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ArchiMer, Institutional Archive of Ifremer (French Research Institute for Exploitation of the Sea) (8.998 recursos)
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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Mostrando recursos 1 - 20 de 49

1. Black scabbardfish, Aphanopus carbo, in the northeast Atlantic: distribution and hypothetical migratory cycle - Farias, Ines; Morales-nin, Beatriz; Lorance, Pascal; Figueiredo, Ivone
The biology, ecology, and dynamics of the deep-sea teleost black scabbardfish in the northeast Atlantic are reviewed. The black scabbardfish is a commercial bathypelagic species found in the NE Atlantic mostly from Iceland to the Canary Islands and Western Sahara, at depths from 800 to 1300 m. The spatial structure of its population is still uncertain, although the existence of one single stock that migrates around the NE Atlantic driven by feeding and reproduction is the most likely hypothesis consistent with available data. This review is based on data from commercial fisheries off the Faroe Islands, Hatton Bank, the west...

2. Detection of microseismic compressional (P) body waves aided by numerical modeling of oceanic noise sources - Obrebski, Mathias; Ardhuin, Fabrice; Stutzmann, Eleonore; Schimmel, Martin
Among the different types of waves embedded in seismic noise, body waves present appealing properties but are still challenging to extract. Here we first validate recent improvements in numerical modeling of microseismic compressional (P) body waves and then show how this tool allows fast detection and location of their sources. We compute sources at similar to 0.2 Hz within typical P teleseismic distances (30-90 degrees) from the Southern California Seismic Network and analyze the most significant discrete sources. The locations and relative strengths of the computed sources are validated by the good agreement with beam-forming analysis. These 54 noise sources...

3. Combining quantitative and qualitative models to identify functional groups for monitoring changes in the Bay of Biscay continental shelf exploited foodweb - Lassalle, Geraldine; Pasqual, Jean-sebastien Nelva; Boet, Philippe; Rochet, Marie-joelle; Trenkel, Verena; Niquil, Nathalie
To develop and implement ecosystem-based management, it is critical to monitor foodweb components or functional groups which are robust to uncertainty in ecosystem structure and functioning yet sensitive to changes. To select such functional groups for the Bay of Biscay continental shelf, both quantitative and qualitative foodweb models were developed. First, functional groups for which predictions of directions of change following an increase in primary productivity, prey or predators, or in fishing activities were identical across alternative qualitative model structures were identified. Second, the robustness to model type was assessed by comparing qualitative predictions with quantitative Ecopath model results. The...

4. Development of a 3D Coupled Physical-Biogeochemical Model for the Marseille Coastal Area (NW Mediterranean Sea): What Complexity Is Required in the Coastal Zone? - Fraysse, Marion; Pinazo, Christel; Faure, Vincent Martin; Fuchs, Rosalie; Lazzari, Paolo; Raimbault, Patrick; Pairaud, Ivane
Terrestrial inputs (natural and anthropogenic) from rivers, the atmosphere and physical processes strongly impact the functioning of coastal pelagic ecosystems. The objective of this study was to develop a tool for the examination of these impacts on the Marseille coastal area, which experiences inputs from the Rhone River and high rates of atmospheric deposition. Therefore, a new 3D coupled physical/biogeochemical model was developed. Two versions of the biogeochemical model were tested, one model considering only the carbon (C) and nitrogen (N) cycles and a second model that also considers the phosphorus (P) cycle. Realistic simulations were performed for a period...

5. Isotopic Diversity Indices: How Sensitive to Food Web Structure? - Brind'Amour, Anik; Dubois, Stanislas
Recently revisited, the concept of niche ecology has lead to the formalisation of functional and trophic niches using stable isotope ratios. Isotopic diversity indices (IDI) derived from a set of measures assessing the dispersion/distribution of points in the δ-space were recently suggested and increasingly used in the literature. However, three main critics emerge from the use of these IDI: 1) they fail to account for the isotopic sources overlap, 2) some indices are highly sensitive to the number of species and/or the presence of rare species, and 3) the lack of standardization prevents any spatial and temporal comparisons. Using simulations...

6. Gene expression pattern of digestive and antioxidant enzymes during the larval development of reared Atlantic bluefin tuna (ABFT), Thunnus thynnus L. - Mazurais, David; Coves, Denis; Papandroulakis, Nikos; Ortega, Aurelio; Desbruyeres, Elisabeth; Huelvan, Christine; Le Gall, Marie-madeleine; De La Gandara, Fernando; Cahu, Chantal
The aim of this study was to determine whether mortality observed during the larval development of reared bluefin tuna (Thunnus thynnus) could be related to improper expression profiles of key genes involved in digestive or antioxidant response capabilities. Tuna larvae were sampled at hatching, 2, 5, 10, 15 and 20 dph (days post hatching) for the relative quantification of transcripts encoded by genes involved in digestive [trypsinogen 1 (TRYP1), alpha-amylase (AMY), aminopeptidase N (ANPEP)] and antioxidant [catalase (CAT)] functions. The levels of expression of ANPEP related to the development and maturation of intestinal function increased from 5 to 20 dph....

