Éditeur(s) : Elsevier
Résumé : Changes in biodiversity may disrupt the ecological functions performed by species assemblages. Hence, we urgently need to examine the implications of biodiversity loss not only in terms of species conservation but also in terms of sustainability of ecosystem services. The ability of protected areas to maintain local species richness has been clearly demonstrated. However, preserving goods and services provided by ecosystems requires not only the conservation of species richness but also the conservation of the most 'original' species, i.e. the ones with the highest average rarity of their attributes which are likely to perform some unique functions in ecosystems. We proposed a new conservation of biological originality (CBO) index as well as associated randomization tests to quantify the ability of piotected areas to maintain viable populations for the most original species. As an application, we used long-term fisheries data collected in the Bonifacio Strait Natural Reserve (BSNR) to determine the species which benefited from the protection reinforcement in 1999. We also estimated a set of 14 ecomorphological functional traits on the 37 fish species caught in the BSNR and we obtained a functional originality value for each species. As a result, we found that functional originality was significantly protected in the fish assemblage of the BSNR: species with the most original functional trait combinations became more abundant after 1999. Our finding suggests that protecting most original species is an insurance against functional diversity erosion in the BSNR. More generally, our new index can be used to test whether protected areas may protect preferentially the most original species and whether restorative management promotes the reestablishment of the most original species with particular habitat requirements. (c) 2008 Elsevier Ltd. All rights reserved.
Biological Conservation (0006-3207) (Elsevier), 2008-06 , Vol. 141 , N. 6 , P. 1569-1580

Droits : 2008 Elsevier Ltd All rights reserved.
http://archimer.ifremer.fr/doc/2008/publication-4480.pdf
DOI:10.1016/j.biocon.2008.04.002
http://archimer.ifremer.fr/doc/00000/4480/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The aim of this study was to establish a new QuEChERS (quick, easy, cheap, effective, rugged and safe) method coupled to gas chromatography-mass spectrometry (GC-MS) detection for the evaluation of the pesticide biodistribution in specific maternal and fetal tissues. This method was validated for the quantification of pesticides such as chlorotriazines (atrazine, simazine and propazine), their chlorinated metabolites (DIA, DEA and DACT). This new QuEChERS method was developed to facilitate extraction from small tissues such as fetal tissues (mean value: 200mg). The limits of detection, quantification, recovery, precision and accuracy were evaluated for different tissues (liver and brain) and blood. LOD and LOQ ranged between 0.34 and 3.27 ng/g and 1.04 to 9.91 ng/g, respectively. Recovery exceeded 80% for all pesticides, except DACT, with an associated RSD<15%. Precision and accuracy satisfied the criteria usually applied in the validation of bioanalytical methods. The results obtained indicate that this technique is suitable for use in studies of the biodistribution of pesticides in fetal tissues and can be used to evaluate the risk of exposure to pesticides during gestation.
ISSN: 0731-7085

hal-01122837
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01122837
PUBMED : 25497890
DOI : 10.1016/j.jpba.2014.10.035

Éditeur(s) : HAL CCSD The Company of Biologists
Résumé : International audience
The ability to produce sound has been known for decades inBalistidae. Sounds of many species have been recorded and a varietyof sound-producing mechanisms have been proposed, includingteeth stridulation, collision of the buccal teeth and movements of thefins. The best-supported hypothesis involves movements of thepectoral fin against the lateral part of the swimbladder, called adrumming membrane. In this study, we describe for the first time thesounds made by the blackbar triggerfish Rhinecanthus aculeatus,which are like short drum rolls with an average duration of 85 ms,193 Hz dominant frequency and 136 dB SPL level at 3 cm distance.The sounds are a series of pulses that result from alternate sweepingmovements of the right and left pectoral fins, which push a system ofthree scutes that are forced against the swimbladder wall. Pulses fromeach fin occur in consecutive pairs. High-speed videos indicate thateach pulse consists of two cycles. The first part of each cyclecorresponds to the inward buckling of the scutes, whereas the secondpart of the cycle corresponds to an apparent passive recoil of thescutes and swimbladder wall. This novel sound productionmechanism is probably found in many members of Balistidaebecause these peculiar scutes occur in other species in the family.Comparison of sound characteristics from fishes of different sizesshows that dominant frequency decreases with size in juveniles butnot in adults.KEY WORDS: Acoustic, Communication, Swimbladder
ISSN: 00220949

hal-01472506
https://hal-univ-perp.archives-ouvertes.fr/hal-01472506
DOI : 10.1242/jeb.146514

