ArchiMer, Institutional Archive of Ifremer (French Research Institute for Exploitation of the Sea)
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Archimer, is the institutional repository of Ifremer (French Research Institute for Exploitation of the Sea). It provides freely available scientific or technical documents online (publications, theses, conference proceedings, etc) in all fields related to oceans (oceanography, aquaculture, fisheries, etc). The site is available in French and English.
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A random effects population dynamics model based on proportions-at-age and removal data for estimating total mortality - Trenkel, Verena; Bravington, Mark V.; Lorance, Pascal
Catch curves are widely used to estimate total mortality for exploited marine populations. The usual population dynamics model assumes constant recruitment across years and constant total mortality. We extend this to include annual recruitment and annual total mortality. Recruitment is treated as an uncorrelated random effect, while total mortality is modelled by a random walk. Data requirements are minimal as only proportions-at-age and total catches are needed. We obtain the effective sample size for aggregated proportion-at-age data based on fitting Dirichlet-multinomial distributions to the raw sampling data. Parameter estimation is carried out by approximate likelihood. We use simulations to study...
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ISAS-Tool Version 6 : Method and configuration - Gaillard, Fabienne
ISAS (In Situ Analysis System) is an analysis tool for the temperature and salinity fields. Originally designed for the synthesis of ARGO dataset, it has been tested for the first time on the POMME area in the North-East Atlantic in 2000, it was later extended to the Atlantic and the Global ocean as the Argo array was setting up. It is developed and maintained at LPO (Laboratoire de Physique des Océans) within the Argo Observing Service (SO-ARGO) where it is used for research purposes on ocean variability. ISAS is made available to the Coriolis datacenter for exploitation in operational mode....
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ISAS-Tool Version 6 : User’s manual - Brion, Emilie; Gaillard, Fabienne
ISAS (In Situ Analysis System) is an analysis tool for producing gridded scalar fields. At the moment it is set to process temperature and salinity. Originally designed for the synthesis of ARGO dataset, it has been tested for the first time on the POMME area in the North-East Atlantic in 2000, it was later extended to the Atlantic and the Global ocean as the Argo array was setting up. It is developed and maintained at LPO (Laboratoire de Physique des Océans) within the Argo Observing Service (SO-ARGO) where it is used for research purposes on ocean variability. ISAS is made...
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A fisheries acoustic multi-frequency indicator to inform on large scale spatial patterns of aquatic pelagic ecosystems - Trenkel, Verena; Berger, Laurent
Fisheries acoustic instruments provide information on four major groups in aquatic ecosystems: fish with and without swim bladder (tertiary and quaternary consumers), fluidlike zooplankton (secondary consumers) and small gas bearing organisms such as larval fish and phytoplankton (predominantly primary producers). We entertain that this information is useable to describe the spatial structure of organism groups in pelagic ecosystems. The proposal we make is based on a multi-frequency indicator that synthesises in a single metric the shape of the acoustic frequency response of different organism groups, i.e. the dependence of received acoustic backscattered energy on emitting echosounder frequency. We demonstrate the...
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Observed acidification trends in North Atlantic water masses - Vazquez-rodriguez, M.; Perez, F.f.; Velo, A.; Rios, A. F.; Mercier, Herle
The lack of observational pH data has made it difficult to assess recent rates of ocean acidification, particularly in the high latitudes. Here we present a time series that spans over 27 yr (1981-2008) of high-quality carbon system measurements in the North Atlantic, which comprises fourteen cruises and covers the important water mass formation areas of the Irminger and Iceland Basins. We provide direct quantification of acidification rates in upper and intermediate North Atlantic waters. The highest rates were associated with surface waters and with Labrador Sea Water (LSW). The Subarctic Intermediate and Subpolar Mode Waters (SAIW and SPMW) showed...
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Space-time modelling of blue ling for fisheries stock management - Augustin, Nicole H.; Trenkel, Verena; Wood, Simon; Lorance, Pascal
Fishery catch data offer a rich potential source of information for management, if modelling can separate out the effects of fishing effort, species behaviour and population abundance. Here, we model catch data from the blue ling fishery off the northwest coast of Scotland, using generalised additive mixed models with a space time interaction represented via a novel tensor product of a soap film smooth of space with a penalized regression spline of time. The use of soap film smoothers avoids imposing correspondences between spatially adjacent areas that are in fact separated by the stock boundary. The comparison of the performance...
