Biodiversity and Conservation

, Volume 21, Issue 1, pp 115–130 | Cite as

Predicting spatially explicit coral reef fish abundance, richness and Shannon–Weaver index from habitat characteristics

  • Jesús Ernesto Arias-González
  • Gilberto Acosta-González
  • Néstor Membrillo
  • Joaquín Rodrigo Garza-Pérez
  • José Manuel Castro-Pérez
Original Paper


The assessment of biodiversity in coral reefs requires the application of geographic information systems (GIS), remote sensing and analytical tools in order to make cost-effective spatially explicit predictions of biodiversity over large geographic areas. Here we present a spatially explicit prediction for coral reef fish diversity index, as well as habitat classification according to reef fish diversity index values in Chinchorro Bank Biosphere Reserve, one of the most important plain/atoll type reef systems in the Caribbean. We have used extensive ecological data on depth, fish and habitat characteristics to perform such prediction. Fish species assemblages and different biotic variables of benthic organisms were characterized using visual censuses and video-transects, respectively at 119 sampling stations. The information was integrated in a GIS, along with satellite imagery (LANSDAT 7 ETM+) and a digital bathymetric model. From the recorded data and a hierarchical classification procedure, we obtained nine different classes of habitats. We used a generalized regression analysis and spatial prediction methodology to create predictive maps (GIS layers) of the different reef benthic components, and a second modeling run produced predictive maps of coral reef fish diversity index. Predictive accuracy of the diversity index map presented a good correlation coefficient (r = 0.87), with maximum diversity index values en reefscapes composed of aggregation of coral colonies with seagrass beds. The implementation of our application was successful for the prediction of fish diversity hot spots and surrogate habitats.


Diversity Caribbean Coral reefs Chinchorro Bank Fish Mexico GRASP Proxies Reefscape Spatial prediction 



