Additional readings

Ecopath with Ecosim (EwE) & ecosystem modelling, overall

• Christensen, Villy. 2013. Ecological networks in fisheries: predicting the future? Fisheries 38 (2):76-81.

• Christensen, V. and C. J. Walters. 2004. Ecopath with Ecosim: methods, capabilities and limitations. Ecological Modelling, 172:109-139

• 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., 2015. Modelling dynamic ecosystems: venturing beyond boundaries with the Ecopath approach. Reviews in Fish Biology and Fisheries 25, 413-424. download

• Colléter, M., Valls, A., Guitton, J., Gascuel, D., Pauly, D., Christensen, V., 2015. Global overview of the applications of the Ecopath with Ecosim modelling approach using the EcoBase models repository. Ecological Modelling 302, 42–53.

• Ecopath with Ecosim 6: A User's Guide: download

• FAO, 2008. Fisheries management. 2. The ecosystem approach to fisheries. 2.1 Best practices in ecosystem modelling for informing an ecosystem approach to fisheries., FAO Fisheries Technical Guidelines for Responsible Fisheries. No. 4, Suppl. 2, Add. 1. Rome, FAO. 2008. 78p. FAO download.

• Heymans, J.J., Coll, M., Link, J.S., Mackinson, S., Steenbeek, J., Christensen, V., 2016. Best practice in Ecopath with Ecosim food-web models for ecosystem-based management. Ecological Modelling

• Palomares, M., & Bailly, N. (2011). Organizing and disseminating marine biodiversity information: The FishBase and SeaLifeBase story. In V. Christensen & J. Maclean (Eds.), Ecosystem Approaches to Fisheries: A Global Perspective (pp. 24-46). Cambridge: Cambridge University Press. Download.

• Pauly, Daniel, Villy Christensen, and C. Walters. 2000. Ecopath, Ecosim, and Ecospace as tools for evaluating ecosystem impact of fisheries. ICES Journal of Marine Science 57 (3):697-706.

• 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., 2016. Ecopath with Ecosim as a model-building toolbox: source code capabilities, extensions, and variations. Ecological Modelling, 319: 178–189.

• Townsend et al., 2019. Progress on implementing ecosystem-based fisheries management in the united states through the use of ecosystem models and analysis) Front. Mar. Sci. https://www.frontiersin.org/articles/10.3389/fmars.2019.00641/full

• Walters and Martell. 2004. Fisheries Ecology and Management, Chapters 6, 10, 11, 12.

Ecopath

• Christensen, V., Steenbeek, J., and Failler, P. A combined ecosystem and value chain modeling approach for evaluating societal cost and benefit of fishing. Ecological Modelling, 222 857-864

• Christensen, Villy, S. De la Puente, J. C. Sueiro, and J. Steenbeek. 2014. Valuing seafood: The Peruvian fisheries sector. Marine Policy 44 302-311.

• Christensen, V. and D. Pauly. 1992. ECOPATH II - A software for balancing steady-state ecosystem models and calculating network characteristics. Ecological Modelling, 61:169-185.

• Essington, T. 2007. Evaluating the sensitivity of a trophic mass-balance model (Ecopath) to imprecise data inputs CJFAS 64:628-637.

• 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.

• Majluf, P., S. de la Puente, V. Christensen. 2017. The little fish that can feed the world. Fish and Fisheries. 4:772-777

• Valls, A., Coll, M., & Christensen, V. 2015. Keystone species: toward an operational concept for marine biodiversity conservation. Ecological Monographs, 85(1), 29–47.

Network analysis and indicators

• Agnetta, D., Badalamenti, F., Colloca, F., D’Anna, G., Di Lorenzo, M., Fiorentino, F., et al. (2019). Benthic-pelagic coupling mediates interactions in Mediterranean mixed fisheries: An ecosystem modeling approach. PLoS ONE, 14(1), e0210659–24. http://doi.org/10.1371/journal.pone.0210659

• Christensen, V. 1995. Ecosystem maturity - towards quantification. Ecological Modelling 77:3-32.

• Coll, M., Steenbeek, J., 2017. Standardized ecological indicators to assess aquatic food webs: The ECOIND software plug-in for Ecopath with Ecosim models. Environmental Modelling & Software 89, 120–130.

• Valls, A. , Coll, M & Christensen, V. 2015. Keystone species: toward an operational concept for marine biodiversity conservation. Ecol. Monographs 85: 29-47

Ecosim

• Walters, C., V. Christensen and D. Pauly. 1997. Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments. Reviews in Fish Biology and Fisheries 7:139-172.

