Publications

2024

  • [DOI] R. Sun, P. Sun, H. Yu, P. Ju, S. Ma, Z. Liang, M. Heino, Y. Shin, N. Barrier, and Y. Tian, “Exploring fishing impacts on the structure and functioning of the yellow sea ecosystem using an individual-based modeling approach,” Journal of marine systems, vol. 242, p. 103946, 2024.
    [Bibtex] 
    @article{SUN2024103946,
title = {Exploring fishing impacts on the structure and functioning of the Yellow Sea ecosystem using an individual-based modeling approach},
journal = {Journal of Marine Systems},
volume = {242},
pages = {103946},
year = {2024},
issn = {0924-7963},
doi = {https://doi.org/10.1016/j.jmarsys.2023.103946},
url = {https://www.sciencedirect.com/science/article/pii/S0924796323000908},
author = {Runlong Sun and Peng Sun and Haiqing Yu and Peilong Ju and Shuyang Ma and Zhenlin Liang and Mikko Heino and Yunne-Jai Shin and Nicolas Barrier and Yongjun Tian},
keywords = {Fishing effect, Ecosystem model, Over-exploitation, Ecological indicators, OSMOSE model},
abstract = {The Yellow Sea is a marginal sea in the Northwestern Pacific where the fishery resources have been overfished and the community structure has greatly changed over the past six decades. Ecosystem modeling approaches are valuable tools to uncover potential mechanisms behind the ecosystem changes. Here, we developed ‘OSMOSE-YS’, an individual-based multi-species OSMOSE model that includes important commercial pelagic and demersal fish and invertebrates in the Yellow Sea. Simulations were carried out under three fishing scenarios to investigate how different levels of fishing pressure may have impacted the Yellow Sea ecosystem. Results indicate that the biomass of demersal fish continued to decline during 1970–2014, while the biomass of pelagic fish and invertebrates fluctuated periodically. Long-term fishing pressure has led to the reduction of total biomass, body sizes, and longevity of the modelled species. Under low-fishing condition, the ecosystem biomass is restored and the proportion of elder and larger individuals increases. On the contrary, high-fishing condition further decreases the proportion of high-trophic-level species. OSMOSE-YS serves as a baseline model to investigate ecosystem responses to different fishing strategies, in support of ecosystem-based fisheries management in the Yellow Sea.}
}

2023

  • [DOI] L. Xing, J. Tang, S. Tian, and N. Barrier, “Simulating impacts of fishing toothfish on the pelagic community in the cooperation sea, southern ocean,” Regional studies in marine science, vol. 68, 2023.
    [Bibtex] 
    @article{ WOS:001098661900001,
Author = {Xing, Lei and Tang, Jianye and Tian, Siquan and Barrier, Nicolas},
Title = {Simulating impacts of fishing toothfish on the pelagic community in the
Cooperation Sea, Southern Ocean},
Journal = {REGIONAL STUDIES IN MARINE SCIENCE},
Year = {2023},
Volume = {68},
Month = {DEC 30},
DOI = {10.1016/j.rsma.2023.103227},
EarlyAccessDate = {OCT 2023},
Article-Number = {103227},
ISSN = {2352-4855},
Unique-ID = {WOS:001098661900001},
}
  • R. Oliveros-Ramos, Y. Shin, D. Gutierrez, and V. M. Trenkel, “A multi-model selection approach for statistical downscaling and bias correction of earth system model outputs for regional impact applications,” Ess open archive, 2023.
    [Bibtex] 
    @article{Downscaling,
title = {A multi-model selection approach for statistical downscaling and bias correction of Earth System Model outputs for regional impact applications},
year = 2023,
journal = {ESS Open Archive},
author = {Ricardo Oliveros-Ramos and Yunne-Jai Shin and Dimitri Gutierrez and Verena M Trenkel},
url = {https://essopenarchive.org/doi/full/10.22541/essoar.167810427.75944849/v1}
}
  • [DOI] R. Sun, P. Sun, C. Fu, G. Liu, Z. Liang, Y. Shin, N. Barrier, and Y. Tian, “Exploring balanced harvest as a potential strategy for highly exploited multispecies fisheries,” Ices journal of marine science, vol. 80, iss. 4, pp. 897-910, 2023.
    [Bibtex] 
    @article{ WOS:000935306400001,
Author = {Sun, Runlong and Sun, Peng and Fu, Caihong and Liu, Guankui and Liang,
Zhenlin and Shin, Yunne-Jai and Barrier, Nicolas and Tian, Yongjun},
Title = {Exploring balanced harvest as a potential strategy for highly exploited
multispecies fisheries},
Journal = {ICES JOURNAL OF MARINE SCIENCE},
Year = {2023},
Volume = {80},
Number = {4},
Pages = {897-910},
Month = {MAY 18},
DOI = {10.1093/icesjms/fsad023},
EarlyAccessDate = {FEB 2023},
ISSN = {1054-3139},
EISSN = {1095-9289},
ResearcherID-Numbers = {Sun, Runlong/JFJ-6406-2023
Shin, Yunne-Jai/A-7575-2012
},
ORCID-Numbers = {Shin, Yunne-Jai/0000-0002-7259-9265
Sun, Peng/0000-0002-0839-1785
Fu, Caihong/0000-0002-6343-9550
Sun, Runlong/0000-0003-1186-0367},
Unique-ID = {WOS:000935306400001},
}
  • [DOI] F. Moullec, N. Barrier, F. Guilhaumon, M. A. Peck, C. Ulses, and Y. Shin, “Rebuilding mediterranean marine resources under climate change,” Marine ecology progress series, vol. 708, pp. 1-20, 2023.
    [Bibtex] 
    @article{ WOS:000989709200001,
Author = {Moullec, Fabien and Barrier, Nicolas and Guilhaumon, Francois and Peck,
Myron A. and Ulses, Caroline and Shin, Yunne-Jai},
Title = {Rebuilding Mediterranean marine resources under climate change},
Journal = {MARINE ECOLOGY PROGRESS SERIES},
Year = {2023},
Volume = {708},
Pages = {1-20},
Month = {MAR 23},
DOI = {10.3354/meps14269},
ISSN = {0171-8630},
EISSN = {1616-1599},
Unique-ID = {WOS:000989709200001},
}
  • [DOI] A. Morell, Y. Shin, N. Barrier, M. Travers-Trolet, G. Halouani, and B. Ernande, “Bioen-osmose: a bioenergetic marine ecosystem model with physiological response to temperature and oxygen,” Progress in oceanography, p. 103064, 2023.
    [Bibtex] 
    @article{MORELL2023103064,
title = {Bioen-OSMOSE: A bioenergetic marine ecosystem model with physiological response to temperature and oxygen},
journal = {Progress in Oceanography},
pages = {103064},
year = {2023},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2023.103064},
url = {https://www.sciencedirect.com/science/article/pii/S0079661123001076},
author = {Alaia Morell and Yunne-Jai Shin and Nicolas Barrier and Morgane Travers-Trolet and Ghassen Halouani and Bruno Ernande},
keywords = {Bioenergetic, Food web, Hypoxia, Marine ecosystem model, Phenotypic plasticity, Thermal tolerance},
}
  • [DOI] A. Morell, Y. Shin, N. Barrier, M. Travers-Trolet, and B. Ernande, “Ev-osmose: an eco-genetic marine ecosystem model,” Biorxiv, p. 2023–02, 2023.
    [Bibtex] 
    @article{morell2023ev,
title={Ev-OSMOSE: An eco-genetic marine ecosystem model},
author={Morell, Alaia and Shin, Yunne-Jai and Barrier, Nicolas and Travers-Trolet, Morgane and Ernande, Bruno},
journal={bioRxiv},
pages={2023--02},
year={2023},
publisher={Cold Spring Harbor Laboratory},
url={https://doi.org/10.1101/2023.02.08.527669},
doi={10.1101/2023.02.08.527669}
}

2022

  • [DOI] L. Xing, Y. Chen, K. R. Tanaka, N. Barrier, and Y. Ren, “Evaluating the hatchery program of a highly exploited shrimp stock (fenneropenaeus chinensis) in a temperate marine ecosystem,” Frontiers in marine science, vol. 9, 2022.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2022.789805,
AUTHOR={Xing, Lei and Chen, Yong and Tanaka, Kisei R. and Barrier, Nicolas and Ren, Yiping},
TITLE={Evaluating the Hatchery Program of a Highly Exploited Shrimp Stock (Fenneropenaeus chinensis) in a Temperate Marine Ecosystem},
JOURNAL={Frontiers in Marine Science},
VOLUME={9},
YEAR={2022},
URL={https://www.frontiersin.org/articles/10.3389/fmars.2022.789805},
DOI={10.3389/fmars.2022.789805},
ISSN={2296-7745},
ABSTRACT={Hatchery programs are commonly used to enhance fishery stocks, while the efforts to minimize potential negative ecological impacts have grown in recent years. In China, Fenneropenaeus chinensis is a fast-growing, short-lived shrimp species with a high commercial value. F. chinensis fishery is heavily dependent on the hatchery program. We evaluated the trade-off between economic profits and ecological impacts of F. chinensis hatchery program in the Jiaozhou Bay of China. The total length of released individuals was 1.4 cm. The results showed that artificially released F. chinensis individuals experienced high predation pressure during the first 2 weeks. The economic profit peaked when 198 million individuals were released. The modeled hatchery program yielded a lower proportion of individuals with the increasing amount of F. chinensis release. The temporally uniform hatchery release was more efficient than other hatchery release scenarios (e.g., increasing the released amount year by year) in a long-term hatchery program. F. chinensis had the negative impacts on two large predatory fishes. Large fishes recovered at a slower rate than small fishes after the F. chinensis release stopped. Reducing fishing pressure could offset negative impacts of F. chinensis release on large fishes. The study indicates that the effectiveness of F. chinensis release cannot be enhanced by simply increasing the released amount. A long-term F. chinensis hatchery program with a large released amount may present additional challenges for managing natural resources in an ecosystem context.}
}
  • [DOI] M. Hill Cruz, I. Frenger, J. Getzlaff, I. Kriest, T. Xue, and Y. Shin, “Understanding the drivers of fish variability in an end-to-end model of the northern humboldt current system,” Ecological modelling, vol. 472, p. 110097, 2022.
    [Bibtex] 
    @article{HILLCRUZ2022110097,
title = {Understanding the drivers of fish variability in an end-to-end model of the Northern Humboldt Current System},
journal = {Ecological Modelling},
volume = {472},
pages = {110097},
year = {2022},
issn = {0304-3800},
doi = {https://doi.org/10.1016/j.ecolmodel.2022.110097},
url = {https://www.sciencedirect.com/science/article/pii/S0304380022002009},
author = {Mariana {Hill Cruz} and Ivy Frenger and Julia Getzlaff and Iris Kriest and Tianfei Xue and Yunne-Jai Shin},
keywords = {Ecosystem modelling, OSMOSE, End-to-end model, CROCO, BioEBUS, Northern Humboldt Current System, Eastern boundary upwelling system, Fisheries, Higher trophic levels, Trophic interactions, physical–biogeochemical model},
abstract = {The Northern Humboldt Current System is the most productive eastern boundary upwelling system, generating about 10 % of the global fish production, mainly coming from small pelagic fish. It is bottom-up and top-down affected by environmental and anthropogenic variability, such as El-Niño Southern Oscillation and fishing pressure, respectively. The high variability of small pelagic fish in this system, as well as their economic importance, call for a careful management aided by the use of end-to-end models. This type of models represent the ecosystem as a whole, from the physics, through plankton up to fish dynamics. In this study, we utilised an end-to-end model consisting of a physical–biogeochemical model (CROCO-BioEBUS) coupled one-way with an individual-based fish model (OSMOSE). We investigated how time-variability in plankton food production affects fish populations in OSMOSE and contrasted it against the sensitivity of the model to two parameters with high uncertainty: the plankton accessibility to fish and fish larval mortality. Relative interannual variability in the modelled fish is similar to plankton variability. It is, however, small compared with the high variability seen in fish observations in this productive ecosystem. In contrast, changes in larval mortality have a strong effect on anchovies. In OSMOSE, it is a common practice to scale plankton food for fish, accounting for processes that may make part of the total plankton in the water column unavailable. We suggest that this scaling should be done constant across all plankton groups when previous knowledge on the different availabilities is lacking. In addition, end-to-end modelling systems should consider environmental impacts on other biological processes such as larval mortality in order to better capture the interactions between environmental processes, plankton and fish.}
}
  • [DOI] F. Moullec, N. Barrier, S. Drira, F. Guilhaumon, T. Hattab, M. A. Peck, and Y. Shin, “Using species distribution models only may underestimate climate change impacts on future marine biodiversity,” Ecological modelling, vol. 464, p. 109826, 2022.
    [Bibtex] 
    @article{MOULLEC2022109826,
title = {Using species distribution models only may underestimate climate change impacts on future marine biodiversity},
journal = {Ecological Modelling},
volume = {464},
pages = {109826},
year = {2022},
issn = {0304-3800},
doi = {https://doi.org/10.1016/j.ecolmodel.2021.109826},
url = {https://www.sciencedirect.com/science/article/pii/S0304380021003690},
author = {Fabien Moullec and Nicolas Barrier and Sabrine Drira and François Guilhaumon and Tarek Hattab and Myron A. Peck and Yunne-Jai Shin},
keywords = {Beta diversity, Climate change, End-to-end model, Osmose model, Species distribution model, Mediterranean sea},
abstract = {In face of global changes, projecting and mapping biodiversity changes are of critical importance to support management and conservation measures of marine ecosystems. Despite the development of a wide variety of ecosystem models capable of integrating an increasing number of ecological processes, most projections of climate-induced changes in marine biodiversity are based on species distribution models (SDMs). These correlative models present a significant advantage when the lack of knowledge on the species physiology is counterbalanced by the availability of relevant environmental variables over the species geographical range. However, correlative SDMs neglect intra- and inter-specific interactions and thereby can lead to biased projections of changes in biodiversity distribution. To evaluate the influence of trophic interactions on projections of species richness and assemblage composition under climate change scenarios, we compared biodiversity projections derived from an ensemble of different SDMs to projections derived from a hybrid model coupling SDMs and a multispecies trophic model in the Mediterranean Sea. Our results show that accounting for trophic interactions modifies projections of future biodiversity in the Mediterranean Sea. Under the RCP8.5 scenario, SDMs tended to overestimate the gains and underestimate the losses of species richness by the end of the 21st century, with marked local differences in projections, both in terms of magnitude and trend, in some biodiversity hotspots. In both SDMs and hybrid approaches, nestedness with gains in species richness was the main pattern driving dissimilarity between present and future fish and macro-invertebrate species assemblages at the Mediterranean basin scale. However, at local scale, we highlighted some differences in the relative contribution of nestedness vs replacement in driving dissimilarity. Our results call for the development of integrated modelling tools that can mechanistically consider multiple biotic and abiotic drivers to improve projections of future marine biodiversity.}
}
  • [DOI] S. Fabri-Ruiz, A. Baudena, F. Moullec, F. Lombard, J. Irisson, and M. L. Pedrotti, “Mistaking plastic for zooplankton: risk assessment of plastic ingestion in the mediterranean sea.,” Ssrn, 2022.
    [Bibtex] 
    @article{Ruiz,
author={Fabri-Ruiz, Salomé and Baudena, Alberto and Moullec, Fabien and Lombard, Fabien and Irisson, Jean-Olivier and Pedrotti, Maria Luiza},
title={Mistaking Plastic for Zooplankton: Risk Assessment of Plastic Ingestion in the Mediterranean Sea.},
journal={SSRN},
doi={https://dx.doi.org/10.2139/ssrn.4182817},
year={2022},
}

