data to derive environmental predictors and use these in random forest models, with field observations, to predict resilience indicator values at unsampled locations. Predictions are compared with those obtained from universal kriging and from a baseline model. Prediction errors are estimated using cross-validation, and the ability to map each resilience indicator is quantified as the percentage reduction in prediction error compared to the baseline model. Results are most promising (percentage reduction = 18.3%) for mapping the cover of live coral and crustose coralline algae and least promising (percentage reduction = 0%) for coral diversity. Our study has demonstrated one approach to map indicators of coral reef resilience. In the context of MPA network planning, the potential to consider reef resilience in addition to habitat and feature representation in decision-support software now exists, allowing planners to integrate aspects of reef resilience in MPA network development.


[1]  Hughes, T.; Baird, A.; Bellwood, D.; Card, M.; Connolly, S.; Folke, C.; Grosberg, R.; Hoegh-Guldberg, O.; Jackson, J.; Kleypas, J.; et al. Climate change, human impacts, and the resilience of coral reefs. Science 2003, 301, 929–933.
[2]  Hoegh-Guldberg, O. Climate change, coral bleaching and the future of the World’s Coral Reefs. Mar. Freshwater Res 1999, 50, 839–866.
[3]  Hoegh-Guldberg, O.; Mumby, P.; Hooten, A.; Steneck, R.; Greenfield, P.; Gomez, E.; Harvell, C.; Sale, P.; Edwards, A.; Caldeira, K.; et al. Coral reefs under rapid climate change and ocean acidification. Science 2007, 318, 1737–1742.
[4]  Kleypas, J.A.; Yates, K.K. Coral reefs and ocean acidification. Oceanography 2009, 22, 108–117.
[5]  Marshall, P.; Shuttenberg, H. A Reef Manager’s Guide to Coral Bleaching; Great Barrier Reef Marine Park Authority: Townsville, Australia, 2006; p. 178.
[6]  McLeod, E.; Salm, R.; Green, A.; Almany, J. Designing marine protected area networks to address the impacts of climate change. Front. Ecol. Environ 2009, 7, 362–370.
[7]  Obura, D.O.; Grimsditch, G. Resilience Assessment of Coral Reefs—Assessment Protocol for Coral Reefs, Focusing on Coral Bleaching and Thermal Stress; IUCN working group on Climate Change and Coral Reefs, IUCN: Gland, Switzerland, 2009; p. 70.
[8]  West, J.; Salm, R. Resistance and resilience to coral bleaching: Implications for coral reef conservation and management. Conserv. Biol 2003, 17, 956–967.
[9]  Pimm, S.L. The complexity and stability of ecosystems. Nature 1984, 307, 321–326.
[10]  Maina, J.; McClanahan, T.R.; Venus, V.; Ateweberhan, M.; Madin, J. Global gradients of coral exposure to environmental stresses and implications for local management. PLoS ONE 2011, doi:10.1371/journal.pone.0023064.
[11]  Maina, J.; Venus, V.; McClanahan, M.R.; Ateweberhan, M. Modelling susceptibility of coral reefs to environmental stress using remote sensing data and GIS models. Ecol. Model 2008, 212, 180–199.
[12]  Purkis, S.J.; Kohler, K.E.; Riegl, B.M.; Rohmann, S.O. The statistics of natural shapes in modern coral reef landscapes. J. Geol 2007, 115, 493–508.
[13]  Cohen, P.J.; Foale, S.J. Sustaining small-scale fisheries with periodically harvested marine reserves. Mar. Policy 2012, 37, 278–287.
[14]  Govan, H. Status and Potential of Locally-Managed Marine Areas in the South Pacific: Meeting Nature Conservation and Sustainable Livelihood Targets through Wide-Spread Implementation of LMMAS; University Library of Munich: Munich, Germany, 2009; p. 95.
[15]  Rowlands, G.; Purkis, S.; Riegl, B.; Metsamaa, L.; Bruckner, A.; Renaud, P. Satellite imaging coral reef resilience at regional scale. A case-study from Saudi Arabia. Mar. Pollut. Bull 2012, 64, 1222–1237.