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : International audience
Context : Functional - structural models (FSM) of tree growth have great potential in forestry, but their development, calibration and validation are hampered by the difficulty of collecting experimental data at organ scale for adult trees. Due to their simple architecture and morphological properties, " model plants " such as Cecropia sciadophylla are of great interest to validate new models and methodologies, since exhaustive descriptions of their plant structure and mass partitioning can be gathered. * Aims : Our objective was to develop a model-based approach to analysing the influence of environmental conditions on the dynamics of trophic competition within C. sciadophylla trees. * Methods : We defined an integrated environmental factor that includes meteorological medium-frequency variations and a relative index representing the local site conditions for each plant. This index is estimated based on model inversion of the GreenLab FSM using data from 11 trees for model calibration and 7 trees for model evaluation. * Results : The resulting model explained the dynamics of biomass allocation to different organs during the plant growth, according to the environmental pressure they experienced. * Perspectives : By linking the integrated environmental factor to a competition index, an extension of the model to the population level could be considered.
ISSN: 1286-4560

hal-00780347
https://hal-ecp.archives-ouvertes.fr/hal-00780347
https://hal-ecp.archives-ouvertes.fr/hal-00780347/document
https://hal-ecp.archives-ouvertes.fr/hal-00780347/file/Letort2011AFS.pdf
DOI : 10.1007/s13595-011-0131-x

Éditeur(s) : HAL CCSD Station Biologique
Résumé : International audience
From fish samplings (rotenone: 6 February 2002 & 13 May 2003; boxtraps: January 2008 to July 2009) in amangrove lagoon, the demographic structure, reproductive period and diet of Lophogobius cyprinoides were studied.Individual fish were measured (< 1 mm), weighed (± 0.01 g), and sexed by observing the urogenital papilla, sex-ratios andtotal length (TL)-standard length and length-mass relationships were calculated. Five individuals per size class (2 mm) wereused to study sexual maturity by macroscopic observation of gonad structure with a sexual maturity scale, and diet byqualitative and quantitative examination of digestive tract contents and calculation of the following indices: levels offullness and vacuity; occurrence, number, and point frequencies of various food items, and quality of nutrition. Growth isisometric and sexual dimorphism in favor of males (78 vs. 64 mm), demographic structure (18 ≤ TL ≤ 78 mm) and conditionevolved over time, with a distinct femininization of the population. Sexual inversion appeared from 46 mm onward, andtotal masculinization at 72 mm. Protogynous hermaphrodism is advantageous in a sedentary, subcryptobenthic species thatis reproductively active almost throughout the year. The species has an omnivorous diet specialized in copepods and plants
ISSN: 0007-9723

hal-00746079
https://hal.univ-antilles.fr/hal-00746079

Éditeur(s) : EDP Sciences
Résumé : The necessity to move from a traditional fishery management to an ecosystem approach is now acknowledged. Indicators are required to support the development of this approach. For example, community indicators have been proposed to assess the impact of fishing. We tested here the applicability of one such community indicator, the abundance-biomass comparison (ABC method), as a measure of the impact of bottom trawling (years of sampling: 2001 and 2003) on the benthic invertebrates-typically starfishes, crabs, squat lobsters, shrimps and large hard-shelled molluscs-of "Grande Vasiere", a major French fishing zone, in the Bay of Biscay. The ABC method is generally used as an impact indicator for different types of physical, biological and anthropogenic disturbances on benthic communities. This method is based on the assumption that increasing disturbance shifts communities from dominance by large-bodied species with low turnover rates toward dominance by small-bodied species with high turnover rates. At less disturbed areas the average biomass of individuals is greater than at more heavily disturbed areas. The ABC method measures this effect by comparing the ranked distributions of abundance and biomass within a given community. We applied the ABC method and compared the size structure and the species diversity at two areas exposed to moderate and high bottom trawl effort. Species diversity was lower in the most exploited area. The highly trawled area was dominated by opportunistic organisms, mainly one species of swimming crab Liocarcinus depurator, one species of squat lobster Munida rugosa and Norway lobsters Nephrops norvegicus, which are large-bodied species. Consequently, the results of the ABC method were inconsistent with the theoretical expectation for these particular macrofaunal communities and the measured levels of fishing intensity.
La nécessité de passer d'une gestion monospécifique des pêches à une approche écosystémique est largement reconnue. Pour mettre en place une telle approche, des indicateurs ont été proposés afin d'estimer l'impact de la pêche sur les communautés. Nous avons testé l'efficacité de l'un de ces indicateurs, la comparaison abondance-biomasse (méthode ABC), pour mesurer l'impact du chalutage de fond (année d'échantillonnage : 2001 et 2003) sur les communautés de la macrofaune benthique de la Grande Vasière, golfe de Gascogne (typiquement des crabes, étoiles de mer, des galathées, de gros mollusques à coquille dure). La méthode ABC est généralement utilisée comme un indicateur d'impact de différents types de perturbations physiques, biologiques et anthropiques sur les communautés benthiques. Cette méthode est basée sur l'hypothèse qu'un régime de perturbation croissant entraîne une modification de la structure des communautés qui deviennent graduellement dominées par des espèces opportunistes de petite taille caractérisées par un renouvellement rapide. Dans une communauté modérément perturbée, la biomasse moyenne des individus est ainsi plus grande que dans une communauté fortement perturbée. La méthode ABC mesure cet effet en comparant les distributions en biomasse et densité dans chaque communauté. Nous avons appliqué la méthode ABC et étudié la structure en taille et la diversité spécifique des communautés benthiques en comparant deux zones, l'une soumise à un effort de pêche modéré et l'autre à un important effort de pêche. La diversité spécifique était plus faible sur les sites fortement chalutés. Ces sites étaient dominés par des organismes opportunistes de grande taille, principalement une espèce de crabe nageur Liocarcinus depurator, une espèce de galathée Munida rugosa et des langoustines Nephrops norvegicus. Dans ces conditions, les résultats de la méthode ABC n'étaient pas cohérents avec la théorie pour ces communautés de macro-invertébrés benthiques et les efforts de pêche mesurés.
Aquatic Living Resources (0990-7440) (EDP Sciences), 2006-07 , Vol. 19 , N. 3 , P. 219-228

