Are we predicting the actual or apparent distribution of temperate marine fishes?

PLoS ONE

Volumn 7, Issue 4, 2012, Pages

  Monk, Jacquomo ^a   Ierodiaconou, Daniel ^a   Harvey, Euan ^b   Rattray, Alex ^a   Versace, Vincent L ^c  

^a DEAKIN UNIVERSITY   (Australia)

^b UNIVERSITY OF WESTERN AUSTRALIA   (Australia)

^c DEAKIN UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; AUSTRALIA; COASTAL WATERS; DATA BASE; ENTROPY; FISH; MARINE SPECIES; NONHUMAN; PREDICTION; PROBABILITY; RELIABILITY; SCIENTIST; SPECIES DISTRIBUTION; SPECIES HABITAT; STATISTICAL MODEL; TAXONOMY; TEMPERATE MARINE FISH; VIDEORECORDING; ANIMAL; AREA UNDER THE CURVE; BIOLOGICAL MODEL; COMPUTER SIMULATION; ECOSYSTEM; ENVIRONMENTAL PROTECTION; INFORMATION PROCESSING; METHODOLOGY; RECEIVER OPERATING CHARACTERISTIC; SEA;

PISCES;

ANIMALS; AREA UNDER CURVE; COMPUTER SIMULATION; CONSERVATION OF NATURAL RESOURCES; DATA COLLECTION; ECOSYSTEM; FISHES; MODELS, BIOLOGICAL; OCEANS AND SEAS; ROC CURVE; VIDEO RECORDING;

EID: 84859840866     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0034558     Document Type: Article

References (74)

