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Assessing the sensitivity of bivalve populations to global warming using an individual-based modelling approach ArchiMer
Thomas, Yoann; Bacher, Cedric.
Climate change exposes benthic species populations in coastal ecosystems to a combination of different stressors (e.g. warming, acidification and eutrophication), threatening the sustainability of the ecological functions they provide. Thermal stress appears to be one of the strongest drivers impacting marine ecosystems, acting across a wide range of scales, from individual metabolic performances to geographic distribution of populations. Accounting for and integrating the response of species functional traits to thermal stress is therefore a necessary step in predicting how populations will respond to the warming expected in coming decades. Here, we developed an individual‐based population model using a mechanistic formulation of metabolic processes...
Tipo: Text Palavras-chave: Benthic species; Biogeography; Climate scenario; Dynamic energy budget; Global warming; Phenology; Population dynamics; Temperature tolerance.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00450/56163/57710.pdf
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Effets d’une exposition alimentaire chronique à un mélange environnemental de PCB et PBDE sur les traits d’histoire de vie, la bioénergétique et la dynamique des populations de poissons ArchiMer
Horri, Khaled.
Persistent organic pollutants (POPs) are a broad group of compounds with varying physicochemical and toxic properties. Among POP, polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are two families of hydrophobic compounds sharing some similar environmental properties such as hydrophobicity, persistence, bioaccumulation and toxicity. Previous studies have demonstrated that these compounds could affect fish life-history traits such as survival, growth and reproductive success. However, few studies have focused on environmental situations as most previous works investigated the effect of either single congeners, or single families of molecules among POP, or high concentrations, so that results can hardly be transposed to natural...
Tipo: Text Palavras-chave: Poisson-zèbre; Écotoxicologie; Polluants organiques persistants; Allocation d’énergie; Modes d’action; Dynamique des populations; Populations structurées; Zebrafish; Ecotoxicology; Persistent organic pollutants; Energy allocation; Modes of action; Population dynamics; Structured populations.
Ano: 2018 URL: http://archimer.ifremer.fr/doc/00444/55592/57219.pdf
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La Baie de Seine: Peuplements et especes benthiques en regime perturbe ArchiMer
Cabioch, L; Retiere, C.
The waters of the Seine River are polluted by urban, industrial and agricultural effluents. In addition direct industrial wastes inputs are emptied into the estuary. Within the limits of the Seine Bay program it was not possible to research pollution impacts on every estuarine ecosystem link; so only benthos have been studied. To take time response of organisms into account, the authors have defined indicators or quantitative evaluation of parameters, reflecting physiological state. They have studied population fluctuations caused by natural or man induced effects.
Tipo: Text Palavras-chave: Hydrodynamics; Population dynamics; Population structure; Bioaccumulation; Pollution effects; Marine pollution; Ecosystem disturbance; Benthos.
Ano: 1985 URL: http://archimer.ifremer.fr/doc/1985/acte-1304.pdf
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Evaluation of the bioeconomic sustainability of multi-species multi-fleet fisheries under a wide range of policy options using ISIS-Fish ArchiMer
Pelletier, Dominique; Mahevas, Stephanie; Drouineau, Hilaire; Vermard, Youen; Thebaud, Olivier; Guyader, Olivier; Poussind, Benjamin.
In order to provide reliable scientific advice and support for fisheries management, it is necessary to evaluate the biological and economic sustainability of complex fisheries, such as multi-species multi-fleet fisheries. Existing policy-screening modelling tools are not fully suitable in this purpose due to either an over-simplified description of population dynamics, or due to the lack of consideration of economic aspects. In this paper, we present a package that enables quantitative bioeconomic assessment of management scenarios. Population dynamics is described through spatially- and seasonally-explicit models. Exploitation dynamics is characterized by several fishing activities with specific spatial and seasonal features, and practiced by several...
Tipo: Text Palavras-chave: Policy screening; Natural resource management; Fisheries dynamics; Bioeconomic model; Population dynamics; Complex systems; Simulation tool.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6782.pdf
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Modelling benthic invasion by the colonial gastropod Crepidula fornicata and its competition with the bivalve Pecten maximus . 1. A new 0D model for population dynamics of colony-forming species ArchiMer
Menesguen, Alain; Gregoris, Thomas.
