Lessons in modelling and management of marine ecosystems: The Atlantis experience

Fish and Fisheries

Volumn 12, Issue 2, 2011, Pages 171-188

  Fulton, Elizabeth A ^a   Link, Jason S ^b   Kaplan, Isaac C ^c   Savina Rolland, Marie ^a   Johnson, Penelope ^a   Ainsworth, Cameron ^c   Horne, Peter ^c   Gorton, Rebecca ^a   Gamble, Robert J ^b   Smith, Anthony D M ^a   Smith, David C ^a  

^a CSIRO   (Australia)

^b NORTHEAST FISHERIES SCIENCE CENTER   (United States)

^c ALASKA FISHERIES SCIENCE CENTER   (United States)

Author keywords

Atlantis; Ecosystem modelling; Ecosystem based management; Exploited marine ecosystems

Indexed keywords

BIOMONITORING; ECONOMIC ANALYSIS; IMPLEMENTATION PROCESS; INTEGRATED APPROACH; MANAGEMENT PRACTICE; MARINE ECOSYSTEM; NUMERICAL MODEL; RESOURCE MANAGEMENT; TRADE-OFF;

ATLANTIC OCEAN;

EID: 79955721997     PISSN: 14672960     EISSN: 14672979     Source Type: Journal    
DOI: 10.1111/j.1467-2979.2011.00412.x     Document Type: Article

References (86)

