Combining environmental gradients to explain and predict the structure of demersal fish distributions

Journal of Biogeography

Volumn 37, Issue 4, 2010, Pages 593-605

  Chatfield, Brenton S ^a,b,c   Van Niel, Kimberly P ^a,b   Kendrick, Gary A ^a,b   Harvey, Euan S ^a,b  

^a UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^b Department of Civil and Environmental Engineering   (Australia)

^c SINCLAIR KNIGHT MERZ   (Australia)

Author keywords

Environmental gradients; Fish distributions; Fish habitat; Generalized additive models; Generalized linear models; Species distribution modelling; Species niche; Western Australia

Indexed keywords

BENTHOS; DEMERSAL FISH; ENVIRONMENTAL GRADIENT; HABITAT TYPE; MACROALGA; MODEL TEST; NICHE; POPULATION MODELING; SAMPLING; SPECIES OCCURRENCE; SUBSTRATE; UNDERWATER CAMERA; VIDEOGRAPHY; WATER DEPTH;

AUSTRALIA; RECHERCHE ARCHIPELAGO; WESTERN AUSTRALIA;

EID: 77952020088     PISSN: 03050270     EISSN: 13652699     Source Type: Journal    
DOI: 10.1111/j.1365-2699.2009.02246.x     Document Type: Article

References (63)