• Walters, C.J., J.F. Kitchell, V. Christensen and D. Pauly. 2000. Representing density dependent consequences of life history strategies in aquatic ecosystems: Ecosim II. Ecosystems 3: 70-83.

• Ahrens, R, CJ. Walters, and V. Christensen. 2012. Foraging arena theory. Fish and Fisheries 13 41-59.

• Ainsworth, C., Walters, C., 2015. Ten common mistakes made in Ecopath with Ecosim modelling. Ecological Modelling 308, 14-17.

• Christensen, V. and C. J. Walters. 2004. Trade-offs in ecosystem-scale optimization of fisheries management policies. Bull. Mar. Sci. 74(3):549-562

• Christensen, V and C. J. Walters. 2011. Progress in the use of ecosystem modeling for fisheries management. Edited by Christensen, Villy and Jay L. Maclean. In Ecosystem Approaches to Fisheries: A Global Perspective, Cambridge: Cambridge University Press. Download

• Espinosa-Romero, M.J., E.J. Gregr, V. Christensen, C. Walters, and K.M.A. Chan. 2011. Representing mediating effects and species reintroductions in Ecopath with Ecosim. Ecological Modeling 222: 1569-1579.

• Harvey, C.J., 2014. Mediation functions in Ecopath with Ecosim: handle with care. CJFAS 71, 1020–1029.

• Forrest, R. E., Savina, M., Fulton, E. A., & Pitcher, T. J. P. (2015). Do marine ecosystem models give consistent policy evaluations? A comparison of Atlantis and Ecosim, Fish Res. 167, 293–312. http://doi.org/10.1016/j.fishres.2015.03.010

• Hilborn, R., Amoroso, R. O., Bogazzi, E., Jensen, O. P., Parma, A. M., Szuwalski, C., & Walters, C. J. (2017). When does fishing forage species affect their predators?, Fisheries Research 191: 211–221.

• Heymans, JJ., Sumaila, UR, Christensen, V. 2009. Policy options for the northern Benguela ecosystem using a multispecies,multifleet ecosystem model. Progress in Oceanography 83: 417–425

• Mackinson, S., Platts, M., Garcia, C., Lynam, C., 2018. Evaluating the fishery and ecological consequences of the proposed North Sea multi-annual plan. PLoS ONE 13, e0190015.

• Pitcher, TJ & Cochrane, K. 2002. The Use of Ecosystem Models to Investigate Multispecies Management Strategies for Capture Fisheries. Fisheries Centre Research Reports 10:2.

• 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(3):731-741.

• Walters, C. J., V Christensen, S. J. Martell, and J. F. Kitchell. 2005. Possible ecosystem impacts of applying MSY policies from single-species assessment. ICES Journal of Marine Science 62 (3):558-568.

• Walters, C. and Kitchell, J.F., 2001. Cultivation/depensation effects on juvenile survival and recruitment: implications for the theory of fishing. Canadian Journal of Fisheries and Aquatic Sciences, 58:39-50.

• Walters, C, Martell, SJD, Christensen, V, and Mahmoudi, B. 2008. An Ecosim model for exploring ecosystem management options for the Gulf of Mexico: implications of including multistanza life history models for policy predictions. Bull. Mar. Sci. 83(1): 251-271.

• Walters, C., Christensen, V., Fulton, B., Smith, A.D.M., Hilborn, R., 2016. Predictions from simple predator-prey theory about impacts of harvesting forage fishes. Ecological Modelling 337, 272–280.

Ecospace

• Walters, C., D. Pauly and V. Christensen. 1999. Ecospace: prediction of mesoscale spatial patterns in trophic relationships of exploited ecosystems, with emphasis on the impacts of marine protected areas. Ecosystems 2: 539-554.stems:

• Walters, C., Christensen, V., Walters, W. and Rose, K., Representation of multi-stanza life histories in Ecospace models for spatial organization of ecosystem trophic interaction patterns. Bulletin of Marine Science 86 439-459.

• Christensen, Villy, Zach Ferdaña, Jeroen Steenbeek. 2009. Spatial optimization of protected area placement incorporating ecological, social and economical criteria. Ecological Modelling, 220: 2583-2593

• Christensen, Villy, Marta Coll, J. Steenbeek, Joe Buszowski, Dave Chagaris, and Carl J. Walters. 2014. Representing variable habitat quality in a spatial food web model. Ecosystems 17 (8):1397-1412.

• Coll, M., Steenbeek, J., Sole, J., Palomera, I., Christensen, V. 2016. Modelling the cumulative spatial-temporal effects of environmental factors and fishing in a NW Mediterranean marine ecosystem. Ecological Modelling, 331:100-114.