1. Ainsworth, C.H., Kaplan, I.C., Levin, P.S. et al. (in press) Atlantis model development for the Northern Gulf of California. NOAA Technical Memo.
2. Baird, S.F. (1872) Report on the Condition of the Sea Fisheries of the South Coast of New England (published as first section of First Report of the Commissioner of Fish and Fisheries). Available at: (accessed 6 February 2011).
3. Ball, I.R. and Possingham, H.P. (2000) MARXAN (V1.8.2): Marine Reserve Design Using Spatially Explicit Annealing, a Manual. GBRMPA report, Townsville.
4. Barton, D.N., Saloranta, T., Moe, S.J., Eggestad, H.O. and Kuikka, S. (2008) Bayesian belief networks as a meta-modelling tool in integrated river basin management - pros and cons in evaluating nutrient abatement decisions under uncertainty in a Norwegian river basin. Ecological Economics 66, 91-104.
5. Beck, M.B. (1999) Coping with ever larger problems, models, and databases. Water Science Technology 39, 1-11.
6. Benoit, H.P. and Swain, D.P. (2008) Impacts of environmental change and direct and indirect harvesting effects on the dynamics of a marine fish community. Canadian Journal of Fisheries and Aquatic Sciences 65, 2088-2104.
7. Box, G.E.P. (1979) Robustness in the strategy of scientific model building. In: Robustness in Statistics (eds R.L. Launer and G.N. Wilkinson ). Academic Press, New York, pp. 201-236.
8. Brand, E.J., Kaplan, I.C., Harvey, C.J. et al. (2007) A Spatially Explicit Ecosystem Model of the California Current's Food Web and Oceanography. U.S. Department of Commerce, NOAA Technical Memo. NMFS-NWFSC-84. Available at: (accessed 6 February 2011).
9. Brander, K.M. (2007) Global fish production and climate change. Proceedings of the National Academy of Sciences of the United States of America 104, 19709-19714.
10. Bundy, A., Shannon, L., Rochet, M.J. et al. (2010) The Good(ish), the Bad and the Ugly: a tripartite classification of ecosystem trends. ICES Journal of Marine Science 67, 745-768.
11. Carpenter, S.R., Pingali, P.L., Bennett, E.M. and Zurek, M.B. (eds) (2005) Ecosystems and Human Well-being: Scenarios: Findings of the Scenarios Working Group, Millennium Ecosystem Assessment. Island Press, Washington, pp. 551.
12. Christensen, V. (2010) MEY=MSY. Fish and Fisheries 11, 105-110.
13. Christensen, V. and Walters, C.J. (2004) Ecopath with Ecosim: methods, capabilities and limitations. Ecological Modelling 172, 109-139.
14. Condie, S.A., Waring, J., Mansbridge, J.V. and Cahill, M.L. (2005) Marine connectivity patterns around the Australian continent. Environmental Modelling & Software 20, 1149-1157.
15. Costello, C., Gaines, S.D. and Lynham, J. (2008) Can catch shares prevent fisheries collapse? Science 321, 1678-1681.
16. Cury, P.M., Shannon, L.J., Roux, J.-P. et al. (2005) Trophodynamic indicators for an ecosystem approach to fisheries. ICES Journal of Marine Science 62, 430-442.
17. Dambacher, J.M., Li, H.W. and Rossignol, P.A. (2002) Relevance of community structure in assessing indeterminacy of ecological predictions. Ecology 83, 1372-1385.
18. Elzinga, C.L., Salzer, D.W. and Willoughby, J.W. (1998) Measuring and Monitoring Plant Populations. Bureau of Land Management, Denver, CO. BLM Technical Reference 1730-1.
19. Fogarty, M.J. and Murawski, S.A. (1998) Large-scale disturbance and the structure of marine systems: fishery impacts on Georges Bank. Ecological Applications 8, S6-S22.
20. Fulton, E.A. (2001) The effects of model structure and complexity on the behaviour and performance of marine ecosystem models. PhD thesis, School of Zoology, University of Tasmania, Hobart, Tasmania.
21. Fulton, E.A. (2010) Approaches to end-to-end ecosystem models. Journal of Marine Systems 81, 171-183.
22. Fulton, E.A. and Smith, A.D.M. (2004) Lessons learnt from the comparison of three ecosystem models for Port Phillip Bay, Australia. African Journal Marine Science 26, 219-243.
23. Fulton, E.A., Smith, A.D.M. and Johnson, C.R. (2003a) Effect of complexity on marine ecosystem models. Marine Ecology Progress Series 253, 1-16.
24. Fulton, E.A., Smith, A.D.M. and Johnson, C.R. (2003b) Mortality and predation in ecosystem models: is it important how these are expressed? Ecological Modelling 169, 157-178.
25. Fulton, E.A., Fuller, M., Smith, A.D.M. and Punt, A.E. (2004a) Ecological indicators of the ecosystem effects of fishing: final report. Australian Fisheries Management Authority Report R99/1546, pp. 116.
26. Fulton, E.A., Parslow, J.S., Smith, A.D.M. and Johnson, C.R. (2004b) Biogeochemical marine ecosystem models II: the effect of physiological detail on model performance. Ecological Modelling 173, 371-406.
27. Fulton, E.A., Smith, A.D.M. and Johnson, C.R. (2004c) Effects of spatial resolution on the performance and interpretation of marine ecosystem models. Ecological Modelling 176, 27-42.
28. Fulton, E.A., Punt, A.E. and Smith, A.D.M. (2005) Which ecological indicators can robustly detect effects of fishing? ICES Journal of Marine Science 62, 540-551.
29. Fulton, E.A., Smith, A.D.M. and Smith, D.C. (2007) Alternative Management Strategies for Southeast Australian Commonwealth Fisheries: Stage 2: Quantitative Management Strategy Evaluation. Australian Fisheries Management Authority, Fisheries Research and Development Corporation Report.