2021

  • [DOI] C. Piroddi, E. Akoglu, E. Andonegi, J. W. Bentley, I. Celić, M. Coll, D. Dimarchopoulou, R. Friedland, K. de Mutsert, R. Girardin, E. Garcia-Gorriz, B. Grizzetti, P. -Y. Hernvann, J. J. Heymans, B. Müller-Karulis, S. Libralato, C. P. Lynam, D. Macias, S. Miladinova, F. Moullec, A. Palialexis, O. Parn, N. Serpetti, C. Solidoro, J. Steenbeek, A. Stips, M. T. Tomczak, M. Travers-Trolet, and A. C. Tsikliras, “Effects of nutrient management scenarios on marine food webs: a pan-european assessment in support of the marine strategy framework directive,” Frontiers in marine science, vol. 8, 2021.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2021.596797,
AUTHOR={Piroddi, Chiara and Akoglu, Ekin and Andonegi, Eider and Bentley, Jacob W. and Celić, Igor and Coll, Marta and Dimarchopoulou, Donna and Friedland, René and de Mutsert, Kim and Girardin, Raphael and Garcia-Gorriz, Elisa and Grizzetti, Bruna and Hernvann, P.-Y. and Heymans, Johanna J. and Müller-Karulis, Bärbel and Libralato, Simone and Lynam, Christopher P. and Macias, Diego and Miladinova, Svetla and Moullec, Fabien and Palialexis, Andreas and Parn, Ove and Serpetti, Natalia and Solidoro, Cosimo and Steenbeek, Jeroen and Stips, Adolf and Tomczak, Maciej T. and Travers-Trolet, Morgane and Tsikliras, Athanassios C.},
TITLE={Effects of Nutrient Management Scenarios on Marine Food Webs: A Pan-European Assessment in Support of the Marine Strategy Framework Directive},
JOURNAL={Frontiers in Marine Science},
VOLUME={8},
YEAR={2021},
URL={https://www.frontiersin.org/articles/10.3389/fmars.2021.596797},
DOI={10.3389/fmars.2021.596797},
ISSN={2296-7745},
ABSTRACT={Eutrophication is one of the most important anthropogenic pressures impacting coastal seas. In Europe, several legislations and management measures have been implemented to halt nutrient overloading in marine ecosystems. This study evaluates the impact of freshwater nutrient control measures on higher trophic levels (HTL) in European marine ecosystems following descriptors and criteria as defined by the Marine Strategy Framework Directive (MSFD). We used a novel pan-European marine modeling ensemble of fourteen HTL models, covering almost all the EU seas, under two nutrient management scenarios. Results from our projections suggest that the proposed nutrient reduction measures may not have a significant impact on the structure and function of European marine ecosystems. Among the assessed criteria, the spawning stock biomass of commercially important fish stocks and the biomass of small pelagic fishes would be the most impacted, albeit with values lower than 2.5%. For the other criteria/indicators, such as species diversity and trophic level indicators, the impact was lower. The Black Sea and the North-East Atlantic were the most negatively impacted regions, while the Baltic Sea was the only region showing signs of improvement. Coastal and shelf areas were more sensitive to environmental changes than large regional and sub-regional ecosystems that also include open seas. This is the first pan-European multi-model comparison study used to assess the impacts of land-based measures on marine and coastal European ecosystems through a set of selected ecological indicators. Since anthropogenic pressures are expanding apace in the marine environment and policy makers need to use rapid and effective policy measures for fast-changing environments, this modeling framework is an essential asset in supporting and guiding EU policy needs and decisions.}
}
  • [DOI] L. Xing, Y. Chen, B. Li, K. R. Tanaka, R. Boenish, Y. Ren, and B. Xu, “Evaluating impacts of trophic interactions on the effectiveness of single-species fisheries management,” Frontiers in marine science, vol. 8, 2021.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2021.698991,
AUTHOR={Xing, Lei and Chen, Yong and Li, Bai and Tanaka, Kisei R. and Boenish, Robert and Ren, Yiping and Xu, Binduo},
TITLE={Evaluating Impacts of Trophic Interactions on the Effectiveness of Single-Species Fisheries Management},
JOURNAL={Frontiers in Marine Science},
VOLUME={8},
YEAR={2021},
URL={https://www.frontiersin.org/articles/10.3389/fmars.2021.698991},
DOI={10.3389/fmars.2021.698991},
ISSN={2296-7745},
ABSTRACT={Single-species fisheries management (SSFM) is applied to many fisheries ecosystems around the world. The associated ecological impacts are usually not well understood due to the lack of considering trophic interactions among species in the ecosystem. This impedes the implementation of SSFM in an ecosystem context and reduces our ability to understand the possible ecological impacts of fishing activities. This study focuses on two economically important species in the Jiaozhou Bay, China: the short-lived, fast-growing, and relatively abundant Japanese mantis shrimp (Oratosquilla oratoria) and the long-lived, slow-growing, and less abundant Korean rockfish (Sebastes schlegelii). We evaluated how varying trophic interactions influenced O. oratoria and S. schlegelii (i.e., target-species) who were managed under constant fishing pressure. The increase of fishing pressure to other species (i.e., non-target species) was beneficial to O. oratoria and S. schlegelii. O. oratoria was more sensitive to the decrease of fishing pressure to other species. The predation mortality of age-0 O. oratoria increased with the increased fishing pressure to other species. The predation mortality of age-1 O. oratoria and age-0 S. schlegelii had negative relationships with the fishing pressure to other species. Age-1 S. schlegelii seemed not to be sensitive to the changes in trophic interactions. The predation mortality of O. oratoria and S. schlegelii had bigger changes than the starvation mortality after fishing changed. It suggested the prey-predator relationship had a bigger impact than the food competition. The increase of high-trophic-level fish Johnius belangerii fishery positively impacted O. oratoria, but negatively impacted S. schlegelii. S. schlegelii was more sensitive to the changes of the low-trophic-level fish Pholis fangi fishery. Given the complex dynamics of ecosystems, this study highlights the importance of species-specific responses of fishes to shifting trophic interactions in fisheries management.}
}
  • [DOI] K. E. van de Wolfshaar, U. Daewel, S. S. Hjøllo, T. A. Troost, M. Kreus, J. Pätsch, R. Ji, and M. Maar, “Sensitivity of the fish community to different prey fields and importance of spatial-seasonal patterns.,” Marine ecology progress series, vol. 680, p. 680:79-95, 2021.
    [Bibtex] 
    @article{Wolfshaar,
author={Karen E. van de Wolfshaar and Ute Daewel and Solfrid Sætre Hjøllo and Tineke A. Troost and Markus Kreus and Johannes Pätsch and Rubao Ji and Marie Maar},
year={2021},
title={Sensitivity of the fish community to different prey fields and importance of spatial-seasonal patterns.},
journal={Marine Ecology Progress Series},
pages={680:79-95},
volume={680},
doi={https://doi.org/10.3354/meps13885}
}
  • [DOI] L. Xing, Y. Chen, R. Boenish, K. R. Tanaka, N. Barrier, and Y. Ren, “Evaluating the impacts of fishing and migratory species in a temperate bay of china using the ecosystem model osmose-jzb,” Fisheries research, vol. 243, p. 106051, 2021.
    [Bibtex] 
    @article{XING2021106051,
title = {Evaluating the impacts of fishing and migratory species in a temperate bay of China using the ecosystem model OSMOSE-JZB},
journal = {Fisheries Research},
volume = {243},
pages = {106051},
year = {2021},
issn = {0165-7836},
doi = {https://doi.org/10.1016/j.fishres.2021.106051},
url = {https://www.sciencedirect.com/science/article/pii/S016578362100179X},
author = {Lei Xing and Yong Chen and Robert Boenish and Kisei R. Tanaka and Nicolas Barrier and Yiping Ren},
keywords = {OSMOSE, Small-scale fisheries, Race to fish, Trophic interactions, Jiaozhou Bay},
abstract = {Small-scale fisheries (SSFs) play a vital role in the sustainability of local economies. Migratory species moving into and out of an ecosystem may influence the dynamics of local fish communities and SSFs. We used the end-to-end model, OSMOSE-JZB (Object-oriented Simulator of Marine ecOSystEms), to evaluate the impacts of fishing and a migratory shrimp (Trachypenaeus curvirostris) on the ecosystem of Jiaozhou Bay, China. Increased fishing intensity (i.e., annual fishing effort) resulted in the decline of four ecological indicators, including the total biomass of the community, mean trophic level of the community, inverse fishing pressure, and large fish index. Compared to managing fish stocks under uniform fishing mortality over the fishing season, landings and community biomass were higher when a “race to fish” (i.e., large catches in a short period) occurred. The results suggested that managing fishing seasonality (i.e., temporal allocation of fishing effort) could mitigate the negative impact of fishing intensity. Two resident high-trophic-level fishes were sensitive to changes in fishing intensity and fishing seasonality. The changes in trophic interactions had larger impacts on species at low trophic levels than fishing. Pearson's correlation analysis showed that T. curvirostris biomass was negatively correlated with the biomass of resident species and positively correlated with the biomass of other migratory species. We also found that fishing changed the impact of varying T. curvirostris migratory biomass on other species. Resident species were more sensitive to changes in fishing and T. curvirostris migratory biomass than other migratory species. We argue that SSFs management can benefit from the development of temporal fishing strategies and consideration of trophic interactions stemming from migratory species dynamics.}
}

2020

  • [DOI] L. Xing, Y. Chen, C. Zhang, B. Li, Y. Shin, and Y. Ren, “Evaluating impacts of pulse fishing on the effectiveness of seasonal closure,” Acta oceanologica sinica, vol. 39, pp. 89-99, 2020.
    [Bibtex] 
    @article{Xing2020,
author = {Xing, Lei and Chen, Yong and Zhang, Chongliang and Li, Bai and Shin, Yunne-Jai and Ren, Yiping},
year = 2020,
title = {Evaluating impacts of pulse fishing on the effectiveness of seasonal closure},
journal = {Acta Oceanologica Sinica},
volume=39,
pages={89-99},
url = {https://doi.org/10.1007/s13131-020-1536-x},
doi = {10.1007/s13131-020-1536-x}
}
  • [DOI] C. Fu, Y. Xu, C. Guo, N. Olsen, A. Grüss, H. Liu, N. Barrier, P. Verley, and Y. Shin, “The cumulative effects of fishing, plankton productivity, and marine mammal consumption in a marine ecosystem,” Frontiers in marine science, vol. 7, p. 840, 2020.
    [Bibtex] 
    @article {132,
title = {The Cumulative Effects of Fishing, Plankton Productivity, and Marine Mammal Consumption in a Marine Ecosystem},
journal = {Frontiers in Marine Science},
volume = {7},
year = {2020},
pages = {840},
abstract = {The marine ecosystem off British Columbia (BC), Canada, has experienced various changes in the last two decades, including reduced lipid-rich zooplankton biomass, increased marine mammals, and deteriorated commercial fisheries, particularly those targeting pelagic species such as Pacific Herring (Clupea pallasii). Understanding how stressors interactively and cumulatively affect commercially important fish species is key to moving toward ecosystem-based fisheries management. Because it is challenging to assess the cumulative effects of multiple stressors by using empirical data alone, a dynamic, individual-based spatially explicit ecosystem modeling platform such as Object-oriented Simulator of Marine Ecosystems (OSMOSE) represents a valuable tool to simulate ecological processes and comprehensively evaluate how stressors cumulatively impact modeled species. In this study, we employed OSMOSE to investigate the cumulative effects of fishing, plankton biomass change, and marine mammal consumption on the dynamics of some fish species and the BC marine ecosystem as a whole. We specifically simulated ecosystem dynamics during the last 20 years under two sets of scenarios: (1) unfavorable conditions from the perspective of commercial fish species (i.e., doubling fishing mortality rates, halving plankton biomass, and doubling marine mammal biomass, acting individually or collectively); and (2) favorable conditions with the three factors having opposite changes (i.e., halving fishing mortality rates, doubling plankton biomass, and halving marine mammal biomass, acting individually or collectively). Our results indicate that, under unfavorable conditions, the degree to which species biomass was reduced varied among species, and that negative synergistic and negative dampened effects were dominant under historical and doubled fishing mortality rates, respectively. Under favorable conditions, species biomasses did not increase as much as expected due to the existence of complex predator-prey interactions among fish species, and positive synergistic and positive dampened effects were prevailing under historical and halved fishing mortality rates, respectively. The ecosystem total biomass and the biomass to fisheries yield ratio were found to be good ecological indicators to represent ecosystem changes and track the impacts from the multiple drivers of change. Our research provides insights on how fisheries management should adapt to prepare for potential future impacts of climate change.},
issn = {2296-7745},
doi = {10.3389/fmars.2020.565699},
url = {https://www.frontiersin.org/article/10.3389/fmars.2020.565699},
author = {Fu, Caihong and Xu, Yi and Guo, Chuanbo and Olsen, Norm and Gr{\"u}ss, Arnaud and Liu, Huizhu and Barrier, Nicolas and Verley, Philippe and Shin, Yunne-Jai}
}
  • [DOI] M. Travers-Trolet, P. Bourdaud, M. Genu, L. Velez, and Y. Vermard, “The risky decrease of fishing reference points under climate change,” Frontiers in marine science, vol. 7, 2020.
    [Bibtex] 
    @ARTICLE{10.3389/fmars.2020.568232,
AUTHOR={Travers-Trolet, Morgane and Bourdaud, Pierre and Genu, Mathieu and Velez, Laure and Vermard, Youen},
TITLE={The Risky Decrease of Fishing Reference Points Under Climate Change},
JOURNAL={Frontiers in Marine Science},
VOLUME={7},
YEAR={2020},
URL={https://www.frontiersin.org/article/10.3389/fmars.2020.568232},
DOI={10.3389/fmars.2020.568232},
ISSN={2296-7745},
ABSTRACT={In Europe, implementation of sustainable fisheries management has been reinforced in the latest common fisheries policy, and presently marine fish stocks are mostly managed through assessment of their exploitation and ecological status compared to reference points such as Maximum Sustainable Yield (MSY). However, MSY and its associated fishing mortality rate FMSY are sensitive to both stock characteristics and environment conditions. In parallel, climate change impacts are increasingly affecting fish stocks directly and indirectly but might also change the exploitation reference points and the associated level of catch. Here we explored the variability of MSY reference points under climate change by using a multi-species model applied to the Eastern English Channel, a highly exploited semi-continental sea. The spatial individual-based OSMOSE explicitly represents the entire fish life cycle of 14 species interacting through size-based opportunistic predation. The model was first parameterized and run to fit the historical situation (2000–2009) and then used to assess the ecosystem state for the 2050–2059 period, using two contrasting climate change scenarios (RCP 4.5 and RCP 8.5). For each condition, a monospecific MSY estimation routine was performed by varying species fishing mortality independently and allowed estimation of reference points for each species. The FMSY estimated with OSMOSE were mostly in accordance with available values derived from stock assessment and used for fishing advice. Evolution of reference points with climate change was compared across species and highlighted that overexploited cold-water species are likely to have both MSY and FMSY declining with climate warming. Considering all species together, MSY under RCP scenarios was expected to be higher than historical MSY for half of them, with no clear link with species temperature preferences, exploitation status or trophic level, but in relation with expected change of species biomass under climate change. By contrast, for 80% of cases FMSY projections showed consistent decreasing pattern as climate conditions changed from historical to RCP scenarios in the Eastern English Channel. This result constitutes a risk for fisheries management, and anticipation of climate change impacts on fish community would require targeting a smaller fishing mortality than FMSY to ensure sustainable exploitation of marine stocks.}
}

