REFERENCES
Abrams, Peter A. "The Fallacies of" Ratio‐Dependent" Predation." Ecology 75, no. 6 (1994): 1842-1850.
Ainsworth, C.H. and Walters, C.J. (2015) Ten common mistakes made in Ecopath with Ecosim modelling. Ecological Modelling 308, 14–17.
Ainsworth, C.H., Morzaria-Luna, H., Kaplan, I.C., Levin, P.S., Fulton, E.A., Cudney-Bueno, R., Turk-Boyer, P., Torre, J., Danemann, G.D., and Pfister, T. 2012a. Effective ecosystem-based management must encourage regulatory compliance: A Gulf of California case study. Mar. Policy 36(6): 1275–1283.
Ainsworth, C.H., Morzaria-Luna, H.N., Kaplan, I.C., Levin, P.S., and Fulton, E.A. 2012b. Full compliance with harvest regulations yields ecological benefits: Northern Gulf of California case study. J. Appl. Ecol. 49(1): 63–72.
Ainsworth, C.H., Schirripa, M.J. and Morzaria Luna, H. (2015) An Atlantis Ecosystem Model for the Gulf of Mexico supporting Integrated Ecosystem Assessment. NOAA Technical Memorandum NMFS-SEFSC-676. Miami, USA.Available from http://dx.doi.org/10.7289/V5X63JVH [accessed 21 December 2015].
Alin, S.R., Feely, R.A., Dickson, A., Hernandez-Ayon, J.M., Juranek, L.W., Ohman, M.D. and Goericke, R. (in revision) Robust empirical relationships for estimating the carbonate system in the southern California Current System using hydrographic data and application to CalCOFI hydrographic cruise data (2005–2011). Journal of Geophysical Research.
Arditi, R., & Ginzburg, L. R. (1989). Coupling in predator-prey dynamics: ratio-dependence. Journal of theoretical biology, 139(3), 311-326.
Audzijonyte, A., Kuparinen A., Gorton R., Fulton E.A. (2013) Ecological consequences of body size decline in harvested fish species: positive feedback loops in trophic interactions amplify human impact. Biology Letters, 9(2):1103
Audzijonyte, A., Kuparinen, A., Fulton, E.A. (2014) Ecosystem effects of contemporary life-history changes are comparable to those of fishing. Marine Ecology Progress Series 495: 219-231
Aydin, K., Gaichas, S., Ortiz, I., Kinzey, D. and Friday, N. (2007) A Comparison of the Bering Sea, Gulf of Alaska, and Aleutian Islands Large Marine Ecosystems Through Food Web Modeling.
Behrenfeld, M.J. and Falkowski, P.G. (1997a) A consumer’s guide to phytoplankton primary productivity models. Limnology and Oceanography 42, 1479–1491.
Behrenfeld, M.J. and Falkowski, P.G. (1997b) Photosynthetic rates derived from satellite-based chlorophyll concentration. Limnology and oceanography 42, 1–20.
Brand, E.J., Kaplan, I.C., Harvey, C.J., Levin, P.S., Fulton, E.A., Hermann, A.J. and Field, J.C. (2007) A Spatially Explicit Ecosystem Model of the California Current’s Food Web and Oceanography. NOAA Technical Memorandum NMFS-NWFSC-84.
Brassington, G.G., Pugh, T., Spillman, C., Schulz, E., Beggs, H., Schiller, A. and Oke, P.R. (2007) BLUElink> Development of operational oceanography and servicing in Australia. Journal of Research and Practice in Information Technology 39, 151–164.
Chassignet, E.P., Hurlburt, H.E., Smedstad, O.M., Halliwell, G.R., Hogan, P.J., Wallcraft, A.J. and Bleck, R. (2006) Ocean prediction with the hybrid coordinate ocean model (HYCOM). Springer.
Christensen, V., and Walters, C.J. 2004. Ecopath with Ecosim: methods, capabilities and limitations. Ecol. Model. 172(2-4): 109–139.
Essington, T.E. and Plagányi, É.E. (2013). "Pitfalls and guidelines for “recycling” models for ecosystem-based fisheries management: evaluating model suitability for forage fish fisheries." ICES Journal of Marine Science 71: 118–127.
Fiechter, J., Rose, K.A., Curchitser, E.N. and Hedstrom, K.S. (2014) The role of environmental controls in determining sardine and anchovy population cycles in the California Current: Analysis of an end-to-end model. Progress in Oceanography.