[16]  Holling, C.S. Resilience and stability of ecological systems. Annu. Rev. Ecol. Syst 1973, 41, 1–23.
[17]  Nystrom, M.; Graham, N.A.J.; Lokrantz, J.; Norstrom, A.V. Capturing the cornerstones of coral reef resilience: Linking theory to practice. Coral Reefs 2008, 27, 795–809.
[18]  McClanahan, T.; Donner, S.; Maynard, J.; MacNeil, A.; Graham, N.; Maina, J.; Baker, A.; Alemu, J.; Beger, M.; Campbell, S.; et al. Prioritizing key resilience indicators to support coral reef management in a changing climate. PLoS ONE, 2012, doi:10.1371/journal.pone.0042884.
[19]  Vermeij, M.J.A.; Smith, J.E.; Smith, C.M.; Thurber, R.V.; Sandin, S.A. Survival and settlement success of coral planulae: Independent and synergistic effects of macroalgae and microbes. Oecologia 2009, 159, 325–336.
[20]  Ball, I.R.; Watts, M.E.; Possingham, H.P. Marxan and Relatives: Software for Spatial Conservation Prioritisation. In Spatial Conservation Prioritization: Quantitative Methods and Computational Tools; Moilanen, A., Wilson, K.A., Possingham, H., Eds.; Oxford University Press: New York, NY, USA, 2009; pp. 185–195.
[21]  Hochberg, E.; Atkinson, M.; Andréfou?t, S. Spectral reflectance of coral reef bottom-types worldwide and implications for coral reef remote sensing. Remote Sens. Environ 2003, 85, 159–173.
[22]  Purkis, S.; Myint, S.; Riegl, B. Enhanced detection of the coral acropora cervicornis from satellite imagery using a textural operator. Remote Sens. Environ 2006, 101, 82–94.
[23]  Mumby, P. Beta and habitat diversity in marine systems: A new approach to measurement, scaling and interpretation. Oecologia 2001, 128, 274–280.
[24]  Harborne, A.R.; Mumby, P.J.; Zychaluk, K.; Hedley, J.D.; Blackwell, P.G. Modeling the beta diversity of coral reefs. Ecology 2006, 87, 2871–2881.
[25]  LeDrew, E.F.; Holden, H.; Wulder, M.A.; Derksen, C.; Newman, C. A spatial statistical operator applied to multidate satellite imagery for identification of coral reef stress. Remote Sens. Environ 2004, 91, 271–279.
[26]  McClanahan, T.R.; Ateweberhan, M.; Sebastian, C.R.; Graham, N.A.J.; Wilson, S.K.; Bruggemann, J.H.; Guillaume, M.M.M. Predictability of coral bleaching from synoptic satellite and in situ temperature observations. Coral Reefs 2007, 26, 695–701.
[27]  Morel, A.; Prieur, L. Analysis of variations in ocean color. Limnol. Oceanogr 1977, 22, 709–722.
[28]  Moses, W.J.; Gitelson, A.A.; Berdnikov, S.; Povazhnyy, V. Estimation of chlorophyll-a concentration in case II waters using MODIS and MERIS data—Successes and challenges. Environ. Res. Lett. 2009, doi:10.1088/1748-9326/4/4/045005.
[29]  Ouillon, S.; Douillet, P.; Petrenko, A.; Neveux, J.; Dupouy, C.; Froidefond, J.; Andréfou?t, S.; Munoz-Caravaca, A. Optical algorithms at satellite wavelengths for total suspended matter in tropical coastal waters. Sensors 2008, 8, 4165–4185.
[30]  Purkis, S.J.; Graham, N.A.J.; Riegl, B.M. Predictability of reef fish diversity and abundance using remote sensing data in Diego Garcia (Chagos Archipelago). Coral Reefs 2008, 27, 167–178.
[31]  Pittman, S.J.; Costa, B.M.; Battista, T.A. Using lidar bathymetry and boosted regression trees to predict the diversity and abundance of fish and corals. J. Coast. Res 2009, 25, 27–38.
