Combining best professional judgement and quantile regression splines to improve characterisation of macrofaunal responses to enrichment

Ecological Indicators

Volumn 12, Issue 1, 2012, Pages 154-166

  Keeley, Nigel B ^a,b   MacLeod, Catriona K ^b,c   Forrest, Barrie M ^a  

^a CAWTHRON INSTITUTE   (New Zealand)

^b UNIVERSITY OF TASMANIA   (Australia)

^c UNIVERSITY OF TASMANIA   (Australia)

Author keywords

AMBI; Benthic impact assessment; Biotic index; Eco group; Enrichment gradient; Salmon farm

Indexed keywords

AMBI; BENTHIC IMPACT; BIOTIC INDEX; ECO-GROUP; SALMON FARM;

ECOLOGY; POLLUTION CONTROL;

REGRESSION ANALYSIS;

ABUNDANCE; DATABASE; DISCRIMINANT ANALYSIS; ENVIRONMENTAL CONDITIONS; ENVIRONMENTAL IMPACT ASSESSMENT; IDENTIFICATION METHOD; NUMERICAL MODEL; PHYSIOLOGICAL RESPONSE; POLLUTION EFFECT; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REGRESSION ANALYSIS; TAXONOMY; TOLERANCE;

NEW ZEALAND;

EID: 80052593514     PISSN: 1470160X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolind.2011.03.022     Document Type: Article

References (66)

