Best practice in Ecopath with Ecosim food-web models for ecosystem-based management

Ecological Modelling

Volumn 331, Issue , 2016, Pages 173-184

  Heymans, Johanna Jacomina ^a   Coll, Marta ^b,c   Link, Jason S ^d   Mackinson, Steven ^e   Steenbeek, Jeroen ^f   Walters, Carl ^g   Christensen, Villy ^g  

^a SCOTTISH MARINE INSTITUTE   (United Kingdom)

^b INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (France)

^c INSTITUT DE CIÈNCIES DEL MAR   (Spain)

^d NORTHEAST FISHERIES SCIENCE CENTER   (United States)

^e CENTRE FOR ENVIRONMENT   (United Kingdom)

^f Ecopath International Initiative Research Association   (Spain)

^g UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

Ecological network analysis; Ecopath with Ecosim; Ecosystem modelling; Ecosystem based management; Monte Carlo; Time series fitting

Indexed keywords

INTELLIGENT SYSTEMS; MANAGERS; MONTE CARLO METHODS; QUALITY ASSURANCE; TIME SERIES; TIME SERIES ANALYSIS;

ECOLOGICAL NETWORK ANALYSIS; ECOLOGICAL PRINCIPLES; ECOPATH WITH ECOSIM; ECOSYSTEM MANAGEMENT; ECOSYSTEM MODELLING; ECOSYSTEM-BASED MANAGEMENT; FITTING PROCEDURE; STATE OF THE ART;

ECOSYSTEMS;

BEST MANAGEMENT PRACTICE; CALIBRATION; ECOSYSTEM MANAGEMENT; ECOSYSTEM MODELING; MONTE CARLO ANALYSIS; NETWORK ANALYSIS; TIME SERIES ANALYSIS; UNCERTAINTY ANALYSIS;

EID: 84955581372     PISSN: 03043800     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ecolmodel.2015.12.007     Document Type: Article

References (93)