2019

  • [DOI] F. Briton, L. Shannon, N. Barrier, P. Verley, and Y. Shin, “Reference levels of ecosystem indicators at multispecies maximum sustainable yield,” Ices journal of marine science, vol. 76, iss. 7, pp. 2070-2081, 2019.
    [Bibtex] 
    @article{10.1093/icesjms/fsz104,
author = {Briton, Florence and Shannon, Lynne and Barrier, Nicolas and Verley, Philippe and Shin, Yunne-Jai},
title = "{Reference levels of ecosystem indicators at multispecies maximum sustainable yield}",
journal = {ICES Journal of Marine Science},
volume = {76},
number = {7},
pages = {2070-2081},
year = {2019},
month = {06},
abstract = "{We investigate reference points for ecosystem indicators in support of an Ecosystem Approach to Fishery. In particular, we assess indicator capacity to detect when the Multispecies Maximum Sustainable Yield (MMSY) is reached, under a wide range of multispecies fishing strategies. The analysis was carried out using a simulation approach based on the ecosystem model OSMOSE in the southern Benguela. We show that the 13 ecosystem indicators have reference points at MMSY that are highly variable across fishing strategies. The state of the ecosystem at MMSY is so variable across fishing strategies that it is not possible to set reference points without considering the fishing strategy. However, strategy-specific reference points were found to constitute robust proxies for MMSY in more than 90\\% of the simulated fishing strategies. For instance, under the current fishing strategy in the southern Benguela, robust reference points at MMSY could be identified for the following indicators: mean length of fish, mean lifespan, biomass over catch ratio, trophic level of the surveys, mean trophic index, proportion of predatory fish, intrinsic vulnerability index, and mean maximum length.}",
issn = {1054-3139},
doi = {10.1093/icesjms/fsz104},
url = {https://doi.org/10.1093/icesjms/fsz104},
eprint = {https://academic.oup.com/icesjms/article-pdf/76/7/2070/31679591/fsz104.pdf},
}
  • [DOI] C. Guo, C. Fu, N. Olsen, Y. Xu, A. Grüss, H. Liu, P. Verley, and Y. Shin, “Incorporating environmental forcing in developing ecosystem-based fisheries management strategies,” Ices journal of marine science, vol. 77, iss. 2, pp. 500-514, 2019.
    [Bibtex] 
    @article{10.1093/icesjms/fsz246,
author = {Guo, Chuanbo and Fu, Caihong and Olsen, Norm and Xu, Yi and Grüss, Arnaud and Liu, Huizhu and Verley, Philippe and Shin, Yunne-Jai},
title = "{Incorporating environmental forcing in developing ecosystem-based fisheries management strategies}",
journal = {ICES Journal of Marine Science},
volume = {77},
number = {2},
pages = {500-514},
year = {2019},
month = {12},
abstract = "{This study incorporated two pathways of environmental forcing (i.e. “larval mortality forcing” and “somatic growth forcing”) into an end-to-end ecosystem model (Object-oriented Simulator of Marine ecOSystEms, OSMOSE) developed for the Pacific North Coast Integrated Management Area (PNCIMA) off western Canada, in order to evaluate alternative fisheries management strategies under environmental changes. With a suite of ecosystem-level indicators, the present study first compared the ecosystem effects of different pathways of environmental forcing scenarios; and then evaluated the alternative fisheries management strategies which encompassed a series of fishing mortality rates relative to FMSY (the fishing mortality rate that produces maximum sustainable yield) and a set of precautionary harvest control rules (HCRs). The main objectives of this study were to (i) explore the ecosystem effects of different environmental forcing scenarios; (ii) identify the impacts of different fishing mortality rates on marine ecosystem structure and function; and (iii) evaluate the ecosystem-level performance of various levels of precautionary HCRs. Results indicated that different pathways of environmental forcing had different ecosystem effects and incorporating appropriate HCRs in the fisheries management process could help maintain ecosystem health and sustainable fisheries. This study provides important information on future fisheries management options within similar marine ecosystems that are facing global changes.}",
issn = {1054-3139},
doi = {10.1093/icesjms/fsz246},
url = {https://doi.org/10.1093/icesjms/fsz246},
eprint = {https://academic.oup.com/icesjms/article-pdf/77/2/500/32881865/fsz246.pdf},
}
  • [DOI] A. Grüss, M. L. D. Palomares, J. H. Poelen, J. R. Barile, C. D. Aldemita, S. R. Ortiz, N. Barrier, Y. Shin, J. Simons, and D. Pauly, “Building bridges between global information systems on marine organisms and ecosystem models,” Ecological modelling, vol. 398, pp. 1-19, 2019.
    [Bibtex] 
    @article {124,
title = {Building bridges between global information systems on marine organisms and ecosystem models},
journal = {Ecological Modelling},
volume = {398},
year = {2019},
month = {04/2019},
pages = {1 - 19},
abstract = {
    To facilitate the wider implementation of ecosystem modeling platforms and, thereby, to help advance ecosystem-based fisheries management (EBFM) worldwide, tools delivering a large quantity of inputs to ecosystem models are needed. We developed a web application providing OSMOSE ecosystem models with values for trophic, growth and reproduction parameters derived from data from two global information systems (FishBase and SeaLifeBase). Our web application guides the user through simple queries to extract information from FishBase and SeaLifeBase data archives, and it delivers all the configuration files necessary for running an OSMOSE model. Here, we present our web application and demonstrate it for the West Florida Shelf ecosystem. Our software architecture can serve as a basis for designing other advanced web applications using FishBase and SeaLifeBase data in support of EBFM.
    
},
keywords = {Ecosystem model, FishBase, OSMOSE, SeaLifeBase, Web application, Web application programming interface},
issn = {0304-3800},
doi = {https://doi.org/10.1016/j.ecolmodel.2019.01.023},
url = {http://www.sciencedirect.com/science/article/pii/S0304380019300432},
author = {Arnaud Gr{\"u}ss and Maria L.D. Palomares and Jorrit H. Poelen and Josephine R. Barile and Casey D. Aldemita and Shelumiel R. Ortiz and Nicolas Barrier and Yunne-Jai Shin and James Simons and Daniel Pauly}
}
  • [DOI] F. Moullec, L. Velez, P. Verley, N. Barrier, C. Ulses, P. Carbonara, A. Esteban, C. Follesa, M. Gristina, A. Jadaud, A. Ligas, E. L. D. ‘i, P. Maiorano, P. Peristeraki, M. T. Spedicato, I. Thasitis, M. Valls, F. Guilhaumon, and Y. Shin, “Capturing the big picture of mediterranean marine biodiversity with an end-to-end model of climate and fishing impacts,” Progress in oceanography, vol. 178, p. 102179, 2019.
    [Bibtex] 
    @article {127,
title = {Capturing the big picture of Mediterranean marine biodiversity with an end-to-end model of climate and fishing impacts},
journal = {Progress in Oceanography},
volume = {178},
year = {2019},
pages = {102179},
abstract = {
    The Mediterranean Sea is one of the main hotspots of marine biodiversity in the world. The combined pressures of fishing activity and climate change have also made it a hotspot of global change amidst increasing concern about the worsening status of exploited marine species. To anticipate the impacts of global changes in the Mediterranean Sea, more integrated modelling approaches are needed, which can then help policymakers prioritize management actions and formulate strategies to mitigate impacts and adapt to changes. The aim of this study was to develop a holistic model of marine biodiversity in the Mediterranean Sea with an explicit representation of the spatial, multispecies dynamics of exploited resources subject to the combined influence of climate variability and fishing pressure. To this end, we used the individual-based OSMOSE model (Object-oriented Simulator of Marine ecOSystEms), including 100 marine species (fish, cephalopods and crustaceans) representing about 95\% of the total declared catch, at a high spatial resolution (400 km2) and a large spatial scale (the entire Mediterranean basin) \– the first time such a resolution and scale have been modelled. We then combined OSMOSE with the NEMOMED 12 physical model and the Eco3M-S biogeochemical low trophic level model to build the end-to-end model, OSMOSE-MED. We fitted OSMOSE-MED model with observed or estimated biomass and commercial catch data using a likelihood approach and an evolutionary optimization algorithm. The outputs of OSMOSE-MED were then verified against observed biomass and catch data, and compared with independent datasets (MEDITS data, diet composition and trophic levels). The model results \– at different hierarchical levels, from individuals to the scale of the ecosystem \– were consistent with current knowledge of the structure, functioning and dynamics of the ecosystems in the Mediterranean Sea. While the model could be further improved in future iterations, all the modelling steps \– the comprehensive representation of key ecological processes and feedback, the selective parameterization of the model, and the comparison with observed data in the validation process \– strengthened the predictive performance of OSMOSE-MED and thus its relevance as an impact model to explore the future of marine biodiversity under scenarios of global change. It is a promising tool to support ecosystem-based fishery management in the Mediterranean Sea.
    
},
keywords = {Eco3M-S model, Ecosystem Approach to Fisheries Management, Ecosystem model, Global change, NEMOMED model, OSMOSE model},
issn = {0079-6611},
doi = {https://doi.org/10.1016/j.pocean.2019.102179},
url = {http://www.sciencedirect.com/science/article/pii/S0079661118303537},
author = {Fabien Moullec and Laure Velez and Philippe Verley and Nicolas Barrier and Caroline Ulses and Pierluigi Carbonara and Antonio Esteban and Cristina Follesa and Michele Gristina and Ang{\'e}lique Jadaud and Alessandro Ligas and Eduardo L{\'o}pez D{\'\i}az and Porzia Maiorano and Panagiota Peristeraki and Maria Teresa Spedicato and Ioannis Thasitis and Maria Valls and Fran{\c c}ois Guilhaumon and Yunne-Jai Shin}
}
  • [DOI] C. Guo, C. Fu, R. E. Forrest, N. Olsen, H. Liu, P. Verley, and Y. Shin, “Ecosystem-based reference points under varying plankton productivity states and fisheries management strategies,” Ices journal of marine science, 2019.
    [Bibtex] 
    @article {123,
title = {Ecosystem-based reference points under varying plankton productivity states and fisheries management strategies},
journal = {ICES Journal of Marine Science},
year = {2019},
month = {06},
abstract = {
    In the context of ecosystem-based fisheries management, which should consider changing and uncertain environmental conditions, the development of ecosystem-based biological reference points (EBRPs) to account for important multi-species (MS) interactions, fishery operations, and climate change, is of paramount importance for sustainable fisheries management. However, EBRPs under varying plankton productivity states and fisheries management strategies are seldom developed, and the ecosystem effects of these changes are still largely unknown. In this study, ecosystem-based FMSY (fishing mortality rate at MSY) values were estimated within an end-to-end ecosystem model (OSMOSE) for three focused fish species (Pacific Herring, Clupea pallasii; Pacific Cod, Gadus macrocephalus; Lingcod, Ophiodon elongatus) under three plankton productivity states of differing plankton biomass at high, current, and low levels. In addition, ecosystem effects were compared across different plankton productivity and fisheries management strategies with the latter consisting of two fishery scenarios (i.e. single-species-focused (SS) and MS-focused), various fishing mortality rates, and two harvest policies (with and without harvest control rules, HCRs). Main findings of this study include: (i) plankton productivity change affected the values of ecosystem-based FMSY, which increased as plankton productivity states changed from low to high plankton biomass; (ii) ecosystem-based FMSY for Pacific Herring and Pacific Cod stocks increased when fishery scenarios shifted from SS-focused to MS-focused; (iii) fisheries management incorporating HCR yielded more stable system catch and system biomass; and (iv) high plankton biomass combined with fisheries management using HCR could maintain stable ecosystem production and sustainable fisheries. Based on our findings, we highlight possible adaptive fisheries management strategies in the face of future climate and ocean changes. Overall, EBRPs complement SS stock assessments by incorporating key ecological processes and ecosystem properties, thus providing supporting evidence for better incorporation of ecosystem considerations into scientific advice for sustainable fisheries management.
    
},
issn = {1054-3139},
doi = {10.1093/icesjms/fsz120},
url = {https://doi.org/10.1093/icesjms/fsz120},
author = {Guo, Chuanbo and Fu, Caihong and Forrest, Robyn E and Olsen, Norm and Liu, Huizhu and Verley, Philippe and Shin, Yunne-Jai}
}
  • [DOI] M. Travers-Trolet, F. Coppin, P. Cresson, P. Cugier, R. Oliveros-Ramos, and P. Verley, “Emergence of negative trophic level-size relationships from a size-based, individual-based multispecies fish model,” Ecological modelling, vol. 410, p. 108800, 2019.
    [Bibtex] 
    @article {125,
title = {Emergence of negative trophic level-size relationships from a size-based, individual-based multispecies fish model},
journal = {Ecological Modelling},
volume = {410},
year = {2019},
month = {09/2019},
pages = {108800},
abstract = {
    Modeling the mechanisms underlying trophic interactions between individuals allows the food web structure to emerge from local interactions, which constitutes a prerequisite for assessing how marine ecosystems respond to various anthropogenic pressures. Using a multispecies spatially explicit individual-based model, the emergence of trophic patterns was explored in the eastern English Channel ecosystem, where pelagic-benthic trophic coupling was recently studied empirically. The OSMOSE model was applied to this ecosystem by explicitly representing the life cycle of 13 fish species and one squid group, forced by pelagic and benthic prey fields that are variable over time and space. A matrix defining possible accessibilities between life stages was added to the model to link benthic and pelagic communities through overlap of vertical distribution. After optimizing some parameters of the model to represent the average state of the fish community during the 2000\–2009 period, the simulated trophic structure was explored and compared to empirical data. The simulated and stable-isotope-derived trophic levels of fish were in relatively good agreement. Intraspecific variability of the trophic level is high in the five stable-isotope datasets but is well encompassed by the model. Despite the hypothesis of opportunistic size-based predation, the simulation showed a decreasing trend of trophic level with size for four benthic species, a pattern observed empirically for a different set of species in the ecosystem. Model exploration showed that this emerging pattern varies spatially and is both explained by the spatial variability of prey availability and by the independence of trophic and size structures of benthic invertebrates. The combination of individual-based models, stomach contents and intrinsic tracers, such as stable isotopes, appears to be a promising tool to better understand the causes of observed trophic patterns.
    