[32]  Jupiter, S.; Roelfsema, C.; Phinn, S. Science and Management. Goodman, J.A., Phinn, S., Purkis, S., Eds.; Springer-Verlag, 2013. in press..
[33]  Bahuguna, A.; Nayak, S.; Roy, D. Impact of the tsunami and earthquake of 26th December 2004 on the Vital Coastal Ecosystems of the Andaman and Nicobar Islands assessed using RESOURCESAT AWiFS Data. Int. J. Appl. Earth Obs. Geoinf 2008, 10, 229–237.
[34]  Mumby, P.J.; Vitolo, R.; Stephenson, D.B. Temporal clustering of tropical cyclones and its ecosystem impacts. Proc. Natl. Acad. Sci. USA 2011, 108, 17626–17630.
[35]  Puotinen, M.L. Modelling the risk of cyclone wave damage to coral reefs using GIS: A case study of the great barrier reef, 1969–2003. Int. J. Geogr. Inf. Sci 2007, 21, 97–120.
[36]  Heron, S.F.; Willis, B.L.; Skirving, W.J.; Eakin, C.M.; Page, C.A.; Miller, I.R. Summer hot snaps and winter conditions: Modelling white syndrome outbreaks on Great Barrier reef corals. PLoS ONE, 2010, doi:10.1371/journal.pone.0012210.
[37]  Mumby, P.; Green, E.; Edwards, A.; Clark, C. Coral reef habitat-mapping: How much detail can remote sensing provide? Mar. Biol 1997, 130, 193–202.
[38]  Zainal, A.J.M. New technique for enhancing the detection and classification of shallow marine habitats. Mar. Technol. Soc. J 1994, 28, 68–77.
[39]  Crabbe, M.J.C. Environmental effects on coral growth and recruitment in the Caribbean. J. Mar. Biol. Assn. UK 2012, 92, 747–752.
[40]  Fabricius, K.; Wild, C.; Wolanski, E.; Abele, D. Effects of transparent exopolymer particles and muddy terrigenous sediments on the survival of hard coral recruits. Estuar. Coast. Shelf. Sci 2003, 57, 613–621.
[41]  Van Woesik, R.; Tomascik, T.; Blake, S. Coral assemblages and physico-chemical characteristics of the Whitsunday Islands: Evidence of recent community changes. Mar. Freshw. Res 1999, 50, 427–440.
[42]  Mumby, P.; Dahlgren, C.; Harborne, A.; Kappel, C.; Micheli, F.; Brumbaugh, D.; Holmes, K.; Mendes, J.; Broad, K.; Sanchirico, J.; et al. Fishing, trophic cascades, and the process of grazing on coral reefs. Science 2006, 311, 98–101.
[43]  Norstrom, A.V.; Lokrantz, J.; Nystrom, M.; Yap, H.T. Influence of dead coral substrate morphology on patterns of juvenile coral distribution. Mar. Biol 2007, 150, 1145–1152.
[44]  Harrington, L.; Fabricius, K.; De’Ath, G.; Negri, A. Recognition and selection of settlement substrata determine post-settlement survival in corals. Ecology 2004, 85, 3428–3437.
[45]  O’Leary, J.K.; Potts, D.C.; Braga, J.C.; McClanahan, T.R. Indirect consequences of fishing: Reduction of coralline algae suppresses juvenile coral abundance. Coral Reefs 2012, 31, 547–559.
[46]  Mumby, P.; Hedley, J.; Chisholm, J.; Clark, C.; Ripley, H.; Jaubert, J. The cover of living and dead corals from airborne remote sensing. Coral Reefs 2004, 23, 171–183.
[47]  Knudby, A.; Roelfsema, C.; Lyons, M.; Phinn, S.; Jupiter, S. Mapping fish community variables by integrating field and satellite data, object-based image analysis and modeling in a traditional Fijian fisheries management area. Remote Sens 2011, 3, 460–483.