• Steenbeek, Jeroen, Marta Coll, Leigh Gurney, Frédéric Mélin, Nicolas Hoepffner, Joe Buszowski, and Villy Christensen. 2013. Bridging the gap between ecosystem modeling tools and geographic information systems: Driving a food web model with external spatial–temporal data. Ecological Modelling 263 139-151.

Ecotracer

• Tierney, K.M., Heymans, J.J., Muir, G.K.P., Cook, G.T., Buszowski, J., Jeroen Steenbeek, Walters, W.J., Christensen, V., MacKinnon, G., Howe, J.A., Xu, S., 2018. Modelling marine trophic transfer of radiocarbon (14C) from a nuclear facility. Environmental Modelling Software 102, 138–154.

• Walters, W., Christensen, V. 2018. Analyzing concentration of contaminants and radioisotopes in an aquatic spatial-dynamic food web model. Journal of Environmental Radioactivity, 181: 118-127.

Suggested

• Walters, C and V. Christensen. 2007. Adding realism to foraging arena predictions of trophic flow rates in Ecosim ecosystem models: shared foraging arenas and bout feeding. Ecological Modelling 209:342-350.

• Christensen, V. 2010. MEY = MSY. Fish and Fisheries

• Coll, M., A. Bundy and L.J. Shannon. Ecosystem Modeling using the Ecopath with Ecosim approach. 2008. In. B. Megrey and E. Moksness. Computers in Fisheries Research. Second edition. Springer. Book chapter. 225-291.

• Fulton, EA, ADM Smith, CR Johnson, 2003. Effect of complexity on marine ecosystem models. MEPS 253: 1-16

• Lorenzen, K. 1996. The relationship between body weight and natural mortality in juvenile and adult fish: a comparison of natural ecosystems and aquaculture. Journal of Fish Biology 49(4): 627-642

• Nielsen et al. 2018. Integrated Ecological-Economic Fisheries Models – Evaluation, Review and Challenges for Implementation. Fish and Fisheries, 19: 1-29.

• Plagányi, É.E., 2007. Models for an ecosystem approach to fisheries, FAO Fisheries Technical Paper, No 477, Rome.

• Walters, C.J. and Martell, S.J.D., 2004. Fisheries Ecology and Management. Princeton University Press, Princeton, 399 p.

• Ulanowicz, R.E. 2000. Growth and Development: Ecosystems Phenomenology. iUniverse.

EcoTracer

• Tierney, K.M., Heymans, J.J., Muir, G.K.P., Cook, G.T., Buszowski, J., Jeroen Steenbeek, Walters, W.J., Christensen, V., MacKinnon, G., Howe, J.A., Xu, S., 2018. Modelling marine trophic transfer of radiocarbon (14C) from a nuclear facility. Environmental Modelling Software 102, 138–154.

• Walters, W., Christensen, V. 2018. Analyzing concentration of contaminants and radioisotopes in an aquatic spatial-dynamic food web model. Journal of Environmental Radioactivity, 181: 118-127

EcoTroph

• Colléter et al., 2013 (http://journal.r-project.org/archive/2013-1/colleter-guitton-gascuel.pdf)

• Gasche & Gascuel, 2013 (http://icesjms.oxfordjournals.org/content/70/3/498)

• Gascuel et al., 2011 (http://icesjms.oxfordjournals.org/content/68/7/1403)

Stock Reduction Analysis (SRA)

• Walters, C. J., Martell, S. J. D., & Korman, J. (2006). A stochastic approach to stock reduction analysis. Canadian Journal of Fisheries and Aquatic Sciences, 63(1), 212–223.

• Lombardi, L., & Walters, C. J. (2011). Stochastic Stock Reduction Analysis (SRA). User Guide (p. 22). NOAA Fisheries Service, Southeast Fisheries Science Center, Panama City Laboratory, 3500 Delwood Beach Road, Panama City, Florida 32408. Panama City Laboratory Contribution 11-03. Program and users guide at this link: http://floridarivers.ifas.ufl.edu/Carl%20Class/SRA/SRA_instructions.htm

• Kimura, D. K., Balsiger, J. W., & Ito, D. H. (1984). Generalized stock reduction analysis. Canadian Journal of Fisheries and Aquatic Sciences, 41(9), 1325–1333. http://www.nrcresearchpress.com/doi/pdf/10.1139/f84-162

• Martell, S., & Froese, R. (2012). A simple method for estimating MSY from catch and resilience. Fish and Fisheries, n/a–n/a. http://doi.wiley.com/10.1111/j.1467-2979.2012.00485.x

Other

• Surplus production: Walters, Carl J., Ray Hilborn, and Villy Christensen. 2008. Surplus production dynamics in declining and recovering fish populations. CJFAS 65 (11):2536-2551.