},
keywords = {Emergent patterns, Fish community, Food web, Individual-based model, Pelagic-benthic coupling},
issn = {0304-3800},
doi = {https://doi.org/10.1016/j.ecolmodel.2019.108800},
url = {http://www.sciencedirect.com/science/article/pii/S0304380019303084},
author = {Morgane Travers-Trolet and Franck Coppin and Pierre Cresson and Philippe Cugier and Ricardo Oliveros-Ramos and Philippe Verley}
}
  • [DOI] F. Moullec, N. Barrier, S. Drira, F. Guilhaumon, P. Marsaleix, S. Somot, C. Ulses, L. Velez, and Y. Shin, “An end-to-end model reveals losers and winners in a warming mediterranean sea,” Frontiers in marine science, vol. 6, p. 345, 2019.
    [Bibtex] 
    @article {119,
title = {An End-to-End Model Reveals Losers and Winners in a Warming Mediterranean Sea},
journal = {Frontiers in Marine Science},
volume = {6},
year = {2019},
pages = {345},
abstract = {
    The Mediterranean Sea is now recognized as a hotspot of global change, ranking among the fastest warming ocean regions. In order to project future plausible scenarios of marine biodiversity at the scale of the whole Mediterranean basin, the current challenge is to develop an explicit representation of the multispecies spatial dynamics under the combined influence of fishing pressure and climate change. Notwithstanding the advanced state-of-the-art modelling of food webs in the region, no previous studies have projected the consequences of climate change on marine ecosystems in an integrated way, considering changes in ocean dynamics, in phyto- and zoo-plankton productions, shifts in Mediterranean species distributions and their trophic interactions at the whole basin scale. We used an integrated modelling chain including a high-resolution regional climate model, a regional biogeochemistry model and a food web model OSMOSE to project the potential effects of climate change on biomass and catches for a wide array of species in the Mediterranean Sea. We showed that projected climate change would have large consequences for marine biodiversity by the end of the 21st century under a business-as-usual scenario (RCP8.5 with current fishing mortality). The total biomass of high trophic level species (fish and macroinvertebrates) is projected to increase by 5\% and 22\% while total catch is projected to increase by 0.3\% and 7\% by 2021-2050 and 2071-2100, respectively. However, these global increases masked strong spatial and inter-species contrasts. The bulk of increase in catch and biomass would be located in the southeastern part of the basin while total catch could decrease by up to 23\% in the western part. Winner species would mainly belong to the pelagic group, are thermophilic and/or exotic, of smaller size and of low trophic level while loser species are generally large-sized, some of them of great commercial interest, and could suffer from a spatial mismatch with potential prey subsequent to a contraction or shift of their geographic range. Given the already poor conditions of exploited resources, our results suggest the need for fisheries management to adapt to future changes and to incorporate climate change impacts in future management strategy evaluation.
    
},
issn = {2296-7745},
doi = {10.3389/fmars.2019.00345},
url = {https://www.frontiersin.org/article/10.3389/fmars.2019.00345},
author = {Moullec, Fabien and Barrier, Nicolas and Drira, Sabrine and Guilhaumon, Fran{\c c}ois and Marsaleix, Patrick and Somot, Samuel and Ulses, Caroline and Velez, Laure and Shin, Yunne-Jai}
}
  • [DOI] G. Halouani, F. L. Loc’h, Y. Shin, L. Velez, T. Hattab, M. S. Romdhane, and F. B. R. Lasram, “An end-to-end model to evaluate the sensitivity of ecosystem indicators to track fishing impacts,” Ecological indicators, vol. 98, pp. 121-130, 2019.
    [Bibtex] 
    @article {111,
title = {An end-to-end model to evaluate the sensitivity of ecosystem indicators to track fishing impacts},
journal = {Ecological Indicators},
volume = {98},
year = {2019},
pages = {121 - 130},
keywords = {Ecological indicators, Ecosystem model, End-to-end model, Fishery, Fishing impacts, Gulf of Gabes, Marine ecosystem, OSMOSE},
issn = {1470-160X},
doi = {https://doi.org/10.1016/j.ecolind.2018.10.061},
url = {http://www.sciencedirect.com/science/article/pii/S1470160X1830846X},
author = {Ghassen Halouani and Fran{\c c}ois Le Loc'h and Yunne-Jai Shin and Laure Velez and Tarek Hattab and Mohamed Salah Romdhane and Frida Ben Rais Lasram}
}
  • [DOI] F. Diaz, D. Bănaru, P. Verley, and Y. Shin, “Implementation of an end-to-end model of the gulf of lions ecosystem (nw mediterranean sea). ii. investigating the effects of high trophic levels on nutrients and plankton dynamics and associated feedbacks,” Ecological modelling, vol. 405, pp. 51-68, 2019.
    [Bibtex] 
    @article{DIAZ201951,
title = "Implementation of an end-to-end model of the Gulf of Lions ecosystem (NW Mediterranean Sea). II. Investigating the effects of high trophic levels on nutrients and plankton dynamics and associated feedbacks",
journal = "Ecological Modelling",
volume = "405",
pages = "51 - 68",
year = "2019",
issn = "0304-3800",
doi = "https://doi.org/10.1016/j.ecolmodel.2019.05.004",
url = "http://www.sciencedirect.com/science/article/pii/S0304380019301693",
author = "Frédéric Diaz and Daniela Bănaru and Philippe Verley and Yunne-Jai Shin",
keywords = "End-to-end model, Two-ways coupling, Plankton, Fisheries, Food web functioning",
abstract = "The end-to-end OSMOSE-GoL model parameterized, calibrated and evaluated for the Gulf of Lions ecosystem (Northwestern Mediterranean Sea) has been used to investigate the effects of introducing two-ways coupling between the dynamics of Low and High Trophic Level groups. The use of a fully dynamic two-ways coupling between the models of Low and High Trophic Levels organisms provided some insights in the functioning of the food web in the Gulf of Lions. On the whole microphytoplankton and mesozooplankton were found to be preyed upon by High Trophic Levels planktivorous groups at rates lower than 20% and 30% of their respective natural mortality rates, but these relatively low rates involved some important alterations in the infra-seasonal and annual cycles of both High and Low Trophic Levels groups. They induced significant changes in biomass, fisheries landings and food web interactions by cascading effects. Spatial differential impacts of High Trophic Levels predation on plankton are less clear except in areas in which primary productivity is high. Higher predation rates on plankton groups were encountered within the area of the Rhone river’s influence and in areas associated to the presence of mesoscale eddies in the Northwestern part of the Gulf of Lions, especially. Generally, the pressure of the High Trophic Levels predation was the highest in areas of highest biomass whatever the plankton group considered. The two-ways coupling between Low and High Trophic Levels models revealed both bottom-up and top-down controls in the ecosystem with effects on planktivorous species similar to those observed in the field. The use of the end-to-end model enabled to propose a set of potential mechanisms that may explain the observed decrease in small pelagic catches by the French Mediterranean artisanal fisheries over the last decade."
}
  • [DOI] D. Bănaru, F. Diaz, P. Verley, R. Campbell, J. Navarro, C. Yohia, R. Oliveros-Ramos, C. Mellon-Duval, and Y. Shin, “Implementation of an end-to-end model of the gulf of lions ecosystem (nw mediterranean sea). i. parameterization, calibration and evaluation,” Ecological modelling, vol. 401, pp. 1-19, 2019.
    [Bibtex] 
    @article{BANARU20191,
title = "Implementation of an end-to-end model of the Gulf of Lions ecosystem (NW Mediterranean Sea). I. Parameterization, calibration and evaluation",
journal = "Ecological Modelling",
volume = "401",
pages = "1 - 19",
year = "2019",
issn = "0304-3800",
doi = "https://doi.org/10.1016/j.ecolmodel.2019.03.005",
url = "http://www.sciencedirect.com/science/article/pii/S0304380019301024",
author = "Daniela Bănaru and Fréderic Diaz and Philippe Verley and Rose Campbell and Jonathan Navarro and Christophe Yohia and Ricardo Oliveros-Ramos and Capucine Mellon-Duval and Yunne-Jai Shin",
keywords = "Ecosystem modeling, Food web, Fisheries, OSMOSE, Eco3M",
abstract = "An end-to-end model named OSMOSE-GoL has been built for the Gulf of Lions, the main French Mediterranean fishing area. This spatialized dynamic model links the coupled hydrodynamic and biogeochemical model Eco3M-S/SYMPHONIE (LTL – low trophic level model) to OSMOSE (HTL – high trophic level model). It includes 15 compartments of living organisms, five from the LTL model (i.e. nanophytoplankton, microphytoplankton, nanozooplankton, microzooplankton and mesozooplankton) and ten from the HTL model (northern krill, southern shortfin squid, European pilchard, European anchovy, European sprat, Atlantic horse mackerel, Atlantic mackerel, blue whiting, European hake and Atlantic bluefin tuna). With the exception of northern krill and European sprat, all HTL species are commercially exploited and undergo fisheries mortality pressure. The modeled species represent more than 70% of annual catches in this area. This paper presents the parameterization, calibration and evaluation of this model with satellite data for phytoplankton and with biomass, landings, diet and trophic level data for HTL groups. For most species, the diets in output of OSMOSE-GoL are similar to field and literature data in terms of dominant prey groups and species. However, some differences were observed. Various reasons may explain the mismatch between the modeled diet and field data. Benthic prey sometimes observed in the stomach content of the HTL predators were not modeled in OSMOSE-GoL. Field studies were carried out at specific periods and locations, while our data concern the period 2001–2004 and the entire modeled domain. Inter- and intra-annual variations in spatial distribution and density of prey may also explain these differences. The model estimates trophic level values similar to those cited in the literature for all the HTL compartments. These values are also close to the trophic levels estimated by a previous Ecopath model for the same area and period. Even though some improvements are still possible, this model may already be of use to explore fishery or Marine Protected Areas scenarios for socio-ecosystem management issues."
}
  • [DOI] C. Guo, C. Fu, N. Olsen, Y. Xu, A. Grüss, H. Liu, P. Verley, and Y. Shin, “Incorporating environmental forcing in developing ecosystem-based fisheries management strategies,” Ices journal of marine science, vol. 77, pp. 500-514, 2019.
    [Bibtex] 
    @article {133,
title = {Incorporating environmental forcing in developing ecosystem-based fisheries management strategies},
journal = {ICES Journal of Marine Science},
volume = {77},
year = {2019},
month = {12},
pages = {500-514},
abstract = {This study incorporated two pathways of environmental forcing (i.e. {\textquotedblleft}larval mortality forcing{\textquotedblright} and {\textquotedblleft}somatic growth forcing{\textquotedblright}) into an end-to-end ecosystem model (Object-oriented Simulator of Marine ecOSystEms, OSMOSE) developed for the Pacific North Coast Integrated Management Area (PNCIMA) off western Canada, in order to evaluate alternative fisheries management strategies under environmental changes. With a suite of ecosystem-level indicators, the present study first compared the ecosystem effects of different pathways of environmental forcing scenarios; and then evaluated the alternative fisheries management strategies which encompassed a series of fishing mortality rates relative to FMSY (the fishing mortality rate that produces maximum sustainable yield) and a set of precautionary harvest control rules (HCRs). The main objectives of this study were to (i) explore the ecosystem effects of different environmental forcing scenarios; (ii) identify the impacts of different fishing mortality rates on marine ecosystem structure and function; and (iii) evaluate the ecosystem-level performance of various levels of precautionary HCRs. Results indicated that different pathways of environmental forcing had different ecosystem effects and incorporating appropriate HCRs in the fisheries management process could help maintain ecosystem health and sustainable fisheries. This study provides important information on future fisheries management options within similar marine ecosystems that are facing global changes.},
issn = {1054-3139},
doi = {10.1093/icesjms/fsz246},
url = {https://doi.org/10.1093/icesjms/fsz246},
author = {Guo, Chuanbo and Fu, Caihong and Olsen, Norm and Xu, Yi and Gr{\"u}ss, Arnaud and Liu, Huizhu and Verley, Philippe and Shin, Yunne-Jai}
}
  • [DOI] C. Fu, Y. Xu, A. Bundy, A. Grüss, M. Coll, J. J. Heymans, E. A. Fulton, L. Shannon, G. Halouani, L. Velez, E. Akoglu, C. P. Lynam, and Y. Shin, “Making ecological indicators management ready: assessing the specificity, sensitivity, and threshold response of ecological indicators,” Ecological indicators, vol. 105, pp. 16-28, 2019.
    [Bibtex] 
    @article {135,
title = {Making ecological indicators management ready: Assessing the specificity, sensitivity, and threshold response of ecological indicators},
journal = {Ecological Indicators},
volume = {105},
year = {2019},
pages = {16 - 28},
abstract = {Moving toward ecosystem-based fisheries management (EBFM) necessitates a suite of ecological indicators that are responsive to fishing pressure, capable of tracking changes in the state of marine ecosystems, and related to management objectives. In this study, we employed the gradient forest method to assess the performance of 14 key ecological indicators in terms of specificity, sensitivity and the detection of thresholds for EBFM across ten marine ecosystems using four modelling frameworks (Ecopath with Ecosim, OSMOSE, Atlantis, and a multi-species size-spectrum model). Across seven of the ten ecosystems, high specificity to fishing pressure was found for most of the 14 indicators. The indicators biomass to fisheries catch ratio (B/C), mean lifespan and trophic level of fish community were found to have wide utility for evaluating fishing impacts. The biomass indicators, which have been identified as Essential Ocean Variables by the Global Ocean Observing System (GOOS), had lower performance for evaluating fishing impacts, yet they were most sensitive to changes in primary productivity. The indicator B/C was most sensitive to low levels of fishing pressure with a generally consistent threshold response around 0.4*FMSY (fishing mortality rate at maximum sustainable yield) across nine of the ten ecosystems. Over 50\% of the 14 indicators had threshold responses at, or below \~{}0.6* FMSY for most ecosystems, indicating that these ecosystems would have already crossed a threshold for most indicators when fished at FMSY. This research provides useful insights on the performance of indicators, which contribute to facilitating the worldwide move toward EBFM.},
keywords = {Ecological modelling, Fishing pressure, Gradient forest method, Indictor performance, Marine ecosystem, Primary productivity},
issn = {1470-160X},
doi = {https://doi.org/10.1016/j.ecolind.2019.05.055},
url = {http://www.sciencedirect.com/science/article/pii/S1470160X19304005},
author = {Caihong Fu and Yi Xu and Alida Bundy and Arnaud Gr{\"u}ss and Marta Coll and Johanna J. Heymans and Elizabeth A. Fulton and Lynne Shannon and Ghassen Halouani and Laure Velez and Ekin Akoglu and Christopher P. Lynam and Yunne-Jai Shin}
}
  • [DOI] C. Fu, Y. Xu, A. Grüss, A. Bundy, L. Shannon, J. J. Heymans, G. Halouani, E. Akoglu, C. P. Lynam, M. Coll, E. A. Fulton, L. Velez, and Y. Shin, “Responses of ecological indicators to fishing pressure under environmental change: exploring non-linearity and thresholds,” Ices journal of marine science, vol. 77, pp. 1516-1531, 2019.
    [Bibtex] 
    @article {134,
title = {Responses of ecological indicators to fishing pressure under environmental change: exploring non-linearity and thresholds},
journal = {ICES Journal of Marine Science},
volume = {77},
year = {2019},
month = {09},
pages = {1516-1531},
abstract = {Marine ecosystems are influenced by multiple stressors in both linear and non-linear ways. Using generalized additive models (GAMs) fitted to outputs from a multi-ecosystem, multi-model simulation experiment, we investigated 14 major ecological indicators across ten marine ecosystems about their responses to fishing pressure under: (i) three different fishing strategies (focusing on low-, high-, or all-trophic-level taxa); and (ii) four different scenarios of directional or random primary productivity change, a proxy for environmental change. From this work, we draw four major conclusions: (i) responses of indicators to fishing mortality in shapes, directions, and thresholds depend on the fishing strategies considered; (ii) most of the indicators demonstrate decreasing trends with increasing fishing mortality, with a few exceptions depending on the type of fishing strategy; (iii) most of the indicators respond to fishing mortality in a linear way, particularly for community and biomass-based indicators; and (iv) occurrence of threshold for non-linear-mixed type (i.e. non-linear with inflection points) is not prevalent within the fishing mortality rates explored. The conclusions drawn from the present study provide a knowledge base in indicators{\textquoteright} dynamics under different fishing and primary productivity levels, thereby facilitating the application of ecosystem-based fisheries management worldwide.},
issn = {1054-3139},
doi = {10.1093/icesjms/fsz182},
url = {https://doi.org/10.1093/icesjms/fsz182},
author = {Fu, Caihong and Xu, Yi and Gr{\"u}ss, Arnaud and Bundy, Alida and Shannon, Lynne and Heymans, Johanna J and Halouani, Ghassen and Akoglu, Ekin and Lynam, Christopher P and Coll, Marta and Fulton, Elizabeth A and Velez, Laure and Shin, Yunne-Jai}
}