Droits : 2006 EDP
http://archimer.ifremer.fr/doc/2006/publication-2133.pdf
DOI:10.1051/alr:2006022
http://archimer.ifremer.fr/doc/00000/2133/

Éditeur(s) : HAL CCSD Nature Publishing Group
Résumé : International audience
Different marine habitats are characterised by different soundscapes. How or which differences may be representative of the habitat characteristics and/or community structure remains however to be explored. A growing project in passive acoustics is to find a way to use soundscapes to have information on the habitat and on its changes. In this study we have successfully tested the potential of two acoustic indices, i.e. the average sound pressure level and the acoustic complexity index based on the frequency spectrum. Inside and outside marine protected areas of Moorea Island (French Polynesia), sound pressure level was positively correlated with the characteristics of the substratum and acoustic complexity was positively correlated with fish diversity. It clearly shows soundscape can be used to evaluate the acoustic features of marine protected areas, which presented a significantly higher ambient sound pressure level and were more acoustically complex than non-protected areas. This study further emphasizes the importance of acoustics as a tool in the monitoring of marine environments and in the elaboration and management of future conservation plans. Coral reef ecosystems are among the most biologically diverse and complex marine ecosystems worldwide. In addition to their biological and ecological importance, coral reefs support major economic and physical functions (e.g. food production, tourism, biotechnology development and coastal protection) that are essential for many countries 1. Unfortunately, coral reefs are severely threatened: 20% of coral reefs can no longer be defined as such, another 25% are currently endangered and another 25% will be endangered by 2050 2. The frequency and severity of natural perturbations (e.g. cyclone, outbreaks of predators, particularly the crown-of-thorns starfish [COTS] Acanthaster planci) and anthropogenic perturbations (e.g. ocean acidification, pesticides, rising seawater temperatures) on coral reefs have greatly increased worldwide in the last three decades, and, as a consequence, reef communities (fish, coral and benthic invertebrates) have suffered unprecedented levels of decline 3,4
ISSN: 2045-2322

hal-01370610
https://hal-uvsq.archives-ouvertes.fr/hal-01370610
https://hal-uvsq.archives-ouvertes.fr/hal-01370610/document
https://hal-uvsq.archives-ouvertes.fr/hal-01370610/file/2016%20Sci.Rep.pdf
DOI : 10.1038/srep33326

Éditeur(s) : Elsevier Science Bv
Résumé : Small-scale fisheries have traditionally received less research effort than large-scale fisheries and are generally under-studied in Europe. In spite of their comparatively low volume of catches and economic importance, small-scale fisheries are socially important and an integral part of the European coastal zone. Considering the high heterogeneity of situations and the paucity of quantitative data, we used an analytical methodology based on the comparative method. We carried out an analysis of small-scale fisheries (SSFs) in Europe based on a selection of nine case studies. Our objective was to obtain a comprehensive description of small-scale fleets covering different areas/fisheries/species, encompassing the diversity and specific conditions under which SSFs operate, in order to demonstrate the ecological and social sustainability of this often overlooked fisheries segment. A common approach formulated so that the case studies could be compared with the case histories of other competing users, required that for each set of criteria – technical, biological, socio-economic, and institutional – a set of relevant items and indicators was established. An analysis of characteristics common to the selected case studies is conducted and an attempt made to extend our comparisons to the whole of the European Union. Our results show that (as compared with large-scale fleets, their main competitor) small-scale fleets: (i) are composed of smaller vessels and, consequently, travel lower distances to fishing grounds, and are more reliant on coastal areas; (ii) have smaller crews (although the global employment figure is similar to that of large-scale fleets in Europe); (iii) use mostly, but not exclusively, passive gears; (iv) use multi-purpose fishing approaches, and can change the fish species they target during the year; (v) have lower extraction rates; (vi) have lower total capital investments (including fishing rights), turnover and costs; and (vii) have lower fuel consumption, making them less sensitive to changing oil prices. Dependence on subsidies is lower (viii). Involvement in fisheries management is variable, conservation and access regulation measures are largely local in origin. For the selected case studies, the most significant competitors are large-scale fleets, and recreational fisheries, but other sources of interaction (water quality, invasive species, etc.) cannot be ignored.
Fisheries Research (0165-7836) (Elsevier Science Bv), 2013-02 , Vol. 140 , P. 1-13

Droits : 2012 Elsevier B.V. All rights reserved
http://archimer.ifremer.fr/doc/00118/22934/20757.pdf
DOI:10.1016/j.fishres.2012.11.008
http://archimer.ifremer.fr/doc/00118/22934/

Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : The natural 15N abundance method for estimating symbiotic biological N2-fixation was tested on legume trees from two rain forests on contrasting soils (oxisols and spodosols) in French Guiana. When possible, the significance of N2-fixing species in the plant community was evaluated in terms of density, biomass and contribution of N2-fixation to the building up of the total nitrogen mass in the leaves. Of the two sites, the rain forest on spodosols was the less favourable for application of the [delta]15N method: the available soil nitrogen was isotopically similar to fixed-N2. Hence, the results showed that a reliable estimate of N2-fixation could not be obtained. A substantial contribution of fixed-N2 to the nitrogen nutrition of legumes was found on oxisols, with an average value of 54 % Ndfa (Nitrogen derived from the atmosphere). The contribution of the N2-fixing legumes to the biomass of the stand was estimated to be 2 t ha[minus sign]1 for the leaf biomass and 136 t ha[minus sign]1 for the total above-ground plant biomass. With 7.5 % of trees in the stand able to fix N2 (462 out of 6156), N2-fixation was estimated to be 7 kg ha[minus sign]1 y[minus sign]1. These results are the first use of the [delta]15N method to estimate nitrogen input by N2-fixing legumes to a natural rain forest. The inter-site variability observed in the [delta]15N of the non-fixing plants suggested different nitrogen-cycling processes in the two soils. The [delta]15N of the non-N2-fixing plants could be related to the soil nitrogen availability and be used as an indicator of efficient or non-efficient nitrogen-cycling rain forests. The spatial variability of the [delta]15N in the plant-available soil nitrogen pool and the nitrogen balance in tropical rain forests are discussed.
ISSN: 0266-4674

hal-01032201
https://hal.archives-ouvertes.fr/hal-01032201
DOI : 10.1017/S0266467499000644

Éditeur(s) : Université de Bretagne Occidentale
Résumé : Study of mineral suspended particulate matter (SPM) is essential to understand ecosystem dynamics. SPM influences light penetration which is closely related to primary production and carries pollutants and nutrients within the water masses. This work aims to study near-surface mineral SPM dynamics in the English Channel using two complementary methods: remote-sensing by satellites and numerical modelling. Firstly, MODIS and MERIS satellite images processed by the IFREMER semi-analytical algorithm and describing non-algal SPM, are analysed to build three statistical models which are able to estimate near-surface SPM using simple variables, e.g., tidal coefficient, significant wave height and mean chlorophyll-a concentration. Secondly, the three-dimensional hydrosedimentary model ROMS (Regional Ocean Modeling System) is applied in the English Channel. It considers tidal forcing along open boundaries, wind stress at the sea-surface, wave-current interactions in the bottom boundary layer and realistic heterogeneous bottom sediments. Results of the more sophisticated statistical model is also used to impose SPM concentrations at open boundaries. Sensitivity tests on SPM boundary conditions show the importance of prescribing realistic sediment concentrations to improve the model predictions. Biological influences on mineral SPM are also tested using settling velocity and critical shear stress for erosion which vary with seasons. Both statistical and numerical models highlight and locate respective influences of tide, waves and biology on mineral SPM. Numerical predictions indicate that near-surface SPM is mainly composed of silts (>70%). Near-surface suspended silts come largely from seabed resuspension alongshore in the Eastern Channel and from the open boundaries of our limited-area coastal model at the West of Cotentin Peninsula and offshore. Near-surface SPM variations are investigated at semi-diurnal, neap-spring tidal cycle time scales and during a wave event. Finally, dynamics of sediments in the turbidity maximum zone around the Isle of Wight is examined depending on hydrodynamical conditions in order to distinguish the role played by advection and local erosion/settling processes in this area. Keywords: Suspended particulate matter, satellite, remote-sensing, modelling, English Channel, sediments, turbidity, tide, wave
L'étude des matières en suspension (MES) minérales est essentielle pour comprendre le fonctionnement des écosystèmes en Manche : les MES influencent la pénétration de la lumière dans la colonne d'eau, paramètre clé pour la production biologique, et sont susceptibles de transporter des polluants et nutriments. Lors de ce travail, la dynamique des MES minérales de surface en Manche est étudiée à l'aide de deux méthodes complémentaires : l'observation par satellite et la modélisation numérique tridimensionnelle. Dans un premier temps, les images satellite MODIS et MERIS, traitées par l'algorithme semi-analytique développé par l'IFREMER et représentant les MES non-algales de surface, sont analysées afin d'élaborer trois modèles statistiques permettant d'estimer la MES de surface en fonction de variables basiques telles que le coefficient de marée, la hauteur significative des vagues et la concentration moyenne en chlorophylle-a. Dans un deuxième temps, le modèle hydrosédimentaire multiclasse tridimensionnel ROMS (Regional Ocean Modeling System) est implémenté en Manche. Il prend en considération le forçage par la marée aux frontières ouvertes, la contrainte exercée par le vent à la surface de la mer, l'interaction houle-courant en couche limite de fond et l’hétérogénéité spatiale réaliste du lit sédimentaire. Les résultats du modèle statistique le plus sophistiqué sont également utilisés pour forcer la concentration en MES aux frontières ouvertes du domaine de calcul. Des tests de sensibilité sur les conditions limites montrent l'importance de considérer de manière réaliste les sédiments entrant en Manche par les frontières ouvertes lors de la modélisation numérique. L'influence de la biologie sur les MES minérales est testée en utilisant une formulation de la vitesse de chute et de la contrainte critique d'érosion variant saisonnièrement. Grâce à ces deux outils associés, les influences respectives de la marée, de la houle et de la biologie sur les MES minérales sont mises en avant et localisées en Manche. Le modèle numérique prédit que les MES de surface sont composées principalement de silts (>70%). Les silts en suspension en surface proviennent majoritairement du lit sédimentaire près des côtes en Manche orientale et des frontières ouvertes du domaine de calcul à l'ouest de la presqu'île du Cotentin et au large en Manche centrale et orientale. Les variations des MES de surface sont ensuite étudiées aux échelles des cycles de marée semi-diurnes, vive-eau/morte-eau et autour d'un épisode de houles. Enfin, l'évolution de la concentration de sédiments dans la zone de forte turbidité autour de l'île de Wight peut être analysée suivant les conditions hydrodynamiques afin d'évaluer les rôles respectifs des processus locaux d'érosion/dépot et d'advection dans la génération de ces turbidités remarquables. Mots-clés : Matière en suspension, télédétection, satellite, modélisation, Manche, sédiments, turbidité, marée, houle