The north-American marine gastropod Crepidula fornicata (Linné 1758), commonly called slipper limpet, has been introduced accidentally in Great Britain, along with American oysters (Crassostrea virginica) at the end of the 19th century. Its spreading, enhanced by oyster transport and international shipping, turned into invasion of a lot of benthic grounds along the North-European coasts. When local conditions are favorable to larval confinement and adult growth, the invasion by very dense populations may deeply change initially sandy or muddy benthic communities into similar “slipper limpet communities”. Competition for space eliminates several species of native infauna, and hampers the survival of some epibenthic bivalves such as the scallop Pecten...
Tipo: Text Palavras-chave: Crepidula fornicata; Invasive species; Benthic gastropod; Colony model; Matching matrix; Pecten maximus; Competition; Population dynamics; Limit cycle.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00415/52601/53491.pdf
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Dynamique des populations marines exploitées. Tome 1. Concepts et modèles ArchiMer
Laurec, Alain; Le Guen, Jean-claude.
This book constitutes the first of a series of three volumes, the purpose of which is to cover the principal methods used in fish population dynamics. It is devoted to the definition of the main concepts, ami the presentation of the usual mathematical models. The second volume will deal with the fitting of the models, and the estimation of parameters. The third will be devoted to sampling problems. These volumes will be recollections of communications presented during ad hoc seminars, hold in Brest (GSG/COB) in 1980 and 1981. The first part deals with the basic concepts related to the two components whose relationship is being described by the population dynamics, namely the fish stock, to its relations with biological populations, and to the partition of...
Tipo: Text Palavras-chave: Pêche; Conservation de la ressource; Modèle mathématique; Dynamique des populations; Gestion de stock; Resource conservation; Mathematical models; Fishery resources; Stock assessment; Population dynamics.
Ano: 1981 URL: https://archimer.ifremer.fr/doc/1981/rapport-1126.pdf
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Crepidula fornicata L. (gastéropode) dans le bassin de Marennes-Oléron : structure, dynamique et production d'une population ArchiMer
Deslous-paoli, Jean-marc.
The reproduction of Crepidula fornicata occurs from the end of February to October. This reproduction determines two periods of juvenile settlement, the first early in June and the second early in October. Because of the lack of distinct cohorts, estimation of production and population dynamics was made according to the location of individuals in the chain. This was confirmed by the agreement between the growth rings of the shells and individual location in the chain. The main chain accounted for 80 per cent of individuals, the others being isolated or in collateral chains. The curvilinear growth of Crepidula fornicata in the bay of Marennes-Oléron follows the equation Le = 81.01 (1-e (-0.400 8(t-0,01)). The average yearly production from a population of...
Tipo: Text Palavras-chave: Production; Marennes-Oléron; Crepidula fornicata; Dynamique de population; Population dynamics; Production; Marennes-Oléron; Crepidula fornicata.
Ano: 1985 URL: http://archimer.ifremer.fr/doc/1985/publication-2956.pdf
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What can exploratory modelling tell us about the ecobiology of European sea bass ( Dicentrarchus labrax ): a comprehensive overview ArchiMer
Lopez, Romain; De Pontual, Helene; Bertignac, Michel; Mahevas, Stephanie.
European sea bass, Dicentrarchus labrax, is a highly valuable species in Europe, both for aquaculture in the Mediterranean Sea and for commercial and recreational fisheries in the North East Atlantic Ocean. Subjected to increasing fishing pressure, the wild population has recently experienced significant recruitment fluctuation as well as a northward extension of its distribution area in the North Sea. While the nature of the ecological and/or physiological processes involved remains unresolved, ontogenetic habitat shifts and adult site fidelity could increase the species’ vulnerability to climate change and overfishing. As managers look for expert information to propose management scenarios leading to sustainable exploitation, exploratory modelling...
Tipo: Text Palavras-chave: Population dynamics; Essential habitats; Connectivity; Bioenergetic modeling; Phenotypic plasticity; Life cycle adaptation.
Ano: 2015 URL: http://archimer.ifremer.fr/doc/00341/45258/44699.pdf
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Geographic variability of sardine dynamics in the Iberian Biscay region ArchiMer
Silva, A.; Skagen, D. W.; Uriarte, A.; Masse, Jacques; Santos, M. B.; Marques, V.; Carrera, P.; Beillois, Pierre; Pestana, G.; Porteiro, C.; Stratoudakis, Y..