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ARGO based statistics for climate monitoring - Gaillard, Fabienne; Reynaud, Thierry; Von Schuckmann, Karina; Roquet, Fabien; Prigent, Annaig; Lagadec, Catherine
The Argo array, by offering simultaneously global coverage and high vertical resolution, made the monitoring of inter-annual and decadal variability of the ocean interior possible. In the ARIVO project, we have initiated the production of gridded monthly fields of temperature and salinity using an optimal analysis tool and designed an iterative approach to combine near-real time and delayed mode data.
The monthly gridded fields are averaged over time to produce the reference state needed by climatological studies, dynamical modeling and reconstruction methods themselves. Higher degree statistics such as variances and extreme values are later derived. Global indices (heat content, dynamical height)...
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Observation of spiciness interannual variability in the Pacific pycnocline - Kolodziejczyk, Nicolas; Gaillard, Fabienne
Monthly gridded fields predominantly based on global Argo in situ temperature and salinity data are used to analyze the density-compensated anomaly of salinity (spiciness anomaly) in the pycnocline of the subtropical and tropical Pacific Ocean between 2004 and 2011. Interannual variability in the formation, propagation and fate of spiciness anomalies are investigated. The spiciness anomalies propagate on the isopycnal surface sq = 25.5 along the subtropical-tropical pycnocline advected by the mean currents. They reach the Pacific Western Tropics in about 5–6 years in the Southern Hemisphere and about 7–8 years in the Northern Hemisphere. Their amplitude strongly diminishes along the...
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Proteomic identification of quality factors for oocytes in the Pacific oyster Crassostrea gigas - Corporeau, Charlotte; Vanderplancke, Gwenaelle; Boulais, Myrina; Suquet, Marc; Quere, Claudie; Boudry, Pierre; Huvet, Arnaud; Madec, Stephanie
We used a 2-DE proteomic approach to identify abundant proteins linked to oocyte quality in the Pacific oyster Crassostrea gigas, an economically important bivalve. Oocyte quality of 14 females was estimated by recording fertilisation and early developmental success until D-larval stage under controlled conditions. Proteins that were differentially expressed between females showing high or low oocyte quality were identified by nano-liquid chromatography tandem mass spectrometry. Twelve up-accumulated spots associated with low quality oocytes revealed 10 distinct proteins, including vitellogenin — breakdown products and metabolic enzymes. Eight up-accumulated spots from high quality oocytes revealed 6 distinct proteins, including chaperone molecules and...
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Using qualitative and quantitative stakeholder knowledge: examples from European deep-water fisheries - Lorance, Pascal; Agnarsson, Sveinn; Damalas, Dimitrios; Des Clers, Sophie; Figueiredo, Ivone; Gil, Juan; Trenkel, Verena
Stakeholder knowledge was collected through questionnaires and cognitive maps and used to summarize biological, environmental, technical, management, and socio-economic factors for several deep-water fisheries, identifying regional management issues and solutions. The questionnaires and cognitive maps revealed different technical, environmental, and management concerns in these fisheries. Dissatisfaction with management was more at an implementation than a conceptual level, because the existing management measures were mostly considered fit for purpose. Further, catch-and-effort data provided by the fishing industry were used to calculate standardized landings per unit effort. The results suggested different trends over time for three deep-water stocks exploited by the same...
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Ecosystem limits to food web fluxes and fisheries yields in the North Sea simulated with an end-to-end food web model - Heath, M
Equilibrium yields from an exploited fish stock represent the surplus production remaining after accounting for losses due to predation. However, most estimates of maximum sustainable yield, upon which fisheries management targets are partly based, assume that productivity and predation rates are constant in time or at least stationary. This means that there is no recognition of the potential for interaction between different fishing sectors. Here, an end-to-end ecosystem model is developed to explore the possible scale and mechanisms of interactions between pelagic and demersal fishing in the North Sea. The model simulates fluxes of nitrogen between detritus, inorganic nutrient and...
