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An integrated Bayesian modeling approach for the growth of Indian Ocean yellowfin tuna ArchiMer
Dortel, Emmanuelle; Sardenne, Fany; Bousquet, N.; Rivot, Etienne; Million, Julien; Le Croizier, Gael; Chassot, Emmanuel.
The Indian Ocean Tuna Tagging Program provided a unique opportunity to collect demographic data on the key commercially targeted tropical tuna species in the Indian Ocean. In this paper, we focused on estimating growth rates for one of these species, yellowfin (Thunnus albacares). Whilst most growth studies only draw on one data source, in this study we use a range of data sources: individual growth rates derived from yellowfin that were tagged and recaptured, direct age estimates obtained through otolith readings, and length-frequency data collected from the purse seine fishery between 2000 and 2010. To combine these data sources, we used an integrated Bayesian model that allowed us to account for the process and measurement errors associated with each...
Tipo: Text Palavras-chave: Indian Ocean yellowfin; Hierarchical Bayesian model; Tagging; Fisheries.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00254/36513/35080.pdf
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Stock assessment of the English Channel stock of cuttlefish with a two-stage biomass model ArchiMer
Alemany, Juliette; Foucher, Eric; Rivot, Etienne; Vigneau, Joel; Robin, Jean-paul.
Among the English Channel fishery, the importance of cuttlefish stock has increased, following the cephalopods global landings and market trend. The stock is currently managed at regional scale but not by European regulations, although it is a shared species targeted by French and British fishing fleets at several stages of its life-cycle and across much of its distributional range. An assessment of this stock was conducted in June 2014 by fitting a two-stage biomass model on a 22 years’ time-series (1992-2013). We present the last update of cuttlefish stock assessment using the same model on years 1992-2014. As the outputs of the model are sensitive to a fix growth parameter, we explore possibilities to improve the model. The use of a Bayesian framework...
Tipo: Text Palavras-chave: Stock assessment; Short-lived species; Data-limited; Cuttlefish; Sepia officinalis; English Channel; Two-stage biomass model; Bayesian methods.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00377/48774/49172.pdf
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Mechanisms of change in human behaviour ArchiMer
Marchal, Paul; Bartelings, Heleen; Bastardie, François; Batsleer, Jurgen; Delaney, Alyne; Girardin, Raphael; Gloaguen, Pierre; Hamon, Katell; Hoefnagel, Ellen; Jouanneau, Charlène; Mahevas, Stephanie; Nielsen, Rasmus; Piwowarczyk, Joanna; Poos, Jan-jaap; Schulze, Torsten; Rivot, Etienne; Simons, Sarah; Tidd, Alex; Vermard, Youen; Woillez, Mathieu.
The scope of this report is to present the science developed within the VECTORS project to improve the understanding of the key processes driving the behaviour of human agents utilising a variety of EU maritime domains. While particular attention has been paid to the spatial interactions between fishing activities and other human uses (e.g., maritime traffic, offshore wind parks, aggregate extractions), the behaviour of non-fishing sectors of activity has also been considered. Various quantitative and semi-qualitative approaches have been pursued to gain better insight into behavioural drivers based on past data, and also forecast how human agents would react if access was constrained by either management (e.g. Marine Protected Areas – MPA), or the...
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Ano: 2014 URL: http://archimer.ifremer.fr/doc/00223/33377/31802.pdf
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Update of the English Channel cuttlefish stock assessment with a Bayesian two-stage biomass model. ArchiMer
Alemany, Juliette; Rivot, Etienne; Foucher, Eric; Vigneau, Joel; Robin, Jean-paul.
A two-stage biomass model is developed in the Bayesian framework that allows us to assimilate various sources of information. A method that makes use of ancillary length frequency data is developed to provide an informative prior distribution for the intrinsic biomass growth rate parameter and its annual variability. The new Bayesian model provides substantial improvement to the existing stock assessment method used by ICES. Considering a time-varying g parameter improves model fit and improves the ecological realisms of the model according to the sensitivity of the cuttlefish population dynamics to environmental fluctuations. We present results of the English Channel cuttlefish stock assessment updated with the new Bayesian model. The model also provides...
