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Auteur Chevrinais, M.; Jacquet, C.; Cloutier, R. doi  openurl
  Titre Early establishment of vertebrate trophic interactions: Food web structure in Middle to Late Devonian fish assemblages with exceptional fossilization Type Article scientifique
  Année 2017 Publication Revue Abrégée Bull. Geosci.  
  Volume 92 Numéro 4 Pages 491-510  
  Mots-Clés north-america; bottom-up; body-size; predator; top-down; bottom-up control; coordinated stasis; Devonian; digestive contents; ecomorphology; escuminac formation; foraging ecology; fossil fish; fossil record; pahteoecology; prey size relationships; top-down control  
  Résumé In past and present ecosystems, trophic interactions determine material and energy transfers among species, regulating population dynamics and community stability. Food web studies in past ecosystems are helpful to assess the persistence of ecosystem structure throughout geological times and to explore the existence of general principles of food web assembly. We determined and compared the trophic structure of two Devonian fish assemblages [(1) the Escuminac assemblage (ca. 380 Ma), Miguasha, eastern Canada and (2) the Lode assemblage (ca. 390 Ma), Straupe, Latvia] with a closer look at the Escuminac assemblage. Both localities are representative of Middle to Late Devonian aquatic vertebrate assemblages in terms of taxonomic richness (ca. 20 species), phylogenetic diversity (all major groups of lower vertebrates) and palaeoenvironment (palaeoestuaries). Fossil food web structures were assessed using different kinds of direct (i.e. digestive contents and bite marks in fossils) and indirect (e.g. ecomoiphological measurements, stratigraphic species co-occurrences) indicators. First, the relationships between predator and prey body size established for the Escuminac fishes are comparable to those of recent aquatic ecosystems, highlighting a consistency of aquatic food web structure across geological time. Second, non-metric dimensional scaling on ecomorphological variables and cluster analysis showed a common pattern of functional groups for both fish assemblages; top predators, predators, primary and secondary consumers were identified. We conclude that Devonian communities were organized in multiple trophic levels and that size-based feeding interactions were established early in vertebrate history.  
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  ISSN 1214-1119 ISBN Médium  
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Auteur Silva Junior, C. a. B.; Mérigot, B.; Lucena-Fredou, F.; Ferreira, B.P.; Coxey, M.S.; Rezende, S.M.; Fredou, T. doi  openurl
  Titre Functional diversity of fish in tropical estuaries: A traits-based approach of communities in Pernambuco, Brazil Type Article scientifique
  Année 2017 Publication Revue Abrégée Estuar. Coast. Shelf Sci.  
  Volume 198 Numéro Pages 413-420  
  Mots-Clés patterns; biodiversity; evolutionary; assemblages; species richness; Monitoring; marine ecosystems; quadratic entropy; Diversity indices; organization; Double principal coordinate analysis; Estuarine ecosystems; Species function; redundancy; services  
  Résumé Environmental changes and human activities may have strong impacts on biodiversity and ecosystem functioning. While biodiversity is traditionally based on species richness and composition, there is a growing concern to take into account functional diversity to assess and manage species communities. In spite of their economic importance, functional diversity quantified by a traits-based approach is still poorly documented in tropical estuaries. In this study, the functional diversity of fishes was investigated within four estuaries in Pernambuco state, northeast of Brazil. These areas are subject to different levels of human impact (e.g. mangrove deforestation, shrimp farming, fishing etc.) and environmental conditions. Fishes were collected during 34 scientific surveys. A total of 122 species were identified and 12 functional traits were quantified describing two main functions: food acquisition and locomotion. Fish abundance and functional dissimilarities data were combined into a multivariate analysis, the Double Principal Coordinate Analysis, to identify the functional typology of fish assemblages according to the estuary. Results showed that Itapissuma, the largest estuary with a wider mangrove forest area, differs from the other three estuaries, showing higher mean values per samples of species richness S and quadratic entropy Q. Similarly, it presented a different functional typology (the first two axes of the DPCoA account for 68.7% of total inertia, while those of a traditional PCA based solely on species abundances provided only 17.4%). Conversely, Suape, Sirinhaem, and to a lower extent Rio Formoso, showed more similarity in their diversity. This result was attributed to their predominantly marine influenced hydrological features, and similar levels of species abundances and in morphological traits. Overall, this study, combining diversity indices and a recent multivariate analysis to access species contribution to functional typology, allows to deepen diversity assessment by providing additional information regarding the functional pattern of fish assemblages. (C) 2016 Elsevier Ltd. All rights reserved.  
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Auteur Sardenne, F.; Hollanda, S.; Lawrence, S.; Albert-Arrisol, R.; Degroote, M.; Bodin, N. doi  openurl
  Titre Trophic structures in tropical marine ecosystems: a comparative investigation using three different ecological tracers Type Article scientifique
  Année 2017 Publication Revue Abrégée Ecol. Indic.  
