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Auteur Bailleul, D.; Stoeckel, S.; Arnaud-Haond, S. doi  openurl
  Titre RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r Type Article scientifique
  Année 2016 Publication Revue Abrégée Methods Ecol. Evol.  
  Volume 7 Numéro 8 Pages 966-970  
  Mots-Clés clonal diversity; clonality; clonal population; diversity; genotype; markers; multilocus genotypes; multilocus lineages; organisms; population-genetics; program; software; spatial autocorrelation  
  Résumé Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements. The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes (MLGs), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs and (iv) describing several spatial components of clonality. RClone allows the one-shot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through next-generation sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClonequickmanual) or several populations (RCloneqmsevpops).  
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  ISSN 2041-210x ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1637  
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Auteur Becheler, R.; Cassone, A.-L.; Noel, P.; Mouchel, O.; Morrison, C.L.; Arnaud-Haond, S. doi  openurl
  Titre Low incidence of clonality in cold water corals revealed through the novel use of a standardized protocol adapted to deep sea sampling Type Article scientifique
  Année 2017 Publication Revue Abrégée Deep-Sea Res. Part II-Top. Stud. Oceanogr.  
  Volume 145 Numéro Pages 120-130  
  Mots-Clés diversity; dispersal; disturbance; Lophelia pertusa; Madrepora oculata; organisms; population-structure; asexual reproduction; Clonality; Cold-water coral; Fine-grained spatial genetic structure; gorgonian coral; lophelia-pertusa; pertusa linnaeus 1758; spatial genetic-structure; Standardized sampling  
  Résumé Sampling in the deep sea is a technical challenge, which has hindered the acquisition of robust datasets that are necessary to determine the fine-grained biological patterns and processes that may shape genetic diversity. Estimates of the extent of clonality in deep-sea species, despite the importance of clonality in shaping the local dynamics and evolutionary trajectories, have been largely obscured by such limitations. Cold-water coral reefs along European margins are formed mainly by two reef-building species, Lophelia pertusa and Madrepora oculata. Here we present a fine-grained analysis of the genotypic and genetic composition of reefs occurring in the Bay of Biscay, based on an innovative deep-sea sampling protocol. This strategy was designed to be standardized, random, and allowed the georeferencing of all sampled colonies. Clonal lineages discriminated through their Multi-Locus Genotypes (MLG) at 6-7 microsatellite markers could thus be mapped to assess the level of clonality and the spatial spread of clonal lineages. High values of clonal richness were observed for both species across all sites suggesting a limited occurrence of clonality, which likely originated through fragmentation. Additionally, spatial autocorrelation analysis underlined the possible occurrence of fine-grained genetic structure in several populations of both L. pertusa and M. oculata. The two cold-water coral species examined had contrasting patterns of connectivity among canyons, with among-canyon genetic structuring detected in M. oculata, whereas L. pertusa was panmictic at the canyon scale. This study exemplifies that a standardized, random and georeferenced sampling strategy, while challenging, can be applied in the deep sea, and associated benefits outlined here include improved estimates of fine grained patterns of clonality and dispersal that are comparable across sites and among species.  
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  ISSN 0967-0645 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2257  
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Auteur Ben Othman, H.; Leboulanger, C.; Le Floc'h, E.; Mabrouk, H.H.; Hlaili, A.S. url  doi
openurl 
  Titre Toxicity of benz(a)anthracene and fluoranthene to marine phytoplankton in culture: Does cell size really matter? Type Article scientifique
  Année 2012 Publication Revue Abrégée J. Hazard. Mater.  
  Volume 243 Numéro Pages 204-211  
  Mots-Clés Benz(a)anthracene; Ecotoxicity; Fluoranthene; Size-sensitivity relationship; aquatic organisms; biodegradation; chlorophyll; fluorescence; food-web; fresh-water phytoplankton; in-vitro; organic pollutants; pahs; phytoplankton; polycyclic aromatic-hydrocarbons; surface sediments  
  Résumé The toxicity of benz(a)anthracene and fluoranthene (polycyclic aromatic hydrocarbons, PAHs) was evaluated on seven species of marine algae in culture belonging to pico-, nano-, and microphytoplankton, exposed to increasing concentrations of up to 2 mg L-1. The short-term (24 h) toxicity was assessed using chlorophyll a fluorescence transients, linked to photosynthetic parameters. The maximum quantum yield Fv/Fm was lower at the highest concentrations tested and the toxicity thresholds were species-dependent. For acute effects, fluoranthene was more toxic than benz(a)anthracene, with LOECs of 50.6 and 186 mu g L-1, respectively. After 72 h exposure, there was a dose-dependent decrease in cell density, fluoranthene being more toxic than benz(a)anthracene. The population endpoint at 72 h was affected to a greater extent than the photosynthetic endpoint at 24 h. EC50 was evaluated using the Hill model, and species sensitivity was negatively correlated to cell biovolume. The largest species tested, the dinoflagellate Alexandrium catenella, was almost insensitive to either PAH. The population endpoint EC50s for fluoranthene varied from 54 mu g L-1 for the picophytoplankton Picochlorum sp. to 418 mu g L-1 for the larger diatom Chaetoceros muelleri. The size/sensitivity relationship is proposed as a useful model when there is a lack of ecotoxicological data on hazardous chemicals, especially in marine microorganisms. (C) 2012 Elsevier B.V. All rights reserved.  