Tipo: Text Palavras-chave: Stock assessment; Short-lived species; Data-limited; Cuttlefish; Sepia officinalis; English Channel; Two-stage biomass model; Bayesian.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00377/48775/49173.pdf
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Is speed through water a better proxy for fishing activities than speed over ground? ArchiMer
Gloaguen, Pierre; Woillez, Mathieu; Mahevas, Stephanie; Vermard, Youen; Rivot, Etienne.
Understanding fishing vessel dynamics at a fine spatial scale is of great interest for defining appropriate spatial management plans. Different models have been developed to detect fishing activity from Vessel Monitoring System (VMS) data. While mathematical and statistical methods differ, all rely on the idea that vessel speed over ground provides information on fishing vessel activity. However, trawling with constant speed relative to the water mass may as well prove a winning strategy for both technical (to ensure sufficient trawl opening) and biological (to limit escapement of fish) reasons. Therefore, considering speed through water instead of speed over ground might provide insights into fishing activities. We developed a method combining surface...
Tipo: Text Palavras-chave: Vessel monitoring system surface currents hidden Markov models; MARS 3D; Obsmer.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00359/47030/46948.pdf
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Identifying fishing trip behaviour and estimating fishing effort from VMS data using Bayesian Hidden Markov Models ArchiMer
Vermard, Youen; Rivot, Etienne; Mahevas, Stephanie; Marchal, Paul; Gascuel, Didier.
Recent advances in technologies have lead to a vast influx of data on movements, based on discrete recorded position of animals or fishing boats, opening new horizons for future analyses. However, most of the potential interest of tracking data depends on the ability to develop suitable modelling strategies to analyze trajectories from discrete recorded positions. A serious modelling challenge is to infer the evolution of the true position and the associated spatio-temporal distribution of behavioural states using discrete, error-prone and incomplete observations. In this paper, a Bayesian Hierarchical Model (HBM) using Hidden Markov Process (HMP) is proposed as a template for analyzing fishing boats trajectories based on data available from...
Tipo: Text Palavras-chave: Bayesian Hierarchical Models; Hidden Markov Model; State-space model; VMS; Fleet behaviour; Fishing effort.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00009/11993/9342.pdf
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Le vivaneau rouge (Lutjanus purpureus) dans la ZEE de Guyane française. Bilan des connaissances sur la biologie de l'espèce. Analyse de quelques aspects de la pêcherie vénézuélienne ArchiMer
Rivot, Etienne.
Tipo: Text
Ano: 2000 URL: http://archimer.ifremer.fr/doc/00085/19655/17285.pdf
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State-space modeling of multi-decadal mark-recapture data reveals low adult dispersal in a nursery-dependent fish metapopulation ArchiMer
Lecomte, Jean-baptiste; Le Pape, Olivier; Baillif, Hélène; Nevoux, Marie; Vermard, Youen; Savina-rolland, Marie; Veron, Matthieu; Lehuta, Sigrid; Hunter, Ewan; Rivot, Etienne.
Quantifying connectivity within fish metapopulations is an important component in understanding population dynamics and providing an evidence base for assessment and management. We investigate meta-population connectivity of the common sole (Solea solea L.) in the Eastern English Channel (EEC). The EEC common sole stock is currently assessed as a single and spatially homogeneous population but connectivity induced through adult movements within this stock and with nearby stocks remains unknown. To fill this knowledge gap, we developed a state-space mark-recovery model, designed to estimate adult connectivity, using mark-recapture data from multiple release experiments from 1970 to 2018 across the EEC and adjacent management areas. The model estimates...
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Ano: 2020 URL: https://archimer.ifremer.fr/doc/00515/62634/67003.pdf
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Stock assessment models for short-lived species in data-limited situations. Case study of the English Channel stock of cuttlefish. ArchiMer
Alemany, Juliette; Foucher, Eric; Rivot, Etienne; Vigneau, Joel; Robin, Jean-paul.
