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Auteur Maury, O.; Poggiale, J.-C. url  openurl
  Titre From individuals to populations to communities: A dynamic energy budget model of marine ecosystem size-spectrum including life history diversity Type Article scientifique
  Année 2013 Publication Revue Abrégée Journal of Theoretical Biology  
  Volume 324 Numéro Pages (up) 52-71  
  Mots-Clés biodiversity; Dynamic Energy Budget theory; predation; Schooling; Size spectrum  
  Résumé  
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  ISSN 0022-5193 ISBN Médium  
  Région Expédition Conférence  
  Notes <p>\textbackslashtextlessp\textbackslashtextgreaterIndividual metabolism, predator–prey relationships, and the role of biodiversity are major factors underlying the dynamics of food webs and their response to environmental variability. Despite their crucial, complementary and interacting influences, they are usually not considered simultaneously in current marine ecosystem models. In an attempt to fill this gap and determine if these factors and their interaction are sufficient to allow realistic community structure and dynamics to emerge, we formulate a mathematical model of the size-structured dynamics of marine communities which integrates mechanistically individual, population and community levels. The model represents the transfer of energy generated in both time and size by an infinite number of interacting fish species spanning from very small to very large species. It is based on standard individual level assumptions of the Dynamic Energy Budget theory (DEB) as well as important ecological processes such as opportunistic size-based predation and competition for food. Resting on the inter-specific body-size scaling relationships of the DEB theory, the diversity of life-history traits (i.e. biodiversity) is explicitly integrated. The stationary solutions of the model as well as the transient solutions arising when environmental signals (e.g. variability of primary production and temperature) propagate through the ecosystem are studied using numerical simulations. It is shown that in the absence of density-dependent feedback processes, the model exhibits unstable oscillations. Density-dependent schooling probability and schooling-dependent predatory and disease mortalities are proposed to be important stabilizing factors allowing stationary solutions to be reached. At the community level, the shape and slope of the obtained quasi-linear stationary spectrum matches well with empirical studies. When oscillations of primary production are simulated, the model predicts that the variability propagates along the spectrum in a given frequency-dependent size range before decreasing for larger sizes. At the species level, the simulations show that small and large species dominate the community successively (small species being more abundant at small sizes and large species being more abundant at large sizes) and that the total biomass of a species decreases with its maximal size which again corroborates empirical studies. Our results indicate that the simultaneous consideration of individual growth and reproduction, size-structured trophic interactions, the diversity of life-history traits and a density-dependent stabilizing process allow realistic community structure and dynamics to emerge without any arbitrary prescription. As a logical consequence of our model construction and a basis for future studies, we define the function Φ as the relative contribution of each species to the total biomass of the ecosystem, for any given size. We argue that this function is a measure of the functional role of biodiversity characterizing the impact of the structure of the community (its species composition) on its function (the relative proportions of losses, dissipation and biological work).\textbackslashtextless/p\textbackslashtextgreater</p> Approuvé pas de  
  Numéro d'Appel LL @ pixluser @ collection 245  
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Auteur Carteron, A.; Jeanmougin, M.; Leprieur, F.; Spatharis, S. url  doi
openurl 
  Titre Assessing the efficiency of clustering algorithms and goodness-of-fit measures using phytoplankton field data Type Article scientifique
  Année 2012 Publication Revue Abrégée Ecol. Inform.  
  Volume 9 Numéro Pages (up) 64-68  
  Mots-Clés 2-norm; Beta diversity; Cophenetic correlation coefficient; Dendrogram; Upgma; Ward's algorithm; beta-diversity; blooms; classification; communities; cophenetic correlation; environment; forest; functional diversity; som  
  Résumé Investigation of patterns in beta diversity has received increased attention over the last years particularly in light of new ecological theories such as the metapopulation paradigm and metacommunity theory. Traditionally, beta diversity patterns can be described by cluster analysis (i.e. dendrograms) that enables the classification of samples. Clustering algorithms define the structure of dendrograms, consequently assessing their performance is crucial. A common, although not always appropriate approach for assessing algorithm suitability is the cophenetic correlation coefficient c. Alternatively the 2-norm has been recently proposed as an increasingly informative method for evaluating the distortion engendered by clustering algorithms. In the present work, the 2-norm is applied for the first time on field data and is compared with the cophenetic correlation coefficient using a set of 105 pairwise combinations of 7 clustering methods (e.g. UPGMA) and 15 (dis)similarity/distance indices (e.g. Jaccard index). In contrast to the 2-norm, cophenetic correlation coefficient does not provide a clear indication on the efficiency of the clustering algorithms for all combinations. The two approaches were not always in agreement in the choice of the most faithful algorithm. Additionally, the 2-norm revealed that UPGMA is the most efficient clustering algorithm and Ward's the least. The present results suggest that goodness-of-fit measures such as the 2-norm should be applied prior to clustering analyses for reliable beta diversity measures. (C) 2012 Elsevier B.V. All rights reserved.  