Biodiversity spatially explicit predictions


Broad-functional groups


Classification and regression trees


Chinchorro Bank Biosphere Reserve


Digital bathymetric model


Generalized additive models


Geographic information systems


Generalized linear models


Generalized additive models and spatial prediction


Morpho-structural groups


Response variables


Predictive variables


  1. Almany GR (2004) Does increased habitat complexity reduce predation and competition in coral reef fish assemblages? Oikos 106:275–284CrossRefGoogle Scholar
  2. Arias-González JE, Done TJ, Page CA, Cheal A, Kininmonth S, Garza-Pérez JR (2006) Towards a reefscape ecology: relating biomass and trophic structure of fish assemblages to habitat at Davies Reef, Australia. Mar Ecol Prog Ser 320:29–41CrossRefGoogle Scholar
  3. Arias-González JE, Legendre P, Rodriguez-Zaragoza FA (2008) Scaling up beta diversity on Caribbean coral reefs. J Exp Mar Biol Ecol 366:28–36CrossRefGoogle Scholar
  4. Arias-González JE, Rodriguez-Zaragoza FA, Nuñez-Lara E, Legendre P (2011) Reefscape proxies for the conservation of Caribbean coral reef biodiversity. Ciencias Marinas 37:87–96Google Scholar
  5. Bellwood DR, Hughes TP (2001) Regional-scale assembly rules and biodiversity of coral reefs. Science 292:1532–1534PubMedCrossRefGoogle Scholar
  6. Bouchon-Navaro Y, Bouchon C, Louis M, Legendre P (2005) Biogeographic patterns of coastal fish assemblages in the West Indies. J Exp Mar Biol Ecol 315:31–47CrossRefGoogle Scholar
  7. Carpenter KE, Abrar M, Aeby G, Aronson BR, Banks S, Bruckner A, Chiriboga A, Cortés J, ChJ Delbeek, DeVantier L, Edgar JG, Edwards JA, Fenner D, Guzmán MH, Hoeksema WB, Hodgson G, Johan O, Licuanan YW, Livingstone RS, Lovell RE, Moore AJ, Obura OD, Ochavillo D, Polidoro, William F, Precht, Miledel C, Quibilan, Reboton C, Richards ZT, Rogers ABAD, Sanciangco J, Sheppard A, Sheppard Ch, Smith J, Stuart S, Turak E, Veron ENJ, Wallace C, Weil E, Wood E (2008) One-third of reef-building corals face elevated extinction risk from climate change and local impacts. Science 321:560–563PubMedCrossRefGoogle Scholar
  8. Cleveland WS, Delvin SJ (1988) Locally weighted regression: an approach to regression analysis by local fitting. J Am Stat Ass 83:596–610CrossRefGoogle Scholar
  9. Ferrier S, Drielsma M, Manion G, Watson G (2002) Extended statistical approaches to modelling spatial pattern in biodiversity in northeast New South Wales II. Community-level modelling. Biodivers Conserv 11:2309–2338CrossRefGoogle Scholar
  10. Friedlander AM, Parish JD (1998) Habitat characteristics affecting fish assemblages on a Hawaiian coral reef. J Exp Mar Biol Ecol 224:1–30CrossRefGoogle Scholar
  11. García-Gil G, Padilla-Saldivar J, Carricart-Ganivet JP, Arias-González JE (2003) Bathymetric chart (1:70, 000) of Chinchorro Bank, Mexican Caribbean. Bull Mar Sci 73:249Google Scholar
  12. Gardner T, Côté IM, Gill JA, Grant A, Watkinson AR (2003) Long-term region-wide declines in Caribbean corals. Science 301:958–960PubMedCrossRefGoogle Scholar
  13. Garza-Pérez JR, Lehmann A, Arias-González JE (2004) Spatial prediction of coral reef habitats: integrating ecology with spatial modeling and remote sensing. Mar Ecol Prog Series 269:241–252CrossRefGoogle Scholar
  14. Gratwicke B, Speight MR (2005) Effects of habitat complexity on Caribbean marine fish assemblages. Mar Ecol Prog Ser 292:301–310CrossRefGoogle Scholar
  15. Grober-Dunsmore R, Frazer TK, Lindberg WJ, Beets JP (2007) Reef fish and habitat relationships in a Caribbean seascape: the importance of reef context. Coral Reefs 26:201–216CrossRefGoogle Scholar
  16. Grober-Dunsmore R, Frazer TK, Beets JP, Lindberg WJ, Zwick P, Funicelli A (2008) Influence of landscape structure on reef fish assemblages. Landscape Ecol 23:37–53CrossRefGoogle Scholar
  17. Harborne AR, Mumby PJ, Zychaluk K, Hedley JD, Blackwell PG (2006) Modeling the beta diversity of coral reefs. Ecology 87:28712881CrossRefGoogle Scholar
  18. Hazin H, Erzinib K (2008) Assessing swordfish distribution in the South Atlantic from spatial predictions. Fish Res 90:45–55CrossRefGoogle Scholar
