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Auteur Cox, S.L.; Embling, C.B.; Hosegood, P.J.; Votier, S.C.; Ingram, S.N. doi  openurl
  Titre Oceanographic drivers of marine mammal and seabird habitat-use across shelf-seas: A guide to key features and recommendations for future research and conservation management Type Article scientifique
  Année 2018 Publication Revue Abrégée Estuar. Coast. Shelf Sci.  
  Volume 212 Numéro Pages (down) 294-310  
  Mots-Clés Bio-physical coupling; bottle-nosed dolphins; california current system; coastal upwelling system; Conservation management; ecosystem-based management; Foraging ecology; Habitat selection; Marine mammals; Oceanography; porpoise phocoena-phocoena; predator-prey interactions; Seabirds; southeastern bering-sea; st-george island; thin zooplankton layers; tidal-stream environments  
  Résumé Mid-latitude (similar to 30-60 degrees) seasonally stratifying shelf-seas support a high abundance and diversity of marine predators such as marine mammals and seabirds. However, anthropogenic activities and climate change impacts are driving changes in the distributions and population dynamics of these animals, with negative consequences for ecosystem functioning. Across mid-latitude shelf-seas marine mammals and seabirds are known to forage across a number of oceanographic habitats that structure the spatio-temporal distributions of prey fields. Knowledge of these and the bio-physical mechanisms driving such associations are needed to improve marine management and policy. Here, we provide a concise and easily accessible guide for both researchers and managers of marine systems on the predominant oceanographic habitats that are favoured for foraging by marine mammals and seabirds across mid-latitude shelf-seas. We (1) identify and describe key discrete physical features present across the continental shelf, working inshore from the shelf-edge to the shore line, (2) provide an overview of findings relating to associations between these habitats and marine mammals and seabirds, (3) identify areas for future research and (4) discuss the relevance of such information to conservation management. We show that oceanographic features preferentially foraged at by marine mammals and seabirds include shelf edge fronts, upwelling and tidal-mixing fronts, offshore banks and internal waves, regions of stratification, and topographically complex coastal areas subject to strong tidal flow. Whilst associations were variable across taxa and through space and time, in the majority of cases interactions between bathymetry and tidal currents appear to play a dominant role, alongside patterns in seasonal stratification and shelf-edge upwelling. We suggest that the ecological significance of these bio-physical structures stems from a capacity to alter the densities, distributions (both horizontally and vertically) and/or behaviours of prey in a persistent and/or predictable manner that increases accessibility for predators, and likely enhances foraging efficiency. Future conservation management should aim to preserve and protect these habitats. This will require adaptive and holistic strategies that are specifically tailored to the characteristics of an oceanographic feature, and where necessary, evolve through space and time in response to spatio-temporal variability. Improved monitoring of animal movements and biophysical conditions across shelf-seas would aid in this. Areas for future research include multi-disciplinary/ trophic studies of the mechanisms linking bio-physical processes, prey and marine mammals and seabirds (which may elucidate the importance of lesser studied features such as bottom fronts and Langmuir circulation cells), alongside a better understanding of how predators perceive their environment and develop foraging strategies during immature/juvenile stages. Estimates of the importance of oceanographic habitat features at a population level should also be obtained. Such information is vital to ensuring the future health of these complex ecosystems, and can be used to assess how anthropogenic activities and future environmental changes will impact the functioning and spatio-temporal dynamics of these bio-physical features and their use by marine predators.  
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  Langue English Langue du Résumé Titre Original  
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  Volume de collection Numéro de collection Edition  
  ISSN 0272-7714 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2428  
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Auteur Grenie, M.; Mouillot, D.; Villeger, S.; Denelle, P.; Tucker, C.M.; Munoz, F.; Violle, C. doi  openurl
  Titre Functional rarity of coral reef fishes at the global scale: Hotspots and challenges for conservation Type Article scientifique
  Année 2018 Publication Revue Abrégée Biol. Conserv.  
  Volume 226 Numéro Pages (down) 288-299  
  Mots-Clés biodiversity; Biodiversity facet; Coral triangle; diversity; ecology; ecosystem processes; Evolutionary distinctiveness; Functional distinctiveness; Funrar; marine-protected areas; ocean acidification; redundancy; species richness; trait; vulnerability  
  Résumé Characterizing functional diversity has become central in ecological research and for biodiversity assessment. Understanding the role of species with rare traits, i.e. functionally rare species, in community assembly, ecosystem dynamics and functioning has recently gained momentum. However, functional rarity is still ignored in conservation strategies. Here, we quantified global functional and evolutionary rarity for 2073 species of coral reef fishes and compared the rarity values to IUCN Red List status. Most species were functionally common but geographically rare. However, we found very weak correlation between functional rarity and evolutionary rarity. Functional rarity was highest for species classified as not evaluated or threatened by the IUCN Red List. The location of functional rarity hotspots (Tropical Eastern Pacific) did not match hotspots of species richness and evolutionary distinctiveness (Indo-Australian Archipelago), nor the currently protected areas. We argue that functional rarity should be acknowledged for both species and site prioritization in conservation strategies.  
