Impact d'une obligation de débarquement sur les dynamiques couplées écosystème-pêcheurs : approche par modélisation individu-centrée appliquée à la Manche Orientale

L'objectif de cette thèse était d'anticiper les effets de l'Obligation de Débarquement (OD) mise en place en UE depuis début 2015 en Manche Orientale (MO). Pour accomplir ces objectifs, il a été prévu de : i) mieux comprendre la distribution spatiale saisonnière d'espèces commerciales à l'aide d'observations embarquées sur des navires commerciaux, ii) les comparer avec la distribution de l'effort de pêche à fine échelle des chalutiers de fonds (OTB), et iii) développer un modèle individu-centré de dynamique des flotilles, DSVM, à intégrer avec le modèle écosystémique OSMOSE pour simuler l'OD. L'utilité des données d'observations embarquées a été prouvée pour une majeure partie des espèces échantillonnées, en utilisant une validation par la bibliographie et un indicateur géostatique. Ensuite la comparaison de l'effort de pêche à fine échelle a fourni une amélioration de la quantification de l'effort de pêche effectif et mis en valeur l'importance de la seiche et du rouget barbet pour la distribution des OTB en MO. De plus, l'intensité de ciblage des OTB a été quantifiée en octobre à l'aide d'un nouvel indicateur, et démontré l'intérêt pour les mêmes espèces, mais aussi la contrainte d'un faible quota de cabillaud pour les pêcheurs. Les résultats du couplage OSMOSE-DSVM montrent que k'OD aurait des effets négatifs à court terme pour le revenu des pêcheurs, induits par le déplacement de l'effort de pêche afin d'éviter les dépassements de quota, mais serait profitable à moyen terme. Cependant, l'OD provoquerait une hausse de la pression de prédation produite par le cabillaud et le merlan sur les autres espèces, ce qui n'améliorerait pas l'état global de l'écosystème.The objective of this thesis was to anticipate the effects if the EU Landing Obligation (LO) implemented since the beginning of 2015 in the Eastern English Channel (EEC). To achieve these objectives, it was planned to : i) better understand seasonal spatial distribution of commercial species using on-board commercial vessels observation data, ii) compare them with the final scale fishing effort distribution of EEC bottom otter trawlers (OTB), and iii) develop an individual-based model of fleet-dynamics, DSVM, to be integrated within the ecosystem model OSMOSE to simulate a LO. The usefulness of on-board observation data was proved for a main part of a species sample, using validation from the literature and a geostatistical indicator. Then the comparison of fine scale fishing effort provided an improvement of the quantification of effective fishing effort and emphasized the importance of cuttlefish and red mullet for the global distribution of EEC OTB. In addition, the targeting intensity of OTB was quantified in October using a newly-developed indicator, and demonstrated the attractiveness of the same species, but also the constraint of low cod quota for fishers. Results of the OSMOSE-DSVM coupling show that the LO would have short-term negative effects on fishers' revenue, induced by a large reallocation of their fishing effort to avoid quota over-shooting, but would be profitable in the medium-term. However, the LO would induce an increase of the predatory pressure operated by cod and withing on the other species, which would not improve the overall ecosystem health

Impact of a landing obligation on coupled dynamics ecosystem-fishers : individual-based modelling approach applied to Eastern English Channel

The objective of this thesis was to anticipate the effects if the EU Landing Obligation (LO) implemented since the beginning of 2015 in the Eastern English Channel (EEC). To achieve these objectives, it was planned to : i) better understand seasonal spatial distribution of commercial species using on-board commercial vessels observation data, ii) compare them with the final scale fishing effort distribution of EEC bottom otter trawlers (OTB), and iii) develop an individual-based model of fleet-dynamics, DSVM, to be integrated within the ecosystem model OSMOSE to simulate a LO. The usefulness of on-board observation data was proved for a main part of a species sample, using validation from the literature and a geostatistical indicator. Then the comparison of fine scale fishing effort provided an improvement of the quantification of effective fishing effort and emphasized the importance of cuttlefish and red mullet for the global distribution of EEC OTB. In addition, the targeting intensity of OTB was quantified in October using a newly-developed indicator, and demonstrated the attractiveness of the same species, but also the constraint of low cod quota for fishers. Results of the OSMOSE-DSVM coupling show that the LO would have short-term negative effects on fishers' revenue, induced by a large reallocation of their fishing effort to avoid quota over-shooting, but would be profitable in the medium-term. However, the LO would induce an increase of the predatory pressure operated by cod and withing on the other species, which would not improve the overall ecosystem health.L'objectif de cette thèse était d'anticiper les effets de l'Obligation de Débarquement (OD) mise en place en UE depuis début 2015 en Manche Orientale (MO). Pour accomplir ces objectifs, il a été prévu de : i) mieux comprendre la distribution spatiale saisonnière d'espèces commerciales à l'aide d'observations embarquées sur des navires commerciaux, ii) les comparer avec la distribution de l'effort de pêche à fine échelle des chalutiers de fonds (OTB), et iii) développer un modèle individu-centré de dynamique des flotilles, DSVM, à intégrer avec le modèle écosystémique OSMOSE pour simuler l'OD. L'utilité des données d'observations embarquées a été prouvée pour une majeure partie des espèces échantillonnées, en utilisant une validation par la bibliographie et un indicateur géostatique. Ensuite la comparaison de l'effort de pêche à fine échelle a fourni une amélioration de la quantification de l'effort de pêche effectif et mis en valeur l'importance de la seiche et du rouget barbet pour la distribution des OTB en MO. De plus, l'intensité de ciblage des OTB a été quantifiée en octobre à l'aide d'un nouvel indicateur, et démontré l'intérêt pour les mêmes espèces, mais aussi la contrainte d'un faible quota de cabillaud pour les pêcheurs. Les résultats du couplage OSMOSE-DSVM montrent que k'OD aurait des effets négatifs à court terme pour le revenu des pêcheurs, induits par le déplacement de l'effort de pêche afin d'éviter les dépassements de quota, mais serait profitable à moyen terme. Cependant, l'OD provoquerait une hausse de la pression de prédation produite par le cabillaud et le merlan sur les autres espèces, ce qui n'améliorerait pas l'état global de l'écosystème

