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Auteur Lagarde, F.; Fiandrino, A.; Ubertini, M.; d'Orbcastel, E.R.; Mortreux, S.; Chiantella, C.; Bec, B.; Bonnet, D.; Roques, C.; Bernard, I.; Richard, M.; Guyondet, T.; Pouvreau, S.; Lett, C. url  doi
openurl 
  Titre Duality of trophic supply and hydrodynamic connectivity drives spatial patterns of Pacific oyster recruitment Type Article scientifique
  Année 2019 Publication Revue Abrégée Marine Ecology Progress Series  
  Volume 632 Numéro Pages 81-100  
  Mots-Clés Coastal lagoon; Connectivity; Crassostrea gigas; Larval ecology; Oligotrophication; Recruitment; Settlement; Spatial patterns  
  Résumé The recent discovery of Pacific oyster Crassostrea gigas (also known as Magallana gigas) spatfields in a Mediterranean lagoon intensely exploited for shellfish farming (Thau lagoon) revealed significant contrasts in spatial patterns of recruitment. We evaluated the processes that drive spatial patterns in oyster recruitment by comparing observed recruitment, simulated hydrodynamic connectivity and ecological variables. We hypothesized that spatial variability of recruitment depends on (1) hydrodynamic connectivity and (2) the ecology of the larval supply, settlement, metamorphosis, survival and biotic environmental parameters. We assessed recruitment at 6-8 experimental sites by larval sampling and spat collection inside and outside oyster farming areas and on an east-west gradient, from 2012-2014. Hydrodynamic connectivity was simulated using a numerical 3D transport model assessed with a Eulerian indicator. The supply of large umbo larvae did not differ significantly inside and outside oyster farming areas, whereas the supply of pediveligers to sites outside shellfish farms was structured by hydrodynamic connectivity. Inside shellfish farming zones, unfavorable conditions due to trophic competition with filter-feeders jeopardized their settlement. In this case, our results suggest loss of settlement competence by oyster larvae. This confirms our hypothesis of top-down trophic control by the oysters inside farming zones of Thau lagoon in summer that fails to meet the ecological requirements of these areas as oyster nurseries. Knowledge of oyster dispersal, connectivity and recruitment in coastal lagoons will help local development of sustainable natural spat collection. On a global scale, our method could be transposed to other basins or used for other species such as mussels, clams or scallops, to better understand the spatial patterns of bivalve recruitment. Management of the oyster industry based on natural spat collection will help develop a sustainable activity, based on locally adapted oyster strains but also by reducing the risks of transferring pathogens between basins and the global carbon footprint of this industry.  
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  Editeur Lieu de Publication Éditeur  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0171-8630, 1616-1599 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2673  
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Auteur Lagarde, F.; Richard, M.; Bec, B.; Roques, C.; Mortreux, S.; Bernard, I.; Chiantella, C.; Messiaen, G.; Nadalini, J.-B.; Hori, M.; Hamaguchi, M.; Pouvreau, S.; ROQUE D'ORBCASTEL, E.; Tremblay, R. url  doi
openurl 
  Titre Trophic environments influence size at metamorphosis and recruitment performance of Pacific oysters Type Article scientifique
  Année 2018 Publication Revue Abrégée Marine Ecology Progress Series  
  Volume 602 Numéro Pages 135-153  
  Mots-Clés Crassostrea gigas; Cryptophytes; Larval ecology; Oligotrophication; Prodissoconch II; Recruitment; Thau lagoon  
  Résumé Reproduction and recruitment of benthic invertebrates are influenced by the climate and by the ecological structure of marine ecosystems, along with local anthropogenic pressures such as eutrophication or oligotrophication. Using the Pacific oyster Crassostrea gigas as a biological model, we tested the hypothesis that the variability in prodissoconch II (PII) size (i.e. size at metamorphosis) depends on ecological functioning. Settlement and recruitment were assessed at 5 sampling sites on the French Mediterranean shellfish farmed Thau lagoon during the main summer recruitment events in 3 consecutive years (2012-2014). Hydrobiological and planktonic analyses were conducted at 3 sampling sites. Our results showed that recruitment was extremely heterogeneous, ranging from 0 to 260 ± 27 SE ind. dm-2 throughout the ecosystem and was linked with variability in PII size, which ranged from 180 to 296 µm. The annual temporal pattern of PII sizes appeared to be controlled by temperature during the settlement period, whereas the spatial pattern depended on phytoplankton biomass and on the trophic functioning of the ecosystem. Smaller PII sizes were significantly correlated with the highest phytoplankton biomass, while larger PII sizes were positively correlated with mixotrophic cryptophyte abundance. We found an inverse relationship between PII size and survival after metamorphosis, showing that recruitment success was associated with smaller PII sizes. Regional climate conditions and local trophic functioning appear to be key factors in metamorphosis and consequently contribute to recruitment heterogeneity. Further studies should be performed in other ecosystems following an oligotrophication trajectory to generalize this result.  