1. Ahrens R.N.M., Walters C.J., Christensen V. Foraging arena theory. Fish Fish. 2012, 13:41-59.
2. Akaike H. A new look at the statistical model identification. IEEE Trans. Autom. Control 1974, 19:716-723.
3. Akoglu E., Libralato S., Salihoglu B., Oguz T., Solidoro C. EwE-F 1.0: an implementation of Ecopath with Ecosim in Fortran 95/2003 for coupling. Geosci. Model Dev. Discuss. 2015, 8:1511-1537.
4. Alexander K.A., Heymans J.J., MaGill S., Tomczak M., Holmes S., Wilding T.A. Investigating the recent decline in gadoid stocks in the west of Scotland shelf ecosystem using a food-web model. ICES J. Mar. Sci. 2015, 72:436-449.
5. Araújo J.N., Bundy A. Effects of environmental change, fisheries and trophodynamics on the ecosystem of the western Scotian Shelf, Canada. Mar. Ecol. Prog. Ser. 2012, 464:51-67.
6. Arreguín-Sánchez F., Ruiz-Barreiro T.M. Approaching a functional measure of vulnerability in marine ecosystems. Ecol. Indic. 2014, 45:130-138.
7. Aydin K., Gaichas S., Ortiz I., Kinzey D., Friday N. A comparison of the Bering Sea, Gulf of Alaska, and Aleutian Islands Large Marine Ecosystems through food web modeling. NOAA Technical Memorandum NMFS-AFSC-178 2007, NOAA.
8. Azam F., Fenchel T., Field J.G., Gray J.S., Meyer-Reil L.A., Thingstad F. The ecological role of water-column microbes in the sea. Mar. Ecol. Prog. Ser. 1983, 10:257-263.
9. Baird D., McGlade J.M., Ulanowicz R.E. The comparative ecology of six marine ecosystems. Philos. Trans. R. Soc. Lond. B 1991, 333:15-29.
10. Brey T. A collection of empirical relations for use in ecological modelling. Naga ICLARM Q. 1999, 22:24-28.
11. Brey T. An empirical model for estimating aquatic invertebrate respiration. Methods Ecol. Evol. 2010, 1:92-101.
12. Brey T. A multi-parameter artificial neural network model to estimate macrobenthic invertebrate productivity and production. Limnol. Oceanogr.: Methods 2012, 10:581-589.
13. Burnham K.P., Anderson D.R. Multimodel inference: understanding AIC and BIC in model selection. Sociol. Methods Res. 2004, 33:261-304.
14. Christensen V. Ecosystem maturity - towards quantification. Ecol. Model. 1995, 77:3-32.
15. Christensen V., Pauly D. ECOPATH II - a software for balancing steady-state ecosystem models and calculating network characteristics. Ecol. Model. 1992, 61:169-185.
16. Christensen V., Pauly D. Trophic models of aquatic ecosystems. ICLARM Conference Proceedings 26. 1st edition 1993, International Center for Living Resources Management, Manila, Philippines.
17. Christensen V., Walters C. Ecopath with ecosim: methods, capabilities and limitations. Pages 79-105. Methods for Evaluating the Impacts of Fisheries on North Atlantic Ecosystems 2000, Fisheries Centre, University of British Columbia, Vancouver, BC. D. Pauly, T.J. Pitcher (Eds.).
18. Christensen V., Walters C.J. Ecopath with Ecosim: methods, capabilities and limitations. Ecol. Model. 2004, 172:109-139.
19. Christensen V., Walters C.J., Pauly D., Forrest R. Ecopath with Ecosim Version 6. User Guide 2008, Fisheries Centre, University of British Columbia, Vancouver, Canada.
20. Christensen V., Coll M., Steenbeek J., Buszowski J., Chagaris D., Walters C.J. Representing variable habitat quality in a spatial food web model. Ecosystems 2014, 1-16.
21. Coll M., Steenbeek J. New software plug-in to calculate biodiversity and conservation-based indicators from EwE food web models. Pages 67-68. Ecopath 30 Years Conference Proceedings: Extended Abstracts. Fisheries Centre Research Reports 22(3) 2014, Fisheries Centre, University of British Columbia, Vancouver. J. Steenbeek, C. Piroddi, M. Coll, J.J. Heymans, S. Villasante, V. Christensen (Eds.).
