How to integrate ecosystem responses with management measures in ecosystem models? The case-study of the Continental Shelf off the Northern coast of Portugal.
Context
This internship will be part of the SEED Project ECO-REACT ‘Forecasting ecosystem responses to management and conservation strategies’.
Marine ecosystems are increasingly exposed to human pressures such as overfishing, pollution, climate change, ocean acidification, and invasive species (Intergovernmental Panel on Climate Change (IPCC) 2022; Halpern et al. 2015). These
pressures can alter community structure, reduce biodiversity, and compromise ecosystem services (Halpern et al. 2008). Since the mid-20th century, it has been recognized that changes affecting a single species can trigger trophic cascades that impact entire food
webs and ecosystem functioning (Worm et al. 2006; Surma et al. 2025).
To address these issues, socio-ecosystem approaches have been developed, offering integrated frameworks to understand ecosystem dynamics and the effects of disturbances (McLeod et Leslie 2012; Pikitch et al. 2004). However, these tools remain
underused because most studies still focus on a single human pressure and a single ecological component, limiting the ability to capture system-wide interactions (Goethel et al. 2023). As a result, management decisions are often made without considering
broader trade-offs, sometimes causing unintended impacts on non-target species and ecosystem services (Richard 2025). However, ecosystem responses to management measures are expected to be both predictable and quantifiable when assessed through an
integrative socio-ecosystem model. Incorporating collateral (both ecological and social) effects would then enhance the accuracy and policy relevance of decision-making, allowing systematic evaluation of trade-offs and supporting adaptative adjustments of
management strategies.
The continental shelf off Portugal lies within an upwelling system and is therefore characterized by highly productive waters (Santos et al. 2007). The ecosystem is dominated by small and medium pelagic species such as sardine Sardina pilchardus, chub
mackerel Scomber colias and horse mackerel Trachurus trachurus. This particularly productive ecosystem supports an important fishing activity in Portugal, mainly targeting sardines, which are the principal product of the fish canning industry (Silva et al. 2015). However, since the early 2000s, sardine stock biomass has declined substantially and is now close to its lowest level in the past 30 years. The causes of this decline remain unclear and likely result from a complex interplay between environmental variability, species interactions, and fishing pressure (Malta et al. 2016). Previously ecosystem models 1developed for the region have highlighted the key role of plankton and small pelagic fishes in ecosystem regulation and have provided essential insights for the development of management scenarios (Veiga-Malta et al. 2019; Szalaj et al. 2021).
Overall, the objective of the project is to go further in developing a conceptual socio-ecosystem model to forecast how introduction and adjustment of management measures drive ecosystem responses.
Internship description
– General objectives
In this context, the student would have to use a widely known and previously implemented ecosystem model framework, such as Ecopath with Ecosim (EwE), and run an already developed model of the Portuguese Northern coast. By doing that and
performing a literature review, he/she will be able to
– Identify the structure of the baseline model;
– Select ecosystem metrics and indicators from the model outputs that can be used to identified changes
From that, the student will have to select two relevant management measures that have been implemented or suggested in the literature and assess limits of the model framework used to explicitly include feedback loops and economic outputs.
Then, from all of these information, he/she will be able to suggest a structure of a new conceptual model allowing to forecast ecosystem responses driven by the introduction of management measures.
– Work to be done
➢ Use an ecosystem model framework (Ecopath with Ecosim).
➢ Define inputs/outputs/structure/amount of data of this modeling framework.
➢ Highlight the pros and cons to investigate the addition of management inputs within the model framework.
➢ Be able to suggest improvements for the model to include feedback loops and economic outputs.
Profile
– Master 2 student or last year of engineering school in ecology with an interest in modeling.
– Interest in ecological modelling
– Interest for applied ecology and resource management issues
– Independence, curiosity, consistency
– Good communication skills in English (spoken and written) are required
– Scientific writing skills
Host laboratory and supervision
The internship will be welcomed at the Interdisciplinary Center of Marine and Environmental Research (CIIMAR) in Matosinhos (near Porto), Portugal. This research institute, located on the Cruise Terminal of the Leixões harbour, is a very dynamic place with several hundreds of people.
– Supervision: Johanna Faure (post-doctoral fellow); the student may benefit from support of the Team, including the PI, Irene Martins.