[48]  Cheal, A.J.; Emslie, M.; MacNeil, M.A.; Miller, I.; Sweatman, H. Spatial variation in the functional characteristics of herbivorous fish communities and the resilience of coral reefs. Ecol. Appl 2013, 23, 174–188.
[49]  Bellwood, D.; Hughes, T.; Folke, C.; Nystrom, M. Confronting the coral reef crisis. Nature 2004, 429, 827–833.
[50]  Mumby, P.J.; Hastings, A.; Edwards, H.J. Thresholds and the resilience of Caribbean coral reefs. Nature 2007, 450, 98–101.
[51]  Bellwood, D.R.; Hughes, T.P.; Hoey, A.S. Sleeping functional group drives coral-reef recovery. Curr. Biol 2006, 16, 2434–2439.
[52]  Kaufman, L.; Sandin, S.; Sala, E.; Obura, D.; Rohwer, F.; Tschirky, T. Coral Health Index: Measuring Coral Community Health; Conservation International: Arlington, VA, USA, 2011; p. 16.
[53]  Hughes, T.P.; Graham, N.A.J.; Jackson, J.B.C.; Mumby, P.J.; Steneck, R.S. Rising to the challenge of sustaining coral reef resilience. Trends Ecol. Evol 2010, 25, 633–642.
[54]  Rasher, D.B.; Hay, M.E. Chemically rich seaweeds poison corals when not controlled by herbivores. Proc. Natl. Acad. Sci. USA 2010, 107, 9683–9688.
[55]  Heyward, A.; Negri, A. Natural inducers for coral larval metamorphosis. Coral Reefs 1999, 18, 273–279.
[56]  Clarke, P.; Jupiter, S.D. Law, custom and community-based natural resource management in Kubulau District (Fiji). Environ. Conserv 2010, 37, 98–106.
[57]  Jupiter, S.; Egli, D. Ecosystem-based management in Fiji: Successes and challenges after five years of implementation. J. Mar. Biol., 2011, doi:10.1155/2011/940765.
[58]  Adams, V.M.; Mills, M.; Jupiter, S.D.; Pressey, R.L. Improving social acceptability of marine protected area networks: A method for estimating opportunity costs to multiple gear types in both fished and currently unfished areas. Biol. Conserv 2011, 144, 350–361.
[59]  Green, A.; Bellwood, D.R. Monitoring Functional Groups of Herbivorous Reef Fishes as Indicators of Coral Reef Resilience: A Practical guide for Coral Reef Managers in the Asia Pacific Region; IUCN: Gland, Switzerland, 2009; p. 70.
[60]  Froese, R.; Pauly, D. Fishbase, Available online: (accessed on 12 January 2009).
[61]  WCS. WCS-Fiji Marine Biological Monitoring Protocol; Wildlife Conservation Society: Suva, Fiji, 2010; p. 50.
[62]  Loya, Y.; Sakai, K.; Yamazato, K.; Nakano, Y.; Sambali, H.; van Woesik, R. Coral bleaching: The winners and the losers. Ecol. Lett 2001, 4, 122–131.
[63]  Marshall, P.; Baird, A. Bleaching of corals on the great barrier reef: Differential susceptibilities among Taxa. Coral Reefs 2000, 19, 155–163.
[64]  McClanahan, T.R.; Ateweberhan, M.; Graham, N.A.J.; Wilson, S.K.; Sebastian, C.R.; Guillaume, M.M.M.; Bruggemann, J.H. Western Indian Ocean coral communities: Bleaching responses and susceptibility to extinction. Mar. Ecol. Prog. Ser 2007, 337, 1–13.
[65]  Blaschke, T. Object based image analysis for remote sensing. ISPRS J. Photogramm 2010, 65, 2–16.
[66]  Lyzenga, D.R. Passive remote-sensing techniques for mapping water depth and bottom features. Appl. Opt 1978, 17, 379–383.
[67]  Knudby, A.; LeDrew, E.; Brenning, A. Predictive mapping of reef fish species richness, diversity and biomass in Zanzibar using IKONOS imagery and machine-learning techniques. Remote Sens. Environ 2010, 114, 1230–1241.