1. F. Aguado-Gimenez, A. Marin, S. Montoya, L. Marin-Guirao, A. Piedecausa, and B. Garcia-Garcia Comparison between some procedures for monitoring offshore cage culture in western Mediterranean Sea: sampling methods and impact indicators in soft substrata Aquaculture 271 2007 357 370 (Pubitemid 47332520)
2. M.J. Anderson Animal-sediment relationships re-visited: characterising species' distributions along an environmental gradient using canonical analysis and quantile regression splines J. Exp. Mar. Biol. Ecol. 366 2008 16 27
3. M.J. Anderson, and J. Robinson Generalized discriminant analysis based on distances Aust. N. Z. Stat. 45 2003 301 318 (Pubitemid 37023230)
4. M.J. Anderson, and T.J. Willis Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology Ecology 84 2003 511 525 (Pubitemid 36893087)
5. Anderson, M.J.; Gorley, R.N.; Clarke, K.R.; 2008. PERMANOVA+ for PRIMER: Guide to Software and Statistical Methods, PRIMER-E, Plymouth, UK.
6. A. Borja The biotic indices and the Water Framework Directive: the required consensus in the new benthic monitoring tools Mar. Pollut. Bull. 48 2004 405 408 (Pubitemid 38234394)
7. A. Borja, D.M. Dauer, R.J. Diaz, R.J. Llanso, I. Muxika, J.G. Rodríguez, and L. Schaffner Assessing estuarine benthic quality conditions in Chesapeake Bay: a comparison of three indices Ecol. Indicators 8 2008 395 403 (Pubitemid 351308120)
8. A. Borja, J. Franco, and V. Perez A marine biotic index to establish the ecological quality of soft-bottom benthos within European estuarine and coastal environments Mar. Pollut. Bull. 40 2000 1100 1114
9. A. Borja, and H. Muxika Guidelines for the use of AMBI (AZTI's Marine Biotic Index) in the assessment of the benthic ecological quality Mar. Pollut. Bull. 50 2005 787 789 (Pubitemid 40898336)
10. A. Borja, J.G. Rodríguez, K. Black, A. Bodoy, A. Emblow, T.F. Fernandes, J. Forte, I. Karakassis, I. Muxika, T.D. Nickell, N. Papageorgiou, F. Pranovi, K. Sevastou, P. Tomassetti, and D. Angel Assessing the suitability of a range of benthic indices in the evaluation of environmental impact of fin and shellfish aqauculture located acress Europe Aquaculture 293 2009 231 240
11. K.M. Brooks, C. Mahnken, and C. Nash Environmental effects associated with marine netpen waste with emphasis on salmon farming in the Pacific northwest Responsible Marine Aquaculture 2002 159 203
12. K.M. Brooks, A.R. Stierns, C.V.W. Mahnken, and D.B. Blackburn Chemical and biological remediation of the benthos near Atlantic salmon farms Aquaculture 219 2003 355 377 (Pubitemid 36345519)
13. M. Burgman Risks and decisions for conservation and environmental management Ecology, Biodiversity and Conservation Series 2005 Cambridge University Press UK 488 pp.
14. K.P. Burnham, and D.R. Anderson Model Selection and Multi-model Inference: A Practical Information-theoretic Approach 2002 Springer New York
15. A.H. Buschmann, V.A. Riquelme, M.C. Hernandez-Gonzalez, D. Varela, J.E. Jimenez, L.A. Henriquez, P.A. Vergara, R. Guinez, and L. Filun A review of the impacts of salmonid farming on marine coastal ecosystems in the southeast Pacific ICES J. Mar. Sci. 63 2006 1338 1345 (Pubitemid 44108693)
16. B.S. Cade, and B.R. Noon A gentle introduction to quantile regression for ecologists Front. Ecol. Environ. 1 2003 412 420
17. B.S. Cade, B.R. Noon, and C.H. Flather Quantile regression reveals hidden bias and uncertainty in habitat models Ecology 86 2005 786 800 (Pubitemid 40383874)
18. B.S. Cade, J.W. Terrell, and R.L. Schroeder Estimating effects of limiting factors with regression quantiles Ecology 80 1999 311 323 (Pubitemid 29054063)
19. M.D. Callier, C.W. McKindsey, and G. Desrosiers Multi-scale spatial variations in benthic sediment geochemistry and macrofaunal communities under a suspended mussel culture Mar. Ecol. Prog. Ser. 348 2007 103 115 (Pubitemid 350189911)
20. M.D. Callier, C.W. McKindsey, and G. Desrosiers Evaluation of indicators used to detect mussel farm influence on the benthos: two case studies in the Magdalen Islands, Eastern Canada Aquaculture 278 2008 77 88
21. M.J. Cardell, R. Sarda, and J. Romero Spatial changes in sublittoral soft-bottom polychaete assemblages due to river inputs and sewage discharges Acta Oecol. Int. J. Ecol. 20 1999 343 351 (Pubitemid 29514683)