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  Editeur Lieu de Publication Éditeur  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0171-8630, 1616-1599 ISBN Médium  
  Région Expédition Conférence  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2398  
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Auteur KIVELA, M.; ARNAUD-HAOND, S.; SARAMAKI, J. url  doi
openurl 
  Titre EDENetworks: A user-friendly software to build and analyse networks in biogeography, ecology and population genetics Type Article scientifique
  Année 2015 Publication Revue Abrégée Molecular Ecology Resources  
  Volume 15 Numéro 1 Pages 117-122  
  Mots-Clés Biogeography; biological communities; graph theory; microbial ecology; network analysis; population genetics  
  Résumé The recent application of graph-based network theory analysis to biogeography, community ecology and population genetics has created a need for user-friendly software, which would allow a wider accessibility to and adaptation of these methods. EDENetworks aims to fill this void by providing an easy-to-use interface for the whole analysis pipeline of ecological and evolutionary networks starting from matrices of species distributions, genotypes, bacterial OTUs or populations characterized genetically. The user can choose between several different ecological distance metrics, such as Bray-Curtis or Sorensen distance, or population genetic metrics such as FST or Goldstein distances, to turn the raw data into a distance/dissimilarity matrix. This matrix is then transformed into a network by manual or automatic thresholding based on percolation theory or by building the minimum spanning tree. The networks can be visualized along with auxiliary data and analysed with various metrics such as degree, clustering coefficient, assortativity and betweenness centrality. The statistical significance of the results can be estimated either by resampling the original biological data or by null models based on permutations of the data.  
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  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1755-098x ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1119  
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Auteur Mazel, F.; Renaud, J.; Guilhaumon, F.; Mouillot, D.; Gravel, D.; Thuiller, W. url  doi
openurl 
  Titre Mammalian phylogenetic diversity-area relationships at a continental scale Type Article scientifique
  Année 2015 Publication Revue Abrégée Ecology  
  Volume 96 Numéro 10 Pages 2814-2822  
  Mots-Clés Biodiversity; Biogeography; community ecology; conservation; conservation biogeography; habitat loss; habitat loss; null models; overestimate extinction rates; patterns; phylogenetic diversity; richness; species-area; species-area relationship; statistics; strict nested design  
  Résumé In analogy to the species-area relationship (SAR), one of the few laws in ecology, the phylogenetic diversity-area relationship (PDAR) describes the tendency of phylogenetic diversity (PD) to increase with area. Although investigating PDAR has the potential to unravel the underlying processes shaping assemblages across spatial scales and to predict PD loss through habitat reduction, it has been little investigated so far. Focusing on PD has noticeable advantages compared to species richness (SR), since PD also gives insights on processes such as speciation/extinction, assembly rules and ecosystem functioning. Here we investigate the universality and pervasiveness of the PDAR at continental scale using terrestrial mammals as study case. We define the relative robustness of PD (compared to SR) to habitat loss as the area between the standardized PDAR and standardized SAR (i.e., standardized by the diversity of the largest spatial window) divided by the area under the standardized SAR only. This metric quantifies the relative increase of PD robustness compared to SR robustness. We show that PD robustness is higher than SR robustness but that it varies among continents. We further use a null model approach to disentangle the relative effect of phylogenetic tree shape and nonrandom spatial distribution of evolutionary history on the PDAR. We find that, for most spatial scales and for all continents except Eurasia, PDARs are not different from expected by a model using only the observed SAR and the shape of the phylogenetic tree at continental scale. Interestingly, we detect a strong phylogenetic structure of the Eurasian PDAR that can be predicted by a model that specifically account for a finer biogeographical delineation of this continent. In conclusion, the relative robustness of PD to habitat loss compared to species richness is determined by the phylogenetic tree shape but also depends on the spatial structure of PD.  