1. Anderson DR, Burnham KP, Thompson WL. Null hypothesis testing: problems, prevalence, and an alternative. Journal of Wildlife Management 2000, 64:912-923.
2. Araújo MB, Pearson RG, Thuiller W, Erhard M. Validation of species-climate impact models under climate change. Global Change Biology 2005, 11:1504-1513.
3. Austin MP. A silent clash of paradigms: some inconsistencies in community ecology. Oikos 1999, 86:170-178.
4. Austin MP. Spatial prediction of species distribution: an interface between ecological theory and statistical modelling. Ecological Modelling 2002, 157:101-118.
5. Austin MP. Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecological Modelling 2007, 200:1-19.
6. Austin MP, Meyers JA. Current approaches to modelling the environmental niche of eucalypts: implication for management of forest biodiversity. Forest Ecology and Management 1996, 85:95-106.
7. Austin MP, Nicholls AO. To fix or not to fix the species limits, that is the ecological question: response to Jari Oksanen. Journal of Vegetation Science 1997, 8:743-748.
8. Ayvazian SG, Hyndes GA. Surf zone fish assemblages in south-western Australia: do adjacent nearshore habitats and the warm Leeuwin Current influence the characteristics of the fish fauna? Marine Biology 1995, 122:527-536.
9. Bio AMF. Does vegetation suit our models? Data and model assumptions and the assessment of species distribution in space 2000, PhD Thesis, Utrecht University, Utrecht
10. Bio AMF, De Becker P, De Bie E, Huybrechts W, Wassen M. Prediction of plant species distribution in lowland river valleys in Belgium: modelling species response to site conditions. Biodiversity and Conservation 2002, 11:2189-2216.
11. Boyce MS, Vernier PR, Nielsen SE, Schmiegelow FKA. Evaluating resource selection functions. Ecological Modelling 2002, 157:281-300.
12. Burnham KP, Anderson DR. Kullback-Leibler information as a basis for strong inference in ecological studies. Wildlife Research 2001, 28:111-119.
13. Cappo M, Speare P, De'ath G. Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in inter-reef areas of the Great Barrier Reef Marine Park. Journal of Experimental Marine Biology and Ecology 2004, 302:123-152.
14. Chambers JM, Hastie TJ. Statistical models in S 1993, Chapman and Hall, New York
15. Chatfield C. Model uncertainty, data mining and statistical inference. Journal of the Royal Statistical Society 1995, 158:419-466.
16. De'ath G, Fabricius KE. Classification and regression trees: a powerful yet simple technique for ecological data analysis. Ecology 2000, 81:3178.
17. Edgar GJ, Shaw C. The production and trophic ecology of shallow-water fish assemblages in southern Australia III. General relationships between sediments, seagrasses, invertebrates and fishes. Journal of Experimental Marine Biology and Ecology 1995, 194:107-131.
18. Elith J, Graham CH, Anderson RP. Novel methods improve prediction of species' distributions from occurrence data. Ecography 2006, 29:129-151.
19. Engel DW, Thayer GW, Evans DW. Linkages between fishery habitat quality, stressors, and fishery populations. Environmental Science and Policy 1999, 2:465-475.
20. Fielding AH, Bell JF. A review of methods for the assessment of prediction errors in conservation presence/absence models. Environmental Conservation 1997, 24:38-49.
21. Franklin J. Predicting the distribution of shrub species in southern California from climate and terrain-derived variables. Journal of Vegetation Science 1998, 9:733-748.
22. Friedlander AM, Parrish JD. Habitat characteristics affecting fish assemblages on a Hawaiian coral reef. Journal of Experimental Marine Biology and Ecology 1998, 224:1-30.
23. Froese R, Pauly D. FishBase, version (08/2009) 2009, http://www.fishbase.org/, Available at:
24. Fulton CJ, Bellwood DR. Wave exposure, swimming performance, and the structure of tropical and temperate reef fish assemblages. Marine Biology 2004, 144:429-437.
25. Gomon MF, Glover JCM, Kuiter RH. The fishes of Australia's south coast 1994, State Print, Adelaide
26. Guisan A, Thuiller W. Predicting species distribution: offering more than simple habitat models. Ecology Letters 2005, 8:993-1009.
27. Guisan A, Zimmermann NE. Predictive habitat distribution models in ecology. Ecological Modelling 2000, 135:147-186.
28. Guisan A, Theurillat JP, Hastie T. Predicting the potential distribution of plant species in an alpine environment. Journal of Vegetation Science 1998, 9:65-74.
29. Guisan A, Edwards TC, Hastie T. Generalized linear and generalized additive models in studies of species distributions: setting the scene. Ecological Modelling 2002, 157:89-100.
30. Hanley JA, McNeil BJ. The meaning and use of the area under a receiver operating characteristic (ROC) curve. Radiology 1982, 143:29-36.
31. Harvey E, Shortis MR. A system for stereo-video measurement of sub-tidal organisms. Marine Technical Society Journal 1996, 29:10-22.
32. Harvey E, Cappo M, Butler J, Hall N, Kendrick GA. Bait attraction affects the performance of remote underwater video stations in assessment of demersal fish community structure. Marine Ecology Progress Series 2007, 350:245-254.
33. Hastie T, Tibshirani R. Generalized additive models 1990, Chapman and Hall, London
34. Hastie T, Tibshirani R, Friedman J. The elements of statistical learning: data mining, inference and prediction 2001, Springer, New York