22. M.L. Carroll, S. Cochrane, R. Fieler, R. Velvin, and P. White Organic enrichment of sediments from salmon farming in Norway: environmental factors, management practices, and monitoring techniques Aquaculture 226 2003 165 180 (Pubitemid 37274121)
23. Clarke, K.R.; Gorley, R.N.; 2006. PRIMER v6: User Manual/Tutorial.; PRIMER-E Ltd.; Plymouth, UK.
24. C.M. Crawford, I.M. Mitchell, and C.K. Macleod Video assessment of environmental impacts of salmon farms ICES J. Mar. Sci. 58 2001 445 452 (Pubitemid 32533241)
25. C.J. Cromey, T.D. Nickell, and K.D. Black DEPOMOD - modelling the deposition and biological effects of waste solids from marine cage farms Aquaculture 214 2002 211 239 (Pubitemid 35224596)
26. DSRSA, 2010. Salmon Aquaculture Dialogue: Draft Standards for Responsible Salmon Aquaculture, August 3. http://www.worldwildlife.org/what/globalmarkets/ aquaculture/WWFBinaryitem17499.pdf.
27. G.J. Edgar, C. Macleod, R.B. Mawbey, and D. Shields Broad-scale effects of marine salmonid aquaculture on macrobenthos and the sediment environment in southeatsern Tasmania J. Exp. Mar. Biol. Ecol. 2005 327
28. B. Forrest, and R.G. Creese Benthic impacts of intertidal oyster culture, with consideration of taxonomic sufficiency Environ. Monit. Assess. 112 2006 159 176
29. B. Forrest, P.A. Gillespie, C. Cornelisen, and K. Rogers Multiple indicators reveal river plume influence on sediments and benthos in a New Zealand coastal embayment N. Z. J. Mar. Freshwat. Res. 41 2007 13 24 (Pubitemid 46658551)
30. M. Glémarec, and C. Hily Perturbations apportees a la macrofaune benthique de la baie de Concatneau par les effluents urbains et portuaires Acta Ecol. 2 1981 139 150 (Pubitemid 11085976)
31. J. Grall, and M. Glémarec Using biotic indices to estimate macrobenthic community perturbations in the Bay of Brest Estuar. Coast. Shelf Sci. 44 1997 43 53
32. J.S. Gray, and T.H. Pearson Objective selection of species indicative of pollution-inducing change in benthic communities: I comparative methodology Mar. Ecol. Prog. Ser. 9 1982 111 119
33. J.S. Gray, M. Waldichuk, A.J. Newton, R.J. Berry, A.V. Holden, and T.H. Pearson Pollution-induced changes in populations [and discussion] Philos. Trans. R. Soc. London: Ser. B Biol. Sci. 286 1979 545 561
34. R.H. Green, and R.C. Young Sampling to detect rare species Ecol. Appl. 3 1993 351 356
35. B.T. Hargrave, M. Holmer, and C.P. Newcombe Towards a classification of organic enrichment in marine sediments based on biogeochemical indicators Mar. Pollut. Bull. 56 2008 810 824
36. B.T. Hargrave, G.A. Phillips, L.I. Doucette, M.J. White, T.G. Milligan, D.J. Wildish, and R.E. Cranston Assessing benthic impacts of organic enrichment from marine aquaculture Water Air Soil Pollut. 99 1997 641 650 (Pubitemid 27397751)
37. M. Holmer, and E. Kristensen Impact of marine fish cage farming on metabolism and sulfate reduction of underlying sediments Mar. Ecol. Prog. Ser. 80 1992 191 201
38. R.D. Jacobs, and R.D. Podolsky Variety is the spice of life histories: comparison of intraspecific variability in marine invertebrates Comp. Biol. 50 2010 630 642
39. I. Kalantzi, and I. Karakassis Benthic impacts of fish farming: meta-analysis of community and geochemical data Mar. Pollut. Bull. 52 2006 484 493 (Pubitemid 43767507)
40. Koenker, R.; 2005. Quantile Regression, New York, USA.
41. R. Koenker, P. Ng, and S. Portnoy Quantile smoothing splines Biometricka 81 1994 673 680
42. J. Lancaster, and L.R. Belyea Defining the limits to local density: alternative views of abundance-environment relationships Freshwat. Biol. 51 2006 783 796
43. C. Luczak, M.A. Janquin, and A. Kupka Simple standard procedure for the routine determination of organic matter in marine sediment Hydrobiologia 345 1997 87 94 (Pubitemid 27284814)
44. C. Macleod, and S. Forbes Guide to the assessment of sediment condition at marine fish farms in Tasmania Aquafin CRC Project 4.1. Tasmanian Fisheries and Aquaculture Institute, Australia 2004 p. 63
45. C.K. Macleod, C. Crawford, and N.A. Miltschaniwskyj Assessment of long term change in sediment condition after organic enrichment defining recovery Mar. Pollut. Bull. 49 2004 79 88 (Pubitemid 38968595)
46. C.K. Macleod, N.A. Moltschaniwskyj, C.M. Crawford, and S.E. Forbes Biological recovery from organic enrichment: some systems cope better than others Mar. Ecol. Prog. Ser. 342 2007 41 53 (Pubitemid 47300557)