22. Coll M., Palomera I., Tudela S., Dowd M. Food-web dynamics in the South Catalan Sea ecosystem (NW Mediterranean) for 1978-2003. Ecol. Model. 2008, 217:95-116.
23. Coll M., Palomera I., Tudela S. Decadal changes in a NW Mediterranean Sea food web in relation to fishing exploitation. Ecol. Model. 2009, 220:2088-2102.
24. Coll M., Akoglu E., Arreguín-Sánchez F., Fulton E.A., Gascuel D., Heymans J.J., Libralato S., Mackinson S., Palomera I., Piroddi C., Shannon L.J., Steenbeek J., Villasante S., Christensen V. Modelling dynamic ecosystems: venturing beyond boundaries with the Ecopath approach. Rev. Fish Biol. Fish. 2015, 25:413-424.
25. Colléter M., Valls A., Guitton J., Morissette J., Arreguín-Sánchez F., Christensen V., Gascuel D., Pauly D. EcoBase: a repository solution to gather and communicate information from EwE models. Fisheries Centre Research Reports 2013, UBC Fisheries Centre.
26. Cox S.P., Essington T.E., Kitchell J.F., Martell S.J.D., Walters C.J., Boggs C., Kaplan I. Reconstructing ecosystem dynamics in the central Pacific Ocean, 1952-1998. II. A preliminary assessment of the trophic impacts of fishing and effects on tuna dynamics. Can. J. Fish. Aquat. Sci. 2002, 59:1736-1747.
27. Darwall W.R.T., Allison E.H., Turner G.F., Irvine K. Lake of flies, or lake of fish? A trophic model of Lake Malawi. Ecol. Model. 2010, 221:713-727.
28. Deehr R.A., Luczkovich J.J., Hart K.J., Clough L.M., Johnson B.J., Johnson J.C. Using stable isotope analysis to validate effective trophic levels from Ecopath models of areas closed and open to shrimp trawling in Core Sound, NC, USA. Ecol. Model. 2014, 282:1-17.
29. FAO Fisheries Management. The Ecosystem Approach To Fisheries. Best Practices in Ecosystem Modelling to Informing an Ecosystem Approach to Fisheries 2008, FAO.
30. Finn J.T. Measures of ecosystem structure and function derived from analysis of flows. J. Theor. Biol. 1976, 56:363-380.
31. Fulton E.A., Smith A.D.M. Lessons learnt from a comparison of three ecosystem models for Port Phillip Bay, Australia. Afr. J. Mar. Sci. 2004, 26:219-243.
32. Gaichas S.K., Aydin K.Y., Francis R.C. What drives dynamics in the Gulf of Alaska? Integrated hypotheses of species, fishing, and climate relationships using ecosystem modeling. Can. J. Fish. Aquat. Sci. 2011, 68:1553-1578.
33. Gaichas S.K., Odell G., Aydin K.Y., Francis R.C. Beyond the defaults: functional response parameter space and ecosystem-level fishing thresholds in dynamic food web model simulations. Can. J. Fish. Aquat. Sci. 2012, 69:2077-2094.
34. Grimm V., Revilla E., Berger U., Jeltsch F., Mooij W.M., Railsback S.F., Thulke H.-H., Weiner J., Wiegand T., DeAngelis D.L. Pattern-oriented modeling of agent-based complex systems: lessons from ecology. Science 2005, 310:987-991.
35. Guesnet V., Lassalle G., Chaalali A., Kearney K., Saint-Béat B., Karimi B., Grami B., Tecchio S., Niquil N., Lobry J. Incorporating food-web parameter uncertainty into Ecopath-derived ecological network indicators. Ecol. Model. 2015, 313:29-40.
36. Heymans J.J. Ecosystem model of the Western and Central Aleutian Islands in 1963, 1979 and 1991. Pages 8-82. The Steller sea lion decline: models and data of the Northeast Pacific, Fisheries Centre Research Reports 13(1) 2005, S. Guénette, V. Christensen (Eds.).
37. Heymans J.J., Tomczak M.T. Regime shifts in the Northern Benguela ecosystem: challenges for management. Ecol. Model. 2016, 331:151-159.
38. Heymans J.J., Ulanowicz R.E., Bondavalli C. Network analysis of the South Florida Everglades graminoid marshes and comparison with nearby cypress ecosystems. Ecol. Model. 2002, 149:5-23.