35. Huntley B. Plant species response to climate change implications for the conservation of European birds. Ibis 1995, 137:S127-S138.
36. Hutchins BJ. A survey of the nearshore reef fish fauna of Western Australia's west and south coasts: the Leeuwin Province 1994, Records of the Western Australian Museum, Supplement No. 46, Western Australian Museum, Perth
37. Kendrick GA, Harvey E, McDonald J, Wells F, Walker DI. Introduction to the marine biology of the Recherche Archipelago, Western Australia. Proceedings of the 12th International Marine Biological Workshop: the marine flora and fauna of Esperance, Western Australia 2005, 1-10. Wells F, Walker DI, Kendrick GA, ed. by, pp, Western Australian Museum, Perth
38. Kupschus S. Development and evaluation of statistical habitat suitability models: an example based on juvenile spotted seatrout Cynoscion nebulosus. Marine Ecology Progress Series 2003, 265:197-212.
39. Leathwick JR. Are New Zealand's Nothofagus species in equilibrium with their environment? Journal of Vegetation Science 1998, 9:719-732.
40. Leathwick JR, Rowe D, Richardson AJ, Elith J, Hastie T. Using multivariate adaptive regression splines to predict the distributions of New Zealand's freshwater diadromous fish. Freshwater Biology 2005, 50:2034-2052.
41. Liu C, Berry PM, Dawson TP, Pearson RG. Selecting thresholds of occurrence in the prediction of species distributions. Ecography 2005, 28:385-393.
42. Lobo JM, Jiménez-Valverde A, Real R. AUC: a misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography 2008, 17:145-151.
43. Maggini R, Lehmann A, Zimmermann NE, Guisan A. Improving generalized regression analysis for the spatial prediction of forest communities. Journal of Biogeography 2006, 33:1729-1749.
44. Maravelias CD. Trends in abundance and geographic distribution of North Sea herring in relation to environmental factors. Marine Ecology Progress Series 1997, 159:151-164.
45. Maravelias CD. Seabed substrate, water depth and zooplankton as determinants of the prespawning spatial aggregation of North Atlantic herring. Marine Ecology Progress Series 2000, 195:249-259.
46. Maravelias CD. Habitat associations of Atlantic herring in the Shetland area: influence of spatial scale and geographic segmentation. Fisheries Oceanography 2001, 10:259-267.
47. Maravelias CD, Reid DG. Identifying the effects of oceanographic features and zooplankton on prespawning herring abundance using generalized additive models. Marine Ecology Progress Series 1997, 147:1-9.
48. McCullagh P, Nelder JA. Generalized linear models 1983, Chapman and Hall, London
49. McPherson JM, Jetz W, Rogers DJ. The effects of species' range sizes on the accuracy of distribution models: ecological phenomenon or statistical artefact? Journal of Applied Ecology 2004, 41:811-823.
50. Nagelkerke NJD. A note on a general definition of the coefficient of determination. Biometrika 1991, 78:691-692.
51. Pikitch EK, Santora C, Babcock EA, Bakun A, Bonfil R, Conover DO, Dayton P, Doukakis P, Fluharty D, Heneman B, Houde ED, Link J, Livingston PA, Mangel M, McAllister MK, Pope J, Sainsbury KJ. ECOLOGY: ecosystem-based fishery management. Science 2004, 305:346-347.
52. Pittman SJ, Christensen JD, Caldow C, Menza C, Monaco ME. Predictive mapping of fish species richness across shallow-water seascapes in the Caribbean. Ecological Modelling 2007, 204:9-21.
53. Ryan DA, Brooke BP, Collins LB, Kendrick GA, Baxter KJ, Bickers AN, Siwabessy PJW, Pattiaratchi CB. The influence of geomorphology and sedimentary processes on shallow-water benthic habitat distribution, Esperance Bay, Western Australia. Estuarine, Coastal and Shelf Science 2007, 72:379-386.
54. Scott MJ, Heglund PJ, Morrison ML, Haufler JB, Raphael MG, Wall WA, Samson FB. Predicting species occurrence: issues of accuracy and scale 2002, Island Press, Washington, DC
55. Stoner AW, Manderson JP, Pessutti JP. Spatially explicit analysis of estuarine habitat for juvenile winter flounder: combining generalized additive models and geographic information systems. Marine Ecology Progress Series 2001, 213:253-271.
56. Swartzman G, Huang C, Kaluzny S. Spatial analysis of Bering Sea groundfish survey data using generalized additive models. Canadian Journal of Fisheries and Aquatic Sciences 1992, 49:1366-1378.
57. Swets JA. Measuring the accuracy of diagnostic systems. Science 1988, 240:1285-1293.
58. Valavanis VD, Georgakarakos S, Kapantagakis A, Palialexis A, Katara I. A GIS environmental modelling approach to essential fish habitat designation. Ecological Modelling 2004, 178:417-427.
59. Venables WN, Dichmont CM. GLMs, GAMs and GLMMs: an overview of theory for applications in fisheries research. Fisheries Research 2004, 70:319-337.
60. Ward TJ, Vanderklift MA, Nicholls AO, Kenchington RA. Selecting marine reserves using habitats and species assemblages as surrogates for biological diversity. Ecological Applications 1999, 9:691-698.
61. Yee TW, Mitchell ND. Generalized additive models in plant ecology. Journal of Vegetation Science 1991, 2:587-602.
62. Ysebaert T, Meire P, Herman PMJ, Verbeek H. Macrobenthic species response surfaces along estuarine gradients: prediction by logistic regression. Marine Ecology Progress Series 2002, 225:79-95.
63. Zweig MH, Campbell G. Receiver-operating characteristic (ROC) plots: a fundamental evaluation tool in clinical medicine. Clinical Chemistry 1993, 39:561-577.