47. B.J.F. Manly Randomization, Bootstrap and Monte Carlo Methods in Biology 2006 Chapman & Hall London
48. A. Mazzola, S. Mirto, T. La Rosa, M. Fabiano, and R. Danovaro Fish-farming effects on benthic community structure in coastal sediments: analysis of meiofanal recovery ICES J. Mar. Sci. 57 2000 1454 1461 (Pubitemid 32108849)
49. I. Muxika, A. Borja, and J. Bald Using historical data, expert judgement and multivariate analysis in assessing reference conditions and benthic ecological status according to the European Water Framework Directive Mar. Pollut. Bull. 55 2007 16 29 (Pubitemid 44779645)
50. L.A. Nickell, K.D. Black, D.J. Hughes, J. Overnell, T. Brand, T.D. Nickell, E. Breuer, and S.M. Harvey Bioturbation, sediment fluxes and benthic community structure around a salmon cage farm in Loch Creran, Scotland J. Exp. Mar. Biol. Ecol. 285 2003 221 233 (Pubitemid 36211186)
51. T.H. Pearson, and R. Rosenberg Macrobenthic succession in relation to organic enrichment and pollution of the marine environment Oceanogr. Mar. Biol. Annu. Rev. 16 1978 229 311
52. Pinedo, S.; Jordana, E.; 2008. Spain (Catalonia and Balearic Islands). In: Carletti, A.; Heiskanen, A.-S. (Eds.), Water Framework Directive Intercalibration Technical Report. Part 3: Coastal and Transitional Waters, JRC Scientific and Technical Reports: 62-70. JRC & ies.
53. G. Pohle, B. Frost, and R. Findlay Assessment of regional benthic impact of salmon mariculture within the Letang Inlet, Bay of Fundy ICES J. Mar. Sci. 58 2001 417 426 (Pubitemid 32540306)
54. H.M. Regan, M. Colyvan, and M.A. Burgman A taxonomy and treatment of uncertainty for ecology and conservation biology Ecol. Appl. 12 2002 618 628 (Pubitemid 36516680)
55. R. Rosenberg, M. Blomqvist, H. C Nilsson, H. Cederwall, and A. Dimming Marine quality assessment by use of benthic species-abundance distributions: a proposed new protocol within the European Union Water Framework Directive Mar. Pollut. Bull. 49 2004 728 739 (Pubitemid 39462763)
56. P. Sampou, and C.A. Oviatt Seasonal patterns of sedimentary carnon and anaerobic respiration along a simulated eutrophication gradient Mar. Ecol. Prog. Ser. 72 1991 271 281
57. N. Simboura Bentix index vs. biotic index in monitoring: an answer to Borja et al. (2003) Mar. Pollut. Bull. 48 2003 403 404
58. N. Simboura, and A. Zenetos Benthic indicators to use in Ecological Quality classification of Mediterranean soft bottom marine ecosystems, including a new Biotic Index Mediterr. Mar. Sci. 3 2002 77 111
59. J. Smith, and S.E. Shackley Effects of commercial mussel Mytilus edulis lay on a sublittoral, soft sediment benthic community Mar. Ecol. Prog. Ser. 282 2004 185 191 (Pubitemid 39661297)
60. L.A. Taylor, P.M. Chapman, R.A. Miller, and R.V. Pym The effects of untreated municipal sewage discharge to the marine environment off Victoria, British Columbia, Canada Water Sci. Technol. 38 1998 285 292
61. R Development Core Team, 2007. R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria.
62. H. Teixeira, Á. Borja, S.B. Weisberg, J. Ananda Ranasinghe, D.B. Cadien, D.M. Dauer, J.-C. Dauvin, S. Degraer, R.J. Diaz, A. Grémare, I. Karakassis, R.J. Llansó, L.L. Lovell, J.C. Marques, D.E. Montagne, A. Occhipinti-Ambrogi, R. Rosenberg, R. Sardá, L.C. Schaffner, and R.G. Velarde Assessing coastal benthic macrofauna community condition using best professional judgement - developing consensus across North America and Europe Mar. Pollut. Bull. 60 2010 589 600
63. J.D. Thomson, G. Weiblen, B.A. Thomson, S. Alfaro, and P. Legendre Untangling multiple factors in spatial distributions: Lilies, Gophers, and Rocks Ecology 77 1996 1698 1715
64. P. Tomassetti, E. Persia, I. Mercatali, D. Vani, V. Marussso, and S. Porrello Effects of mariculture on macrobenthic assemblages in a western mediterranean site Mar. Pollut. Bull. 58 2009 533 541
65. S.B.T.B. Weisberg, J.A. Ranasinghe, D.E. Montagne, D.B. Cadien, D.M. Dauer, D. Diener, J. Oliver, D.J. Reish, R.G. Velarde, and J.Q. Word The level of agreement among experts applying best professional judgement to assess the condition of benthic infaunal communities Ecol. Indicators 8 2008 389 394 (Pubitemid 351308118)
66. Word, J.Q.; 1978. The Infaunal Trophic Index. Annual Report 1978, Coastal Water Research Project, El Sequndo, CA, USA, pp. 19-39.