1. Jackson JBC, Kirby MX, Berger WH, Bjorndal KA, Botsford LW, et al. (2001) Historical overfishing and the recent collapse of coastal ecosystems. Science 293: 629-637.
2. Aswani S, Lauer M, (2006) Benthic mapping using local aerial photo interpretation and resident taxa inventories for designing marine protected areas. Environmental Conservation 33: 263-273.
3. Harris PT, Whiteway T, (2009) High seas marine protected areas: benthic environmental conservation priorities from a GIS analysis of global ocean biophysical data. Ocean and Coastal Management 52: 22-38.
4. Jordan A, Lawler M, Halley V, Barrett N, (2005) Seabed habitat mapping in the Kent Group of islands and its role in marine protected area planning. Aquatic Conservation-Marine and Freshwater Ecosystems 15: 51-70.
5. Ward TJ, Vanderklift MA, Nicholls AO, Kenchington RA, (1999) Selecting marine reserves using habitats and species assemblages as surrogates for biological diversity. Ecological Applications 9: 691-698.
6. Zacharias MA, Gregr EJ, (2005) Sensitivity and vulnerability in marine environments: an approach to identifying vulnerable marine areas. Conservation Biology 19: 86-97.
7. Guisan A, Zimmermann NE, (2000) Predictive habitat distribution models in ecology. Ecological Modelling 135: 147-186.
8. Myers N, Mittermeier RA, Mittermeier CG, da Fonseca GAB, Kent J, (2000) Biodiversity hotspots for conservation priorities. Nature 403: 853-858.
9. Vanderklift MA, Ward TJ, (2000) Using biological survey data when selecting Marine Protected Areas: an operational framework and associated risks. Pacific Conservation Biology 6: 152-161.
10. Austin M, (2007) Species distribution models and ecological theory: a critical assessment and some possible new approaches. Ecological Modelling 200: 1-19.
11. Hirzel AH, Helfer W, Metral F, (2001) Assessing habitat-suitability models with a virtual species. Ecological Modelling 145: 111-121.
12. Gibson L, Barrett B, Burbidge AH, (2007) Dealing with uncertain absences in habitat modelling: a case study of a rare ground-dwelling parrot. Diversity and Distributions 13: 704-713.
13. Engler R, Guisan A, Rechsteiner L, (2004) An improved approach for predicting the distribution of rare and endangered species from occurrence and pseudo-absence data. Journal of Applied Ecology 41: 263-274.
14. Elith J, Graham CH, Anderson RP, Dudik M, Ferrier S, et al. (2006) Novel methods improve prediction of species' distributions from occurrence data. Ecography 29: 129-151.
15. Wisz M, Guisan A, (2009) Do pseudo-absence selection strategies influence species distribution models and their predictions? An information-theoretic approach based on simulated data. BMC Ecology 9: 8.
16. VanDerWal J, Shoo LP, Graham C, Williams SE, (2009) Selecting pseudo-absence data for presence-only distribution modeling: how far should you stray from what you know? Ecological Modelling 220: 589-594.
17. Murphy HM, Jenkins GP, (2010) Observational methods used in marine spatial monitoring of fishes and associated habitats: a review. Marine and Freshwater Research 61: 236-252.
18. Moore CH, Harvey ES, Van Niel KP, (2009) Spatial prediction of demersal fish distributions: enhancing our understanding of species-environment relationships. ICES Journal of Marine Science 66: 2068-2075.
19. Stoner AW, Spencer ML, Ryer CH, (2007) Flatfish-habitat associations in Alaska nursery grounds: Use of continuous video records for multi-scale spatial analysis. Journal of Sea Research 57: 137-150.
20. Harvey ES, Cappo M, Butler JJ, Hall N, Kendrick GA, (2007) Bait attraction affects the performance of remote underwater video stations in assessment of demersal fish community structure. Marine Ecology-Progress Series 350: 245-254.
21. Colton MA, Swearer SE, (2010) A comparison of two survey methods: differences between underwater visual census and baited remote underwater video. Marine Ecology-Progress Series 400: 19-36.
22. Wintle BA, Kavanagh RP, McCarthy MA, Burgman MA, (2005) Estimating and dealing with detectability in occupancy surveys for forest owls and arboreal marsupials. Journal of Wildlife Management 69: 905-917.
23. Warren DL, Glor RE, Turelli M, (2008) Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62: 2868-2883.
24. Roubicek AJ, VanDerWal J, Beaumont LJ, Pitman AJ, Wilson P, et al. (2010) Does the choice of climate baseline matter in ecological niche modelling? Ecological Modelling 221: 2280-2286.