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  Langue English Langue du Résumé Titre Original  
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  Volume de collection Numéro de collection Edition  
  ISSN 1574-9541 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 457  
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Auteur Granger, V.; Fromentin, J.-M.; Bez, N.; Relini, G.; Meynard, C.; GAERTNER, J.-C.; Maiorano, P.; Garcia Ruiz, C.; Follesa, C.; Gristina, M.; Peristeraki, P.; BRIND'AMOUR, A.; Carbonara, P.; Charilaou, C.; Esteban, A.; Jadaud, A.; Joksimovic, A.; Kallianiotis, A.; Kolitari, J.; Manfredi, C.; Massuti, E.; Mifsud, R.; Quetglas, T.; Refes, W.; Sbrana, M.; Vrgoc, N.; SPEDICATO, M.T.; Mérigot, B. url  doi
openurl 
  Titre Large-scale spatio-temporal monitoring highlights hotspots of demersal fish diversity in the Mediterranean Sea Type Article scientifique
  Année 2015 Publication Progress in Oceanography Revue Abrégée  
  Volume 130 Numéro Pages (up) 65-74  
  Mots-Clés Functional diversity; Phylogenetic diversity; Rao’s quadratic entropy; Regression tree; Large scale  
  Résumé Increasing human pressures and global environmental change may severely affect the diversity of species assemblages and associated ecosystem services. Despite the recent interest in phylogenetic and functional diversity, our knowledge on large spatio-temporal patterns of demersal fish diversity sampled by trawling remains still incomplete, notably in the Mediterranean Sea, one of the most threatened marine regions of the world. We investigated large spatio-temporal diversity patterns by analysing a dataset of 19,886 hauls from 10 to 800 m depth performed annually during the last two decades by standardized scientific bottom trawl field surveys across the Mediterranean Sea, within the MEDITS program. A multi-component (eight diversity indices) and multi-scale (local assemblages, biogeographic regions to basins) approach indicates that only the two most traditional components (species richness and evenness) were sufficient to reflect patterns in taxonomic, phylogenetic or functional richness and divergence. We also put into question the use of widely computed indices that allow comparing directly taxonomic, phylogenetic and functional diversity within a unique mathematical framework. In addition, demersal fish assemblages sampled by trawl do not follow a continuous decreasing longitudinal/latitudinal diversity gradients (spatial effects explained up to 70.6% of deviance in regression tree and generalized linear models), for any of the indices and spatial scales analysed. Indeed, at both local and regional scales species richness was relatively high in the Iberian region, Malta, the Eastern Ionian and Aegean seas, meanwhile the Adriatic Sea and Cyprus showed a relatively low level. In contrast, evenness as well as taxonomic, phylogenetic and functional divergences did not show regional hotspots. All studied diversity components remained stable over the last two decades. Overall, our results highlight the need to use complementary diversity indices through different spatial scales when developing conservation strategies and defining delimitations for protected areas.  