7. The relative importance of environmental stochasticity, interspecific interactions, and observation error: Insights from sardine and anchovy landings - Hosack, Geoffrey R.; Trenkel, Verena; Dambacher, Jeffrey M.
Long-term time series of sardine and anchovy landings often suggest negative dependence between these species, and an array of mechanisms have been proposed as explanations. We reduce these propositions to four basic hypotheses of (1) independence, (2) correlated process noise, (3) interspecific interactions, and (4) correlated observational error. We use a Bayesian approach to develop priors for parsimonious state space models with both process noise and observation error that represent each of these hypotheses, and apply this approach to five long-term time series of landings collected from the Pacific and Atlantic Oceans. Model comparison criteria suggest that the hypothesis of...

8. Supporting Fisheries Management by Means of Complex Models: Can We Point out Isles of Robustness in a Sea of Uncertainty? - Gasche, Loic; Mahevas, Stephanie; Marchal, Paul
Ecosystems are usually complex, nonlinear and strongly influenced by poorly known environmental variables. Among these systems, marine ecosystems have high uncertainties: marine populations in general are known to exhibit large levels of natural variability and the intensity of fishing efforts can change rapidly. These uncertainties are a source of risks that threaten the sustainability of both fish populations and fishing fleets targeting them. Appropriate management measures have to be found in order to reduce these risks and decrease sensitivity to uncertainties. Methods have been developed within decision theory that aim at allowing decision making under severe uncertainty. One of these...

9. A quantitative estimate of the function of soft-bottom sheltered coastal areas as essential flatfish nursery habitat - Trimoreau, E.; Archambault, Benoit; Brind'Amour, Anik; Lepage, Mario; Guitton, Jerome; Le Pape, Olivier
Essential fish habitat suitability (EFHS) models and geographic information system (GIS) were combined to describe nursery habitats for three flatfish species (Solea solea, Pleuronectes platessa, Dicologlossa cuneata) in the Bay of Biscay (Western Europe), using physical parameters known or suspected to influence juvenile flatfish spatial distribution and density (i.e. bathymetry, sediment, estuarine influence and wave exposure). The effects of habitat features on juvenile distribution were first calculated from EFHS models, used to identify the habitats in which juvenile are concentrated. The EFHS model for S. solea confirmed previous findings regarding its preference for shallow soft bottom areas and provided new...

10. A hierarchical Bayesian model for embedding larval drift and habitat models in integrated life cycles for exploited fish - 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...

11. How Do Fishing and Environmental Effects Propagate Among and Within Functional Groups? - Rochet, Marie-joelle; Collie, Jeremy S.; Trenkel, Verena
Competition and predation can play different roles in mediating the influence of external pressures, such as fishing or environmental variations, on marine communities. Pressure effects propagate through food webs along predation links. These predator-prey interactions may result in trophic cascades, but they can be buffered by competitive interactions. We investigated these mechanisms by taking a functional-group approach. Are functional groups affected by external pressures in a predictable way? Within functional groups, do all species respond in the same way, or does competitive release allow for compensation among species? We constructed a simple community model, with functional groups connected by predation...

12. Interannual variability of fisheries economic returns and energy ratios is mostly explained by gear type - Trenkel, Verena; Daures, Fabienne; Rochet, Marie-joelle; Lorance, Pascal
According to portfolio theory applied to fisheries management, economic returns are stabilised by harvesting in a portfolio stocks of species whose returns are negatively correlated and for which the portfolio economic return variance is smaller than the sum of stock specific return variances. Also, variability is expected to decrease with portfolio width. Using a range of indicators, these predictions were tested for the French fishing fleets in the Bay of Biscay (Northeast Atlantic) during the period 2001–2009. For this, vessels were grouped into eight fishing fleets based on the gears used and exploited species were grouped into five functional groups....