Droits : 2013 UBO
http://archimer.ifremer.fr/doc/00157/26783/24884.pdf
http://archimer.ifremer.fr/doc/00157/26783/

Éditeur(s) : Gauthier-Villars
Résumé : Long tropical instability waves are described at around 3-4 degrees N based on results of a simulation performed with a general circulation model for the Atlantic Ocean. This description is in agreement with earlier observations of organized undulations of the summer thermal front associated with anti-cyclonic eddies propagating westward at 30-40 km/day along 3-4 degrees N from 10 to 40 degrees W through the Atlantic basin. However, the simulation indicated the presence of long waves in early boreal winter. In this respect, satellite observations during short cold events in winter show thermal front undulations similar to those associated with long wave propagations. The simulation clearly demonstrated large vertical movements between the surface and a depth of 70 m, associated with anti-cyclonic eddies at around 3 degrees N. These vertical movements could commonly reach the thermocline in the central part of the Atlantic basin (10-20 degrees W). In this region, long instability waves could subsequently affect biological production by ''eddy pumping''. During the PIRAL cruise at 4 degrees N-20 degrees W in June 1986, remarkably high chlorophyll concentrations (the highest values in our data bank for the equatorial Atlantic and typical of a very productive zone) were associated with currents similar to those of an anticyclonic eddy and characterized by a surface temperature distribution typical of the long instability wave pattern. These high chlorophyll concentrations may have resulted from ''eddy pumping'' and/or strong meridian advection since each of these mechanisms is associated with long instability waves.
Oceanologica Acta (0399-1784) (Gauthier-Villars), 1994 , Vol. 17 , N. 6 , P. 585-596

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00099/21034/18660.pdf
http://archimer.ifremer.fr/doc/00099/21034/

Éditeur(s) : HAL CCSD Cambridge University Press (CUP)
Résumé : International audience
We studied the monogenean communities of 34 species of butterflyfish from the tropical Indo-West Pacific, identifying 13 dactylogyrid species (including two species that are presently undescribed). Monogenean assemblages differed significantly between host species in terms of taxonomic structure, intensity and prevalence. Parasite richness ranged from 0 (Chaetodon lunulatus) to 11 (C. auriga, C. citrinellus and C. lunula). Host specificity varied between the dactylogyrids species, being found on 2-29 of the 34 chaetodontid species examined. Sympatric butterflyfish species were typically parasitized by different combinations of dactylogyrid species, suggesting the existence of complex host-parasite interactions. We identified six clusters of butterflyfish species based on the similarities of their dactylogyrid communities. Dactylogyrid richness and diversity were not related to host size, diet specialization, depth range or phylogeny of butterflyfish species. However, there was a weak positive correlation between monogenean richness and diversity and host geographical range. Most communities of dactylogyrids were dominated by Haliotrema aurigae and H. angelopterum, indicating the importance of the genus Haliotrema in shaping monogenean communities of butterflyfishes. This study casts light on the structure of the monogenean communities of butterflyfishes, suggesting that the diversity and complexity of community structures arises from a combination of host species-specific parameters.
ISSN: 0031-1820

hal-01380679
https://hal-univ-perp.archives-ouvertes.fr/hal-01380679
DOI : 10.1017/S0031182016001463