2018

  • M. Maar, M. Butenschön, U. Daewel, A. Eggert, W. Fan, S. Sætre Hjollo, M. Hufnagl, M. Huret, R. Ji, G. Lacroix, M. Peck, H. Radtke, S. Sailley, M. Sinerchia, M. Skogen, M. Travers-Trolet, T. Troost, and K. E. Van de Wolfshaar, “Responses of summer phytoplankton biomass to changes in top-down forcing: insights from comparative modelling,” Ecological modelling, vol. 376, 2018.
    [Bibtex] 
    @article {109,
title = {Responses of summer phytoplankton biomass to changes in top-down forcing: Insights from comparative modelling},
journal = {Ecological Modelling},
volume = {376},
year = {2018},
month = {03},
author = {Maar, Marie and Butensch\"{o}n, Momme and Daewel, Ute and Eggert, A and Fan, W and S{\ae}tre Hjollo, Solfrid and Hufnagl, Marc and Huret, Martin and Ji, Rubao and Lacroix, Genevi{\`e}ve and Peck, Myron and Radtke, Hagen and Sailley, Sevrine and Sinerchia, Matteo and Skogen, MD and Travers-Trolet, Morgane and Troost, T and Van de Wolfshaar, K.E.}
}
  • C. Fu, M. Travers-Trolet, L. Velez, A. Grüss, A. Bundy, L. J Shannon, E. Fulton, E. Akoglu, J. E Houle, M. Coll, P. Verley, J. Heymans, E. John, and Y. Shin, “Risky business: the combined effects of fishing and changes in primary productivity on fish communities,” Ecological modelling, vol. 368, pp. 265-276, 2018.
    [Bibtex] 
    @article {105,
title = {Risky business: The combined effects of fishing and changes in primary productivity on fish communities},
journal = {Ecological Modelling},
volume = {368},
year = {2018},
month = {01},
pages = {265-276},
author = {Fu, Caihong and Travers-Trolet, Morgane and Velez, Laure and Gr{\"u}ss, Arnaud and Bundy, Alida and J Shannon, Lynne and Fulton, Elizabeth and Akoglu, Ekin and E Houle, Jennifer and Coll, Marta and Verley, Philippe and Heymans, Johanna and John, Emma and Shin, Yunne-Jai}
}
  • Y. Shin, J. E Houle, E. Akoglu, J. L Blanchard, A. Bundy, M. Coll, H. Demarcq, C. Fu, E. Fulton, J. Heymans, B. Salihoglu, L. Shannon, M. Sporcic, and L. Velez, “The specificity of marine ecological indicators to fishing in the face of environmental change: a multi-model evaluation,” Ecological indicators, vol. 89, pp. 317-326, 2018.
    [Bibtex] 
    @article {104,
title = {The specificity of marine ecological indicators to fishing in the face of environmental change: A multi-model evaluation},
journal = {Ecological Indicators},
volume = {89},
year = {2018},
month = {01},
pages = {317-326},
author = {Shin, Yunne-Jai and E Houle, Jennifer and Akoglu, Ekin and L Blanchard, Julia and Bundy, Alida and Coll, Marta and Demarcq, Herve and Fu, Caihong and Fulton, Elizabeth and Heymans, Johanna and Salihoglu, Baris and Shannon, Lynne and Sporcic, Miriana and Velez, Laure}
}

2017

  • L. Xing, Z. Chongliang, Y. Chen, Y. Shin, P. Verley, H. Yu, and Y. Ren, “An individual-based model for simulating the ecosystem dynamics of jiaozhou bay, china,” Ecological modelling, vol. 360, pp. 120-131, 2017.
    [Bibtex] 
    @article {107,
title = {An individual-based model for simulating the ecosystem dynamics of Jiaozhou Bay, China},
journal = {Ecological Modelling},
volume = {360},
year = {2017},
month = {09},
pages = {120-131},
author = {Xing, Lei and Chongliang, Zhang and Chen, Yong and Shin, Yunne-Jai and Verley, Philippe and Yu, Haiqing and Ren, Yiping}
}
  • D. Tittensor, T. Eddy, H. Lotze, E. Galbraith, W. Cheung, M. Barange, J. L. Blanchard, L. Bopp, A. Bryndum-Buchholz, M. Büchner, C. Bulman, D. A. Carozza, V. Christensen, M. Coll, J. Dunne, J. Fernandes, E. Fulton, A. Hobday, V. Huber, and N. Walker, “A protocol for the intercomparison of marine fishery and ecosystem models: fish-mip v1.0,” Geoscientific model development discussions, pp. 1-39, 2017.
    [Bibtex] 
    @article {92,
title = {A protocol for the intercomparison of marine fishery and ecosystem models: Fish-MIP v1.0},
journal = {Geoscientific Model Development Discussions},
year = {2017},
month = {10},
pages = {1-39},
author = {Tittensor, Derek and Eddy, Tyler and Lotze, Heike and Galbraith, Eric and Cheung, William and Barange, Manuel and L. Blanchard, Julia and Bopp, Laurent and Bryndum-Buchholz, Andrea and B{\"u}chner, Matthias and Bulman, Catherine and A. Carozza, David and Christensen, Villy and Coll, Marta and Dunne, J and Fernandes, Jose and Fulton, Elizabeth and Hobday, Alistair and Huber, Veronika and Walker, Nicola}
}
  • R. Oliveros-Ramos, P. Verley, V. Echevin, and Y. Shin, “A sequential approach to calibrate ecosystem models with multiple time series data,” Progress in oceanography, vol. 151, pp. 227-244, 2017.
    [Bibtex] 
    @article {94,
title = {A sequential approach to calibrate ecosystem models with multiple time series data},
journal = {Progress In Oceanography},
volume = {151},
year = {2017},
month = {01},
pages = {227-244},
author = {Oliveros-Ramos, Ricardo and Verley, Philippe and Echevin, V and Shin, Yunne-Jai}
}
  • [DOI] C. Fu, N. Olsen, N. Taylor, A. Grüss, S. Batten, H. Liu, P. Verley, Y. Shin, and H. J. editor: Link, “Spatial and temporal dynamics of predator-prey species interactions off western canada,” Ices journal of marine science, vol. 74, pp. 2107-2119, 2017.
    [Bibtex] 
    @article {113,
title = {Spatial and temporal dynamics of predator-prey species interactions off western Canada},
journal = {ICES Journal of Marine Science},
volume = {74},
year = {2017},
pages = {2107-2119},
doi = {10.1093/icesjms/fsx056},
url = {http://dx.doi.org/10.1093/icesjms/fsx056},
author = {Fu, Caihong and Olsen, Norm and Taylor, Nathan and Gr{\"u}ss, Arnaud and Batten, Sonia and Liu, Huizhu and Verley, Philippe and Shin, Yunne-Jai and Handling editor: Jason Link}
}

2016

  • [DOI] J. Reed, L. Shannon, L. Velez, E. Akoglu, A. Bundy, M. Coll, C. Fu, E. A. Fulton, A. Grüss, G. Halouani, J. J. Heymans, J. E. Houle, E. John, F. Le Loc’h, B. Salihoglu, P. Verley, and Y. Shin, “Ecosystem indicators—accounting for variability in species’ trophic levels,” Ices journal of marine science, vol. 74, iss. 1, pp. 158-169, 2016.
    [Bibtex] 
    @article{10.1093/icesjms/fsw150,
author = {Reed, Jodie and Shannon, Lynne and Velez, Laure and Akoglu, Ekin and Bundy, Alida and Coll, Marta and Fu, Caihong and Fulton, Elizabeth A. and Grüss, Arnaud and Halouani, Ghassen and Heymans, Johanna J. and Houle, Jennifer E. and John, Emma and Le Loc'h, François and Salihoglu, Baris and Verley, Philippe and Shin, Yunne-Jai},
title = "{Ecosystem indicators—accounting for variability in species’ trophic levels}",
journal = {ICES Journal of Marine Science},
volume = {74},
number = {1},
pages = {158-169},
year = {2016},
month = {08},
abstract = "{Trophic level (TL)-based indicators are commonly used to track the ecosystem effects of fishing as the selective removal of organisms from the food web may result in changes to the trophic structure of marine ecosystems. The use of a fixed TL per species in the calculation of TL-based indicators has been questioned, given that species’ TLs vary with ontogeny, as well as over time and space. We conducted a model-based assessment of the performance of fixed TL-based indicators vs. variable TL-based indicators for tracking the effects of fishing pressure. This assessment considered three TL-based indicators (the trophic level of the landed catch (TLc), the marine trophic index (MTI) and the trophic level of the surveyed community (TLsc)), three fishing scenarios that targeted specific model groups (the low TL scenario (LTL), the high TL scenario (HTL) and a scenario encompassing broad-scale exploitation (ALL)) and ten contrasting marine ecosystems with four types of ecosystem modelling approaches that differ in their structure and assumptions. Results showed that, overall, variable TL-based indicators have a greater capacity for detecting the effects of fishing pressure than fixed TL-based indicators. Across TL-based indicators, TLsc displayed the most consistent response to fishing whether fixed or variable species' TLs were used, as well as the highest capacity for detecting fishing effects. This result supports previous studies that promote the use of survey-based indicators over catch-based indicators to explore the impacts of fishing on the structure of marine ecosystems. Across fishing scenarios, the low trophic level fishing scenario (LTL) resulted in the lowest consistency between fixed and variable TL-based indicator responses and the lowest capacity of TL-based indicators for detecting fishing effects. Overall, our results speak to the need for caution when interpreting TL-based indicator trends, and knowledge of the broader context, such as fishing strategies and exploitation history.}",
issn = {1054-3139},
doi = {10.1093/icesjms/fsw150},
url = {https://doi.org/10.1093/icesjms/fsw150},
eprint = {https://academic.oup.com/icesjms/article-pdf/74/1/158/31243716/fsw150.pdf},
}
  • [DOI] A. Grüss, M. J. Schirripa, D. Chagaris, L. Velez, Y. Shin, P. Verley, R. Oliveros-Ramos, and C. H. Ainsworth, “Estimating natural mortality rates and simulating fishing scenarios for gulf of mexico red grouper (epinephelus morio) using the ecosystem model osmose-wfs,” Journal of marine systems, vol. 154, Part B, pp. 264-279, 2016.
    [Bibtex] 
    @article {71,
title = {Estimating natural mortality rates and simulating fishing scenarios for Gulf of Mexico red grouper (Epinephelus morio) using the ecosystem model OSMOSE-WFS},
journal = {Journal of Marine Systems},
volume = {154, Part B},
year = {2016},
pages = {264 - 279},
abstract = {
    Abstract The ecosystem model OSMOSE-WFS was employed to evaluate natural mortality rates and fishing scenarios for Gulf of Mexico (GOM) red grouper (Epinephelus morio). OSMOSE-WFS represents major high trophic level (HTL) groups of species of the West Florida Shelf, is forced by the biomass of plankton and benthos groups, and has a monthly time step. The present application of the model uses a recently developed \‘stochastic mortality algorithm\’ to resolve the mortality processes of HTL groups. OSMOSE-WFS predictions suggest that the natural mortality rate of juveniles of GOM red grouper is high and essentially due to predation, while the bulk of the natural mortality of adult red grouper results from causes not represented in OSMOSE-WFS such as, presumably, red tides. These results were communicated to GOM red grouper stock assessments. Moreover, OSMOSE-WFS indicate that altering the fishing mortality of GOM red grouper may have no global impact on the biomass of the major prey of red grouper, due to the high complexity and high redundancy of the modeled system. By contrast, altering the fishing mortality of GOM red grouper may have a large impact on the biomass of its major competitors. Increasing the fishing mortality of red grouper would increase the biomass of major competitors, due to reduced competition for food. Conversely, decreasing the fishing mortality of red grouper would diminish the biomass of major competitors, due to increased predation pressure on the juveniles of the major competitors by red grouper. The fishing scenarios that we evaluated may have slightly different impacts in the real world, due to some discrepancies between the diets of red grouper and its major competitors predicted by OSMOSE-WFS and the observed ones. Modifications in OSMOSE-WFS are suggested to reduce these discrepancies.
    
},
keywords = {Gulf of Mexico},
issn = {0924-7963},
doi = {http://dx.doi.org/10.1016/j.jmarsys.2015.10.014},
url = {http://www.sciencedirect.com/science/article/pii/S0924796315001815},
author = {Arnaud Gr{\"u}ss and Michael J. Schirripa and David Chagaris and Laure Velez and Yunne-Jai Shin and Philippe Verley and Ricardo Oliveros-Ramos and Cameron H. Ainsworth}
}
  • A. Grüss, W. Harford, M. Schirripa, L. Velez, S. Sagarese, Y. Shin, and P. Verley, “Management strategy evaluation using the individual-based,multispecies modeling approach osmose,” Ecological modelling, vol. 340, p. 86{–}105, 2016.
    [Bibtex] 
    @article {101,
title = {Management strategy evaluation using the individual-based,multispecies modeling approach OSMOSE},
journal = {Ecological Modelling},
volume = {340},
year = {2016},
month = {09},
pages = {86{\textendash}105},
author = {Gr{\"u}ss, Arnaud and Harford, William and Schirripa, Michael and Velez, Laure and Sagarese, Skyler and Shin, Yunne-Jai and Verley, Philippe}
}
  • G. Halouani, F. Lasram, Y. Shin, L. Velez, P. Verley, T. Hattab, R. Oliveros-Ramos, F. Diaz, F. Ménard, M. Baklouti, A. Guyennon, R. Ms, and F. Le Loc{’}h, “Modelling food web structure using an end-to-end approach in the coastal ecosystem of the gulf of gabes (tunisia),” Ecological modelling, vol. 339, pp. 45-57, 2016.
    [Bibtex] 
    @article {102,
title = {Modelling food web structure using an end-to-end approach in the coastal ecosystem of the Gulf of Gabes (Tunisia)},
journal = {Ecological Modelling},
volume = {339},
year = {2016},
month = {08},
pages = {45-57},
author = {Halouani, Ghassen and Lasram, Frida and Shin, Yunne-Jai and Velez, Laure and Verley, Philippe and Hattab, Tarek and Oliveros-Ramos, Ricardo and Diaz, Fr{\'e}d{\'e}ric and M{\'e}nard, Fr{\'e}d{\'e}ric and Baklouti, Melika and Guyennon, Arnaud and Ms, Romdhane and Le Loc{\textquoteright}h, Fran{\c c}ois}
}

2015

  • [DOI] M. Smith, E. Fulton, R. Day, L. Shannon, and Y-J. Shin, “Ecosystem modelling in the southern benguela: comparisons of atlantis, ecopath with ecosim, and osmose under fishing scenarios,” African journal of marine science, vol. 37, pp. 65-78, 2015.
    [Bibtex] 
    @article {69,
title = {Ecosystem modelling in the southern Benguela: comparisons of Atlantis, Ecopath with Ecosim, and OSMOSE under fishing scenarios},
journal = {African Journal of Marine Science},
volume = {37},
year = {2015},
pages = {65-78},
abstract = {
    Ecosystem-based management of marine fisheries requires the use of simulation modelling to investigate the system-level impact of candidate fisheries management strategies. However, testing of fundamental assumptions such as system structure or process formulations is rarely done. In this study, we compare the output of three different ecosystem models (Atlantis, Ecopath with Ecosim, and OSMOSE) applied to the same ecosystem (the southern Benguela), to explore which ecosystem effects of fishing are most sensitive to model uncertainty. We subjected the models to two contrasting fishing pressure scenarios, applying high fishing pressure to either small pelagic fish or to adult hake. We compared the resulting model behaviour at a system level, and also at the level of model groups. We analysed the outputs in terms of various commonly used ecosystem indicators, and found some similarities in the overall behaviour of the models, despite major differences in model formulation and assumptions. Direction of change in system-level indicators was consistent for all models under the hake pressure scenario, although discrepancies emerged under the small-pelagic-fish scenario. Studying biomass response of individual model groups was key to understanding more integrated system-level metrics. All three models are based on
    
existing knowledge of the system, and the convergence of model results increases confidence in the robustness of the model outputs. Points of divergence in the model results suggest important areas of future study. The use of feeding guilds to provide indicators for fish species at an aggregated level was explored, and proved to be an interesting alternative to aggregation by trophic level.
    