New trophic indicators and target values for an ecosystem-based management of fisheries

In the present study, we tested five trophic indicators and we demonstrated their usefulness to assess the environmental status of marine ecosystems and to implement an ecosystem approach to fisheries management (EAFM). The tested indicators include the slope of the biomass spectrum, the mean trophic level (MTL), the marine trophic index (MTI) and two newly developed indicators, the high trophic level indicator (HTI) and the apex predator indicator (API). Indicators are compared between current state and potential reference situations, using as case studies: the Celtic Sea/Bay of Biscay, North Sea and English Channel ecosystems. Trophic spectra are obtained from Ecopath models while reference situations are estimated, simulating with EcoTroph and Ecosim different fishing pressures including three candidate scenarios for an EAFM. Inter-ecosystems assessments are done using Ecopath models, simulations outputs and scientific surveys data to assess the current states of the studied ecosystems, contrast the reference situations and analyze the responses of all indicators. Sensitivity analyses are also conducted on the main simulation parameters to test the robustness of the chosen indicators. Ecosystems specific targets for EAFM are proposed for the five trophic indicators estimated from whole-ecosystem models, while in the Celtic Sea/Bay of Biscay ecosystem targets are proposed for the MTL (=3.85) and HTI (48%) estimated from standard bottom-trawl surveys. The HTI is proposed to be relevant for survey data and the API is recommended using whole-ecosystem models. We conclude that HTI and API show trends in ecosystems health better than MTI

Importance of grey mullets on coastal food webs in a context of omega-3 deficiency: from sub-individual level to trophic dynamics

International audienc

Improving the interpretation of fishing effort and pressures in mixed fisheries using spatial overlap metrics

Managing mixed fisheries requires understanding fishers’ behaviour to allow predicting future fisheries distribution and impact on marine ecosystems. A new approach was developed to compare fine scale fishing effort distribution of Eastern English Channel (EEC) bottom trawlers, to the monthly- and spatially-resolved abundance distributions of commercial species. First, the added-value of using species-specific spatial overlap metric to quantify effective fishing effort and improve the relationship between fishing effort and fishing mortality was assessed. Second, based on the Ideal Free Distribution (IFD) theory, the species-specific weights given by fishers to different species were estimated by maximizing the overlap between target species assemblage and effort distributions in October. At a seasonal scale our results emphasized the importance of cuttlefish and red mullet for the global distribution of EEC bottom trawlers. In October, cuttlefish and red mullet were clearly more determining fishers’ location choice than historically harvested species, and also than the overall expected revenue. This is likely due to external constraints such as low cod quota, causing IFD assumptions violated. This study evidenced the importance of getting good insights into spatio-temporal distributions of stocks and fleets to understand fishers’ behaviour and improve mixed fisheries management advic

The Risky Decrease of Fishing Reference Points Under Climate Change

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

Inferring the annual, seasonal, and spatial distributions of marine species from complementary research and commercial vessels’ catch rates