Among the English Channel fishery, the importance of cuttlefish stock has increased, following the cephalopods global landings and market trend. The stock is currently managed at regional scale but not by European regulations, although it is a shared species targeted by French and British fishing fleets at several stages of its life-cycle and across much of its distributional range. An assessment of this stock was conducted in June 2014 by fitting a two-stage biomass model on a 22 years’ time-series (1992-2013). As the assumptions of the model are based on a simplified life-cycle, it would be appropriate to compare the results with outputs from other models in order to obtain reliable biomass estimations. The final aim is to produce reliable management...
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Ano: 2015 URL: http://archimer.ifremer.fr/doc/00377/48773/49171.pdf
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A hierarchical Bayesian model for embedding larval drift and habitat models in integrated life cycles for exploited fish ArchiMer
Rochette, Sebastien; Le Pape, Olivier; Vigneau, Joel; Rivot, Etienne.
This paper proposes a hierarchical Bayesian framework for modeling the life cycle of marine exploited fish with a spatial perspective. The application was developed for a nursery-dependent fish species, the common sole (Solea solea), on the Eastern Channel population (Western Europe). The approach combined processes of different natures and various sources of observations within an integrated framework for life-cycle modeling: (1) outputs of an individual-based model for larval drift and survival that provided yearly estimates of the dispersion and mortality of eggs and larvae, from spawning grounds to settlement in several coastal nurseries; (2) a habitat suitability model, based on juvenile trawl surveys coupled with a geographic information system, to...
Tipo: Text Palavras-chave: Eastern Channel (Western Europe); Habitat suitability model; Hierarchical Bayesian model; Hydrodynamic models; Integrated model; Larval drift; Life cycle; Nursery; Recruitment; Sole; Solea solea; Spatially structured.
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00161/27243/25454.pdf
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The duration of migration of Atlantic Anguilla larvae ArchiMer
Bonhommeau, Sylvain; Castonguay, Martin; Rivot, Etienne; Sabatie, Richard; Le Pape, Olivier.
Oceanic larvae of the European (Anguilla anguilla) and American (A. rostrata) eels have to cross the Atlantic Ocean from the Sargasso Sea to European or North American coasts before entering continental habitats. In some European rivers, eel recruitment is now < 1% of levels in the 1980s. A better understanding of the effects of anthropogenic pressures and environmental fluctuations on eel larvae and subsequent recruitment is a prerequisite to build efficient management plans. The present paper provides insight into the critical oceanic phase of the eel life cycle with a focus on the duration of the larval migration whose estimates varies between 7 months and more than 2 years in both species. Does this range correspond to a natural variability in...
Tipo: Text Palavras-chave: Lagrangian modelling; Leptocephali; North Atlantic; Otoliths; Sargasso Sea.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00011/12208/9033.pdf
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Integrating mark-recapture data within a Bayesian life-cycle model to evaluate spatial structure and population dynamics of sole. A coastal and nursery dependent flatfish : Eastern Channel Sole ArchiMer
Veron, Matthieu; Archambault, Benoit; Rochette, Sebastien; Hunter, Ewan; Lehuta, Sigrid; Randon, Marine; Savina-rolland, Marie; Vermard, Youen; Reveillac, Elodie; Rivot, Etienne; Le Pape, Olivier.
The common sole -Solea solea- is one of the most harvested flatfish population in the Eastern English Channel -EEC; ICES area VIId-. In the EEC, this population is currently assessed and managed as a homogeneous single stock. However, some ecological clues indicate that a metapopulation structure formed by a set of three loosely connected subpopulations associated with local coastal nurseries areas cannot be ruled out. Results show that key estimates of population dynamics parameters, stock assessment and management reference points are highly sensitive to the hypotheses made on the spatial structure. A Bayesian integrated life-cycle model was developed to explore the sensitivity of population dynamics and stock assessment to the level of connectivity in...