39. Heymans J.J., Shannon L.J., Jarre A. Changes in the northern Benguela ecosystem over three decades: 1970s, 1980s and 1990s. Ecol. Model. 2004, 172:175-195.
40. Heymans J.J., Guénette S., Christensen V. Evaluating network analysis indicators of ecosystem status in the Gulf of Alaska. Ecosystems 2007, 10:488-502.
41. Heymans J.J., Coll M., Libralato S., Morissette L., Christensen V. Global patterns in ecological indicators of marine food webs: a modelling approach. PLOS ONE 2014, 9:e95845.
42. Hilborn R., Walters C.J. Quantitative Fisheries Stock Assessment: Choice, Dynamics and Uncertainty 1992, Kluwer Academic Publishers, Boston.
43. Hurvich C.M., Tsai C.-L. A crossvalidatory AIC for hard wavelet thresholding in spatially adaptive function estimation. Biometrika 1998, 85:701-710.
44. Hyder K., Rossberg A.G., Allen J.I., Austen M.C., Barciela R.M., Blanchard J., Burrows M.T., Defriez E., Dorrington T., Edwards K., Garcia-Carreras B., Heath M.R., Hembury D.J., Heymans J.J., Holt J., Houle J.E., Jennings S., Mackinson S., McPike R., Mee L., Mills D.K., Montgomery C., Pearson D., Pinnegar J.K., Pollicino M., Popova E.E., Rae L., Rogers S.I., Speirs D., Spence M., Thorpe R., Turner R.K., van der Molen J., Yool A., Paterson D.M. Making modelling count - increasing the contribution of shelf-seas community and ecosystem models to policy development and management. Mar. Policy 2015, 61:291-302.
45. ICES Report of the Working Group on Multispecies Assessment Methods (WGSAM), 5-9 October 2009, ICES Headquarters, Copenhagen 2009, ICES CM 2009/RMC:10 ICES CM 2009/RMC:10, ICES, Copenhagen.
46. ICES Report of the Working Group on Multispecies Assessment Methods (WGSAM), 10-14 October 2011, Woods Hole, USA 2012, ICES CM 2011/SSGSUE:10 ICES CM 2011/SSGSUE:10, ICES, Copenhagen.
47. ICES Interim Report of the Working Group on Multispecies Assessment Methods (WGSAM), 21-25 October 2013, Stockholm, Sweden 2013, ICES CM 2013/SSGSUE:10 ICES CM 2013/SSGSUE:10, ICES, Copenhagen.
48. ICES Interim Report of the Working Group on Multispecies Assessment Methods (WGSAM), 9-13 November 2015, Woods hole, USA 2016, ES CM 2016/SSGSUE ICES CM 2016/SSGSUE, ICES, Copenhagen.
49. Innes S., Lavigne D.M., Earle W.M., Kovacs K.M. Feeding rates of seals and whales. J. Anim. Ecol. 1987, 56:115-130.
50. Kearney K.A., Stock C., Sarmiento J.L. Amplification and attenuation of increased primary production in a marine food web. Mar. Ecol. Prog. Ser. 2013, 491:1-14.
51. Kramer-Schadt S., Revilla E., Wiegand T., Grimm V. Patterns for parameters in simulation models. Ecol. Model. 2007, 204:553-556.
52. Lassalle G., Bourdaud P., Saint-Béat B., Rochette S., Niquil N. A toolbox to evaluate data reliability for whole-ecosystem models: application on the Bay of Biscay continental shelf food-web model. Ecol. Model. 2014, 285:13-21.
53. Link J.S. Adding rigor to ecological network models by evaluating a set of pre-balance diagnostics: a plea for PREBAL. Ecol. Model. 2010, 221:1582-1593.
54. Link J., Overholtz W., O'Reilly J., Green J., Dow D., Palka D., Legault C., Vitaliano J., Guida V., Fogarty M., Brodziak J., Methratta L., Stockhausen W., Col L., Griswold C. The Northeast US continental shelf Energy Modeling and Analysis exercise (EMAX): ecological network model development and basic ecosystem metrics. Contributions from Advances in Marine Ecosystem Modelling Research II 23-26 June 2008, Plymouth, UK. J. Mar. Syst. 2008, 74:453-474.
55. Lucey S.M., Aydin K.Y., Gaichas S.K., Fogarty M.J., Hyun S.-Y., Cadrin S.X. Improving the EBFM toolbox with an alternative open source mass balance model. Pages 204-205. Ecopath 30 years conference proceedings: Extended Abstracts, Fisheries Centre Research Reports 22(3) 2014, Fisheries Centre UBC, Vancouver. J. Steenbeek, C. Piroddi, M. Coll, J.J. Heymans, S. Villasante, V. Christensen (Eds.).