},
doi = {10.2989/1814232X.2015.1013501},
url = {http://dx.doi.org/10.2989/1814232X.2015.1013501},
author = {MD Smith and EA Fulton and RW Day and LJ Shannon and Y-J Shin}
}
  • [DOI] A. Grüss, M. J. Schirripa, D. Chagaris, M. Drexler, J. Simons, P. Verley, Y. Shin, M. Karnauskas, R. Oliveros-Ramos, and C. H. Ainsworth, “Evaluation of the trophic structure of the west florida shelf in the 2000s using the ecosystem model osmose,” Journal of marine systems, vol. 144, pp. 30-47, 2015.
    [Bibtex] 
    @article {70,
title = {Evaluation of the trophic structure of the West Florida Shelf in the 2000s using the ecosystem model OSMOSE},
journal = {Journal of Marine Systems},
volume = {144},
year = {2015},
pages = {30 - 47},
abstract = {
    Abstract We applied the individual-based, multi-species OSMOSE modeling approach to the West Florida Shelf, with the intent to inform ecosystem-based management (EBM) in this region. Our model, referred to as \‘OSMOSE-WFS\’, explicitly considers both pelagic-demersal and benthic high trophic level (HTL) groups of fish and invertebrate species, and is forced by the biomass of low trophic level groups of species (plankton and benthos). We present a steady-state version of the OSMOSE-WFS model describing trophic interactions in the West Florida Shelf in the 2000s. OSMOSE-WFS was calibrated using a recently developed evolutionary algorithm that allowed simulated biomasses of HTL groups to match observed biomasses over the period 2005\–2009. The validity of OSMOSE-WFS was then evaluated by comparing simulated diets to observed ones, and the simulated trophic levels to those in an Ecopath model of the West Florida Shelf (WFS Reef fish Ecopath). Finally, OSMOSE-WFS was used to explore the trophic structure of the West Florida Shelf in the 2000s and estimate size-specific natural mortality rates for a socio-economically important species, gag grouper (Mycteroperca microlepis). OSMOSE-WFS outputs were in full agreement with observations as to the body size and ecological niche of prey of the different HTL groups, and to a lesser extent in agreement with the observed species composition of the diet of HTL groups. OSMOSE-WFS and WFS Reef fish Ecopath concurred on the magnitude of the instantaneous natural mortality of the different life stages of gag grouper over the period 2005\–2009, but not always on the main causes of natural mortality. The model evaluations conducted here provides a strong basis for ongoing work exploring fishing and environmental scenarios so as to inform EBM. From simple size-based predation rules, we were indeed able to capture the complexity of trophic interactions in the West Florida Shelf, and to identify the predators, prey and competitors of socio-economically important species as well as pivotal prey species of the ecosystem.
    
},
keywords = {Gag grouper},
issn = {0924-7963},
doi = {http://dx.doi.org/10.1016/j.jmarsys.2014.11.004},
url = {http://www.sciencedirect.com/science/article/pii/S0924796314003091},
author = {Arnaud Gr{\"u}ss and Michael J. Schirripa and David Chagaris and Michael Drexler and James Simons and Philippe Verley and Yunne-Jai Shin and Mandy Karnauskas and Ricardo Oliveros-Ramos and Cameron H. Ainsworth}
}

2014

  • [DOI] M. Travers-Trolet, Y. Shin, L. J. Shannon, C. L. Moloney, and J. G. Field, “Combined fishing and climate forcing in the southern benguela upwelling ecosystem: an end-to-end modelling approach reveals dampened effects,” PLoS ONE, vol. 9, p. e94286, 2014.
    [Bibtex] 
    @article {61,
title = {Combined Fishing and Climate Forcing in the Southern Benguela Upwelling Ecosystem: An End-to-End Modelling Approach Reveals Dampened Effects},
journal = {{PLoS} {ONE}},
volume = {9},
year = {2014},
pages = {e94286},
abstract = {
    The effects of climate and fishing on marine ecosystems have usually been studied separately, but their interactions make ecosystem dynamics difficult to understand and predict. Of particular interest to management, the potential synergism or antagonism between fishing pressure and climate forcing is analysed in this paper, using an end-to-end ecosystem model of the southern Benguela ecosystem, built from coupling hydrodynamic, biogeochemical and multispecies fish models ({ROMS}-N2P2Z2D2-{OSMOSE}). Scenarios of different intensities of upwelling-favourable wind stress combined with scenarios of fishing top-predator fish were tested. Analyses of isolated drivers show that the bottom-up effect of the climate forcing propagates up the food chain whereas the top-down effect of fishing cascades down to zooplankton in unfavourable environmental conditions but dampens before it reaches phytoplankton. When considering both climate and fishing drivers together, it appears that top-down control dominates the link between top-predator fish and forage fish, whereas interactions between the lower trophic levels are dominated by bottom-up control. The forage fish functional group appears to be a central component of this ecosystem, being the meeting point of two opposite trophic controls. The set of combined scenarios shows that fishing pressure and upwelling-favourable wind stress have mostly dampened effects on fish populations, compared to predictions from the separate effects of the stressors. Dampened effects result in biomass accumulation at the top predator fish level but a depletion of biomass at the forage fish level. This should draw our attention to the evolution of this functional group, which appears as both structurally important in the trophic functioning of the ecosystem, and very sensitive to climate and fishing pressures. In particular, diagnoses considering fishing pressure only might be more optimistic than those that consider combined effects of fishing and environmental variability.
    
},
doi = {10.1371/journal.pone.0094286},
url = {http://dx.doi.org/10.1371/journal.pone.0094286},
author = {Travers-Trolet, Morgane and Shin, Yunne-Jai and Shannon, Lynne J. and Moloney, Coleen L. and Field, John G.}
}
  • [DOI] M. Travers-Trolet, Y-J. Shin, and J. Field, “An end-to-end coupled model ROMS-n2p2z2d2-OSMOSE of the southern benguela foodweb: parameterisation, calibration and pattern-oriented validation,” African journal of marine science, vol. 36, iss. 1, p. 11{–}29, 2014.
    [Bibtex] 
    @article{travers-trolet_end_2014,
title = {An end-to-end coupled model {ROMS}-N2P2Z2D2-{OSMOSE} of the southern Benguela foodweb: parameterisation, calibration and pattern-oriented validation},
journal = {African Journal of Marine Science},
volume = {36},
number = {1},
year = {2014},
pages = {11{\textendash}29},
abstract = {In order to better understand ecosystem functioning under simultaneous pressures (e.g. both climate change and fishing pressures), integrated modelling approaches are advocated. We developed an end-to-end model of the southern Benguela ecosystem by coupling the high trophic level model {OSMOSE} with a biophysical model ({ROMS}-N2P2Z2D2). {OSMOSE} is a spatial, multispecies, individual-based model simulating the whole life cycle of fish with fish schools interacting through opportunistic and size-based predation. It is linked to the biogeochemical model through the predation process; plankton groups are food for fish and fish apply a predation mortality on plankton. Here we describe the two-way coupling between the models and follow a pattern-oriented modelling approach to validate the simulations. At the individual level, model outputs are consistent with observed diets for several species from small pelagic fish to top predatory fish, although biases emerge from underestimation of macrozooplankton and lack of vertical structure. At the population level, the seasonality of the size structure is similar between the model and data. At the community level, the modelled trophic structure is consistent with the knowledge available for this ecosystem. The structure of the foodweb is an emergent property of the model, showing trophic links between species, their strength and the strong connectivity observed. We also highlight the capacity of this model for tracking indicators at various hierarchical levels.},
issn = {1814-232X},
doi = {10.2989/1814232X.2014.883326},
url = {http://dx.doi.org/10.2989/1814232X.2014.883326},
author = {Travers-Trolet, M and Shin, Y-J and Field, JG}
}
  • R. Oliveros-Ramos, “End–to–end modelling for an ecosystem approach to fisheries in the northern humboldt current ecosystem,” phd Master Thesis, 2014.
    [Bibtex] 
    @mastersthesis{100,
title = {End{\textendash}to{\textendash}end modelling for an ecosystem approach to fisheries in the Northern Humboldt Current Ecosystem},
year = {2014},
month = {12},
type = {phd},
author = {Oliveros-Ramos, Ricardo},
school = {University of Montpellier}
}

2013

  • [DOI] C. Fu, I. R. Perry, Y. Shin, J. Schweigert, and H. Liu, “An ecosystem modelling framework for incorporating climate regime shifts into fisheries management,” Progress in oceanography, vol. 115, p. 53{–}64, 2013.
    [Bibtex] 
    @article {fu_ecosystem_2013,
title = {An ecosystem modelling framework for incorporating climate regime shifts into fisheries management},
journal = {Progress in Oceanography},
volume = {115},
year = {2013},
month = {aug},
pages = {53{\textendash}64},
abstract = {Ecosystem-based approaches to fisheries management ({EBM}) attempt to account for fishing, climate variability and species interactions when formulating fisheries management advice. Ecosystem models that investigate the combined effects of ecological processes are vital to support the implementation of {EBM} by assessing the effectiveness of management strategies in an ecosystem context. In this study, an individual-based ecosystem model was used to demonstrate how species at different trophic levels and of different life histories responded to climate regimes and how well different single- or various multi-species fisheries at different intensities perform in terms of human benefits (yield) and trade-offs (fishery closures) as well as their impacts on the ecosystem. In addition, other performance indicators were also used to evaluate management strategies. The simulations indicated that under no fishing, each species responded to the regimes differently due to different life history traits and different trophic interactions. Fishing at the level of natural mortality (F = M) produced the highest yields within each fishery, however, an F adjusted for the current productivity conditions (regime) resulted in much fewer fishery closures compared with F = M, indicating the advantage of implementing a policy of a regime-specific F from the stand point of conservation and fishery stability. Furthermore, a regime-specific F strategy generally resulted in higher yield and fewer fishery closures compared with F = 0.5M. Other performance indicators also pointed to the advantage of using a regime-specific F strategy in terms of the stability of both ecosystem and fishery production. As a specific example, fishing the predators of Pacific herring under all multi-species fisheries scenarios increased the yield of Pacific herring and reduced the number of herring fishery closures. This supports the conclusion that an exploitation strategy which is balanced across all trophic levels produces better outcomes, as advocated by other researchers.},
issn = {0079-6611},
doi = {10.1016/j.pocean.2013.03.003},
url = {http://www.sciencedirect.com/science/article/pii/S0079661113000281},
author = {Fu, Caihong and Perry, R. Ian and Shin, Yunne-Jai and Schweigert, Jake and Liu, Huizhu}
}
  • [DOI] T. Brochier, J. M. Ecoutin, L. T. de Morais, D. M. Kaplan, and R. Lae, “A multi-agent ecosystem model for studying changes in a tropical estuarine fish assemblage within a marine protected area,” Aquatic living resources, vol. 26, iss. 02, p. 147{–}158, 2013.
    [Bibtex] 
    @article {brochier_multi-agent_2013,
title = {A multi-agent ecosystem model for studying changes in a tropical estuarine fish assemblage within a marine protected area},
journal = {Aquatic Living Resources},
volume = {26},
number = {02},
year = {2013},
pages = {147{\textendash}158},
abstract = {As marine protected areas ({MPAs}) are increasingly being utilised as a tool for fishery management, their impact on the food web needs to be fully understood. However, little is known about the effect of {MPAs} on fish assemblages, especially in the presence of different life history and ecological traits. Modelling the observed changes in fish population structures may provide a mechanistic understanding of fish assemblage dynamics. In addition, modelling allows a quantitative estimate of {MPA} spill-over. To achieve this purpose, we adapted an existing ecosystem model, {OSMOSE} (Object-oriented simulator of marine biodiversity exploitation), to the specific case of the presence of fish with multiple life histories. The adapted model can manage 4 main categories of life history identified in an estuary {MPA}: fish that (1) spend their entire life cycle locally, (2) are present only as juveniles, (3) enter the area as juveniles and stay permanently except during reproduction periods, which occur outside the estuary, and (4) are present occasionally and for a short time for foraging purposes. To take into account these specific life-history traits, the {OSMOSE} code was modified. This modelling approach was developed in the context of the Bamboung Bolong {MPA}, located in a mangrove area in the Sine-Saloum Delta, Senegal. This was the ideal case to develop our approach as there has been scientific monitoring of the fish population structure inside the {MPA} before fishery closure, providing a reference state, and continuous monitoring since the closure. Ecologically similar species were pooled by trophic traits into 15 groups that represented 97\% of the total biomass. Lower trophic levels ({LTL}) were represented by 6 compartments. The biomass of the model species was calibrated to reproduce the reference situation before fishery closure. Model predictions of fish assemblage changes after fishery closure corresponding to the Bamboung {MPA} creation scenario were compared to field observations; in most cases the model reproduces observed changes in biomass (at least in direction). We suggest the existence of a {\textquotedblleft}sanctuary effect{\textquotedblright}, that was not taken into account in the model, this could explain the observed increase in biomass of top predators not reproduced by the model. Finally, the annual {MPA} fish spill-over was estimated at 11 tons ({\textasciitilde}33\% of the fish biomass) from the model output, mainly due to diffusive effects.},
keywords = {Ecosystem model, Life history, Marine Protected Area, Spill-over, Trophic level, Tropical estuarine fish assemblage, West Africa},
doi = {10.1051/alr/2012028},
author = {Brochier, Timoth{\'e}e and Ecoutin, Jean Marc and de Morais, Luis Tito and Kaplan, David M. and Lae, Raymond}
}
  • C. Fu, R. Perry, Y. Shin, J. Schweigert, and H. Z. Liu, “Strait of georgia ecosystem research initiative (eri),” Researchgate, 2013.
    [Bibtex] 
    @article {108,
title = {Strait of Georgia Ecosystem Research Initiative (ERI)},
year = {2013},
month = {01},
author = {Fu, Caihong and Perry, R and Shin, Yunne-Jai and Schweigert, J and Liu, H.Z.},
journal = {Researchgate}
}

