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Travers, M., Shin, Y. - J., Jennings, S., Machu, E., Huggett, J. A., Field, J. G., et al. (2009). Two-way coupling versus one-way forcing of plankton and fish models to predict ecosystem changes in the Benguela. Ecological Modelling, 220(21), 3089–3099.
Résumé: 'End-to-end' 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-N(2)P(2)Z(2)D(2)) and high trophic levels(OSMOSE). ROMS-N(2)P(2)Z(2)D(2) 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.
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Walker, E., & Bez, N. (2010). A pioneer validation of a state-space model of vessel trajectories (VMS) with observers' data. Ecological Modelling, 221, 2008–2017.
Résumé: In the context of the expansion of animal tracking and bio-logging, state-space models have been developed with the objective to characterise animals' trajectories and to understand the factors controlling their behaviour. In the fisheries community, the electronic tagging of vessels commonly designated by Vessel Monitoring Systems (VMS) is developing and provides a new insight for the understanding, the analysis and the modelling of the trajectories of vessels and their prospecting behaviour. VMS data are thus a clue for the proper definition of fishing effort which remains a fundamental parameter of tuna stock assessments. In this context, we used the VMS (recording of hourly positions) of the French tropical tuna purse-seiners operating in the Indian Ocean to characterise three types of movement (states) on the VMS trajectories (stillness, tracking, and cruising). Based on empirical evidences, and on the regular frequency of VMS acquisition, this was achieved by the development of a Bayesian Hidden Markov model for the speeds and turning angles derived from the hourly steps of the trajectories. In a second phase, states were related to activities disentangling stillness into fishing or stop at sea. Finally the quality of the model performances was rigorously quantified thanks to observers' data. Confronting model prediction and true activities allowed estimating that 10% of the hourly steps were misclassified. The assumptions and model' choices are discussed, highlighting the fact that VMS data and observers' data having different time resolutions, the effective use of validating data was troublesome. However, without validation, these analyses remain speculative. The validation part of this work represents an important step for the operational use of state-space models in ecology in the broad sense (predators' tracking data, e.g. birds or mammals trajectories).
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Xing, L., Zhang, C., Chen, Y., Shin, Y. - J., Verley, P., Yu, H., et al. (2017). An individual-based model for simulating the ecosystem dynamics of Jiaozhou Bay, China. Ecological Modelling, 360(Supplement C), 120–131.
Résumé: The Object-oriented Simulator of Marine ecoSystem Exploitation (OSMOSE) is one of the end-to-end models developed for ecosystem dynamic simulation and management strategy evaluation (MSE) in support of ecosystem-based fishery management (EBFM). However, the implementation of such integrated models has been limited due to lack of data, and their performance in advising fisheries management has been rarely evaluated. We developed an end-to-end model (OSMOSE-JZB) representing organisms of high and low trophic levels in the Jiaozhou Bay, a temperate bay in China with limited available data. We evaluated the performance of the model for simulating the ecosystem dynamics by comparing the model-predicted species biomass, size structure, trophic level, and mortality with relevant data derived from scientific surveys and literature. In general, the model-predicted species biomass and size ranges were consistent with observations. However, the size structure of the two dominant fish species showed some discrepancies between the model simulations and observations. The predicted mean trophic levels from OSMOSE-JZB were closer to the values derived from an Ecopath model of the same region, compared to the values derived from empirical isotope analysis. The model's output suggested that predation mortality appeared to be the main source of mortality for younger individuals compared to starvation and fishing mortality. This study suggests that the OSMOSE-JZB performs well under a data-poor situation and can be considered as a baseline ecosystem model for developing EBFM.
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