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Ano: 2017 URL: http://archimer.ifremer.fr/doc/00410/52134/52844.pdf
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Effect of nursery habitat degradation on flatfish population: Application to Solea solea in the Eastern Channel (Western Europe) ArchiMer
Rochette, S.; Rivot, Etienne; Morin, Jocelyne; Mackinson, S.; Riou, Philippe; Le Pape, Olivier.
Estuaries and coastal waters are essential nursery habitats for many marine species, and especially for flatfishes. Thus, investigating how anthropogenic disturbances affect the quality of these habitats is of major importance to understand their consequences on the population renewal of marine species. The aim of the present study was to analyse the effects of estuarine habitat degradation on the population of the common sole in the Eastern Channel, a key species in the fish community and fisheries in this area. We especially focused on the drastic drop in the surface area and on the low water quality of the Seine estuary, the main river of the Eastern Channel. A geographic Information System (GIS) was used to develop quantitative maps of sole nursery...
Tipo: Text Palavras-chave: Solea solea; Nursery; Habitat Mapping; Anthropogenic Disturbance; Seine Estuary; Recruitment.
Ano: 2010 URL: http://archimer.ifremer.fr/doc/00008/11921/9799.pdf
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A Bayesian two-stage biomass model for stock assessment of data-limited species: An application to cuttlefish ( Sepia officinalis ) in the English Channel ArchiMer
Alemany, Juliette; Rivot, Etienne; Foucher, Eric; Vigneau, Joel; Robin, Jean-paul.
Cuttlefish is a key commercial species in the English Channel fishery in terms of landings and value. Age-based assessment methods are limited by time-consuming age determination with statoliths and the lack of stock assessment models tailored to this data-limited species. A two-stage biomass model is developed in the Bayesian state-space modelling framework that allows inferences to be made on the stock biomass at the start, middle and end of each fishing seasons between 1992 and 2014, while accounting for both process and measurement errors and to assimilate various sources of information. A method that uses ancillary length-frequency data is developed to provide an informative prior distribution for the biomass growth rate parameter g (E = 0.89) and its...
Tipo: Text Palavras-chave: English Channel; Cuttlefish; Sepia officinalis; Bayesian state-space model; Data-limited stock; Two-stage biomass model.
Ano: 2017 URL: http://archimer.ifremer.fr/doc/00376/48766/49289.pdf
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Modelling Fishing Vessels Movement and Activity ArchiMer
Gloaguen, Pierre; Mahevas, Stephanie; Rivot, Etienne; Woillez, Mathieu; Guitton, Jérome; Vermard, Youen; Etienne, Marie-pierre.
Tipo: Text
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00371/48181/48296.pdf
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Coupling hydrodynamic and individual-based models to simulate long-term larval supply to coastal nursery areas ArchiMer
Rochette, Sebastien; Huret, Martin; Rivot, Etienne; Le Pape, Olivier.
For many marine fish species, recruitment is strongly related to larval survival and dispersal to nursery areas. Simulating larval drift should help assessing the sensitivity of recruitment variability to early life history. An individual-based model (IBM) coupled to a hydrodynamic model was used to simulate common sole larval supply from spawning areas to coastal and estuarine nursery grounds at the population scale in the eastern Channel on a 14-yr time series, from 1991 to 2004. The IBM allowed each particle released to be transported by currents from the hydrodynamic model, to grow with temperature, to migrate vertically giving stage development, and possibly to die according to drift duration, representing the life history from spawning to...
Tipo: Text Palavras-chave: Eastern Channel; Hydrodynamic model; Individual-based model; Larval supply; Nursery grounds; Recruitment variability; Solea solea.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00085/19598/17236.pdf
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A future for marine fisheries in Europe (Manifesto of the Association Francaise d'Halieumetrie) ArchiMer
Gascuel, D.; Bez, Nicolas; Forest, Andre; Guillotreau, P.; Laloe, F.; Lobry, Jeremy; Mahevas, Stephanie; Mesnil, Benoit; Rivot, Etienne; Rochette, S.; Trenkel, Verena.