  19. Hoegh-Guldberg O, Mumby PJ, Hooten AJ, Steneck RS, Greenfield P, Gomez E, Harvell CD, Sale PF, Edwards AJ, Caldeira K, Knowlton N, Eakin CM, Iglesias-Prieto R, Muthiga N, Bradbury RH, Dubi A, Hatziolos ME (2007) Coral reefs under rapid climate change and ocean acidification. Science 318:1737–1742PubMedCrossRefGoogle Scholar
  20. Hughes TP (1994) Catastrophes, phase shifts, and large-scale degradation of a Caribbean coral reef. Science 265:1547–1551PubMedCrossRefGoogle Scholar
  21. Hughes A, Baird H, Bellwood DR, Card M, Connolly SR, Folke C, Grosberg R, Hoegh-Guldberg O, Jackson JBC, Kleypas J, Lough JM, Marshall P, Nyström M, Palumbi SR, Pandolfi JM, Rosen B, Roughgarden J (2003) Climate change, human impacts, and the resilience of coral reefs. Science 301:929–933PubMedCrossRefGoogle Scholar
  22. Jones GP, Syms C (1998) Disturbance, habitat structure and the ecology of fishes on coral reefs. Aust J Ecol 23:287–297CrossRefGoogle Scholar
  23. Jones GP, McCormick MI, Srinivasan M, Eagle JV (2004) Coral decline threatens biodiversity in marine reserves. Proc Nat Acad Sci USA 101:8251–8253PubMedCrossRefGoogle Scholar
  24. Jost L (2007) Partitioning diversity into independent alpha and beta components. Ecology 88:2427–2439PubMedCrossRefGoogle Scholar
  25. Knudby A, LeDrew E, Newman C (2007) Progress in the use of remote sensing for coral reef biodiversity studies. Prog Phys Geogr 31:421–434CrossRefGoogle Scholar
  26. Knudby A, LeDrew E, Brenning A (2010) Predictive mapping of reef fish species richness, diversity and biomass in Zanzibar using IKONOS imagery and machine-learning techniques. Remote Sensing Environ 114:1230–1241CrossRefGoogle Scholar
  27. Lapointe BE (1997) Nutrient thresholds for bottom-up control of macroalgal blooms on coral reefs in Jamaica and southeast Florida. Limnol Oceanogr 42:1119–1131CrossRefGoogle Scholar
  28. Lehmann A, Overton JMC, Leathwick JR (2002a) GRASP: generalized regression analysis and spatial predictions. Ecol Model 157:189–207CrossRefGoogle Scholar
  29. Lehmann A, Overton JMcC, Austin MP (2002b) Regression models for spatial prediction: their role for biodiversity and conservation. Biodivers Conser 11:2085–2092CrossRefGoogle Scholar
  30. Lizenga D (1978) Passive remote sensing techniques for mapping water depth and bottom features. Appl Opt 17:379–383CrossRefGoogle Scholar
  31. Luckhurst BE, Luckhurst K (1978) Analysis of the influence of substrate variables on coral reef fish communities. Mar Biol 49:317–323CrossRefGoogle Scholar
  32. Maggini R, Lehmann A, Zimmermann NE, Guisan A (2006) Improving generalized regression analysis for the spatial prediction of forest communities. J Biogeogr 33:1729–1749CrossRefGoogle Scholar
  33. Mellin C, Andréfouët S, Ponton D (2007) Spatial predictability of juvenile fish species richness and abundance in a coral reef environment. Coral Reefs 26:895–990CrossRefGoogle Scholar
  34. Mellin C, Bradshaw CJA, Meekan MG, Caley MJ (2010) Environmental and spatial predictors of species richness and abundance in coral reef fishes. Glob Ecol Biogeogr 19:212–222CrossRefGoogle Scholar
  35. Mellin C, Delean S, Caley J, Edgar G, Meekan M, Pitcher R, Przeslawski R, Williams A, Bradshaw C (2011) Effectiveness of biological surrogates for predicting patterns of marine biodiversity: a global meta-analysis. PLoS ONE 6(6): e20141. doi:10.1371/journal.pone.0020141
  36. Mora C (2008) A clear human footprint in the coral reefs of the Caribbean. Proc R Soc B 271:149–155Google Scholar
  37. Moser D, Dullinger S, Englisch T, Niklfeld H, Plutzar C, Sauberer N, Zechmeister HG, Grabherr G (2005) Environmental determinants of vascular plant species richness in the Austrian Alps. J Biogeogr 32:1117–1127CrossRefGoogle Scholar
  38. Mumby PJ, Chisholm JRM, Clark CD, Hedley JD, Jaubert J (2001) A bird’s-eye view of the health of coral reefs. Nature 413:36PubMedCrossRefGoogle Scholar
  39. Mumby PJ, Hastings A, Edwards HJ (2007) Thresholds and the resilience of Caribbean coral reefs. Nature 450:98–101PubMedCrossRefGoogle Scholar
  40. Naeem S, Bunker DE, Hector A, Loreau M, Perrings Ch (2009). Introduction: the ecological and social implications of changing biodiversity. An overview of a decade of biodiversity and ecosystem functioning research. In: Naeem S, Bunker DE, Hector A, Loreau M, Perrings Ch (eds) Biodiversity, ecosistema functioning, and human wellbeing: an ecological and economic perspective. Oxford University Press, Oxford pp 3–13Google Scholar