56. Mackinson S. Combined analyses reveal environmentally driven changes in the North Sea ecosystem and raise questions regarding what makes an ecosystem model's performance credible?. Can. J. Fish. Aquat. Sci. 2014, 71:31-46.
57. Mackinson S., Daskalov G. An ecosystem model of the North Sea for use in research supporting the ecosystem approach to fisheries management: description and parameterisation. Cefas Technical Report Cefas Science Series Technical Report 142 2007, CEFAS, Lowestoft.
58. Mackinson S., Daskalov G., Heymans J.J., Neira S., Arancibia H., Zetina-Rejón M., Jiang H., Cheng H.Q., Coll M., Arreguin-Sanchez F., Keeble K., Shannon L. Which forcing factors fit? Using ecosystem models to investigate the relative influence of fishing and changes in primary productivity on the dynamics of marine ecosystems. Ecol. Model. 2009, 220:2972-2987.
59. Mackinson S., Deas B., Beveridge D., Casey J. Mixed-fishery or ecosystem conundrum? Multispecies considerations inform thinking on long-term management of North Sea demersal stocks. Can. J. Fish. Aquat. Sci. 2009, 66:1107-1129.
60. Mann K.H. Production and use of detritus in various freshwater, estuarine, and coastal marine ecosystems. Limnol. Oceanogr. 1988, 33:910-930.
61. Moloney C.L., Jarre A., Arancibia H., Bozec Y.-M., Neira S., Roux J.-P., Shannon L.J. Comparing the Benguela and Humboldt marine upwelling ecosystems with indicators derived from inter-calibrated models. ICES J. Mar. Sci. 2005, 62:493-502.
62. Morissette L. Complexity, Cost and Quality of Ecosystem Models and Their Impact on Resilience: A Comparative Analysis, with Emphasis on Marine Mammals and the Gulf of St. Lawrence 2007, University of British Columbia, Vancouver.
63. Nilsson S.G., Nilsson I.N. Numbers, Food Consumption, and Fish Predation by Birds in Lake Möckeln, Southern Sweden. Ornis Scand. 1976, 7:61-70.
64. Odum E.P. The strategy of ecosystem development. Science 1969, 164:262-270.
65. Orr K.K. Predicting the Ecosystem Effects of Harvesing Beach-cast Kelp for Biofuel 2013, University of Aberdeen, Oban.
66. Palomares M.L.D., Pauly D. Predicting food consumption of fish populations as functions of mortality, food type, morphometrics, temperature and salinity. Mar. Freshw. Res. 1998, 49:447-453.
67. Pauly D. On the interrelationships between natural mortality, growth parameters, and mean environmental temperature in 175 fish stocks. Journal du Conseil international pour l'Exploration de la Mer 1980, 39:175-192.
68. Pérez-España H., Arreguín-Sánchez F. An inverse relationship between stability and maturity in models of aquatic ecosystems. Ecol. Model. 2001, 145:189-196.
69. Peters R.H. The Ecological Implications of Body Size 1983, Cambridge University Press, Cambridge. 1st ed.
70. Pinnegar J.K., Blanchard J.L., Mackinson S., Scott R.D., Duplisea D.E. Aggregation and removal of weak-links in food-web models: system stability and recovery from disturbance. Ecol. Model. 2005, 184:229-248.
71. Pitcher T.J., Heymans J.J. Ecosystem models of Newfoundland for the time periods 1995, 1985, 1900 and 1450. Fisheries Centre Research Reports 10(5) 2002.
72. Plagányi É.E. Models for an ecosystem approach to fisheries. FAO Fisheries Technical Paper No. 477. FAO Fisheries Technical Paper No. 477. 477 2007, FAO, Rome.
73. Platts M., Mackinson S. Assessing the Effect of Model Parameter Uncertainty on the Performance Management Strategies in Ecosim 2015.
74. Polovina J.J. Model of a coral reef ecosystem I. The ECOPATH model and its application to French Frigate Shoals. Coral Reefs 1984, 3:1-11.