[68]  Mills, M.; Jupiter, S.D.; Pressey, R.L.; Ban, N.C.; Comley, J. Incorporating effectiveness of community-based management in a national marine gap analysis for Fiji. Conserv. Biol 2011, 25, 1155–1164.
[69]  Breiman, L. Random forests. Mach. Learn 2001, 45, 5–32.
[70]  Krige, D.G. A Statistical Approach to Some Mine Valuations and Allied Problems at the Witswatersrand; University of Witswatersrand: Johannesburg, South Africa, 1951.
[71]  Knudby, A.; Brenning, A.; LeDrew, E. New approaches to modelling fish-habitat relationships. Ecol. Model 2010, 221, 503–511.
[72]  Breiman, L.; Friedman, J.; Stone, C.J.; Olshen, R.A. Classification and Regression Trees; Chapman & Hall/CRC: Boca Raton, FL, USA, 1984; p. 358.
[73]  R Core Development Team. R: A Language and Environment for Statistical Computing. Version 2.15; R Foundation for Statistical Computing: Vienna, Austria, 2012.
[74]  Liaw, A.; Wiener, M. Classification and regression with randomForest. R News 2002, 2, 18–22.
[75]  Goovaerts, P. Geostatistics for Natural Resource Evaluation; Oxford University Press: Oxford, UK, 1997; p. 496.
[76]  Pebesma, E. Multivariable geostatistics in S: The gstat package. Comput. Geosci 2004, 30, 683–691.
[77]  Hiemstra, P.H.; Pebesma, E.J.; Twenhofel, C.J.W.; Heuvelink, G.B.M. Real-time automatic interpolation of ambient gamma dose rates from the dutch radioactivity monitoring network. Comput. Geosci 2009, 35, 1711–1721.
[78]  Efron, B.; Tibshirani, R. An Introduction to the Bootstrap; Chapman & Hall: New York, NY, USA, 1993; p. 225.
[79]  Efron, B.; Gong, G. A leisurely look at the bootstrap, the jackknife, and cross-validation. Am. Stat 1983, 37, 36–48.
[80]  Adam, T.C.; Schmitt, R.J.; Holbrook, S.J.; Brooks, A.J.; Edmunds, P.J.; Carpenter, R.C.; Bernardi, G. Herbivory, Connectivity, and ecosystem resilience: Response of a coral reef to a large-scale perturbation. PLoS ONE 2011, doi:10.1371/journal.pone.0023717.
[81]  Dinesen, Z.D. Shade-dwelling corals of the great barrier-reef. Mar. Ecol. Prog. Ser 1983, 10, 173–185.
[82]  Rasher, D.B.; Hoey, A.S.; Hay, M.E. Consumer diversity interacts with prey defenses to drive ecosystem function. Ecology, 2013.
[83]  Cowen, R.; Lwiza, K.; Sponaugle, S.; Paris, C.; Olson, D. Connectivity of marine populations: Open or closed? Science 2000, 287, 857–859.
[84]  Roberts, C. Connectivity and management of caribbean coral reefs. Science 1997, 278, 1454–1457.
[85]  Newman, C.M.; Knudby, A.J.; LeDrew, E.F. Assessing the effect of management zonation on live coral cover using multi-date IKONOS satellite imagery. J. Appl. Remote Sens. 2007, doi:10.1117/1.2822612.
[86]  Isoun, E.; Fletcher, C.; Frazer, N.; Gradie, J. Multi-spectral mapping of reef bathymetry and coral cover; Kailua Bay, Hawaii. Coral Reefs 2003, 22, 68–82.
[87]  McClanahan, T.R.; Graham, N.A.J.; Maina, J.; Chabanet, P.; Bruggemann, J.H.; Polunin, N.V.C. Influence of instantaneous variation on estimates of coral reef fish populations and communities. Mar. Ecol. Prog. Ser 2007, 340, 221–234.
[88]  Andutta, F.P.; Kingsford, M.J.; Wolanski, E. ‘Sticky Water’ enables the retention of larvae in a reef mosaic. Estuar. Coast. Shelf Sci 2012, 101, 54–63.