Fulton, E.A., M. Fuller, A.D.M. Smith, and A.E. Punt. 2004a. Ecological Indicators of the Ecosystem Effects of Fishing: Final Report. Australian Fisheries Management Authority Report, R99/1546.
Fulton, E.A., A.D.M. Smith and C.R. Johnson. 2004b. Effects of spatial resolution on the performance and interpretation of marine ecosystem models. Ecological Modelling 176: 27 – 42.
Fulton E.A,. J.S. Parslow, A.D.M. Smith and C.R. Johnson. 2004c. Biogeochemical Marine Ecosystem Models II: The Effect of Physiological Detail on Model Performance. Ecological Modelling, 173: 371-406.
Fulton, E., Smith, A. and Punt, A. (2005) Which ecological indicators can robustly detect effects of fishing? ICES Journal of Marine Science 62, 540–551.
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 Report.
Fulton, E.A., Link, J.S., Kaplan, I.C., et al. (2011) Lessons in modelling and management of marine ecosystems: the Atlantis experience. Fish and Fisheries 12, 171–188.
Fulton, E.A., Smith, A.D.M., Smith, D.C. and Johnson, P. (2014) An Integrated Approach Is Needed for Ecosystem Based Fisheries Management: Insights from Ecosystem-Level Management Strategy Evaluation. PLoS ONE 9, e84242.
Gray, R., Fulton, E.A., Little, L.R., Scott, R., 2006. Operating Model Specification Within an Agent Based Framework. North West Shelf Joint Environmental Management Study Technical Report, vol 16. CSIRO, Hobart, Tasmania. 127pp.
Griffith, G.P., Fulton, E.A. and Richardson, A.J. (2011) Effects of fishing and acidification-related benthic mortality on the southeast Australian marine ecosystem. Global Change Biology 17, 3058–307.
Griffith, G.P., Fulton, E.A., Gorton, R., and Richardson, A.J. 2012. Predicting Interactions among Fishing, Ocean Warming, and Ocean Acidification in a Marine System with Whole-Ecosystem Models. Conserv. Biol. 26(6): 1145–1152.
Haidvogel, D., Arango, H., Budgell, W., et al. (2008) Ocean forecasting in terrain-following coordinates: Formulation and skill assessment of the Regional Ocean Modeling System. Journal of Computational Physics 227, 3595–3624.
Horne, P.J., Kaplan, I.C., Marshall, K.N., Levin, P.S., Harvey, C.J., Hermann, A.J., and Fulton, E.A. 2010. Design and parameterization of a spatially explicit ecosystem model of the central California Current.
Hunsicker, Mary E., et al. "Functional responses and scaling in predator–prey interactions of marine fishes: contemporary issues and emerging concepts." Ecology Letters 14.12 (2011): 1288-1299.
Ihde, T. F., I. C. Kaplan, E. A. Fulton, I. A. Gray, M. Hasan, D. Bruce, W. Slacum, and H. M. Townsend. 2016. Design and parameterization of the Chesapeake Bay Atlantis Model: A spatially explicit end-to-end ecosystem model. U.S. Dept. of Commer., NOAA. NOAA Technical Memorandum NMFS-F/SPO-166, 145 p.
Johnson, P., Fulton, E., Smith, D. C., Jenkins, G. P., & Barrett, N. (2011). The use of telescoping spatial scales to capture inshore to slope dynamics in marine ecosystem modeling. Natural Resource Modeling, 24(3), 335-364.
Juranek, L.W., Feely, R.A., Peterson, W.T., et al. (2009) A novel method for determination of aragonite saturation state on the continental shelf of central Oregon using multi-parameter relationships with hydrographic data. Geophysical Research Letters 36.
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.
Kaplan, I.C., Horne, P.J., and Levin, P.S. 2012. Screening California Current Fishery Management Scenarios using the Atlantis End-to-End Ecosystem Model. Prog. Oceanogr. 102: 5–18.
Kaplan, I.C., Holland, D.S., and Fulton, E.A. 2014. Finding the accelerator and brake in an individual quota fishery: linking ecology, economics, and fleet dynamics of US West Coast trawl fisheries. ICES J. Mar. Sci. J. Cons. 71(2): 308–319.
Kroeker, K.J., Kordas, R.L., Crim, R., et al. (2013) Impacts of ocean acidification on marine organisms: quantifying sensitivities and interaction with warming. Global change biology.