We, members of the Association Francaise d'Halieumetrie, share the conviction that European fisheries have a future. It is time to get off the wrong track. Radical change is required to embark on the path of sustainable development and truly implement the ecosystem approach to fisheries. Today, high fishing pressure is deployed to catch a rare resource, which in return is responsible for the rarity. We must reverse the situation: an abundant resource that affords high catches applying moderate fishing pressure. All management tools and especially all actors must be mobilized. The transition is not simple, and European solidarity must accompany the changes. It is well worth the effort. By reducing fishing pressure, it will be possible in the medium term to...
Tipo: Text Palavras-chave: Access regulation; Ecosystem approach to fisheries; European Common Fishery Policy; ITQ; MPA; MSY; Management plan; Overcapacity; Subsidies.
Ano: 2011 URL: http://archimer.ifremer.fr/doc/00035/14598/11947.pdf
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An autoregressive model to describe fishing vessel movement and activity ArchiMer
Gloaguen, Pierre; Mahevas, Stephanie; Rivot, Etienne; Woillez, Mathieu; Guitton, Jerome; Vermard, Youen; Etienne, Marie-pierre.
The understanding of the dynamics of fishing vessels is of great interest to characterize the spatial distribution of the fishing effort and to define sustainable fishing strategies. It is also a prerequisite for anticipating changes in fishermen's activity in reaction to management rules, economic context, or evolution of exploited resources. Analyzing the trajectories of individual vessels offers promising perspectives to describe the activity during fishing trips. A hidden Markov model with two behavioral states (steaming and fishing) is developed to infer the sequence of non-observed fishing vessel behavior along the vessel trajectory based on Global Positioning System (GPS) records. Conditionally to the behavior, vessel velocity is modeled with an...
Tipo: Text Palavras-chave: Hidden Markov model; Vessels dynamics; RECOPESCA; Autoregressive process; Baum-Welch algorithm.
Ano: 2015 URL: https://archimer.ifremer.fr/doc/00179/29049/27485.pdf
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A Bayesian two-stage biomass model applied to the English Channel stock of cuttlefish (Sepia officinalis) ArchiMer
Alemany, Juliette; Rivot, Etienne; Foucher, Eric; Vigneau, Joel; Robin, Jean-paul.
Among the English Channel fishery, the importance of cuttlefish stock has increased, following the cephalopods global landings and market trend. An adapted stock assessment model is needed in order to give good management advice with accurate uncertainties. Age based methods in this species are hampered by time consuming age determination with statoliths. A model requiring few data and adapted to the species life-history is therefore proposed. An assessment of this stock was conducted in June 2015 by fitting a two-stage biomass model on a 22 years’ time-series (1992-2014). The use of a Bayesian framework is particularly adapted for decision making, allowing the propagation of uncertainty in the model. It also permits the use of different sources of...
Tipo: Text
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00379/49066/49514.pdf
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Adult-mediated connectivity affects inferences on population dynamics and stock assessment of nursery-dependent fish populations ArchiMer
Archarnbault, Benoit; Le Pape, Olivier; Baulier, Loic; Vermard, Youen; Veron, Matthieu; Rivot, Etienne.
We explore how alternative hypotheses on the degree of mixing among local subpopulations affect statistical inferences on the dynamics and stock assessment of a harvested flatfish population, namely, the common sole population in the Eastern Channel (ICES area VIId). The current paradigm considers a single, well-mixed, spatially homogeneous population with juveniles from all coastal nursery grounds along the French and UK coasts that contribute to a single adult population and one pool of eggs. Based on the available data and ecological knowledge, we developed a spatial Bayesian integrated life-cycle model that consists of three subpopulations (one near the UK coast and two near the French coast, denoted UK, West FR and East FR, respectively) supported by...
Tipo: Text Palavras-chave: Solea solea; Spatial life-cycle model; Coastal nurseries; Connectivity; Stock assessment; Hierarchical bayesian model.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00333/44430/44231.pdf
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