[89]  Mallela, J.; Crabbe, M.J.C. Hurricanes and coral bleaching linked to changes in coral recruitment in Tobago. Mar. Environ. Res 2009, 68, 158–162.
[90]  O’Leary, J.K.; Potts, D.C. Using hierarchical sampling to understand scales of spatial variation in early coral recruitment. Coral Reefs 2011, 30, 1013–1023.
[91]  Connell, J.; Hughes, T.; Wallace, C.; Tanner, J.; Harms, K.; Kerr, A. A long-term study of competition and diversity of corals. Ecol. Monogr 2004, 74, 179–210.
[92]  Done, T.J.; DeVantier, L.M.; Turak, E.; Fisk, D.A.; Wakeford, M.; van Woesik, R. Coral growth on three reefs: Development of recovery benchmarks using a space for time approach. Coral Reefs 2010, 29, 815–833.
[93]  De Vantier, L.M.; De’ath, G.; Turak, E.; Done, T.J.; Fabricius, K.E. Species richness and community structure of reef-building corals on the nearshore great barrier reef. Coral Reefs 2006, 25, 329–340.
[94]  Tulloch-McShane, V.J.D. Designing Robust Marine Reserves Using Uncertain Habitat Information; University of Queensland: Brisbane, Australia, 2012.
[95]  Roelfsema, C.; Phinn, S. Integrating field data with high spatial resolution multispectral satellite imagery for calibration and validation of coral reef benthic community maps. J. Appl. Remote Sens. 2010, doi:10.1117/1.3430107.
[96]  Wedding, L.M.; Friedlander, A.M.; McGranaghan, M.; Yost, R.S.; Monaco, M.E. Using bathymetric lidar to define nearshore benthic habitat complexity: implications for management of reef fish assemblages in Hawaii. Remote Sens. Environ 2008, 112, 4159–4165.
[97]  GeoEye. GeoEye Product Specifications, Available online: (accessed on 28 July 2012).
[98]  Digital Globe. Digitalglobe Basic Satellite Imagery Specifications, Available online: (accessed on 28 July 2012).
[99]  Connell, J. Diversity in tropical rain forests and coral reefs—High diversity of trees and corals is maintained only in a non-equilibrium state. Science 1978, 199, 1302–1310.
[100]  Connell, J.; Hughes, T.; Wallace, C. A 30-year study of coral abundance, recruitment, and disturbance at several scales in space and time. Ecol. Monogr 1997, 67, 461–488.
[101]  Done, T.; Turak, E.; Wakeford, M.; DeVantier, L.; McDonald, A.; Fisk, D. Decadal changes in turbid-water coral communities at Pandora Reef: Loss of resilience or too soon to tell? Coral Reefs 2007, 26, 789–805.
[102]  Done, T.J. Patterns in the distribution of coral communities across the central great barrier reef. Coral Reefs 1982, 1, 95–107.
[103]  Hengl, T.; Heuvelink, G.; Stein, A. A generic framework for spatial prediction of soil variables based on regression-kriging. Geoderma 2004, 120, 75–93.
[104]  Andréfou?t, S.; Muller-Krager, F.E.; Robinson, J.A. Millennium Coral Reef Landsat Archive, Available online: (accessed on 14 August 2012).
[105]  Phinn, S.; Roelfsema, C.; Stumpf, R. Remote Sensing: Discerning the Promise from the Reality. In Integrating and Applying Science: A Handbook for Effective Coastal Ecosystem Assessment; Longstaff, B.J., Carruthers, T.J.B., Dennison, W.C., Lookingbill, T.R., Hawkey, J.M., Thomas, J.F., Wicks, E.C., Woerner, J., Eds.; IAN Press: Cambridge, MD, USA, 2010; pp. 201–222.
[106]  Maynard, J.A.; Marshall, P.A.; Johnson, J.E.; Harman, S. Building resilience into practical conservation: Identifying local management responses to global climate change in the Southern Great Barrier Reef. Coral Reefs 2010, 29, 381–391.


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