Lehodey, P., Senina, I., and Murtugudde, R. 2008. A spatial ecosystem and populations dynamics model (SEAPODYM) – Modeling of tuna and tuna-like populations. Prog. Oceanogr. 78(4): 304–318. doi:10.1016/j.pocean.2008.06.004.
Link, J.S. (2010) Adding rigor to ecological network models by evaluating a set of pre-balance diagnostics: a plea for PREBAL. Ecological Modelling 221, 1580–1591.
Link, J.S., Fulton, E.A. and Gamble, R.J. (2010) 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.
Methot Jr., R.D., and Wetzel, C.R. 2013. Stock synthesis: A biological and statistical framework for fish stock assessment and fishery management. Fish. Res. 142: 86–99. doi:10.1016/j.fishres.2012.10.012.
Morato, T., E.A. Fulton and T. Pitcher. In press. Approaches to the modelling of seamounts and their fisheries. In, Seamounts, Ecology, Fisheries and Conservation. Fish and Aquatic Resources Series (FAR), Blackwell Publishing, Oxford.
Nihoul, J.C.J. and S. Djenidi, 1998. Chapter 18: Coupled physical, chemical and biological models. In: K.H. Brink and A.R. Robinson (eds), The Sea. John Wiley & Sons Inc: New York, London.
Persson, L., Van Leeuwen, A., & De Roos, A. M. (2014). The ecological foundation for ecosystem-based management of fisheries: mechanistic linkages between the individual-, population-, and community-level dynamics. ICES Journal of Marine Science: Journal du Conseil, fst231.
Rose, K., Allen, J.I., Artioli, Y., et al. (2010) End-To-End Models for the Analysis of Marine Ecosystems: Challenges, Issues, and Next Steps. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 2, 115–130.
Rose, K.A., Fiechter, J., Curchitser, E.N., et al. (2015) Demonstration of a fully-coupled end-to-end model for small pelagic fish using sardine and anchovy in the California Current. Progress in Oceanography.
Sainsbury, K.J., A.E. Punt A.E. and A.D.M. Smith. 2000. Design of operational management strategies for achieving fishery ecosystem objectives. ICES Journal of Marine Science, 57: 731–741
Savina, M., Condie, S.A., and Fulton, E.A. 2013. The role of pre-existing disturbances in the effect of marine reserves on coastal ecosystems: A modelling approach. PloS One 8(4): e61207.
Shchepetkin, A.F. and McWilliams, J.C. (2005) The regional oceanic modeling system (ROMS): a split-explicit, free-surface, topography-following-coordinate oceanic model. Ocean Modelling 9, 347–404.
Shin, Y.-J., and Cury, P. 2004. Using an individual-based model of fish assemblages to study the response of size spectra to changes in fishing. Can. J. Fish. Aquat. Sci. 61(3): 414–431. doi:10.1139/f03-154.
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
Uitz, J., Huot, Y., Bruyant, F., Babin, M. and Claustre, H. (2008) Relating phytoplankton photophysiological properties to community structure on large scales. Limnology and Oceanography 53, 614–630.
Uitz, J., Claustre, H., Gentili, B. and Stramski, D. (2010) Phytoplankton class-specific primary production in the world’s oceans: Seasonal and interannual variability from satellite observations: PHYTOPLANKTON CLASS-SPECIFIC PRODUCTION. Global Biogeochemical Cycles 24, n/a–n/a.
Walters, C., Pauly, D., & Christensen, V. (1999). Ecospace: prediction of mesoscale spatial patterns in trophic relationships of exploited ecosystems, with emphasis on the impacts of marine protected areas. Ecosystems, 2(6), 539-554.
Walters, Carl, and James F. Kitchell. "Cultivation/depensation effects on juvenile survival and recruitment: implications for the theory of fishing." Canadian Journal of Fisheries and Aquatic Sciences 58, no. 1 (2001): 39-50.
Weijerman, M., Fulton, E.A., Kaplan, I.C., Gorton, R., Leemans, R., Mooij, W.M., and Brainard, R.E. 2015. An integrated coral reef ecosystem model to support resource management under a changing climate. PloS One 10(12): e0144165.
Wittmann, A.C. and Pörtner, H.-O. (2013) Sensitivities of extant animal taxa to ocean acidification. Nature Climate Change 3, 995–1001.