Éditeur(s) : HAL CCSD Coastal Education and Research Foundation
Résumé : International audience
The ichthyofauna of the Manche-à-Eau mangrove lagoon was regularly sampled in 2002 with a fixed net at seven stations during 4 months corresponding to two hydrological seasons. Physicochemical variables (depth, temperature, salinity, dissolved oxygen, pH) and population descriptors (species and family richness, density and biomass) were measured. The Whitefield and the well-being indexes were calculated to appreciate species equilibrium. Canonical correspondence analysis and generalized linear models were used to link species assemblages to physicochemical variables and to search for a special link with salinity. A total of 30,733 individuals belonging to 34 species and 23 families were collected. The Gerreidae, Clupeidae, Engraulidae, Scianidae, and Sparidae represented almost 98% of the total number of individuals. Our results show that organization of the fish assemblages in the lagoon is poorly dependent on salinity, whereas dissolved oxygen, temperature, and pH could have a stronger role. Looking at response curves to salinity change, most fishes species appeared to be visitors, either temporarily present or regular migrators. Only a few species compose the year-round resident population. They have a high patrimonial value and could be considered bioindicator species for long-term studies (e.g., of global change and natural or anthropogenic disturbances). The Euclidean distance and biomass variables were not useful descriptors of confinement and biological zonation in the lagoon, whereas the negative gradient of specific richness, number of individuals, Whitefield index, and index of well-being better described confinement. On the basis of these last parameters, biological zonation in the Manche-à- Eau lagoon was established and is provided.
ISSN: 0749-0208

hal-00755285
https://hal.univ-antilles.fr/hal-00755285
DOI : 10.2112/06-0804.1

Éditeur(s) : HAL CCSD Tecpar
Résumé : International audience
The general structure and organization of the shallow water (<1.5 m) fish assemblages were studied in two southern Brazilian ecosystems, a bay and a lagoon, under different marine or continental influences. The abiotic factors were measured to define the hydrology of the sites and the biotic descriptors were evaluated to characterize the assemblage structures. Transparency, salinity and organic matter were the abiotic factors which best distinguished the sites. A total richness of 69 species was observed. Ecological guilds, density, diversity and evenness indices values were different in each site. Hydrodynamism and geomorphology determined the structure and the organization of the fish assemblages in these shallow waters. It was observed that variations in the hydrological attributes generated by the marine or continental water movements are able to alter the conditions in the lagoon more quickly and at more regular frequencies than those in the bay.
ISSN: 1516-8913

hal-00753018
https://hal.univ-antilles.fr/hal-00753018
https://hal.univ-antilles.fr/hal-00753018/document
https://hal.univ-antilles.fr/hal-00753018/file/BRAZILIAN_2010.pdf

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Motivation: Gene fusion is an important evolutionary process. It can yield valuable information to infer the interactions and functions of proteins. Fused genes have been identified as non-transitive patterns of similarity in triplets of genes. To be computationally tractable, this approach usually imposes an a priori distinction between a dataset in which fused genes are searched for, and a dataset that may have provided genetic material for fusion. This reduces the `genetic space' in which fusion can be discovered, as only a subset of triplets of genes is investigated. Moreover, this approach may have a high-false-positive rate, and it does not identify gene families descending from a common fusion event. Results: We represent similarities between sequences as a network. This leads to an efficient formulation of previous methods of fused gene identification, which we implemented in the Python program FusedTriplets. Furthermore, we propose a new characterization of families of fused genes, as clique minimal separators of the sequence similarity network. This well-studied graph topology provides a robust and fast method of detection, well suited for automatic analyses of big datasets. We implemented this method in the C++ program MosaicFinder, which additionally uses local alignments to discard false-positive candidates and indicates potential fusion points. The grouping into families will help distinguish sequencing or prediction errors from real biological fusions, and it will yield additional insight into the function and history of fused genes.
ISSN: 1367-4803

hal-01544795
https://hal.archives-ouvertes.fr/hal-01544795
DOI : 10.1093/bioinformatics/btt049

Éditeur(s) : HAL CCSD Walter de Gruyter
Résumé :  
A method for measuring shrinkage resulting from drying in the three anisotropic directions is developed and tested. Measurements are performed on sawn discs, a technique which simplifies preparation and enables large numbers of measurements. Shrinkage values can be represented as a map of the disc surface. The results indicate that comparisons between shrinkage distribution and tension wood distribution on the discs show a clear relationship and can be measured with relatively high accuracy in reference to the "shrinkage map". In the long term, this method could be useful in the timber industry as a means for choosing the direction in which logs are cut depending on their type of wood composition.
Holzforschung

hal-01032055
https://hal.archives-ouvertes.fr/hal-01032055
DOI : 10.1515/HF.2003.100