  Adresse Institute of Oceanography and Fisheries, Split, Croatia  
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  Editeur Elsevier BV Lieu de Publication Éditeur  
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  ISSN 0079-6611 ISBN Médium  
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  Notes Co-auteur au Sud Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ 32743 collection 980  
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Auteur Catherine, A.; Selma, M.; Mouillot, D.; Troussellier, M.; Bernard, C. url  doi
openurl 
  Titre Patterns and multi-scale drivers of phytoplankton species richness in temperate peri-urban lakes Type Article scientifique
  Année 2016 Publication Revue Abrégée Science of The Total Environment  
  Volume 559 Numéro Pages (up) 74-83  
  Mots-Clés Lake- and catchment-scale; Phytoplankton; Productivity–diversity relationship; Random forest; Residuals analysis; species richness  
  Résumé Local species richness (SR) is a key characteristic affecting ecosystem functioning. Yet, the mechanisms regulating phytoplankton diversity in freshwater ecosystems are not fully understood, especially in peri-urban environments where anthropogenic pressures strongly impact the quality of aquatic ecosystems. To address this issue, we sampled the phytoplankton communities of 50 lakes in the Paris area (France) characterized by a large gradient of physico-chemical and catchment-scale characteristics. We used large phytoplankton datasets to describe phytoplankton diversity patterns and applied a machine-learning algorithm to test the degree to which species richness patterns are potentially controlled by environmental factors. Selected environmental factors were studied at two scales: the lake-scale (e.g. nutrients concentrations, water temperature, lake depth) and the catchment-scale (e.g. catchment, landscape and climate variables). Then, we used a variance partitioning approach to evaluate the interaction between lake-scale and catchment-scale variables in explaining local species richness. Finally, we analysed the residuals of predictive models to identify potential vectors of improvement of phytoplankton species richness predictive models. Lake-scale and catchment-scale drivers provided similar predictive accuracy of local species richness (R2 = 0.458 and 0.424, respectively). Both models suggested that seasonal temperature variations and nutrient supply strongly modulate local species richness. Integrating lake- and catchment-scale predictors in a single predictive model did not provide increased predictive accuracy; therefore suggesting that the catchment-scale model probably explains observed species richness variations through the impact of catchment-scale variables on in-lake water quality characteristics. Models based on catchment characteristics, which include simple and easy to obtain variables, provide a meaningful way of predicting phytoplankton species richness in temperate lakes. This approach may prove useful and cost-effective for the management and conservation of aquatic ecosystems.  
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  ISSN 0048-9697 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1566  
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Auteur Reichel, K.; Masson, J.-P.; Malrieu, F.; Arnaud-Haond, S.; Stoeckel, S. doi  openurl
  Titre Rare sex or out of reach equilibrium? The dynamics of F-IS in partially clonal organisms Type Article scientifique
  Année 2016 Publication Revue Abrégée BMC Genet.  
  Volume 17 Numéro Pages (up) 76  
  Mots-Clés consequences; diversity; evolution; genetic diversity; genetic-structure; Heterozygote excess; hybridization; Inbreeding coefficient; loci; Mating system; microsatellite primers; mutation; Parthenogenesis; Partial asexuality; population-genetics; reproduction  
  Résumé Background: Partially clonal organisms are very common in nature, yet the influence of partial asexuality on the temporal dynamics of genetic diversity remains poorly understood. Mathematical models accounting for clonality predict deviations only for extremely rare sex and only towards mean inbreeding coefficient (F-IS) over bar < 0. Yet in partially clonal species, both F-IS < 0 and F-IS > 0 are frequently observed also in populations where there is evidence for a significant amount of sexual reproduction. Here, we studied the joint effects of partial clonality, mutation and genetic drift with a state-and-time discrete Markov chain model to describe the dynamics of F-IS over time under increasing rates of clonality. Results: Results of the mathematical model and simulations show that partial clonality slows down the asymptotic convergence to F-IS = 0. Thus, although clonality alone does not lead to departures from Hardy-Weinberg expectations once reached the final equilibrium state, both negative and positive F-IS values can arise transiently even at intermediate rates of clonality. More importantly, such “transient” departures from Hardy Weinberg proportions may last long as clonality tunes up the temporal variation of F-IS and reduces its rate of change over time, leading to a hyperbolic increase of the maximal time needed to reach the final mean (F-IS,F-infinity) over bar value expected at equilibrium. Conclusion: Our results argue for a dynamical interpretation of F-IS in clonal populations. Negative values cannot be interpreted as unequivocal evidence for extremely scarce sex but also as intermediate rates of clonality in finite populations. Complementary observations (e.g. frequency distribution of multiloci genotypes, population history) or time series data may help to discriminate between different possible conclusions on the extent of clonality when mean (F-IS) over bar values deviating from zero and/or a large variation of F-IS over loci are observed.  
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  ISSN 1471-2156 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1648  
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