13. Gene-associated markers provide tools for tackling illegal fishing and false eco-certification - Nielsen, Einar E.; Cariani, Alessia; Mac Aoidh, Eoin; Maes, Gregory E.; Milano, Ilaria; Ogden, Rob; Taylor, Martin; Hemmer-hansen, Jakob; Babbucci, Massimiliano; Bargelloni, Luca; Bekkevold, Dorte; Diopere, Eveline; Grenfell, Leonie; Helyar, Sarah; Limborg, Morten T.; Martinsohn, Jann T.; Mcewing, Ross; Panitz, Frank; Patarnello, Tomaso; Tinti, Fausto; Van Houdt, Jeroen K. J.; Volckaert, Filip A. M.; Waples, Robin S.; Carvalho, Gary; Albin, Jan Ej; Vieites Baptista, Juan M; Barmintsev, Vladimir; Bautista, Jose M.; Bendixen, Christian; Berge, Jean-pascal; Blohm, Dietmar; Cardazzo, Barbara; Diez, Amalia; Espineira, Montserrat; Geffen, Audrey J.; Gonzalez, Elena; Gonzalez-lavin, Nerea; Guaniero, Ilaria; Jerome, Marc; Kochzius, Marc; Krey, Grigorius; Mouchel, Olivier; Negrisolo, Enrico; Piccinetti, Corrado; Puyet, Antonio; Rastorguev, Sergey; Smith, Jane P; Trentini, Massimo; Verrez-bagnis, Veronique; Volkov, Alexander; Zanzi, Antonella
Illegal, Unreported and Unregulated fishing has had a major role in the overexploitation of global fish populations. In response, international regulations have been imposed and many fisheries have been 'eco-certified' by consumer organizations, but methods for independent control of catch certificates and eco-labels are urgently needed. Here we show that, by using gene-associated single nucleotide polymorphisms, individual marine fish can be assigned back to population of origin with unprecedented high levels of precision. By applying high differentiation single nucleotide polymorphism assays, in four commercial marine fish, on a pan-European scale, we find 93-100% of individuals could be correctly assigned to...

14. Mixed fisheries management: protecting the weakest link - Batsleer, Jurgen; Poos, J. J.; Marchal, Paul; Vermard, Youen; Rijnsdorp, A. D.
North Sea cod Gadus morhua stock is outside safe biological limits, and total allowable catch (TAC) management has proved ineffective to rebuild the stock. The European Commission is considering the imposition of a discard ban to preserve vulnerable and economically important fish stocks. We explored the potential effects of a discard ban in mixed fisheries management using the French mixed fisheries in the Eastern English Channel as a model system. We examined in particular the performance of 2 different management scenarios: (1) individual quota management with a tolerance for discarding and (2) individual quota management in combination with a discard...

15. Multiplex PCR sets of novel microsatellite loci for the great scallop Pecten maximus and their application in parentage assignment - Morvezen, Romain; Cornette, Florence; Charrier, Gregory; Guinand, Bruno; Lapegue, Sylvie; Boudry, Pierre; Laroche, Jean
We report the isolation, development and multiplex optimisation of 12 new microsatellite loci for the great scallop, Pecten maximus. Diversity was moderate to high, with number of alleles ranging from 4 to 20 and observed heterozygosity between 0.28 and 0.88. Progeny produced in a commercial hatchery was used to test locus power for parentage assignment. The percentage of offspring that was unambiguously assigned to a unique pair of parents was 97% (software package CERVUS-COLONY). Parentage assignment revealed that 22% of the studied progeny resulted from unplanned crosses. Effective population size of the study progeny was also estimated. Our study illustrates...

16. Oyster sex determination is influenced by temperature - First clues in spat during first gonadic differentiation and gametogenesis - Santerre, Christelle; Sourdaine, Pascal; Marc, Nicolas; Mingant, Christian; Robert, Rene; Martinez, Anne-sophie
The sex-determining system of Crassostrea gigas is still poorly known, especially regarding the potential influence of temperature. In order to address this question, mRNA expressions of actors of the molecular cascade (Cg-DMI, Cg-SoxE, Cg-beta-catenin, Cg-Foxl2/Cg-FoxI2os) and of Oyvlg, a germ cell marker, were investigated by real-time PCR in spat grown at different temperatures (18, 22, 25 and 28 degrees C). In parallel, gonadic differentiation, gametogenesis and sex ratios were assessed by histology at each of these temperatures. Whatever the temperature, Cg-DMI, Cg-SoxE, Cg-beta-catenin and Oyvlg expressions peaked at the same developmental stage, always after Cg-Foxl2/Cg-Foxl2os (around 40-44 dpf for spat...

17. The challenge of domestication of bluefin tuna Thunnus thynnus: highlights of the selfdott project from 2008-2009 - De La Gandara, Fernando; Mylonas, Constantinos C.; Coves, Denis; Bridges, Christopher R.; Belmonte Rios, Antonio; Vassallo-agius, Robert; Rosenfeld, Hanna; Medina, Antonio; Demetrio, G; Falcon, Jack; Sveinsvoll, K; Ghysen, Alain; Deguara, S

18. 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...

19. 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....

20. 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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