25. Monk J, Ierodiaconou D, Versace V, Bellgrove A, Harvey E, et al. (2010) Habitat suitability for marine fishes using presence-only modelling and multibeam sonar. Marine Ecology-Progress Series 420: 157-174.
26. Segurado P, Araújo MB, (2004) An evaluation of methods for modelling species distributions. Journal of Biogeography 31: 1555-1568.
27. Tsoar A, Allouche O, Steinitz O, Rotem D, Kadmon R, (2007) A comparative evaluation of presence-only methods for modelling species distribution. Diversity and Distributions 13: 397-405.
28. Lobo JM, Jiménez-Valverde A, Real R, (2008) AUC: a misleading measure of the performance of predictive distribution models. Global Ecology and Biogeography 17: 145-151.
29. Peterson AT, Papes M, Soberón J, (2008) Rethinking receiver operating characteristic analysis applications in ecological niche modeling. Ecological Modelling 213: 63-72.
30. Moore CH, Harvey ES, Van Niel K, (2010) The application of predicted habitat models to investigate the spatial ecology of demersal fish assemblages. Marine Biology 157: 2717-2729.
31. Monk J, Ierodiaconou D, Bellgrove A, Harvey E, Laurenson L, (2011) Remotely sensed hydroacoustics and observation data for predicting fish habitat suitability. Continental Shelf Research 31: S17-S27.
32. Wilson MFJ, O'Connell B, Brown C, Guinan JC, Grehan AJ, (2007) Multiscale terrain analysis of multibeam bathymetry data for habitat mapping on the continental slope. Marine Geodesy 30: 3-35.
33. Pittman SJ, Costa BM, Battista TA, (2009) Using LiDAR bathymetry and boosted regression trees to predict the diversity and abundance of fish and corals Journal of Coastal Research 53: 27-38.
34. Leathwick JR, Elith J, Hastie T, (2006) Comparative performance of generalized additive models and multivariate adaptive regression splines for statistical modelling of species distributions. Ecological Modelling 199: 188-196.
35. Ready J, Kaschner K, South AB, Eastwood PD, Rees T, et al. (2010) Predicting the distributions of marine organisms at the global scale. Ecological Modelling 221: 467-478.
36. Kadmon R, Farber O, Danin A, (2003) A systematic analysis of factors affecting the performance of climatic envelope models. Ecological Applications 13: 853-867.
37. Sérgio C, Figueira R, Draper D, Menezes R, Sousa AJ, (2007) Modelling bryophyte distribution based on ecological information for extent of occurrence assessment. Biological Conservation 135: 341-351.
38. MacNeill MA, Tyler EHM, Fonnesbeck CJ, Rushton SP, Polunin NVC, et al. (2008) Accounting for detectability in reef-fish biodiversity estimates. Marine Ecology-Progress Series 367: 249-260.
39. Bozec Y-M, Kulbicki M, Laloë F, Mou-Tham G, Gascuel D, (2011) Factors affecting the detection distances of reef fish: implications for visual counts. Marine Biology pp. 1-13.
40. Godø OR, Huse I, Michalsen K, (1997) Bait defence behaviour of wolffish and its impact on long-line catch rates. ICES Journal of Marine Science 54: 273-275.
41. Thomsen B, Humborstad O-B, Furevik DM, (2010) Fish Pots: Fish Behavior, Capture Processes, and Conservation Issues. Behavior of Marine Fishes Wiley-Blackwell pp. 143-158.
42. Sarà G, Dean JM, Amato DD, Buscaino G, Oliveri A, et al. (2007) Effect of boat noise on the behaviour of bluefin tuna Thunnus thynnus in the Mediterranean Sea. Marine Ecology-Progress Series 331: 243-253.
43. Popper A, Hastings M, (2009) The effects of anthropogenic sources of sound on fishes. Journal of Fish Biology 75: 455-489.
44. Stoner AW, Ryer CH, Parker SJ, Auster PJ, Wakefield WW, (2008) Evaluating the role of fish behavior in surveys conducted with underwater vehicles. Canadian Journal of Fisheries and Aquatic Sciences 65: 1230-1243.
45. Watson DL, Harvey ES, Anderson MJ, Kendrick GA, (2005) A comparison of temperate reef fish assemblages recorded by three underwater stereo-video techniques. Marine Biology 148: 1189-1189.
46. Willis TJ, Babcock RC, (2000) A baited underwater video system for the determination of relative density of carnivorous reef fish. Marine and Freshwater Research 51: 755-763.
47. Willis TJ, Millar RB, Babcock RC, (2000) Detection of spatial variability in relative density of fishes: comparison of visual census, angling, and baited underwater video. Marine Ecology-Progress Series 198: 249-260.
48. Edgar G, (2000) Australian marine life: the plants and animals of temperate waters. Sydney Reed Books. 544.