2012

  • C. Fu, Y. Shin, R. Perry, J. King, and H. Liu, “Exploring climate and fishing impacts in an ecosystem framework,” Global progress in ecosystem-based fisheries management, pp. 65-85, 2012.
    [Bibtex] 
    @article {103,
title = {Exploring climate and fishing impacts in an ecosystem framework},
journal = {Global Progress in Ecosystem-based Fisheries Management},
year = {2012},
month = {01},
pages = {65-85},
author = {Fu, Caihong and Shin, Yunne-Jai and Perry, R and King, J and Liu, H}
}
  • C. Fu, Y. J. Shin, R. I. Perry, J. King, and H. Liu, “Exploring climate and fishing impacts in an ecosystem model of the strait of georgia, british columbia,” in Global progress in ecosystem-based fisheries management, Alaska sea grant, university of alaska fairbanks, 2012, p. 65{–}86.
    [Bibtex] 
    @inbook {kruse_exploring_2012,
title = {Exploring Climate and Fishing Impacts in an Ecosystem Model of the Strait of Georgia, British Columbia},
booktitle = {Global Progress in Ecosystem-Based Fisheries Management},
year = {2012},
pages = {65{\textendash}86},
publisher = {Alaska Sea Grant, University of Alaska Fairbanks},
organization = {Alaska Sea Grant, University of Alaska Fairbanks},
isbn = {9781566121668},
url = {http://seagrant.uaf.edu/bookstore/pubs/item.php?id=11932},
author = {Fu, C. and Shin, Y.J. and Perry, R.I. and King, J. and Liu, H.}
}
  • [DOI] L. Gasche, D. Gascuel, L. Shannon, and Y. -J. Shin, “Global assessment of the fishing impacts on the southern benguela ecosystem using an EcoTroph modelling approach,” Journal of marine systems, vol. 90, iss. 1, p. 1{–}12, 2012.
    [Bibtex] 
    @article {gasche_global_2012,
title = {Global assessment of the fishing impacts on the Southern Benguela ecosystem using an {EcoTroph} modelling approach},
journal = {Journal of Marine Systems},
volume = {90},
number = {1},
year = {2012},
pages = {1{\textendash}12},
abstract = {{\textquoteleft}We show that the {EcoTroph} model based on trophic spectra is an efficient tool to build ecosystem diagnoses of the impact of fishing. Using the Southern Benguela case study as a pretext, we present the first thorough application of the model to a real ecosystem. We thus review the structure and functioning of {EcoTroph} and we introduce the user to the steps that should be followed, showing the various possibilities of the model while underlining the most critical points of the modelling process. We show that {EcoTroph} provides an overview of the current exploitation level and target factors at the ecosystem scale, using two distinct trophic spectra to quantify the fishing targets and the fishing impact per trophic level. Then, we simulate changes in the fishing mortality, facilitating differential responses of two groups of species within the Southern Benguela ecosystem to be distinguished. More generally, we highlight various trends in a number of indicators of the ecosystem{\textquoteright}s state when increasing fishing mortality and we show that this ecosystem is moderately exploited, although predatory species are at their {MSY}. Finally, trophic spectra of the fishing effort multipliers {EMSY} and E0.1 are proposed as tools for monitoring the ecosystem effects of fishing.},
keywords = {Ecosystem indicators, Fishing impact, Overfishing, Southern Benguela, Trophic modelling, {EcoTroph}},
issn = {0924-7963},
doi = {10.1016/j.jmarsys.2011.07.012},
url = {http://www.sciencedirect.com/science/article/pii/S0924796311001709},
author = {Gasche, L. and Gascuel, D. and Shannon, L. and Shin, Y. -J.}
}

2011

  • [DOI] A. D. M. Smith, C. J. Brown, C. M. Bulman, E. A. Fulton, P. Johnson, I. C. Kaplan, H. Lozano-Montes, S. Mackinson, M. Marzloff, L. J. Shannon, Y. Shin, and J. Tam, “Impacts of fishing low–trophic level species on marine ecosystems,” Science, vol. 333, iss. 6046, p. 1147{–}1150, 2011.
    [Bibtex] 
    @article {smith_impacts_2011,
title = {Impacts of Fishing Low{\textendash}Trophic Level Species on Marine Ecosystems},
journal = {Science},
volume = {333},
number = {6046},
year = {2011},
pages = {1147{\textendash}1150},
abstract = {Low{\textendash}trophic level species account for more than 30\% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low{\textendash}trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield ({MSY}) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80\% of {MSY}.},
issn = {0036-8075, 1095-9203},
doi = {10.1126/science.1209395},
url = {http://www.sciencemag.org/content/333/6046/1147},
author = {Smith, Anthony D. M. and Brown, Christopher J. and Bulman, Catherine M. and Fulton, Elizabeth A. and Johnson, Penny and Kaplan, Isaac C. and Lozano-Montes, Hector and Mackinson, Steven and Marzloff, Martin and Shannon, Lynne J. and Shin, Yunne-Jai and Tam, Jorge}
}

2010

  • [DOI] R. Duboz, D. Versmisse, M. Travers, E. Ramat, and Y. Shin, “Application of an evolutionary algorithm to the inverse parameter estimation of an individual-based model,” Ecological modelling, vol. 221, iss. 5, p. 840{–}849, 2010.
    [Bibtex] 
    @article {duboz_application_2010,
title = {Application of an evolutionary algorithm to the inverse parameter estimation of an individual-based model},
journal = {Ecological Modelling},
volume = {221},
number = {5},
year = {2010},
month = {mar},
pages = {840{\textendash}849},
abstract = {Inverse parameter estimation of individual-based models ({IBMs}) is a research area which is still in its infancy, in a context where conventional statistical methods are not well suited to confront this type of models with data. In this paper, we propose an original evolutionary algorithm which is designed for the calibration of complex {IBMs}, i.e. characterized by high stochasticity, parameter uncertainty and numerous non-linear interactions between parameters and model output. Our algorithm corresponds to a variant of the population-based incremental learning ({PBIL}) genetic algorithm, with a specific {\textquotedblleft}optimal individual{\textquotedblright} operator. The method is presented in detail and applied to the individual-based model {OSMOSE}. The performance of the algorithm is evaluated and estimated parameters are compared with an independent manual calibration. The results show that automated and convergent methods for inverse parameter estimation are a significant improvement to existing ad hoc methods for the calibration of {IBMs}.},
keywords = {Evolutionary and genetic algorithms, Individual-based model, Marine ecosystem model, Model calibration, Parameter estimation},
issn = {0304-3800},
doi = {10.1016/j.ecolmodel.2009.11.023},
url = {http://www.sciencedirect.com/science/article/pii/S0304380009008102},
author = {Duboz, Rapha{\"e}l and Versmisse, David and Travers, Morgane and Ramat, Eric and Shin, Yunne-Jai}
}
  • [DOI] M. Travers, K. Watermeyer, L. J. Shannon, and Y. -J. Shin, “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, vol. 79, iss. 1{–}2, p. 101{–}111, 2010.
    [Bibtex] 
    @article {travers_changes_2010,
title = {Changes in food web structure under scenarios of overfishing in the southern Benguela: Comparison of the Ecosim and {OSMOSE} modelling approaches},
journal = {Journal of Marine Systems},
volume = {79},
number = {1{\textendash}2},
year = {2010},
month = {jan},
pages = {101{\textendash}111},
abstract = {Ecosystem models provide a platform allowing exploration into the possible responses of marine food webs to fishing pressure and various potential management decisions. In this study we investigate the particular effects of overfishing on the structure and function of the southern Benguela food web, using two models with different underlying assumptions: the spatialized, size-based individual-based model, {OSMOSE}, and the trophic mass-balance model, Ecopath with Ecosim ({EwE}). Starting from the same reference state of the southern Benguela upwelling ecosystem during the 1990s, we compare the response of the food web to scenarios of overfishing using these two modelling approaches. A scenario of increased fishing mortality is applied to two distinct functional groups: i) two species of Cape hake, representing important target predatory fish, and ii) the forage species anchovy, sardine and redeye. In these simulations, fishing mortality on the selected functional groups is doubled for 10 years, followed by 10 years at the initial fishing mortality. We compare the food web states before the increase of fishing mortality, after 10 years of overfishing and after a further 10 years during which fishing was returned to initial levels. In order to compare the simulated food web structures with the reference state, and between the two modelling approaches, we use a set of trophic indicators: the mean trophic level of the community and in catches, the trophic pyramid (biomass per discrete trophic level), and the predatory/forage fish biomass ratio. {OSMOSE} and {EwE} present globally similar results for the trophic functioning of the ecosystem under fishing pressure: the biomass of targeted species decreases whereas that of their potential competitors increases. The reaction of distant species is more diverse, depending on the feeding links between the compartments. The mean trophic level of the community does not vary enough to be used for assessing ecosystem impacts of fishing, and the mean trophic level in the catch displays a surprising increase due to the short period of overfishing. The trophic pyramids behave in an unexpected way compared to trophic control theory, because at least two food chains with different dynamics are intertwined within the food web. We emphasize the importance of biomass information at the species level for interpreting dynamics in aggregated indicators, and we highlight the importance of competitive groups when looking at ecosystem functioning under fishing disturbance. Finally, we discuss the results within the scope of differences between models, in terms of the way they are formulated, spatial dimensions, predation formulations and the representation of fish life cycles.},
keywords = {Benguela upwelling, Ecosystem model, Ecosystem structure and function, Fishing, Food web, Trophic indicators},
issn = {0924-7963},
doi = {10.1016/j.jmarsys.2009.07.005},
url = {http://www.sciencedirect.com/science/article/pii/S0924796309002346},
author = {Travers, M. and Watermeyer, K. and Shannon, L. J. and Shin, Y. -J.}
}
  • [DOI] M. Travers and Y. -J. Shin, “Spatio-temporal variability in fish-induced predation mortality on plankton: a simulation approach using a coupled trophic model of the benguela ecosystem,” Progress in oceanography, vol. 84, iss. 1{–}2, p. 118{–}120, 2010.
    [Bibtex] 
    @article {travers_spatio-temporal_2010,
title = {Spatio-temporal variability in fish-induced predation mortality on plankton: A simulation approach using a coupled trophic model of the Benguela ecosystem},
journal = {Progress in Oceanography},
volume = {84},
number = {1{\textendash}2},
year = {2010},
month = {jan},
pages = {118{\textendash}120},
abstract = {We investigate the potential predation pressure that would affect plankton communities spatially and seasonally using a coupled model, where fish-induced predation mortality is explicit. In the southern Benguela ecosystem, the fish model {OSMOSE} is forced by a biogeochemical model providing plankton prey fields. We analyse the resulting potential predation mortality rate on copepods. Spatially, this mortality rate is higher on the South coast (Agulhas bank) than on the West coast (upwelling zone), reflecting a lower plankton concentration compared to food requirement for fish. Temporally, fish-induced predation mortality decreases at the beginning of the upwelling season, due to a rapid increase of plankton concentration combined with a lag in the subsequent increase of fish biomass. Such strong spatio-temporal patterns in fish-induced predation mortality encourage the development of two-ways coupling between fish and plankton models for better representing the dynamics of the southern Benguela food web.},
issn = {0079-6611},
doi = {10.1016/j.pocean.2009.09.014},
url = {http://www.sciencedirect.com/science/article/pii/S0079661109001475},
author = {Travers, M. and Shin, Y. -J.}
}

2009

  • [DOI] D. Yemane, Y. Shin, and J. G. Field, “Exploring the effect of marine protected areas on the dynamics of fish communities in the southern benguela: an individual-based modelling approach,” ICES journal of marine science: journal du conseil, vol. 66, iss. 2, p. 378{–}387, 2009.
    [Bibtex] 
    @article {yemane_exploring_2009,
title = {Exploring the effect of Marine Protected Areas on the dynamics of fish communities in the southern Benguela: an individual-based modelling approach},
journal = {{ICES} Journal of Marine Science: Journal du Conseil},
volume = {66},
number = {2},
year = {2009},
month = {jan},
pages = {378{\textendash}387},
abstract = {Yemane, D., Shin, Y-J., and Field, J. G. 2009. Exploring the effect of Marine Protected Areas on the dynamics of fish communities in the southern Benguela: an individual-based modelling approach. {\textendash} {ICES} Journal of Marine Science, 66: 378{\textendash}387. Marine Protected Areas ({MPAs}) have been suggested as a tool that can achieve some of the goals of an Ecosystem Approach to Fisheries ({EAF}), e.g. prevention of overexploitation, biodiversity conservation, recovery of overexploited population, but the consequences of their establishment on the dynamics of protected components are often unclear. Spatial and multispecies models can be used to investigate the effects of their introduction. An individual-based, spatially explicit, size-structured, multispecies model (known as {OSMOSE}) is used to investigate the likely consequences of the introduction of three {MPAs} off the coast of South Africa, individually or in combination. The simultaneous introduction of the {MPAs} affected varying proportions of the distribution of the modelled species (5{\textendash}17\%) and 12\% of the distribution of the whole community. In general, the introduction of the {MPAs} in the different scenarios resulted in a relative increase in the biomass of large predatory fish and a decrease in the biomass of small pelagic fish. The simulation demonstrates that consideration of trophic interactions is necessary when introducing {MPAs}, with indirect effects that may be detrimental to some (mainly smaller prey) species.},
keywords = {ecosystem models, individual-based models, Marine Protected Areas, Southern Benguela},
issn = {1054-3139, 1095-9289},
doi = {10.1093/icesjms/fsn171},
url = {http://icesjms.oxfordjournals.org/content/66/2/378},
author = {Yemane, Dawit and Shin, Yunne-Jai and Field, John G.}
}
  • [DOI] M. Marzloff, Y. Shin, J. Tam, M. Travers, and A. Bertrand, “Trophic structure of the peruvian marine ecosystem in 2000–2006: insights on the effects of management scenarios for the hake fishery using the IBM trophic model osmose,” Journal of marine systems, vol. 75, iss. 1{–}2, p. 290{–}304, 2009.
    [Bibtex] 
    @article {marzloff_trophic_2009,
title = {Trophic structure of the Peruvian marine ecosystem in 2000{\textendash}2006: Insights on the effects of management scenarios for the hake fishery using the {IBM} trophic model Osmose},
journal = {Journal of Marine Systems},
volume = {75},
number = {1{\textendash}2},
year = {2009},
pages = {290{\textendash}304},
abstract = {The individual-based trophic model Osmose is applied to the upwelling marine ecosystem off the coast of Peru. The dynamics and life cycle of eight major species of the Peruvian marine ecosystem are explicitly considered in the model. Reference simulations provide an overview of the trophic structure of the Peruvian ecosystem during the period 2000{\textendash}2006. Results of model calibration and simulations are discussed in the light of current empirical knowledge on the trophic functioning of the Peruvian ecosystem and are compared to outputs obtained recently using the trophic model Ecopath. The impacts on the ecosystem of restoration plans for the depleted hake (Merluccius gayi peruanus) population are explored through two management scenarios: a) a long term reduction of fishing effort targeting hake and b) a moratorium on the hake fishery. The simulations help better understand the recent failure of a 20~month hake moratorium and provide long-term strategic support to ecosystem-based management. Limits of our approach are discussed and recommendations are detailed for future developments of the Osmose model and ecosystem approach to fishery management in the Peruvian context.},
keywords = {anchovy, Hake, Humboldt current system, individual-based modelling, Marine ecosystem modelling, Peru, Predation},
issn = {0924-7963},
doi = {10.1016/j.jmarsys.2008.10.009},
url = {http://www.sciencedirect.com/science/article/pii/S0924796308002960},
author = {Marzloff, Martin and Shin, Yunne-Jai and Tam, Jorge and Travers, Morgane and Bertrand, Arnaud}
}
  • [DOI] M. Travers, Y. -J. Shin, S. Jennings, E. Machu, J. A. Huggett, J. G. Field, and P. M. Cury, “Two-way coupling versus one-way forcing of plankton and fish models to predict ecosystem changes in the benguela,” Ecological modelling, vol. 220, iss. 21, p. 3089{–}3099, 2009.
    [Bibtex] 
    @article {travers_two-way_2009,
title = {Two-way coupling versus one-way forcing of plankton and fish models to predict ecosystem changes in the Benguela},
journal = {Ecological Modelling},
volume = {220},
number = {21},
year = {2009},
pages = {3089{\textendash}3099},
abstract = {{\textquoteleft}End-to-end{\textquoteright} models have been adopted in an attempt to capture more of the processes that influence the ecology of marine ecosystems and to make system wide predictions of the effects of fishing and climate change. Here, we develop an end-to-end model by coupling existing models that describe the dynamics of low ({ROMS}{\textendash}N2P2Z2D2) and high trophic levels ({OSMOSE}). {ROMS}{\textendash}N2P2Z2D2 is a biogeochemical model representing phytoplankton and zooplankton seasonal dynamics forced by hydrodynamics in the Benguela upwelling ecosystem. {OSMOSE} is an individual-based model representing the dynamics of several species of fish, linked through opportunistic and size-based trophic interactions. The models are coupled through a two-way size-based predation process. Plankton provides prey for fish, and the effects of predation by fish on the plankton are described by a plankton mortality term that is variable in space and time. Using the end-to-end model, we compare the effects of two-way coupling versus one-way forcing of the fish model with the plankton biomass field. The fish-induced mortality on plankton is temporally variable, in part explained by seasonal changes in fish biomass. Inclusion of two-way feedback affects the seasonal dynamics of plankton groups and usually reduces the amplitude of variation in abundance (top-down effect). Forcing and coupling lead to different predicted food web structures owing to changes in the dominant food chain which is supported by plankton (bottom-up effect). Our comparisons of one-way forcing and two-way coupling show how feedbacks may affect abundance, food web structure and food web function and emphasise the need to critically examine the consequences of different model architectures when seeking to predict the effects of fishing and climate change.},
keywords = {Benguela upwelling, End-to-end approach, Marine ecosystem model coupling, Marine food web, Predation, {ECEM} 07},
issn = {0304-3800},
doi = {10.1016/j.ecolmodel.2009.08.016},
url = {http://www.sciencedirect.com/science/article/pii/S0304380009005766},
author = {Travers, M. and Shin, Y. -J. and Jennings, S. and Machu, E. and Huggett, J. A. and Field, J. G. and Cury, P. M.}
}