– Team: Marine Ecosystem Modelling (MEMO) – CIIMAR, Matosinhos
– Period: up to 6 months from February to September 2026
Application
Send a CV and a cover letter before the 15th of December 2025 to Johanna Faure: jfaure@ciimar.up.pt . Mail subject: “Application Internship ECO-REACT”
References
Goethel, Daniel R., Kristen L. Omori, André E. Punt, et al. 2023. « Oceans of Plenty? Challenges, Advancements, and Future Directions for the Provision of Evidence-Based Fisheries Management Advice ». Reviews in Fish Biology andFisheries 33 (2): 375‐410. https://doi.org/10.1007/s11160-022-09726-7.
Halpern, Benjamin S., Melanie Frazier, John Potapenko, et al. 2015. « Spatial and Temporal Changes in Cumulative Human Impacts on the World’s Ocean ». Nature Communications 6 (1): 7615. https://doi.org/10.1038/ncomms8615.
Halpern, Benjamin S., Shaun Walbridge, Kimberly A. Selkoe, et al. 2008. « A Global Map of Human Impact on Marine Ecosystems » . Science, publication en ligne anticipée, février 15. world. https://doi.org/10.1126/science.1149345.
Intergovernmental Panel on Climate Change (IPCC). 2022. The Ocean and Cryosphere in a Changing Climate: Special Report of the Intergovernmental Panel on Climate Change. Cambridge University Press. https://doi.org/10.1017/9781009157964.
Malta, T., P. T. Santos, A. M. P. Santos, M. Rufino, et A. Silva. 2016. « Long-term variations in Ibero-Atlantic sardine (Sardina pilchardus) population dynamics: Relation to environmental conditions and exploitation history » . Fisheries Research 179 (juillet): 47‐56. https://doi.org/10.1016/j.fishres.2016.02.009.
McLeod, Karen, et Heather Leslie. 2012. Ecosystem-Based Management for the Oceans. Island Press.
Pikitch, E. K., C. Santora, E. A. Babcock, et al. 2004. « Ecosystem-Based Fishery Management » . Science, publication en ligne anticipée, juillet 16. world. https://doi.org/10.1126/science.1098222.
Richard, Glory. 2025. « Ecosystem Dynamics and Environmental Health Management: Linking Processes » . In Innovative Approaches in Environmental Health Management: Processes, Technologies, and Strategies for a Sustainable Future, par Sylvester Chibueze Izah et Matthew Chidozie Ogwu. Springer Nature.
Santos, A. Miguel P., Alexandra Chícharo, Antonina Dos Santos, et al. 2007. « Physical–biological interactions in the life history of small pelagic fish in the Western Iberia Upwelling Ecosystem » . Progress in Oceanography, Ecological Functioning of the Iberian Seas: A synthesis of GLOBEC Research in Spain and Portugal, vol. 74 (2): 192‐209. https://doi.org/10.1016/.pocean.2007.04.008.
Silva, A., I. Riveiro, A. Moreno, et al. 2015. « Sardine Fisheries: Resource Assessment and Social and Economic Situation. » European Parliament, Brussels.
Surma, Szymon, Evgeny A. Pakhomov, et Tony J. Pitcher. 2025. « Trophic Cascades and Top-down Control: Found at Sea ». Frontiers in Ecology and Evolution 13 (juillet): 1587171. https://doi.org/10.3389/fevo.2025.1587171.
Szalaj, D., M.A. Torres, T. Veiga-Malta, et al. 2021. « Food-Web Dynamics in the Portuguese Continental Shelf Ecosystem between 1986 and 2017: Unravelling Drivers of Sardine Decline ». Estuarine, Coastal and Shelf Science 251 (avril):
107259. https://doi.org/10.1016/j.ecss.2021.107259.
Veiga-Malta, T, D Szalaj, Mm Angélico, et al. 2019. « First Representation of the Trophic Structure and Functioning of the Portuguese Continental Shelf Ecosystem: Insights into the Role of Sardine ». Marine Ecology Progress Series
617‐618 (mai): 323‐40. https://doi.org/10.3354/meps12724.
Worm, Boris, Edward B. Barbier, Nicola Beaumont, et al. 2006. « Impacts of Biodiversity Loss on Ocean Ecosystem Services ». Science, publication en ligne anticipée, novembre 3. world. https://doi.org/10.1126/science.1132294.