49. Gomon MF, Bray D, Kuiter RH, (2008) The fishes of Australia's south coast; Gomon MF, Bray D, Kuiter RH, editors. Sydney New Holand. 928.
50. Kéry M, Gardner B, Monnerat C, (2010) Predicting species distributions from checklist data using site-occupancy models. Journal of Biogeography 37: 1851-1862.
51. Kéry M, Schmidt BR, (2008) Imperfect detection and its consequences for monitoring for conservation. Community Ecology 9: 207-216.
52. Tyre AJ, Tenhumberg B, Field SA, Niejalke D, Parris K, et al. (2003) Improving precision and reducing bias in biological surveys: estimating false-negative error rates. Ecological Applications 13: 1790-1801.
53. Ward G, Hastie T, Barry S, Elith J, Leathwick JR, (2009) Presence-only data and the EM algorithm. Biometrics 65: 554-563.
54. Breiman L, (2001) Statistical modeling: the two cultures. Statistical Science 16: 199-215.
55. Elith J, Leathwick JR, Hastie T, (2008) A working guide to boosted regression trees. Journal of Animal Ecology 77: 802-813.
56. MacKenzie DI, Nichols JD, Lachman GB, Droege S, Royle JA, et al. (2002) Estimating site occupancy rates when detection probabilities are less than one. Ecology 83: 2248-2255.
57. Kulbicki M, Sarramégna S, (1999) Comparison of density estimates derived from strip transect and distance sampling for underwater visual censuses: a case study of Chaetodontidae and Pomacanthidae. Aquatic Living Resources 12: 315-325.
58. Ierodiaconou D, Laurenson L, Burq S, Reston M, (2007) Marine benthic habitat mapping using multibeam data, georeferenced video and image classification techniques in Victoria, Australia. Journal of Spatial Sciences 52: 93-104.
59. Harvey E, Shortis M, (1996) A system for stereo-video measurement of subtidal organisms. Marine Technology Society Journal 29: 10-22.
60. Harvey ES, Shortis MR, (1998) Calibration stability of an underwater stereo-video system: Implications for measurement accuracy and precision. Marine Technology Society Journal 32: 3-17.
61. Watson DL, (2006) Use of underwater stereo-video to measure fish assemblage structure, spatial distribution of fishes and change in assemblages with protection from fishing [PhD Thesis]: The University of Western Australia.
62. Cappo M, Speare P, Wassenberg TJ, Harvey E, Rees M, et al. (2001) Use of baited remote underwater video stations (BRUVS) to survey demersal fish-how deep and meaningful? Australia Fisheries Research and Development Corporation pp. 63-71.
63. Watson D, Harvey E, Fitzpatrick B, Langlois T, Shedrawi G, (2010) Assessing reef fish assemblage structure: how do different stereo-video techniques compare? Marine Biology 157: 1237-1250.
64. Langlois TJ, Radford BT, Van Niel KP, Meeuwig JJ, Pearce AF, et al. (2011) Consistent abundance distributions of marine fishes in an old, climatically buffered, infertile seascape. Global Ecology and Biogeography doi 10.1111/j.1466-8238.2011.00734.x.
65. Willis TJ, Badalamenti F, Milazzo M, (2006) Diel variability in counts of reef fishes and its implications for monitoring. Journal of Experimental Marine Biology and Ecology 331: 108-120.
66. Cappo M, Speare P, De'ath G, (2004) Comparison of baited remote underwater video stations (BRUVS) and prawn (shrimp) trawls for assessments of fish biodiversity in inter-reefal areas of the Great Barrier Reef Marine Park. Journal of Experimental Marine Biology and Ecology 302: 123-152.
67. Moisen GG, Frescino TS, (2002) Comparing five modelling techniques for predicting forest characteristics. Ecological Modelling 157: 209-225.
68. R Core Development Team (2008) R: a language and environment for statistical computing.
69. Hastie T, (2008) GAM: Generalized Additive Models. R Package.
70. Phillips SJ, Anderson RP, Schapire RE, (2006) Maximum entropy modelling of species geographic distributions. Ecological Modelling 190: 231-259.
71. Fielding AH, Bell JF, (1997) A review of methods for the assessment of prediction errors in conservation presence/absence models. Environmental Conservation 24: 38-49.
72. Dormann CF, McPherson JM, Araujo MB, Bivand R, Bolliger J, et al. (2007) Methods to account for spatial autocorrelation in the analysis of species distributional data: a review. Ecography 30: 609-628.
73. Barrett NS, (1995) Short- and long-term movement patterns of six temperate reef fishes (Families Labridae and Monacanthidae). Marine and Freshwater Research 46: 853-860.
74. Anderson MJ, (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecology 26: 32-46.