30. Fulton, E.A., Smith, A.D.M., Smith, D.C. and van Putten, E.I. (in press) Human behaviour, the forgotten component of fisheries failures. Fish and Fisheries.
31. Grafton, R.Q., Hilborn, R., Ridgeway, L. et al. (2008) Positioning fisheries in a changing world. Marine Policy 32, 630-634.
32. Greenstreet, S.P.R. and Hall, S.J. (1996) Fishing and the ground-fish assemblage structure in the northwestern North Sea: an analysis of long-term and spatial trends. Journal of Animal Ecology 65, 577-598.
33. Halfon, E. (1979) Computer-based development of large-scale ecological models: problems and prospects. In: Systems Analysis of Ecosystems (eds G.S. Innis and R.V. O'Neill ). International Co-operative Publishing House, Fairland, MD, pp. 197-209.
34. Hayes, D., Fulton, E., Condie, S.A. et al. (2007) Ecosystem modelling: a tool for sustainable regional development in the Clarence estuary. Proceedings of 16th NSW Coastal Conference, Yamba, NSW 7-9 November 2007.
35. Healey, M.C. and Hennessey, T. (1998) The paradox of fairness: the impact of escalating complexity on fishery management. Marine Policy 22, 109-118.
36. Hilborn, R., Punt, A.E. and Orensanz, J. (2004) Beyond band-aids in fisheries management: fixing world fisheries. Bulletin of Marine Science 74, 493-507.
37. Horne, P., Kaplan, I.C., Marshall, K. et al. (2010) Design and Parameterization of a Spatially Explicit Ecosystem Model of the Central California Current. U.S. Dept. of Commerce, NOAA Technical Memo, NMFS-NWFSC-104, 140 p. Available at: (accessed 6 February 2011).
38. IPCC (2007) Climate Change 2007 Synthesis Report. Cambridge University Press, New York.
39. Jennings, S. and Dulvy, N.K. (2005) Reference points and reference directions for size-based indicators of community structure. ICES Journal of Marine Science 62, 397-404.
40. Jennings, S., Kaiser, M.J. and Reynolds, J.D. (2001) Marine Fisheries Ecology. Blackwell Science, London, pp. 417.
41. Johnson, P., Fulton, E.A. and Grist, E.P.M. (2008) Ecosystem impacts of high fishing mortality on squid and myctophid stocks in south eastern Tasmania. MSc qualifying paper, University of Tasmania, Hobart.
42. Jones, G. (2009) The adaptive management system for the Tasmanian Wilderness World Heritage Area - linking management planning with effectiveness evaluation. In: Adaptive Environmental Management A Practitioner's Guide (eds C. Allan and G. Stankey ). Jointly published by Springer with CSIRO Publishing, Collingwood, Australia, pp. 360.
43. Kaplan, I.C. and Levin, P.S. (2009) Ecosystem based management of what? An emerging approach for balancing conflicting objectives in marine resource management. In: The Future of Fisheries in North America (eds R.J. Beamish and B.J. Rothschild ). Springer, NY, pp. 736.
44. Kaplan, I.C., Levin, P.S., Burden, M. and Fulton, E.A. (2010) Fishing catch shares in the face of global change: a framework for integrating cumulative impacts and single species management. Canadian Journal of Fisheries and Aquatic Sciences 67, 1968-1982.
45. Koch, E.W., Barbier, E.B., Silliman, B.R. et al. (2009) Non-linearity in ecosystem services: temporal and spatial variability in coastal protection. Frontiers in Ecology and Environment 7, 29-37. doi: .
46. Kramer-Schadt, S., Revilla, E., Wiegand, T. and Grimm, V. (2007) Patterns for parameters in simulation models. Ecological Modelling 204, 553-556.
47. Lee, K.N. (1999) Appraising adaptive management. Conservation Ecology 3, 3.
48. Levin, P.S., Fogarty, M.J., Murawski, S.A. and Fluharty, D. (2009) Integrated ecosystem assessments: developing the scientific basis for ecosystem-based management of the ocean. PLoS Biology 7, e1000014. doi: .
49. Link, J.S. (2005) Translating ecosystem indicators into decision criteria. ICES Journal of Marine Science 62, 569-576.
50. Link, J.S. (2007) Under-appreciated species in ecology: "ugly fish" in the Northwest Atlantic Ocean. Ecological Applications 17, 2037-2060.
51. Link, J.S., Gamble, R.J. and Fulton, E.A. (2010) NEUS - ATLANTIS: Construction, Calibration and Application of an Ecosystem Model with Ecological Interactions, Physiographic Conditions, and Fleet Behavior. NOAA NMFS NEFSC Center Reference Document.
52. Link, J.S., Fulton, E.A. and Gamble, R.J. (in press) The Northeast US Application of ATLANTIS: a full system model exploring marine ecosystem dynamics in a living marine resource management context. Progress in Oceanography 87, 214-234.
53. Methot, R.M. (2009) User Manual for Stock Synthesis Model Version 3.03a. Available at: (accessed 6 February 2011).
54. Moore, R.V. and Tindall, C.I. (2005) An overview of the open modelling interface and environment (the OpenMI). Environmental Science & Policy 8, 279-286.
55. National Research Council (NRC), Committee on Models in the Regulatory Decision Process (2007) Models in Environmental Regulatory Decision Making. National Academies Press, Washington, pp. 267.
56. NEFSC (2008) 47th Northeast Regional Stock Assessment Workshop (47th SAW) Assessment Report Appendixes. US Department Commerce, Northeast Fisheries Science Centre Reference Document. 08-12b; 2, 097 p. Available at: (accessed 6 February 2011).
57. Pantus, F.J. (2007) Sensitivity analysis for complex ecosystem models. PhD thesis, School of Physical Sciences, The University of Queensland. Available at: (accessed 6 February 2011).
