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Auteur (up) Ménard, F.; Potier, M.; Jaquemet, S.; Romanov, E.; Sabatié, R.; Cherel, Y. url  doi
openurl 
  Titre Pelagic cephalopods in the western Indian Ocean: New information from diets of top predators Type Article scientifique
  Année 2013 Publication Revue Abrégée Deep Sea Research Part II: Topical Studies in Oceanography  
  Volume 95 Numéro Pages 83-92  
  Mots-Clés ecology; Trophic  
  Résumé Using a combination of diverse large predatory fishes and one seabird, we collected information on the cephalopod fauna of the western Indian Ocean. We analyzed the stomach contents of 35 fishes representing ten families (Xiphiidae, Istiophoridae, Scombridae, Carangidae, Coryphaenidae, Alepisauridae, Dasyatidae, Carcharhinidae, Alopiidae and Sphyrnidae) and of the sooty tern Onychoprion fuscata of the Mozambique Channel from 2000 to 2010. Both fresh and accumulated beaks were used for identifying cephalopod prey. Cephalopods were important prey for twelve predators; swordfish Xiphias gladius had the highest cephalopod proportion; sooty tern (O. fuscata) and bigeye tuna (Thunnus obesus) had high proportions too. We recovered 23 cephalopod families and identified 38 species. Ten species from four Teuthida families (Ommastrephidae, Onychoteuthidae, Histioteuthidae and Ancistrocheiridae) and two Octopoda families (Argonautidae and Bolitaenidae) occurred very frequently in the stomach contents, while Sepiida were rare. Ommastrephidae were the most cephalopod food sources: the purpleback flying squid Sthenoteuthis oualaniensis was the most prevalent prey by far, Ornithoteuthis volatilis was important for eleven predators and few but large specimens of the neon flying squid Ommastrephes bartramii were recovered in the stomachs of swordfish in the Indian South Subtropical Gyre province only. Predators' groups were identified based on cephalopod prey composition, on depth in which they forage, and on prey size. Surface predators' diets were characterized by lower cephalopod diversity but greater average numbers of cephalopod prey, whereas the deep-dwelling predators (swordfish and bigeye tuna) preyed on larger specimens than surface predators (O. fuscata or yellowfin tunas Thunnus albacares). Our findings emphasized the usefulness of a community of marine predators to gain valuable information on the biology and the distribution of the cephalopod forage fauna that are discussed with regard to biogeographic province, marine predator, fishing gear to catch the large pelagic fishes, and size of the beaks recovered in the stomachs.  
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  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0967-0645 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel LL @ pixluser @ collection 291  
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Auteur (up) Meynard, C.N.; Kaplan, D. url  doi
openurl 
  Titre Using virtual species to study species distributions and model performance Type Article scientifique
  Année 2013 Publication Revue Abrégée Journal of Biogeography  
  Volume 40 Numéro 1 Pages 1-8  
  Mots-Clés Auc; predictive ecology; presence-absence; prevalence; Sensitivity; simulations; specificity; threshold; virtual species  
  Résumé Simulations of virtual species (i.e. species for which the environmentoccupancy relationships are known) are increasingly being used to test the effects of different aspects of modelling and sampling strategy on performance of species distribution models (SDMs). Here we discuss an important step of the simulation process: the translation of simulated probabilities of occurrence into patterns of presence and absence. Often a threshold strategy is used to generate virtual occurrences, where presence always occurs above a specific simulated probability value and never below. This procedure effectively translates any shape of simulated species response into a threshold one and eliminates any stochasticity from the species occupancy pattern. We argue that a probabilistic approach should be preferred instead because the threshold response can be treated as a particular case within this framework. This also allows one to address questions relating to the shape of functional responses and avoids convergence issues with some of the most common SDMs. Furthermore, threshold-based virtual species studies generate over-optimistic performance measures that lack classification error or incorporate error from a mixture of sampling and modelling choices. Incorrect use of a threshold approach can have significant consequences for the practising biogeographer. For example, low model performance may be interpreted as due to sample bias or poor model choice, rather than being related to fundamental biological responses to environmental gradients. We exemplify these shortcomings with a case study where we compare results from threshold and probabilistic simulation approaches.  
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  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 0305-0270 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel LL @ pixluser @ collection 246  
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Auteur (up) Meynard, C.N.; Kaplan, D.M.; Leroy, B. doi  openurl
  Titre Detecting outliers in species distribution data: Some caveats and clarifications on a virtual species study Type Article scientifique
  Année 2019 Publication Revue Abrégée J. Biogeogr.  