Éditeur(s) : CNEXO
Résumé : 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 catchabtiity into its components (vulnerability, availability...). The second chapter of this part is devoted to the quantification of exploitation. This leads to a discussion of nominal and effective fishing effort and fishing intensity. A brief review of the use of catch per unit of effort as an index of abundance is followed by a discussion of the concept of fishing power. The second part starts with some general remarks on mathematical modelling (chapter III), then comes to the two classical categories of models : global (surplus production) models (chapter IV), and structural models (chapter V). Chapter IV is mainly a review, based upon the SCHAEFER and PELLATOMLINSON models. Some less classical formulas from the recent literature are also introduced. Attention is paid to the underlying hypotheses and to the limitation of such models. The reader is finally referred to papers presenting the developments that could make it possible to overcome some of these limitations. Chapter V is based upon the classical BEVERTON and HOLT and RlCKER models, and the yield per recruit concepts. This field is however inlarged. Other commonly used variants of structural models are presented with an effort being made to clarify the real differences between all these variants. Special attention is also paid to so-called regenerative models and to the use of spawing-biomass or fecundity per recruit, which are likely to become commonly used in the coming years. In all cases, special attention is paid to the presentation of the basic formulas, that the reader might have to use if faced with a practical problem. Finally, a discussion of the underlying hypotheses takes place, before a brief review of the main developments, where the reader is referred to the appropriate literature.
Ce livre constitue le premier volet d'un tryptique destiné à effectuer une revue des méthodes essentielles en dynamique des populations marines exploitées. Il est consacré à la définition des concepts de base, à la présentation des modèles courants. Dans la discussion des concepts, ce volume s'attache à clarifier les notions relatives aux deux parties dont les relations font l'objet de la dynamique des populations exploitées : le stock et la flottille de pêche. Ceci amène notamment à préciser la définition d'un stock, sa relation avec la notion de population biologique, à analyser les problèmes de définition de la capturabilité. Les concepts d'intensité, d'effort, de puissance de pêche, une analyse des relations entre abondance et capture par unité d'effort sont ensuite présentés. Après une brève réflexion générale sur la modélisation, la deuxième partie de cet ouvrage présente les modèles eux-mêmes, en abordant successivement les modèles dits globaux et structuraux. Un effort est fait pour couvrir non seulement les versions les plus anciennes, mais aussi les variantes récentes, pour détailler les relations entre ces différentes variantes, offrir un formulaire de base, enfin, discuter les hypothèses majeures et les prolongements souhaitables ou en cours.
Publications du C.N.E.X.O. Série "Rapports scientifiques et techniques" (0339-2899) (CNEXO), 1981 , N. 45 , P. 1-120

Droits : Centre National pour l'Exploitation des Océans, 1981
http://archimer.ifremer.fr/doc/1981/rapport-1126.pdf
http://archimer.ifremer.fr/doc/00000/1126/

Éditeur(s) : Interciencia
Résumé : Zooplankton abundance, biomass and composition were evaluated in various temporal scales in a seasonal coastal upwelling system at Margarita Island, Venezuela. Scales of temporal variation include weeks, months and seasons (relaxation, upwelling and transition). Seasons were delimitated by upwelling index and sea temperature. The sampling period comprise Sept/2002 - July/2003. Zooplankton samplings were made by horizontal trawls (1-10m depth), using 200,mu m nets, 2-6km from the coastal margin. Total abundance show important variation at week scales, with different patterns between locations, while seasonal differences of abundance are marginal. Biomass only shows seasonal variation due significant reduction in the transition season. Zooplankton assemblages show changes at scale of weeks, with different local patterns, and seasonal changes. Changes in assemblage between the relaxation and upwelling seasons include reduction (during upwelling) of abundance in copepods, cladocerans, salpidae, chaetognates, fish and crustacea larvae. Except by cirripedia larvae, those were important in the upwelling assemblages. Transition shows high variation, with reduction of biomass and assemblage composition similar to upwelling, except by an isolated event. Small scale variation in the zooplankton could be related to physical processes at small scales, eg. turbulence, local circulation, small eddies and filaments, and biological response. Additional sources of nutrient input, eg. riverine input and internal waves, could support local plankton productivity and abundance during relaxation. Detection of high variation in zooplankton abundance and composition at small scales, with local interaction, bring a new light over zooplankton estimation in time series in this system.
La abundancia, la biomasa y la composición del zooplancton costero fueron analizadas a varias escalas temporales en un área afectada por surgencia costera estacional (Isla de Margarita, Venezuela); considerando para ello escalas de semanas, meses y periodos, así como la variación local. La estimación del zooplancton fue realizada a partir de arrastres horizontales (1-10m de profundidad) utilizando redes de 200μ entre 2 y 6 km de la línea de costa, entre set/2002 y jul/2003. La abundancia total presentó alta variabilidad a escala de semanas, con patrones diferentes entre localidades, mientras que la diferencia entre periodos es marginal. La biomasa únicamente mostró variación a escala de periodos por una disminución durante el periodo de transición. La composición presentó fluctuaciones a escalas temporales pequeñas, con patrones de variación diferentes localmente, así como a escala de periodos. Los cambios en composición entre el periodo de relajación y el de surgencia incluyen disminución en la abundancia de copépodos, cladóceros, salpas, quetognatos, larvas de peces y crustáceos; excepto por las larvas de cirrípedos que forman un componente importante durante la surgencia. Se postula que procesos físicos a pequeña escala, como la turbulencia, la circulación local o la formación de pequeños giros o filamentos, y los procesos biológicos, condicionan esta elevada variabilidad a escalas pequeñas. La existencia de fuentes de enriquecimiento adicionales como aportes de ríos y ondas internas pudiera condicionar la presencia de elevada abundancia y biomasa, en especial durante periodos de relajación. Los cambios en composición resaltan la importancia del aporte de merozooplancton costero. Palabras clave / Biomasa / Escalas Temporales / Surgencia / Venezuela / Zooplancton Costero /
Interciencia (0378-1844) (Interciencia), 2014-02 , Vol. 39 , N. 2 , P. 122-128

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00187/29851/28297.pdf
http://archimer.ifremer.fr/doc/00187/29851/