75. Prato G., Gascuel D., Valls A., Francour P. Towards a balance between complexity and feasibility in food-web models of Mediterranean coastal ecosystems: addressing uncertainty while accounting for data collection constraints. Fish. Centre Res. Rep. 2014, 22:70-71.
76. Ramsvatn S. Investigating Coastal Ecosystem Structure and Dynamics using Ecopath Mass-Balance Modelling and Stable Isotope Data 2013, University of Tromso, Tromso.
77. Scott E., Serpetti N., Steenbeek J., Heymans J.J. A Stepwise Fitting Procedure for Automated Fitting of Ecopath with Ecosim Models. SoftwareX 2015, under review.
78. Shannon L.J., Moloney C.L., Jarre A., Field J.G. Trophic flow in the southern Benguela during the 1980s and 1990s. Contributions from Advances in Marine Ecosystem Modelling Research II 23-26 June 2008, Plymouth, UK, 39. J. Mar. Syst. 2003, 83-116.
79. Shannon L.J., Christensen V., Walters C.J. Modelling stock dynamics in the southern Benguela ecosystem for the period 1978-2002. Afr. J. Mar. Sci. 2004, 26:179-196.
80. STECF Multiannual Management Plans (North Sea), Working Graoup 16-20th March 2015, Ispra, Italy. STECF EWG 15 02 2015.
81. Steenbeek J., Coll M., Gurney L., Mélin F., Hoepffner N., Buszowski J., Christensen V. Bridging the gap between ecosystem modeling tools and geographic information systems: driving a food web model with external spatial-temporal data. Ecol. Model. 2013, 263:139-151.
82. Steenbeek J., Piroddi C., Coll M., Heymans J.J., Villasante S., Christensen V. Ecopath 30 Years Conference Proceedings: Extended Abstracts. Fisheries Centre Research Reports 2014.
83. Steenbeek J., Buszowski J., Christensen V., Akoglu E., Aydin K., Ellis N., Felinto D., Guitton J., Lucey S., Kearney K., Mackinson S., Pan M., Platts M., Walters C. Ecopath with Ecosim as a model-building toolbox: source code capabilities, extensions, and variations. Ecol. Model. 2015, 10.1016/j.ecolmodel.2015.06.031.
84. Stergiou K.I., Karpouzi V.S. Feeding habits and trophic levels of Mediterranean fish. Rev. Fish Biol. Fish. 2002, 11:217-254.
85. Tecchio S., Coll M., Christensen V., Company J.B., Ramírez-llodra E., Sardà F. Food web structure and vulnerability of a deep-sea ecosystem in the NW Mediterranean Sea. Deep Sea Res. Part I: Oceanogr. Res. Pap. 2013, 75:1-15.
86. Tomczak M.T., Niiranen S., Hjerne O., Blenckner T. Ecosystem flow dynamics in the Baltic Proper-using a multi-trophic dataset as a basis for food-web modelling. Ecol. Model. 2012, 230:123-147.
87. Tomczak M.T., Heymans J.J., Yletyinen J., Niiranen S., Otto S.A., Blenckner T. Ecological network indicators of ecosystem status and change in the Baltic Sea. PLOS ONE 2013, 8:e75439.
88. Walters C.J., Martell S.J.D. Fisheries Ecology and Management 2004, Princeton University Press, Princeton.
89. Walters C., Christensen V., Pauly D. Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments. Rev. Fish Biol. Fish. 1997, 7:139-172.
90. Walters C., Pauly D., Christensen V. Ecospace: predicting of mesoscale spatial patterns in trophic relationships of exploited ecosystems, with emphasis on the impacts of marine protected areas. Ecosystems 1999, 2:539-554.
91. Walters C.J., Christensen V., Martell S.J., Kitchell J.F. Possible ecosystem impacts of applying MSY policies from single-species assessment. ICES J. Mar. Sci./Journal du Conseil 2005, 62:558-568.
92. Winberg G.G. Rate of Metabolism and Food Requirements of Fishes 1956.
93. Zetina-Rejón M.J., Cabrera-Neri E., López-Ibarra G.A., Arcos-Huitrón N.E., Christensen V. Trophic modeling of the continental shelf ecosystem outside of Tabasco, Mexico: a network and modularity analysis. Ecol. Model. 2015, 313:314-324.