  Volume 81 Numéro Pages 315-324  
  Mots-Clés feeding-behavior; Stable isotopes; food webs; Fatty acids; Mercury; western indian-ocean; gulf-of-mexico; amino-acid; stable-isotope; bioaccumulation; fatty-acid compositions; Indian ocean; mercury exposure; pelagic fishes; Tropical food web  
  Résumé We looked at how three ecological tracers may influence the characterization and interpretation of trophic structures in a tropical marine system, with a view to informing tracer(s) selection in future trophic ecology studies. We compared the trophic structures described by stable isotope compositions (carbon and nitrogen), the total mercury concentration (THg) and levels of essential fatty acids (EFA) at both the individual and species level. Analyses were undertaken on muscle tissue samples from fish and crustacean species caught in the waters surrounding the Seychelles. The carbon isotope composition (delta C-13) correlated to the proportion of arachidonic acid (ARA), whereas the nitrogen isotope composition (delta N-15) correlated to the proportion of docosahexaenoic acid (DHA) and THg. At the individual level, trophic position obtained with these three last tracers are similar. In ' contrast, the eicosapentaenoic acid (EPA) was not clearly correlated to any of the tracers. At the species level, the use of EFA (ARA and DHA), as compared to stable isotopes, resulted in slight structural modifications, mainly in the middle trophic levels. For example, the EFA overestimated the trophic positions of Thunnus alalunga and Etelis coruscans but underestimated the trophic positions of other snappers and groupers. While ARA mainly originates from coastal/benthic areas, DHA is conserved throughout the food web and may be used as a proxy indicator of trophic position. However, metabolic disparities can affect ecological tracers and in turn, distort the trophic structures derived from their results. This is especially true for species with close trophic ecologies. Despite these caveats, we think that analysing at the individual level the wealth of ARA, DHA and THg data that has already been obtained through earlier nutrition or food security studies would enhance our understanding of trophic structures.  
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  ISSN 1470-160x ISBN Médium  
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Auteur Sirot, C.; Ferraton, F.; Panfili, J.; Childs, A.-R.; Guilhaumon, F.; Darnaude, A.M. doi  openurl
  Titre elementr: An R package for reducing elemental data from LA-ICPMS analysis of biological calcified structures Type Article scientifique
  Année 2017 Publication Revue Abrégée Methods Ecol. Evol.  
  Volume 8 Numéro 12 Pages 1659-1667  
  Mots-Clés fish; temperature; estuarine; microchemistry; otolith microchemistry; graphical user interface; spot and transect reduction; fingerprints; laser ablation; melt inclusions; ms; object-oriented programming; plasma-mass-spectrometry; portuguese coast; trace  
  Résumé 1. Elemental analysis of biological calcified structures (e.g. fish otoliths, mollusc shelves, coral skeletons or fish and shark bones) provides invaluable information regarding ecological processes for many aquatic species. Despite this importance, the reduction of the raw data obtained through Laser-ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICPMS) (i.e. the conversion of the machine raw signal into elemental concentrations) remains a challenge as the tools developed so far for carrying out this task have important limitations for aquatic ecologists. 2. Here, we introduce the elementr R-package which provides a handy, reliable and transparent way to reduce elemental data acquired from spot or transect LA-ICPMS analysis of biological calcified structures. This free and open-source software, implemented based on state-of-the-art literature, handles data from both standards and samples, allowing fast and simultaneous calculations of concentration for any chemical element, correction for potential machine drift, and realignment and averaging for sample replicates when needed. 3. The major attributes of elementr are: (i) its user-friendly graphical interface which provides widgets to set all the reduction settings (i.e. no programming skills are required to run it), (ii) its reactivity whereby the software continuously observes any setting change made by the user, re-calculates and displays all updated results, allowing therefore users to visually check the validity of their settings and to tune them if needed and (iii) an object oriented underlying that facilitates subsequent handling of LA-ICPMS data in R. 4. Despite the elementr design being most suited to the needs of aquatic ecologists, its use could be broadened to other research fields (i.e. geology, material engineering) due to its flexibility. Moreover, the open-source approach used for programming this software allows its expansion in order to refine calculation procedures or to add new functionalities.  
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  ISSN 2041-210x ISBN Médium  
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Auteur Bakker, J.; Wangensteen, O.S.; Chapman, D.D.; Boussarie, G.; Buddo, D.; Guttridge, T.L.; Hertler, H.; Mouillot, D.; Vigliola, L.; Mariani, S. doi  openurl
  Titre Environmental DNA reveals tropical shark diversity in contrasting levels of anthropogenic impact Type Article scientifique
  Année 2017 Publication Revue Abrégée Sci Rep  
  Volume 7 Numéro Pages 16886  
  Mots-Clés management; ecosystem; conservation; fish communities; rays; populations; collapse; aquatic biodiversity; coral-reef fisheries; wilderness  
  Résumé Sharks are charismatic predators that play a key role in most marine food webs. Their demonstrated vulnerability to exploitation has recently turned them into flagship species in ocean conservation. Yet, the assessment and monitoring of the distribution and abundance of such mobile species in marine environments remain challenging, often invasive and resource-intensive. Here we pilot a novel, rapid and non-invasive environmental DNA (eDNA) metabarcoding approach specifically targeted to infer shark presence, diversity and eDNA read abundance in tropical habitats. We identified at least 21 shark species, from both Caribbean and Pacific Coral Sea water samples, whose geographical patterns of diversity and read abundance coincide with geographical differences in levels of anthropogenic pressure and conservation effort. We demonstrate that eDNA metabarcoding can be effectively employed to study shark diversity. Further developments in this field have the potential to drastically enhance our ability to assess and monitor elusive oceanic predators, and lead to improved conservation strategies.  
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