  41. Núñez-Lara E, Arias-González JE (1998) The relationship between reef fish community structure and environmental variables in the southern Mexican Caribbean. J Fish Biol 53:209–221CrossRefGoogle Scholar
  42. Núñez-Lara E, Arias-González JE, Legendre P (2005) Spatial patterns of Yucatan reef fish communities: testing models using a multi-scale survey design. J Exp Mar Biol Ecol 324:157–169CrossRefGoogle Scholar
  43. Overton JMcC, Stephens RTT, Leathwick JR, Lehmann A (2002) Information pyramids for informed biodiversity conservation. Biodivers Conserv 11:2093–2116CrossRefGoogle Scholar
  44. Paddack MJ, Reynolds JD, Aguilar C, Appeldoorn RS, Beets J, Burkett WE, Chittaro PM, Clarke Kr, Esteves R, Fonseca AC, Forrester EG, Friedlander MA, García-Sais J, González-Sansón G, Jordan KBL, McClellan BD, Miller WM, Molloy PP, Mumby JP, Nagelkerken I, Nemeth M, Navas-Camacho R, Pitt J, Polunin VCN, Reyes-Nivia CM, Robertson RD, Rodríguez-Ramírez A, Salas E, Smith RS, Spieler ER, Steele AM, Williams DI, Wormald LC, Watkinson RA, Côté MI (2009) Recent region-wide declines in Caribbean reef fish abundance. Curr Biol 19:590–595PubMedCrossRefGoogle Scholar
  45. Pandolfi JM, Bradbury RH, Sala E, Hughes TP, Bjorndal KA, Cooke RG, McArdle D, McClenachan L, Newman MJH, Paredes G, Warner RR, Jackson JBC (2003) Global trajectories of the long-term decline of coral reef ecosystems. Science 301:955–958PubMedCrossRefGoogle Scholar
  46. Perrings C, Naeem S, Ahrestani F, Bunker DE, Burkill P, Canziani G, Elmqvist T, Ferrati R, Fuhrman J, Jaksic F, Kawabata Z, Kinzig A, Mace GM, Milano F, Mooney H, Prieur-Richard A-H, Tschirhart J, Weisser W (2010) Ecosystem services for 2020. Science 330:323–324PubMedCrossRefGoogle Scholar
  47. Pittman SJ, Brown KA (2011) Multi-scale approach for predicting fish species distributions across coral reef seascapes. PLoS ONE 6(5): e20583. doi:10.1371/journal.pone.0020583
  48. Pittman SJ, Christensen JD, Caldow C, Menza C, Monaco ME (2007) Predictive mapping of fish species richness across shallow-water seascapes in the Caribbean. Ecol Model 204:9–21CrossRefGoogle Scholar
  49. Pittman SJ, Costa MB, Battista TA (2009) Using lidar bathymetry and boosted regression trees to predict the diversity and abundance of fish and corals. J Coast Res S1:27–38CrossRefGoogle Scholar
  50. Purkis SJ, Graham NAJ, Riegl BM (2007) Predictability of reef fish diversity and abundance using remote sensing data in Diego Garcia (Chagos Archipelago). Coral Reefs 27:16–18Google Scholar
  51. Risk MJ (1972) Fish diversity on a coral reef in the Virgin Islands. Atoll Res Bull 153:1–6Google Scholar
  52. Rossier O, Kulbicki M (2000) A comparison of fish assemblages from two types of algal beds and coral reefs in the south-west lagoon of New Caledonia. Cybium 24:3–26Google Scholar
  53. Wedding L, Friedlander AM, McGranaghan M, Yost R, Monaco M (2008) Using bathymetric LIDAR to define nearshore benthic habitat complexity: implications for management of reef fish assemblages in Hawaii. Remote Sensing Environ 112:4159–4165CrossRefGoogle Scholar
  54. Wilson SK, Graham NAJ, Polunin NVC (2007) Appraisal of visual assessments of habitat complexity and benthic composition on coral reefs. Mar Biol 151:1069–1076CrossRefGoogle Scholar
  55. Worm B, Barbier EB., Beaumont N, Duffy JE, Folke C, Halpern BS, Jackson JBC, Lotze HK, Micheli F, Palumbi SR, Sala E, Selkoe KA, Stachowicz JJ, Watson R. (2006) Services impacts of biodiversity loss on ocean ecosystem. Science 314. doi:10.1126/science.1132294
  56. Yee TW, Mitchell ND (1991) Generalized additive models in plant ecology. J Veg Sci 2:587–602CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Jesús Ernesto Arias-González
    • 1
  • Gilberto Acosta-González
    • 1
  • Néstor Membrillo
    • 1
  • Joaquín Rodrigo Garza-Pérez
    • 2
  • José Manuel Castro-Pérez
    • 3
  1. 1.Laboratorio de Ecología de Ecosistemas de Arrecifes CoralinosCentro de Investigación y Estudios Avanzados del I.P.N-Unidad MéridaMéridaMexico
  2. 2.Unidad Multidisciplinaria de Docencia e Investigación Sisal, Facultad de CienciasUniversidad Nacional Autónoma de MéxicoSisalMexico
  3. 3.Laboratorio de EcologíaInstituto Tecnológico de ChetumalChetumalMexico

Personalised recommendations