  Volume 46 Numéro 9 Pages 2141-2144  
  Mots-Clés enm; observation errors; outliers; prevalence; probabilistic approach; sample bias; simulations; species distribution models; thresholds; virtual ecology; virtual species  
  Résumé Liu et al. (2018) used a virtual species approach to test the effects of outliers on species distribution models. In their simulations, they applied a threshold value over the simulated suitabilities to generate the species distributions, suggesting that using a probabilistic simulation approach would have been more complex and yield the same results. Here, we argue that using a probabilistic approach is not necessarily more complex and may significantly change results. Although the threshold approach may be justified under limited circumstances, the probabilistic approach has multiple advantages. First, it is in line with ecological theory, which largely assumes non-threshold responses. Second, it is more general, as it includes the threshold as a limiting case. Third, it allows a better separation of the relevant intervening factors that influence model performance. Therefore, we argue that the probabilistic simulation approach should be used as a general standard in virtual species studies.  
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  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 0305-0270 ISBN Médium  
  Région Expédition Conférence  
  Notes WOS:000483602900019 Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2640  
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Auteur (up) Mostajir, B.; Amblard, C.; Buffan-Dubau, E.; De Wit, R.; Lensi, R.; Sime-Ngando, T. url  isbn
openurl 
  Titre Microbial Food Webs in Aquatic and Terrestrial Ecosystems Type Chapitre de livre
  Année 2015 Publication Revue Abrégée  
  Volume Numéro Pages 485-509  
  Mots-Clés Biodiversity; Biogeochemical cycles; Ecological interactions; Microbial Ecology; Microbial food webs; Microbial loop  
  Résumé In microbial food webs, different types of interactions occur between microorganisms themselves and with meio- and macroorganisms. After an historical and general introduction, the biological components of the microbial food webs in the pelagic and benthic marine and lake ecosystems, as well as in the terrestrial ecosystems, are presented. The functioning of the microbial food webs in different ecosystems is illustrated and explained, including the trophic pathways and transfer of matter from microbial food webs toward meio- and macroorganisms of the superior trophic levels, the nutrient recycling in the aquatic environments, and the decomposition of organic matter in soils. Finally, the factors regulating microbial food webs, primarily “top-down” and “bottom-up” controls, are described with a special focus on the role of viruses in the aquatic microbial food webs.  
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  Editeur Springer Netherlands Lieu de Publication Éditeur Bertrand, J.-C.; Caumette, P.; Lebaron, P.; Matheron, R.; Normand, P.; Sime-Ngando, T.  
  Langue en Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé Environmental Microbiology: Fundamentals and Applications  
  Volume de collection Numéro de collection Edition  
  ISSN ISBN 978-94-017-9117-5 978-94-017-9118-2 Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ alain.herve @ collection 1394  
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Auteur (up) Mouquet, N.; Devictor, V.; Meynard, C.N.; Munoz, F.; Bersier, L.-F.; Chave, J.; Couteron, P.; Dalecky, A.; Fontaine, C.; Gravel, D.; Hardy, O.J.; Jabot, F.; Lavergne, S.; Leibold, M.; Mouillot, D.; Münkemüller, T.; Pavoine, S.; Prinzing, A.; Rodrigues, A.S.L.; Rohr, R.P.; Thébault, E.; Thuiller, W. url  doi
openurl 
  Titre Ecophylogenetics: advances and perspectives Type Article scientifique
  Année 2012 Publication Revue Abrégée Biological Reviews  
  Volume 87 Numéro 4 Pages 769-785  
  Mots-Clés community ecology; conservation biology; ecological networks; ecophylogenetics; Ecosystem functioning; evolution; phylogenetics  
  Résumé Ecophylogenetics can be viewed as an emerging fusion of ecology, biogeography and macroevolution. This new and fast-growing field is promoting the incorporation of evolution and historical contingencies into the ecological research agenda through the widespread use of phylogenetic data. Including phylogeny into ecological thinking represents an opportunity for biologists from different fields to collaborate and has provided promising avenues of research in both theoretical and empirical ecology, towards a better understanding of the assembly of communities, the functioning of ecosystems and their responses to environmental changes. The time is ripe to assess critically the extent to which the integration of phylogeny into these different fields of ecology has delivered on its promise. Here we review how phylogenetic information has been used to identify better the key components of species interactions with their biotic and abiotic environments, to determine the relationships between diversity and ecosystem functioning and ultimately to establish good management practices to protect overall biodiversity in the face of global change. We evaluate the relevance of information provided by phylogenies to ecologists, highlighting current potential weaknesses and needs for future developments. We suggest that despite the strong progress that has been made, a consistent unified framework is still missing to link local ecological dynamics to macroevolution. This is a necessary step in order to interpret observed phylogenetic patterns in a wider ecological context. Beyond the fundamental question of how evolutionary history contributes to shape communities, ecophylogenetics will help ecology to become a better integrative and predictive science.  
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  Langue Langue du Résumé Titre Original  
  Éditeur de collection Titre de collection Titre de collection Abrégé  
  Volume de collection Numéro de collection Edition  
  ISSN 1469-185x ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 556  
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