The African Marine Ecosystem Modelling Hub is core to the Marine Sustainability research group of MARIS, and its home is in the Department of Biological Sciences, UCT. We undertake trophic modelling of African marine ecosystems, particularly using the Ecopath-Ecosim-Ecospace1 and Atlantis2 modelling approaches. Our modelling work centers around understanding African marine ecosystem structure and functioning, and the combined environmental and anthropogenic (especially fisheries) drivers underlying observed and future marine ecosystem dynamics. We aim to provide scientific outputs in the form of conceptual understanding, quantitative indicators and spatial-temporal mapping related to African marine food webs in support of ecosystem based management. We welcome collaborators, project partners and end-users with shared skills and/or objectives, as we advocate for team-based, collaborative ecosystem modelling that is meaningful and useful in the quest for improved health and sustainability of African Marine Ecosystems. 

1Christensen, V., & Walters, C. J. (2004). Ecopath with Ecosim: methods, capabilities and limitations. Ecological modelling, 172(2-4), 109-139.

2Fulton, E. A., Link, J. S., Kaplan, I. C., Savina‐Rolland, M., Johnson, P., Ainsworth, C., ... & Smith, D. C. (2011). Lessons in modelling and management of marine ecosystems: the Atlantis experience. Fish and fisheries, 12(2), 171-188.

 

The UCT Team consists of Lynne Shannon, Kelly Ortega-Cisneros, Samantha Grusd, Darcie Anderson and Natalie Le Roux.

Our UCT Team

Assorted Publications

Ortega-Cisneros, K., Cochrane, K., & Fulton, E. A. (2017). An Atlantis model of the southern Benguela upwelling system: Validation, sensitivity analysis and insights into ecosystem functioning. Ecological Modelling, 355, 49-63. 

Ortega‐Cisneros, K., Cochrane, K. L., Fulton, E. A., Gorton, R., & Popova, E. (2018). Evaluating the effects of climate change in the southern Benguela upwelling system using the Atlantis modelling framework. Fisheries Oceanography, 27(5), 489-503.

Ortega-Cisneros, K.; Weigum, E., Chalmers, R., Grusd, S., Lombard, AT., Shannon, L. 2022. Supporting marine spatial planning with an ecosystem model in Algoa Bay, South Africa. African Journal of Marine Science 44(2):189-204.

Ortega‐Cisneros, K., Fierros‐Arcos, D., Lindmark, M., Novaglio, C., Woodworth‐Jefcoats, P., Eddy, T.D., Coll, M., Fulton, E., Oliveros‐Ramos, R., Reum, J. and Shin, Y.J.,…Shannon, L.J., … Blanchard, J.L. 2025. An integrated global‐to‐regional scale workflow for simulating climate change impacts on marine ecosystems. Earth's Future, 13(2), p.e2024EF004826.

Roux, J.-P. and Shannon, L.J. 2004. Ecosystem approach to fisheries management in the northern Benguela: the Namibian experience. In Ecosystem Approaches to Fisheries in the Southern Benguela.

Sadchatheeswaran, S., Branch, G.M., Shannon, L.J., Moloney, C.L., Coll, M. and Robinson, T.B., 2020. Modelling changes in trophic and structural impacts of alien ecosystem engineers on a rocky-shore island. Ecological Modelling, 433, p.109227.

Shannon, L.J., Moloney, C.L., Jarre, A. and Field, J.G. 2003. Trophic flows in the southern Benguela during the 1980s and 1990s. Journal of Marine Systems  39 (1-2):83-116.

Shannon, L.J., Christensen, V. and Walters, C. 2004b. Modelling stock dynamics in the southern Benguela ecosystem for the period 1978-2002. In Ecosystem Approaches to Fisheries in the Southern Benguela. Shannon, L.J., Cochrane, K.L. and S.C. Pillar (Eds). Afr. J. mar. Sci. 26:179-196.

Shannon, L.J., Roux, J.-P., Jarre, A. and Cochrane, K.L. 2000. Trophic interactions in the Benguela ecosystem and their implications for multispecies management of fisheries. Report on the northern Benguela ecosystem modelling workshop, Swakopmund, Namibia, 16-18 August 1999. BENEFIT/FAO/Government of Japan Cooperative Programme GCP/INT/JPN, Report no. 2.2. 16pp.

Shannon, L.J. and Roux, J.-P. 2000. Trophic interactions in the Benguela ecosystem and their implications for multispecies management of fisheries. Report for period December 1998-December 1999. BENEFIT/FAO/Government of Japan Cooperative Programme GCP/INT/JPN, Report no. 2.3. 6pp.