The spatio-temporal variability in the distribution, demographic structure, recruitment, and mortality of sardine within the Iberian Biscay region is described using area-disaggregated data collected during acoustic surveys and at ports since the mid-1980s. Multiple regression models were used to describe log numbers-at-age obtained annually in ten areas covered by three surveys to test the existence of geographic differences in selectivity-at-age, recruitment strength, and mortality and to infer plausible migration routes. Within Iberian waters, sardine biomass was mainly concentrated off western Portugal and the Gulf of Cadiz. In the Bay of Biscay, biomass levels were comparable with those off western Portugal. Recruitment was localized in a few areas...
Tipo: Text Palavras-chave: Stock structure; Small pelagic fish; Population dynamics; Iberian Peninsula.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/publication-6459.pdf
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Modelling and numerical simulations of larval migration of the sole (Solea solea (L.)) of the Bay of Biscay. Part 1: modelling ArchiMer
Ramzi, Azeddine; Arino, Ovide; Koutsikopoulos, Constantine; Boussouar, Ahmed; Lazure, Pascal.
A spatio-temporal model describing the dynamics of a population of sole is presented. The model is an extension to a 2D-space structure of a 1D model published by the three first authors. Spatial migration is modelled by an advection-diffusion second order operator with constant coefficients. The physical domain is represented by a half-plane with the coast as its boundary. A formula for estimating the proportion of eggs reaching the juvenile stage, depending upon climatic, transport, growth and mortality processes, is derived. Numerical results are deferred to elsewhere.
Tipo: Text Palavras-chave: Recruitment; Diffusion and advection processes; Population dynamics; Recrutement; Processus de diffusion et d'advection; Dynamique de population.
Ano: 2001 URL: https://archimer.ifremer.fr/doc/2001/publication-531.pdf
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A Bayesian state-space model to estimate population biomass with catch and limited survey data: application to the thornback ray (Raja clavata) in the Bay of Biscay ArchiMer
Marandel, Florianne; Lorance, Pascal; Trenkel, Verena M..
The thornback ray (Raja clavata) in the Bay of Biscay is presumed to have declined during the 20th Century. To evaluate this decline and estimate biomass trajectories, a hypothetical catch time series was created for the period 1903-2013. A Bayesian state-space biomass production model with a Schaefer production function was fitted to the hypothetical catch time series and to a shorter research vessel Catch Per Unit Eeffort (CPUE) time series (1973-2013, with missing years). A censored likelihood made it possible to obtain biomass estimates without a CPUE time series or only with an estimate of biomass depletion. A simulation-estimation approach showed a high sensitivity of results to the prior for the intrinsic growth rate. The model provided biomass...
Tipo: Text Palavras-chave: Population dynamics; Stock assessment; Data poor; Censored data; Bayes; Thornback ray; State-space model.
Ano: 2016 URL: http://archimer.ifremer.fr/doc/00359/47032/46947.pdf
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Dynamique des populations de poissons. ArchiMer
Daget, J..
The author explains that the population dynamics study, descriptive and explicative way, the changes which happen in the structure and the parameters (growth rate, sex ratio, fecundity, mortality etc.) of a monospecific population, by the use of mathematical models which permit prediction and simulation. If the fish population is not exploited, it is necessary to sample it directly and obtain samples representative of the demographical structure by experimental fishing (like electrical fishing) or by selectivity corrections. If the population is exploited, often the exploited phasis of the stock is only studied from samples representative of the whole captures. Now it happens that there is an important difference between the demographical structure of the...
Tipo: Text Palavras-chave: Pisces; Catch statistics; Mathematical models; Population dynamics.
Ano: 1976 URL: http://archimer.ifremer.fr/doc/1976/publication-1999.pdf
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Coastal phytoplankton community dynamics and coexistence driven by intragroup density-dependence, light and hydrodynamics ArchiMer
Barraquand, F.; Picoche, C.; Maurer, Daniele; Carassou, L.; Auby, Isabelle.