2008

  • [DOI] R. Vergnon, Y. Shin, and P. Cury, “Cultivation, allee effect and resilience of large demersal fish populations,” Aquatic living resources, vol. 21, iss. 03, p. 287{–}295, 2008.
    [Bibtex] 
    @article {vergnon_cultivation_2008,
title = {Cultivation, Allee effect and resilience of large demersal fish populations},
journal = {Aquatic Living Resources},
volume = {21},
number = {03},
year = {2008},
pages = {287{\textendash}295},
abstract = {In the marine environment, small forage species can predate on, or compete with, the pre-recruits of their larger predators. The {\textquotedblleft}cultivation effect{\textquotedblright} hypothesis proposes that this mechanism can slow down the recovery of depleted populations of large demersal fishes by creating Allee effects that lower their recruitment success. Using an individual based fish community model applied to the southern Benguela ecosystem, we simulate situations of potential cultivation effect on a population of shallow water hake Merluccius capensis. We search for evidence of Allee effects due to cultivation and investigate how complex trophic interactions could influence their underlying mechanisms and impact. The resilience of the shallow water hake population was measured by following the variations of the ratio R/S (the number of recruits over the number of spawners) when population size decreases and the predators and competitors of shallow water hake pre-recruits were identified. Simulations suggest that cultivation effects are likely to emerge within the fish community of the southern Benguela ecosystem. Our twelve species model emphasizes that cultivation effects result from complex influences of predation and competition on the different pre-recruit stages, whose trophic role depends on both body size and geographical distribution. For realistic linkages between forage species and shallow water hake pre-recruits, cultivation effects occurring in the limits of the southern Benguela fish community are predicted to delay population recovery by several decades. These significant delays are not characterized by a decrease of R/S at low stock size, which is the sign usually tracked when looking for Allee effects. Our study suggests that cultivation effects could play a major role in the dynamics of overexploited large demersal fish populations and pleads for the development of improved detection techniques for these processes.},
keywords = {Benguela system, Fish competitors, Fishery exploitation, Marine ecosystem dynamics, Model, Predators, Recruitment, Spawning abundance},
doi = {10.1051/alr:2008042},
author = {Vergnon, R{\'e}mi and Shin, Yunne-Jai and Cury, Philippe}
}

2006

  • [DOI] M. Travers, Y. Shin, L. Shannon, and P. Cury, “Simulating and testing the sensitivity of ecosystem-based indicators to fishing in the southern benguela ecosystem,” Canadian journal of fisheries and aquatic sciences, vol. 63, iss. 4, pp. 943-956, 2006.
    [Bibtex] 
    @article{doi:10.1139/f06-003,
author = {Travers, Morgane and Shin, Yunne-Jai and Shannon, Lynne and Cury, Philippe},
title = {Simulating and testing the sensitivity of ecosystem-based indicators to fishing in the southern Benguela ecosystem},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
volume = {63},
number = {4},
pages = {943-956},
year = {2006},
doi = {10.1139/f06-003},
URL = { https://doi.org/10.1139/f06-003 },
eprint = { https://doi.org/10.1139/f06-003 },
abstract = { The sensitivity of size-based, species-based, and trophodynamic indicators is examined for the fish community of the southern Benguela ecosystem (South Africa) through simulations of different fishing scenarios using the multispecies model OSMOSE. The simulations suggest that it may be erroneous to consider one absolute reference direction of change for any indicator because the direction of change is specific to both the multispecies assemblage and the fishing scenario considered. The analysis of species versus community indicators is helpful for understanding which processes drive the emergent properties of the ecosystem. Informative about the structure and state of the ecosystem, both types of indicators weighted by biomass or by abundance should be used to evaluate ecosystem changes. Indicators characterizing size distribution (e.g., slope of size spectrum) appear to be more helpful in distinguishing the cause of ecosystem changes than mean community indicators because their response is specific to the fishing scenario simulated (i.e., global or hake-targeting fishing). Some indicators do not seem to be sensitive to fishing pressure (slope of the diversity size spectrum) or do not vary consistently with other studies (W statistic). }
}

2004

  • [DOI] Y-J. Shin, L. J. Shannon, and P. M. Cury, “Simulations of fishing effects on the southern benguela fish community using an individual-based model: learning from a comparison with ECOSIM,” African journal of marine science, vol. 26, iss. 1, p. 95{–}114, 2004.
    [Bibtex] 
    @article {shin_simulations_2004,
title = {Simulations of fishing effects on the southern Benguela fish community using an individual-based model: learning from a comparison with {ECOSIM}},
journal = {African Journal of Marine Science},
volume = {26},
number = {1},
year = {2004},
pages = {95{\textendash}114},
abstract = {By applying an individual-based model ({OSMOSE}) to the southern Benguela ecosystem, a multispecies analysis is proposed, complementary to that provided by the application of {ECOPATH}/{ECOSIM} models. To reconstruct marine foodwebs, {OSMOSE} is based on the hypothesis that predation is a size-structured process. In all, 12 fish species, chosen for their importance in terms of biomass and catches, are explicitly modelled. Growth, reproduction and mortality parameters are required to model their dynamics and trophic interactions. Maps of mean spatial distribution of the species are compiled from published literature. Taking into account the spatial component is necessary because spatial co-occurrence determines potential interactions between predatory fish and prey fish of suitable size. To explore ecosystem effects of fishing, different fishing scenarios, previously examined using {ECOSIM}, are simulated using the {OSMOSE} model. They explore the effects of targeting fish species in the southern Benguela considered to be predators (Cape hake Merluccius capensis and M. paradoxus) or prey (anchovy Engraulis encrasicolus, sardine Sardinops sagax, round herring Etrumeus whiteheadi). Simulation results are compared and are generally consistent with those obtained using an {ECOSIM} model. This cross-validation appears to be a promising means of evaluating the robustness of model outputs, when separate validation of marine ecosystem models are still difficult to perform.},
issn = {1814-232X},
doi = {10.2989/18142320409504052},
url = {http://www.tandfonline.com/doi/abs/10.2989/18142320409504052},
author = {Shin, Y-J. and Shannon, L. J. and Cury, P. M.}
}
  • [DOI] Y. Shin and P. Cury, “Using an individual-based model of fish assemblages to study the response of size spectra to changes in fishing,” Canadian journal of fisheries and aquatic sciences, vol. 61, iss. 3, p. 414{–}431, 2004.
    [Bibtex] 
    @article {shin_using_2004,
title = {Using an individual-based model of fish assemblages to study the response of size spectra to changes in fishing},
journal = {Canadian Journal of Fisheries and Aquatic Sciences},
volume = {61},
number = {3},
year = {2004},
month = {mar},
pages = {414{\textendash}431},
abstract = {For most fish species, strong environmental constraints imposed by living in an aquatic medium have produced converging streamlined body forms without prehensile appendices. This similarity in body shapes highlights a common predation constraint: a predatory fish must have a jaw large enough to swallow its prey. Fish diets may then reflect local prey availability and predator–prey size ratios. Based on this size-based opportunistic predation process, the multispecies individual-based model {OSMOSE} (Object-oriented Simulator of Marine {ecOSystem} Exploitation) is used to investigate to what extent the size distribution of fish communities can contribute to better our understanding of the functioning of marine food webs and the ecosystem effects of fishing. Strong similarity in shape is found between simulated size spectra and those described in empirical studies. The existence of a curvature towards small size classes is discussed in the light of the size-based predation hypothesis, which implies that smaller..., Chez la plupart des esp{\`e}ces de poissons, les fortes contraintes environnementales reli{\'e}es {\`a} la vie en milieu aquatique ont men{\'e} au d{\'e}veloppement de corps fusiformes sans appendices pr{\'e}hensiles. Une telle similarit{\'e} morpho lo gique met en lumi{\`e}re une contrainte commune chez les pr{\'e}dateurs qui exige qu{\textquoteright}ils aient une m{\^a}choire suffisamment grande pour avaler leurs proies. Les r{\'e}gimes alimentaires des poissons sont donc le reflet de la disponibilit{\'e} locale des proies et des rapports de tailles pr{\'e}dateurs–proies. Le mod{\`e}le multisp{\'e}cifique individus-centr{\'e} {OSMOSE} ({\guillemotleft} Object-oriented Simulator of Marine {ecOSystem} Exploitation {\guillemotright}), qui est fond{\'e} sur ce processus de pr{\'e}dation opportuniste bas{\'e} sur la taille, nous a servi {\`a} v{\'e}rifier dans quelle mesure la distribution des tailles des communaut{\'e}s de poissons peut aider {\`a} mieux comprendre le fonctionnement des r{\'e}seaux alimentaires marins et les effets de la p{\^e}che sur les {\'e}cosyst{\`e}mes. Il existe une forte similarit{\'e} entre les spectres de taille simul{\'e}s et ceux d{\'e}crits dans...},
issn = {0706-652X},
doi = {10.1139/f03-154},
url = {http://www.nrcresearchpress.com/doi/abs/10.1139/f03-154},
author = {Shin, Yunne-Jai and Cury, Philippe}
}

2001

  • [DOI] Y. Shin and P. Cury, “Exploring fish community dynamics through size-dependent trophic interactions using a spatialized individual-based model,” Aquatic living resources, vol. 14, iss. 2, p. 65{–}80, 2001.
    [Bibtex] 
    @article {shin_exploring_2001,
title = {Exploring fish community dynamics through size-dependent trophic interactions using a spatialized individual-based model},
journal = {Aquatic Living Resources},
volume = {14},
number = {2},
year = {2001},
pages = {65{\textendash}80},
abstract = {An individual-based model named {OSMOSE} (Object-oriented Simulator of Marine Ecosystems Exploitation) is used to investigate the dynamics of exploited marine fish communities. It allows the representation of age- and size-structured populations comprised of groups of individuals that interact within a spatialized food web. Within each group, which constitutes the basic interaction entity (the {\textquoteleft}super-individual{\textquoteright} in individual-based modelling terminology), fish belong to the same species, have similar biological parameters and behaviour rules. Somatic growth, reproduction, predation and starvation processes are modelled. Two rules apply for the predation process: for a given fish group, prey selection depends both on the spatial and temporal co-occurrence of the predator and its prey, and on the respective lengths of the prey versus the predator. Thus, fish feed regardless of the taxonomy of their prey. The strength of both predation and competition relationships therefore vary according to changes in relative species abundance. Preliminary investigations are conducted on a theoretical community comprising seven interacting species. The simulation results show how community stability can emerge from variability in species biomass. It is thus suggested that size-based trophic interactions, along with the existence of multiple weak links and species redundancy, favour community persistence and stability.},
keywords = {ecosystem stability, Individual-based model, interactions trophiques, mod{\`e}le individus-centr{\'e}, mod{\`e}le multisp{\'e}cifique, multispecific model, pr{\'e}dation taille-d{\'e}pendante, size-based predation, stabilit{\'e}, trophic interactions},
issn = {0990-7440},
doi = {10.1016/S0990-7440(01)01106-8},
url = {http://www.sciencedirect.com/science/article/pii/S0990744001011068},
author = {Shin, Yunne-Jai and Cury, Philippe}
}
  • Y. Shin and P. Cury, “Simulation of the effects of marine protected areas on yield and diversity using a multispecies, spatially explicit, individual-based model,” in Spatial processes and management of marine populations : proceedings of the symposium on spatial processes and management of marine populations, Fairbanks: University of alaska sea grant, 2001, p. 105{–}122.
    [Bibtex] 
    @inbook {shin_simulation_2001,
title = {Simulation of the effects of marine protected areas on yield and diversity using a multispecies, spatially explicit, individual-based model},
booktitle = {Spatial processes and management of marine populations : proceedings of the symposium on spatial processes and management of marine populations},
year = {2001},
pages = {105{\textendash}122},
publisher = {University of Alaska Sea Grant},
organization = {University of Alaska Sea Grant},
address = {Fairbanks},
keywords = {simulation, {AIRE} {MARINE} {PROTEGEE}, {AMENAGEMENT} {DES} {PECHES}, {IMPACT} {DE} L{\textquoteright}{ENVIRONNEMENT}, {MODELE}, {MORTALITE}, {PECHE} {MARITIME}, {REPRODUCTION}, {RESSOURCES} {HALIEUTIQUES}},
isbn = {1566120683},
url = {http://www.documentation.ird.fr/hor/fdi:010055052},
author = {Shin, Yunne-Jai and Cury, Philippe},
}