Shannon, L.J., Roux, J.-P. and Jarre, A. 2001. Trophic interactions in the Benguela ecosystem and their implications for multispecies management of fisheries. Report on progress to January 2001: exploring multispecies management options using the completed northern Benguela ecosystem model. BENEFIT/FAO/Government of Japan Cooperative Programme GCP/INT/JPN, Report no. 2.4. 56 pp.

Shannon, L.J., Coll, M., Neira, S., Cury, P.M., and Roux, J.-P. 2009. Impacts of fishing and climate change explored using trophic models. Chapter 8, pp. 158-190  in Checkley, D.M., C. Roy, J. Alheit, and Y. Oozeki (eds.), Climate Change and Small Pelagic Fish. Cambridge University Press 7.

Shannon, L.J., Ortego Cisneros, K., Lamont, T., Winker, H., Crawford, R., Jarre, A. and Coll, M. 2020. Exploring temporal variability in the Southern Benguela ecosystem over the past four decades using a time-dynamic ecosystem model. Frontiers in Marine Science.  doi: 10.3389/fmars.2020.00540

Shin, Y., Shannon, L.J. and Cury, P.M. 2004. Simulations of fishing effects on the southern Benguela fish community using the individual-based model Osmose. Lessons from a comparison with Ecosim simulations. In Ecosystem Approaches to Fisheries in the Southern Benguela. Shannon, L.J., Cochrane, K.L. and S.C. Pillar (Eds). Afr. J. mar. Sci. 26: 95-114.

Smith, A.D.M., Brown, C.J., Bulman, C.M., Fulton, E.A., Johnson, P., Kaplan, I.C., Lozano-Montes, H., Mackinson, S., Marzloff, M., Shannon, L.J., Shin, Y.-J., Tam, J. 2011. Impacts of fishing low-trophic level species on marine ecosystems. Science 333: 1147-1150.

Smith, M.D., Fulton, E.A., Day, R.W., Shannon, L.J. and Shin, Y.-J. 2015. Ecosystem modelling in the southern Benguela: comparisons of Atlantis, Ecopath with Ecosim, and OSMOSE under fishing scenarios,  African Journal of Marine Science, 37(1): 65-78. DOI: 10.2989/1814232X.2015.1013501

Steyn, C., Shannon, L.J., Blamey, L.K. 2021. Changes in food-web structure and energy flow in kelp forest ecosystems on the south-west coast of South Africa following the invasion of Jasus lalandii. Food Webs. https://doi.org/10.1016/j.fooweb.2021.e00200

Travers, M., Watermeyer, K., Shannon, L.J., Shin, Y.-J. 2010. Changes in food web structure under scenarios of overfishing in the southern Benguela: Comparison of the Ecosim and OSMOSE modelling approaches. Journal of Marine Systems 79(1-2):101-111.

Watermeyer, K., Shannon, L.J. and Griffiths, C.L. 2008. Changes in the trophic structure of the southern Benguela before and after the onset of industrial fishing. African Journal of Marine Science 30(2): 351-382.

Watermeyer, K., Shannon, L.J., Roux, J.-P. and Griffiths, C.L. 2008. Changes in the trophic structure of the northern Benguela before and after the onset of industrial fishing. African Journal of Marine Science 30(2): 383-403.

Current associated projects

Key projects associated with our African marine ecosystem modelling in the past

  • Benguela Environment, Fisheries, Interaction and Training (BENEFIT) research programme: 
    Hampton, I., & Sweijd, N. (2008). Achievements and lessons learned from the Benguela Environment, Fisheries, Interaction and Training (BENEFIT) research programme. African Journal of Marine Science, 30(3), 541-564.
  • The South African–French ecosystem research programmes (1997-2004): Viability of Exploited Pelagic FishResources in the Benguela Ecosystems in Relation to theEnvironment and Spatial Aspects (VIBES) which became the IDYLE project (Interactions and Spatial Dynamics ofRenewable Resources in Upwelling Ecosystems).
  • South African Research Chair in Marine Ecology and Fisheries (SARCHI ME&F). Astrid Jarre. https://maris.uct.ac.za/eafsa
  • South African Research Chair in Marine Spatial Planning. Amanda Lombard. https://oceansciences.mandela.ac.za/Research-Chairs-and-Entities/Chair-in-Marine-Spatial-Planning
  • One Ocean Hub. https://oneoceanhub.org/
  • Triatlas Tropical and South Atlantic climate-based marine ecosystem prediction for sustainable management. https://triatlas.w.uib.no/