Phytoplanktonic communities maintain a high diversity in a seemingly homogeneous environment, competing for the same set of resources. Many theories have been proposed to explain this coexistence despite likely competition, such as contrasted responses to temporal environmental variation. However, theory has developed at a faster pace than empirical evaluation using field data, which requires inferring drivers of community dynamics from observational time series. Here, we combine autoregressive models with a data set spanning more than 20 years of phytoplankton counts every two weeks, together with nutrients and physical variables. By comparing models dominated by nutrients or physical variables (hydrodynamics and climate), we first explore which abiotic...
Tipo: Text Palavras-chave: Competition; Diatoms; Dinoflagellates; Hydrodynamics; Interactions; MAR; Mutualism; Network; Population dynamics; Seasonality; Time series.
Ano: 2018 URL: https://archimer.ifremer.fr/doc/00461/57257/59285.pdf
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Dynamique des populations de palourdes japonaises (Ruditapes philippinarum) dans le bassin d'Arcachon : conséquences sur la gestion des populations exploitées ArchiMer
Dang, Cecile.
The Manila clam Ruditapes philippinarum was introduced into Arcachon Bay at the beginning of the 1980s for aquaculture purposes. It rapidly naturalized in all intertidal flats of the lagoon. Nowadays, Arcachon Bay ranks at the first French place in terms of exploitable stock. However, recent stock assessments have shown an unbalance size structure with a deficit in juvenile and adult clams (> 38 mm shell length). These alarming patterns asked many questions on the sustainability of Manila clam populations within Arcachon Bay and have motivated the present thesis. This study aimed to better understand the population dynamics of this species and also some factors controlling this dynamic. The final objective was to improve the Manila clam fishing...
Tipo: Text Palavras-chave: Management; Trophic sources; Pathogens; Population dynamics; Ruditapes philippinarum; Gestion; Resources trophiques; Pathogènes; Dynamique de population; Ruditapes philippinarum.
Ano: 2009 URL: http://archimer.ifremer.fr/doc/2009/these-7382.pdf
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Relations entre l’état d’une ressource et son exploitation via la compréhension et la formalisation des interactions de socio-écosystèmes. Application à la palourde japonaise (Venerupis philippinarum) du bassin d’Arcachon. ArchiMer
Caill-milly, Nathalie.
Significant component of the marine benthic ecosystem, exploited bivalves are mainly located inside the coastal area, which temporal and spatial features generate natural population fluctuations and contribute to considerable biomass and demographic structure changes added to anthropogenic activities’ effects (fishing, pollution,…). Understanding of the relationships between the species, its environment and its exploitation is crucial and their formalization, including for management purposes, requires development of mathematical models that aim at describing the functioning of the system, to explain the observed phenomenon in terms of cause and effect or predict effects of new causes. Originating from venerid culture trials carried out in France in the...
Tipo: Text Palavras-chave: Bivalve; Morphométrie; Allométrie; Dynamique des populations; Système dynamique; Gestion; Palourde japonaise; Venerupis philippinarum; Bivalve; Morphometry; Allometry; Population dynamics; Dynamic system; Management; Manila clam; Venerupis philippinarum.
Ano: 2012 URL: http://archimer.ifremer.fr/doc/00139/25034/23143.pdf
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Les pêcheries de buccin (Buccinum undatum L. : Gastropoda) du Golfe Normand-Breton. Eléments de gestion de la ressource ArchiMer
Santarelli Chaurand, Leonardo.
The whelk (Buccinum undatum) fisheries in the gulf between Brittany and Normandy have grown quickly over the past ten years. In 1983, 35 potters and 14 dories from Granville harbour and the Blainville maritime station landed 3,900 tonnes of whelk (for a value of 7.5 million francs). In spite of a sharp drop in profitability, the number of fishers is still growing. This study aimed to provide decision-making elements for rational management of the resource : stock abundance, catches per unit effort, mortality due to fishing effort and biological properties. In order to assess the impact of measures to organise the fishing effort on total catches in balance, two predictive models were used: Pella and Tomlinson's generalised production model and Ricker's...
Tipo: Text Palavras-chave: Bio economic modelling; Sampling; Population dynamics; Stock management; Mollusc; Modélisation bioéconomique; Echantillonnage; Dynamique de populations; Gestion de stocks; Mollusque.