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  ISSN 0304-3894 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 915  
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Auteur Bouvy, M.; Got, P.; Domaizon, I.; Pagano, M.; Leboulanger, C.; Bouvier, C.; Carré, C.; Roques, C.; Dupuy, C. url  doi
openurl 
  Titre Plankton communities in the five Iles Eparses (Western Indian Ocean) considered to be pristine ecosystems Type Article scientifique
  Année 2016 Publication Revue Abrégée Acta Oecologica  
  Volume Numéro Pages 9-20  
  Mots-Clés Distribution; Enrichment experiment; Iles Eparses; Islands; Microorganisms; Mozambique Channel; Nutrient limitation  
  Résumé Coral reef environments are generally recognized as being the most threatened of marine ecosystems. However, it is extremely difficult to distinguish the effects of climate change from other forcing factors, mainly because it is difficult to study ecosystems that are isolated from human pressure. The five Iles Eparses (Scattered Islands) are located in the Western Indian Ocean (WIO) and can be considered to be “pristine” ecosystems not subject to anthropogenic pressure. This study characterized their plankton assemblages for the first time, by determining the abundances of microbial (virus, bacteria, heterotrophic protists and phytoplankton) and metazooplankton communities in various lagoon and ocean sites around each island. The Europa lagoon has extensive, productive mangrove forests, which have the highest nutrient concentrations (nitrogen forms, dissolved organic carbon) and whose microbial communities present a peculiar structure and functioning. By means of bioassay experiments, we observed that bacterial production and growth rates are higher in Europa than those reported for the other islands. Tromelin, which lies outside the Mozambique Channel, had the lowest biological productivity, nutrient concentrations, and bacterial growth rates. Multivariate analysis indicated that distinct microbial assemblages occur in association to varying nutrient concentrations. Molecular fingerprinting showed clear discrimination of the structure of the archaea, bacteria and eukaryotes community between the sites. Our results suggest that the geographical distance can influence the diversity of dominant microbial taxa in the WIO.  
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  Éditeur de collection Titre de collection Îles Éparses (French Scattered Islands, SW Indian Ocean) as reference ecosystems for environmental research. Titre de collection Abrégé  
  Volume de collection 72 Numéro de collection Edition  
  ISSN 1146-609x ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1494  
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Auteur Lefort, S.; Aumont, O.; Bopp, L.; Arsouze, T.; Gehlen, M.; Maury, O. url  doi
openurl 
  Titre Spatial and body-size dependent response of marine pelagic communities to projected global climate change Type Article scientifique
  Année 2015 Publication Revue Abrégée Global Change Biology  
  Volume 21 Numéro 1 Pages 154-164  
  Mots-Clés biogeochemical model; body-size of organisms; climate change; climate scenario; high trophic level model; pelagic communities; trophic transfer  
  Résumé Temperature, oxygen, and food availability directly affect marine life. Climate models project a global warming of the ocean's surface (similar to+3 degrees C), a de-oxygenation of the ocean's interior (similar to-3%) and a decrease in total marine net primary production (similar to-8%) under the business as usual' climate change scenario (RCP8.5). We estimated the effects of these changes on biological communities using a coupled biogeochemical (PISCES) – ecosystems (APECOSM) model forced by the physical outputs of the last generation of the IPSL-CM Earth System Model. The APECOSM model is a size-structured bio-energetic model that simulates the 3D dynamical distributions of three interactive pelagic communities (epipelagic, mesopelagic, and migratory) under the effects of multiple environmental factors. The PISCES-APECOSM model ran from 1850 to 2100 under historical forcing followed by RCP8.5. Our RCP8.5 simulation highlights significant changes in the spatial distribution, biomass, and maximum body-size of the simulated pelagic communities. Biomass and maximum body-size increase at high latitude over the course of the century, reflecting the capacity of marine organisms to respond to new suitable environment. At low- and midlatitude, biomass and maximum body-size strongly decrease. In those regions, large organisms cannot maintain their high metabolic needs because of limited and declining food availability. This resource reduction enhances the competition and modifies the biomass distribution among and within the three communities: the proportion of small organisms increases in the three communities and the migrant community that initially comprised a higher proportion of small organisms is favored. The greater resilience of small body-size organisms resides in their capacity to fulfill their metabolic needs under reduced energy supply and is further favored by the release of predation pressure due to the decline of large organisms. These results suggest that small body-size organisms might be more resilient to climate change than large ones.  
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  ISSN 1354-1013 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1108  
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