The objective of this study is to analyse at fine scale the annual, seasonal and spatial distributions of several species in the Eastern English Channel (EEC). On the one hand, data obtained from scientific surveys are not available all year through, but are considered to provide consistent yearly and spatially resolved abundance indices. On the other hand, on-board commercial data do cover the whole year, but generally provide a biased perception of stock abundance. The combination of scientific and commercial catches per unit of effort (CPUEs), standardized using a delta-generalized linear model, allowed to infer spatial and monthly dynamics of fish distributions in the EEC, which could be compared with previous knowledge on their life cycles. Considering the scientific survey as a repository, the degree of reliability of commercial CPUEs was assessed with survey-based distribution using the Local Index of Collocation. Large scale information was in agreement with literature, especially for cuttlefish. Fine scale consistency between survey and commercial data was significant for half of the 19 tested species (e.g. whiting, cod). For the other species (e.g. plaice, thornback ray), the results were inconclusive, mainly owing to poor commercial data coverage and/or to particular aspects of the species biology

A toolbox to evaluate data reliability for whole-ecosystem models: Application on the Bay of Biscay continental shelf food-web model

Ecosystem models are always simplifications of reality and as such their application for ecosystem-based management requires standard validation. Here, the “DataReli” toolbox is proposed to evaluate the quality of the data used during the construction of ecosystem models, their coherence across trophic levels, and whether data limitations prevent the model long-term applications. This toolbox is the combination of three operational and complementary analyses: (i) the pedigree index to determine to what extent a model was calibrated on data of local origin; (ii) the graphical analysis known as PREBAL to assess whether a model respects some basic ecological and fisheries principles; and (iii) a sensitivity analysis to evaluate the robustness of model predictions to small variations in input data. The toolbox is delivered to potential users with main generic recommendations on how interpreting results conjointly and on which decisions to make about parameters’ revisions or model uses’ restrictions. (i) Corrections of parameters should be preferentially envisaged when modelling data-rich environments. (ii) For those models with an overall pedigree index above 0.4, a closer look at the pedigree routine, i.e. values by parameters and compartments, and the PREBAL analysis would help to prioritize parameters needing improvement. (ii)’ For Ecopath models of no overall acceptable quality (overall pedigree index <0.4), we recommend stopping the DataReli procedure at this point. (iii) In terms of sensitivity analysis, marked responses of model predictions to small variations in the input values must preferentially lead to restrictions in the model applications compared to corrections of parameter estimates. A concrete application of the “DataReli” toolbox to the pre-existing Ecopath model of the Bay of Biscay continental shelf food web is presented. For the present case study, the general level of input data reliability is considered as satisfying with regard to the model applications

Gene expression variation in natural populations of hexaploid and allododecaploid Spartina species (Poaceae)

International audienceAllopolyploidy is a peculiar process entailing the cohabitation of two (or more) divergent genomes. Consequences on plant genomes are varied and can utlimately alter gene expression and regulatory interactions. Most studies have explored polyploid expression evolution in experimental controlled conditions. Here, we analyzed global gene expression variation in natural populations of the Spartina polyploid complex including hexaploid parental species (S. maritima and S. alterniflora), two F1 hybrids (S. x townsendii and S. x neyrautii) and the allododecaploid S. anglica. In situ sampling and quantitative PCR were performed for comparing global expression of candidate genes involved in responses to abiotic stresses, lignin and cellulose metabolisms between five Spartina taxa. Illumina sequencing datasets and dedicated bioinformatic pipelines were employed to explore sequence heterogeneity in these highly duplicated genomes. Levels of gene expression were significantly higher in S. alterniflora (compared to the other hexaploid parent S. maritima) for seven of the analyzed genes. Effects of both hybridization and polyploidization are detected and consistent with previous global transcriptome analyses performed on Spartina plants grown in controlled conditions. Duplicated copies present in the hybrids and the allododecaploid were successfully assigned to either one of the parental genomes. Phylogenetic analyses identified for each of the parental hexaploid species, the presence of two distinct clades including two or more expressed copies. We provide here a comprehensive gene expression study based on individuals sampled in their natural habitat and detected the superimposed effect of environmental heterogeneity, hybridization and allopolyploidy

An ecosystem-wide approach for assessing the spatialized cumulative effects of local and global changes on coastal ecosystem functioning

Coastal ecosystems are subjected to an increasing number of anthropogenic drivers, including marine renewable energies and climate change (CC). These drivers can interact in complex ways, which may lead to cumulative effects (CEs) whose potential consequences on the ecosystems need to be addressed. We used a holistic approach—ecological network analysis (ENA)—coupled with a two-dimensional food web model—Ecospace—to conduct an ecosystem study of the CEs of CC plus the operation of an offshore wind farm on ecosystem functioning in the extended Bay of Seine (English Channel). Mapped ENA indices showed that CEs were not restricted to the wind farm area, i.e. where anthropogenic drivers are concomitant. CEs varied both in space and among ecosystem properties, displaying that ENA indices can distinguish between different cumulative pathways that modify ecosystem functioning in multiple ways. Moreover, the effects seemed to be tied to the structuring role of CC, and differed under the 2050 and 2100 conditions. Such changes resulted in stronger loss of ecosystem resilience under the 2100 conditions despite the benefits of the reef and reserve effects of the wind farm