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  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  Langue English Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0012-9658 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1423  
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Auteur Bodin, N.; Chassot, E.; Sardenne, F.; Zudaire, I.; Grande, M.; Dhurmeea, Z.; Murua, H.; Barde, J. url  doi
openurl 
  Titre Ecological data for western Indian Ocean tuna Type Article scientifique
  Année 2018 Publication Revue Abrégée Ecology  
  Volume 99 Numéro 5 Pages 1245-1245  
  Mots-Clés energetics; fatty acids; lipids; morphometrics; multi-tissues; proteins; stable isotopes; trophic ecology; tropical marine ecosystems; tuna fisheries  
  Résumé Tuna are marine apex predators that inhabit the tropical and sub-tropical waters of the Indian Ocean where they support socially and economically important fisheries. Key component of pelagic communities, tuna are bioindicator species of anthropogenic and climate-induced changes through modifications of the structure and related energy-flow of food webs and ecosystems. The IndianEcoTuna dataset provides a panel of ecological tracers measured in four soft tissues (white muscle, red muscle, liver, gonads) from 1,364 individuals of four species, i.e., the albacore (ALB, Thunnus alalunga), the bigeye (BET, T. obesus), the skipjack (SKJ, Katsuwomus pelamis), and the yellowfin (YFT, T. albacares), collected throughout the western Indian Ocean from 2009 to 2015. Sampling was carried out during routine monitoring programs, at sea by observers onboard professional vessels or at landing. For each record, the type of fishing gear, the conservation mode, as well as the fishing date and catch location are provided. Individuals were sampled to span a wide range of body sizes: 565 ALB with fork length from 58 to 118 cm, 155 BET from 29.5 to 173 cm, 304 SKJ from 30 to 74 cm, and 340 YFT from 29 to 171.5 cm. The IndianEcoTuna dataset combines: (1) 9,512 records of carbon and nitrogen stable isotopes (percent element weights, δ13C and δ15N values) in 1,185 fish, (2) 887 concentrations of total proteins in 242 fish, (3) 8,356 concentrations of total lipids and three lipid classes (triacylglycerols TAG; phospholipids PL; sterols ST) in 695 fish, and (4) 1,150 and 1,033 profiles of neutral and polar fatty acids in 397 and 342 fish, respectively. Information on sex and weights of the whole fish, gonads, liver and stomach is provided. Because of the essential trophic role and wide-ranging of tuna in marine systems, and the large panel of tropho-energetic tracers and derived-key quantitative parameters provided (e.g., niche width, trophic position, condition indices), the IndianEcoTuna dataset should be of high interest for global and regional research on marine trophic ecology and food web analysis, as well as on the impacts of anthropogenic changes on Indian Ocean marine ecosystems. There are no copyright restrictions for research and/or teaching purposes. Usage of the dataset must include citation of this Data Paper.  
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  Auteur institutionnel Thèse  
  Editeur Lieu de Publication Éditeur  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1939-9170 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2373  
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