Ano: 1985 URL: http://archimer.ifremer.fr/doc/1985/these-1203.pdf
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Peche de l'anchois (Engraulis encrasicholus ) dans le golfe de Gascogne et sur le littoral atlantique de Galice depuis 1920. Variations quantitatives. ArchiMer
Junquera, Susana.
Using the fishing records from the most relevant ports of the Cantabrian and Galician coasts, th history of the anchovy (Engraulis encrasicholus ) fishery in this area is reconstituted. The crisis observed and the variations in the fishing areas throughout the time are analyzed. An estimation of the age classes composition in the catches founded on commercial classification data can be made. The hypothesis of existence of a core population in the Southern part of the Bay of Biscay is presented and that only under certain advantageous condition the expansion of this species throughout all the Cantabrian Sea was possible.
Tipo: Text Palavras-chave: Pisces; Age composition; Population dynamics; Catch/effort; Fishery statistics.
Ano: 1984 URL: http://archimer.ifremer.fr/doc/1984/publication-1795.pdf
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Impact of the reproduction dynamics on genetic variation in the European flat oyster Ostrea edulis ArchiMer
Lapegue, Sylvie; Taris, Nicolas; Lallias, Delphine; Bonhomme, Francois; Boudry, Pierre.
The European flat oyster (Ostrea edulis L.) is a marine bivalve whose natural geographical distribution ranges along the European Atlantic coast from Norway to Morocco, in addition to the Mediterranean and Black Sea. The latest results obtained on the genetic differentiation between these populations have led us to pursue studies at a finer scale, in order to estimate the effective number of breeders and the temporal dynamics of reproduction and, more specially, recruitment. Several experiments were performed to document (1) the variance in allele frequencies during a natural settlement period; (2) the paternal contribution to fertilization by analyzing larvae sampled at the brooding stage within individual females; (3) the variance of individual...
Tipo: Text Palavras-chave: Ostrea edulis; Oyster; Sexual reproduction; Population dynamics; Oyster culture; Inbreeding; Heterosis; Genetic isolation; Genetic diversity; Breeding success; Biological fertilization.
Ano: 2004 URL: http://archimer.ifremer.fr/doc/2004/acte-3436.pdf
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Does the concept of spawning per recruit make sense? ArchiMer
Rochet, Marie-joelle.
Density dependence means that exploited fish populations exhibit earlier maturity, a faster growth rate, increased fecundity and reduced egg size. Here, the consequences of these effects on population dynamics, the estimation of spawning biomass per recruit and associated biological reference points are examined by a simulation model. The model is a self-regenerating model in which the population parameters (age at maturity, growth, fecundity, egg size) vary according to three classes of population abundance. Early life stages are characterized by a size-dependent growth and mortality model. It is concluded that spawning per recruit is an ambiguous concept because, if density dependence occurs in the adult population, the spawning biomass of a cohort is...
Tipo: Text Palavras-chave: Teleost fishes; Population dynamics; Life history; Density dependence; Biological reference points.
Ano: 2000 URL: http://archimer.ifremer.fr/doc/2000/publication-485.pdf
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The collapse and recovery potential of carbon sequestration by baleen whales in the Southern Ocean ArchiMer
Durfort, Anaelle; Mariani, Gael; Troussellier, Marc; Tulloch, Vivitskaia; Mouillot, David.
Limiting climate warming below 2°C requires both reducing anthropic greenhouse gas emissions and sequestering more atmospheric carbon. Natural Climate Solutions (NCS) rely on the ability of ecosystems to capture and store carbon. Despite the important role of marine megafauna on the ocean carbon cycle, its potential as a NCS has not yet been explored. Here, we quantify the amount of carbon potentially sequestered by five baleen whale species across the Southern Hemisphere between 1890 and 2100 through both the sinking of carcasses after natural death and the fertilisation of phytoplankton by nutrients in faeces. At their pre-exploitation abundances, the five whales could sequester 10.6 106 tonnes of carbon per year (tC.yr-1) but this natural carbon sink...
Tipo: Text Palavras-chave: Natural Climate Solutions; Climate change; Population dynamics; Modelling; Krill.
Ano: 2021 URL: https://archimer.ifremer.fr/doc/00682/79434/82038.pdf
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