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Horizontal distribution and overlap of planktivorous fish stocks in the Norwegian Sea during summers 1995–2006 - Rong Utne, Kjell; Huse, Geir; Ottersen, Geir; Holst, Jens C.; Zabavnikov, Vladimir; Jacobsen, Jan A.; Óskarsson, Guđmundur J.; Nøttestad, Leif
The Norwegian Sea harbours several large pelagic fish stocks, which use the area for feeding during the summer. The period 1995–2006 had some of the highest biomass of pelagic fish feeding in the Norwegian Sea on record. Here we address the horizontal distribution and overlap between herring, blue whiting and mackerel in this period during the summers using a combination of acoustic, trawl and LIDAR data. A newly developed temperature atlas for the Norwegian Sea is used to present the horizontal fish distributions in relation to temperature. The centre of gravity of the herring distribution changed markedly several times during...
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The rise and fall of the NE Atlantic blue whiting (Micromesistius poutassou) - Payne, Mark; Egan, Afra; Fassler, Sascha; Hatun, Hjalmar; Holst, Jens C.; Jacobsen, Jan A.; Slotte, Aril; Loeng, Harald
The Northeast Atlantic blue whiting (Micromesistius poutassou) stock has undergone striking changes in abundance in the last 15 years. The stock increased dramatically in the late 1990s due to a succession of eight unusually strong year classes and dropped again equally dramatically after 2005 when the recruitment collapsed to former levels. The North Atlantic subpolar gyre has previously been shown to have a strong influence on the behaviour of this stock: synchronous changes in the gyre and recruitment suggest a causal linkage and the possibility of forecasting recruitment. A range of mechanisms are reviewed that may explain these observed changes,...
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Modelling secondary production in the Norwegian Sea with a fully coupled physical/primary production/individual-based Calanus finmarchicus model system - Hjøllo, Solfrid Sætre; Huse, Geir; Skogen, Morten D.; Melle, Webjørn
The copepod Calanus finmarchicus is the dominant species of the meso-zooplankton in the Norwegian Sea, and constitutes an important link between the phytoplankton and the higher trophic levels in the Norwegian Sea food chain. An individual-based model for C. finmarchicus, based on super-individuals and evolving traits for behaviour, stages, etc., is two-way coupled to the NORWegian ECOlogical Model system (NORWECOM). One year of modelled C. finmarchicus spatial distribution, production and biomass are found to represent observations reasonably well. High C. finmarchicus abundance is found along the Norwegian shelf-break in the early summer, while the overwintering population is found along the...
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History and dynamics of the overexploitation of the blackspot sea bream (Pagellus bogaraveo) in the Bay of Biscay - Lorance, Pascal
The blackspot sea bream (Pagellus bogaraveo) used to be a major species in the landings from the Bay of Biscay up to the early 1980s. Nowadays, it is only a minor bycatch. Up to the mid-70s, more than 15 000 tonnes of blackspot sea bream were landed annually in Spanish and French ports. Then, catches declined sharply from 1975 to 1985 and have stayed at low levels ever since. Here, the full history of the fishery collapse is described using time-series of landings since the 1900s. Fishing mortalities of the main demersal stocks (hake, anglerfish, sole) were in the range...
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Comparing copepod time-series in the north of Spain: Spatial autocorrelation of community composition - Bode, Antonio; Alvarez-ossorio, Maria Teresa; Miranda, Ana; López-urrutia, Angel; Valdés, Luis
Four time-series of copepod species biomass in the north of Spain were contrasted to demonstrate spatial autocorrelation of local communities and their responses to short-term local and regional variability in oceanographic conditions. The series represented coastal and oceanic environments along a marked gradient of influence of seasonal upwelling from Galicia to the Mar Cantábrico (S Bay of Biscay), and each one included at least 10 years of continuous data collected at monthly frequency. Community composition (i.e. species number and diversity) was very consistent through the region, but local variations in the presence of new species and the relative proportions of...
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A framework for qualitatively evaluating management plans in a results-based perspective - Rochet, Marie-joelle; Trenkel, Verena; Rice, Jake
Currently many multi-year management plans are being developed either for rebuilding depleted stocks or for avoiding difficult negotiations when management decisions must be revisited on a regular basis. Management plans are commonly evaluated by intensive model simulations that describe the ecological and economic dynamics, and the management loop. Under the results-based management paradigm, the fishing industry or particular fishing sectors will develop their own management plans, potentially leading to a huge number of plans to be evaluated. Guidelines for evaluating the plans on a qualitative level before launching quantitative evaluations will be essential.
Here we propose a framework for evaluating management...
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