58. Plagányi, E. (2007) Models for an Ecosystem Approach to Fisheries. FAO Fisheries Technical Paper, 477. FAO, Rome, pp. 108.
59. Plagányi, É.E., Rademeyer, R.A., Butterworth, D.S., Cunningham, C.L. and Johnston, S.J. (2007) Making management procedures operational - innovations implemented in South Africa. ICES Journal of Marine Science 64, 626-632.
60. Possingham, H.P., Ball, I.R. and Andelman, S. (2000) Mathematical methods for identifying representative reserve networks. In: Quantitative Methods for Conservation Biology (eds S. Ferson and M. Burgman ). Springer-Verlag, New York, pp. 291-305.
61. Rice, J.C. and Rochet, M.J. (2005) A framework for selecting a suite of indicators for fisheries management. ICES Journal of Marine Science 62, 516-527.
62. Rochet, M.J. and Trenkel, V.M. (2003) Which community indicators can measure the impact of fishing? A review and proposals. Canadian Journal of Fisheries and Aquatic Science 60, 86-99.
63. Rockström, J., Steffen, W., Noone, K. et al. (2009) A safe operating space for humanity. Nature 461, 472-475.
64. Rodionov, S. and Overland, J.E. (2005) Application of a sequential regime shift detection method to the Bering Sea ecosystem. ICES Journal of Marine Science 62, 328-332.
65. Russ, G.R. and Alcala, A.C. (1996) Marine reserves: rates and patterns of recovery and decline of large predatory fish. Ecological Applications 6, 947-961.
66. Sainsbury, K.J., Punt, A.E. and Smith, A.D.M. (2000) Design of operational management strategies for achieving fishery ecosystem objectives. ICES Journal of Marine Science 57, 731-741.
67. Savina, M. (2009) Atlantis-INFORMD: Scoping and Potential of a Regional Ecosystem Model: Final Report. CSIRO, Wealth From Oceans Report, Hobart, pp. 29.
68. Savina, M., Grist, E., Boschetti, F., Fulton, E.A. and McDonald, A.D. (2005) Implementation of the Atlantis Ecological Model in the Westernport Scoping Study. CSIRO, Wealth From Oceans Report, Hobart, pp. 43.
69. Savina, M., Fulton, E., Condie, S. et al. (2008) Ecologically sustainable development of the regional marine and estuarine resources of NSW: modelling of the NSW continental shelf ecosystem. CSIRO and NSW DPI Report, pp. 71.
70. Smith, T.D. (1994) Scaling Fisheries: The Science of Measuring the Effects of Fishing, 1855-1955. Cambridge University Press, Cambridge, UK.
71. Smith, A.D.M., Sainsbury, K.J. and Stevens, R.A. (1999) Implementing effective fisheries management systems - management strategy evaluation and the Australian partnership approach. ICES Journal of Marine Science 56, 967-979.
72. Smith, D.C., Smith, A.D.M. and Punt, A.E. (2001) Approach and process for stock assessment in the South East Fishery: a perspective. Marine and Freshwater Research 52, 671-681.
73. Smith, A.D.M., Sachse, M., Smith, D.C. et al. (2004) Alternative Management Strategies for the Southern and Eastern Scalefish and Shark Fishery - Qualitative Assessment Report. Australian Fisheries Management Authority, Canberra.
74. Smith, A.D.M., Smith, D.C., Tuck, G.N. et al. (2008) Experience in implementing harvest strategies in Australia's south-eastern fisheries. Fisheries Research 94, 373-379.
75. Smith, D.C., Johnson, P. and Fulton, E.A. (2010) Developing integrated performance measures for spatial management of marine systems. Fisheries Research and Development Corporation Report.
76. Stow, C.A., Jolliff, J., McGillicuddy Jr, D.J. et al. (2009) Skill assessment for coupled biological/physical models of marine systems. Journal of Marine Systems 76, 4-15.
77. Townsend, H.M., Link, J.S., Osgood, K.E. et al. (eds) (2008) Report of the NEMoW (National Ecosystem Modeling Workshop). NOAA Technical Memorandum NMFS-F/SPO-87, pp. 93.
78. Travers, M., Shin, Y.-J., Jennings, S. and Cury, P. (2007) Towards end-to-end models for investigating the effects of climate and fishing in marine ecosystems. Progress in Oceanography 75, 751-770.
79. Travers, M., Shin, Y.-J., Jennings, S. et al. (2009) Two-way coupling versus one-way forcing of plankton and fish models to predict ecosystem changes in the Benguela. Ecological Modelling 220, 3089-3099.
80. Trenkel, V.M. and Rochet, M.J. (2003) Performance of indicators derived from abundance estimates for detecting the impact of fishing on a fish community. Canadian Journal of Fisheries and Aquatic Science 60, 67-85.
81. Trenkel, V.M., Rochet, M.-J. and Mesnil, B. (2007) From model-based prescriptive advice to indicator-based interactive advice. ICES Journal of Marine Science 64, 768-774.
82. Walters, C., Christensen, V. and Pauly, D. (1997) Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments. Reviews in Fish Biology and Fisheries 7, 139-172.
83. Walters, C., Christensen, V., Walters, W. and Rose, K. (2010) Representation of multistanza life histories in Ecospace models for spatial organization of ecosystem trophic interaction patterns. Bulletin of Marine Science 86, 439-459.
84. Watt, K.E.F. (1975) Critique and comparison of biome ecosystem modeling. In: System Analysis and Simulation in Ecology, III (ed. B.C. Patten ). Academic Press, New York, London, pp. 139-152.
85. Worm, B., Barbier, E.B., Beaumont, N. et al. (2006) Impacts of biodiversity loss on ocean ecosystem services. Science 314, 787-790.
86. Worm, B., Hilborn, R., Baum, J. et al. (2009) Rebuilding global fisheries. Science 325, 578-585.