Éditeur(s) : HAL CCSD Society for Range Management
Résumé : Grasslands and agroecosystems occupy one-third of the terrestrial area, but their contribution to the global carbon cycle remains uncertain. We used a set of 316 site-years of CO(2) exchange measurements to quantify gross primary productivity, respiration, and light-response parameters of grasslands, shrublands/savanna, wetlands, and cropland ecosystems worldwide. We analyzed data from 72 global flux-tower sites partitioned into gross photosynthesis and ecosystem respiration with the use of the light-response method (Gilmanov, T. G., D. A. Johnson, and N. Z. Saliendra. 2003. Growing season CO(2) fluxes in a sagebrushsteppe ecosystem in Idaho: Bowen ratio/energy balance measurements and modeling. Basic and Applied Ecology 4:167-183) from the RANGEFLUX and WORLDGRASSAGRIFLUX data sets supplemented by 46 sites from the FLUXNET La Thuile data set partitioned with the use of the temperature-response method (Reichstein, M., E. Falge, D. Baldocchi, D. Papale, R. Valentini, M. Aubinet, P. Berbigier, C. Bernhofer, N. Buchmann, M. Falk, T. Gilmanov, A. Granier, T. Grunwald, K. Havrankova, D. Janous, A. Knohl, T. Laurela, A. Lohila, D. Loustau, G. Matteucci, T. Meyers, F. Miglietta, J.M. Ourcival, D. Perrin, J. Pumpanen, S. Rambal, E. Rotenberg, M. Sanz, J. Tenhunen, G. Seufert, F. Vaccari, T. Vesala, and D. Yakir. 2005. On the separation of net ecosystem exchange into assimilation and ecosystem respiration: review and improved algorithm. Global Change Biology 11: 1.424-1439). Maximum values of the quantum yield (alpha = 75 mmol.mol(-1)), photosynthetic capacity (A(max) = 3.4 mg CO(2) . m(-2).s-1), gross photosynthesis (P(g,max) = 1.16 g CO(2) . m(-2).d(-1)), and ecological light-use efficiency (epsilon(ecol) = 59 mmol . mol(-1)) of managed grasslands and high-production croplands exceeded those of most forest ecosystems, indicating the potential of nonforest ecosystems for uptake of atmospheric CO(2). Maximum values of gross primary production (8 600 g CO(2) . m(-2).yr(-1)), total ecosystem respiration (7 900 g CO(2) . m(-2).yr(-1)), and net CO(2) exchange (2 400 g CO(2) . m(-2).yr(-1)) were observed for intensively managed grasslands and high-yield crops, and are comparable to or higher than those for forest ecosystems, excluding some tropical forests. On average, 80% of the nonforest sites were apparent sinks for atmospheric CO(2), with mean net uptake of 700 g CO(2) . m(-2).yr(-1) for intensive grasslands and 933 g CO(2) . m(-2).d(-1) for croplands. However, part of these apparent sinks is accumulated in crops and forage, which are carbon pools that are harvested, transported, and decomposed off site. Therefore, although agricultural fields may be predominantly sinks for atmospheric CO(2), this does not imply that they are necessarily increasing their carbon stock.
ISSN: 1550-7424

hal-01190754
https://hal.archives-ouvertes.fr/hal-01190754
DOI : 10.2111/rem-d-09-00072.1
PRODINRA : 214043

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
This study describes the structure of the digestive gland of Strombus gigas in individuals from Guadeloupe and discusses the function of its cell types and their relationship with intracellular Apicomplexa-like parasites. Three cellular types were found in the epithelium of the blind-ending tubules of the digestive gland according to histological and transmission electron microscopy (TEM) observations; these were: digestive cells, pyramidal crypt cells and vacuolated cells. Columnar digestive cells were characterized by large Alcian blue-positive granules, which have not been previously described in digestive cells of other caenogastropods. Such granules contain large quantities of proteoglycans that are exported to the stomach through the physiological destruction of the digestive cells, which undergo a holocrine secretion. Their cytoplasm appears vacuolar due to lipid extraction by solvents used for tissue preparation. Vacuolated cells also appear to be lipid-storage cells. Small triangular-shaped crypt cells, on the other hand, appear to be metabolically active as suggested by a strong positive in situ hybridization of eukaryotic ribosomes, which was confirmed by their large content of ribosomes and rough endoplasmic reticulum compared to the other cell types. These observations suggest that crypt cells may be immature cells that are involved in the replacement of eliminated digestive cells. However, their spherocrystal inclusions indicate that they may be excretory cells or calcium cells. Large brown inclusions were frequently observed in vacuolated cells; these were identified as parasitic protozoans and were present in the digestive gland of all sampled specimens. These protozoans have previously been described from a queen conch population in the San Andres Archipelago (Colombia). Several life cycle stages of the parasite were identified by scanning electron microscopy and TEM; trophozoites were characterized by their conoid-like structure, sporocysts by their thick walls, and gamonts by their thin walls. These observations suggest that this parasite completes its entire life cycle within the same host and type of tissue. Although previous investigations place this parasite within the Apicomplexa group, further investigations are necessary in order to confirm the identification of the parasite.
ISSN: 0260-1230

hal-00755287
https://hal.univ-antilles.fr/hal-00755287
DOI : 10.1093/mollus/eyn041