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  Volume de collection Numéro de collection Edition  
  ISSN 0006-3207 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2434  
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Auteur Young, J.W.; Olson, R.J.; Ménard, F.; Kuhnert, P.M.; Duffy, L.M.; Allain, V.; Logan, J.M.; Lorrain, A.; Somes, C.J.; Graham, B.; Goñi, N.; Pethybridge, H.; Simier, M.; Potier, M.; Romanov, E.; Pagendam, D.; Hannides, C.; Choy, C.A. url  doi
openurl 
  Titre Setting the stage for a global-scale trophic analysis of marine top predators: a multi-workshop review Type Article scientifique
  Année 2015 Publication Revue Abrégée Rev Fish Biol Fisheries  
  Volume 25 Numéro 1 Pages (down) 261-272  
  Mots-Clés climate change; Freshwater & Marine Ecology; Global diet data; Global nitrogen model; Global stable isotope data; Predictive analyses; top predators; Tuna trophic ecology; Zoology  
  Résumé Global-scale studies of marine food webs are rare, despite their necessity for examining and understanding ecosystem level effects of climate variability. Here we review the progress of an international collaboration that compiled regional diet datasets of multiple top predator fishes from the Indian, Pacific and Atlantic Oceans and developed new statistical methods that can be used to obtain a comprehensive ocean-scale understanding of food webs and climate impacts on marine top predators. We loosely define top predators not as species at the apex of the food web, but rather a guild of large predators near the top of the food web. Specifically, we present a framework for world-wide compilation and analysis of global stomach-contents and stable-isotope data of tunas and other large pelagic predatory fishes. To illustrate the utility of the statistical methods, we show an example using yellowfin tuna in a “test” area in the Pacific Ocean. Stomach-contents data were analyzed using a modified (bagged) classification tree approach, which is being prepared as an R statistical software package. Bulk δ15N values of yellowfin tuna muscle tissue were examined using a Generalized Additive Model, after adjusting for spatial differences in the δ15N values of the baseline primary producers predicted by a global coupled ocean circulation-biogeochemical-isotope model. Both techniques in tandem demonstrated the capacity of this approach to elucidate spatial patterns of variations in both forage species and predator trophic positions and have the potential to predict responses to climate change. We believe this methodology could be extended to all marine top predators. Our results emphasize the necessity for quantitative investigations of global-scale datasets when evaluating changes to the food webs underpinning top ocean predators under long-term climatic variability.  
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  Volume de collection Numéro de collection Edition  
  ISSN 0960-3166, 1573-5184 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1263  
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Auteur Lett, C.; Semeria, M.; Thiebault, A.; Tremblay, Y. url  doi
openurl 
  Titre Effects of successive predator attacks on prey aggregations Type Article scientifique
  Année 2014 Publication Revue Abrégée Theor Ecol  
  Volume 7 Numéro 3 Pages (down) 239-252  
  Mots-Clés Animal aggregation; Animal group; Attraction-repulsion model; Flock; Plant Sciences; School; Swarm; Theoretical Ecology/Statistics; Zoology  
  Résumé We study the cumulative effect of successive predator attacks on the disturbance of a prey aggregation using a modelling approach. Our model intends to represent fish schools attacked by both aerial and underwater predators. This individual-based model uses long-distance attraction and short-distance repulsion between prey, which leads to prey aggregation and swarming in the absence of predators. When intermediate-distance alignment is added to the model, the prey aggregation displays a cohesive displacement, i.e., schooling, instead of swarming. Including predators, i.e. with repulsion behaviour for prey to predators in the model, leads to flash expansion of the prey aggregation after a predator attack. When several predators attack successively, the prey aggregation dynamics is a succession of expanding-grouping-swarming/schooling phases. We quantify this dynamics by recording the changes in the simulated prey aggregation radius over time. This radius is computed as the longest distance of individual prey to the aggregation centroid, and it is assumed to increase along with prey disturbance. The prey aggregation radius generally increases during flash expansion, then decreases during grouping until reaching a constant lowest level during swarming/schooling. This general dynamics is modulated by several parameters: the frequency, direction (vertical vs. horizontal) and target (centroid of the prey aggregation vs. random prey) of predator attacks; the distance at which prey detect predators; the number of prey and predators. Our results suggest that both aerial and underwater predators are more efficient at disturbing fish schools by increasing their attack frequency at such level that the fish cannot return to swarming/schooling. We find that a mix between aerial and underwater predators is more efficient at disturbing a fish school than a single type of attack, suggesting that aerial and underwater foragers may gain mutual benefits in forming foraging groups.  
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  Volume de collection Numéro de collection Edition  
  ISSN 1874-1738, 1874-1746 ISBN Médium  
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  Numéro d'Appel LL @ pixluser @ collection 350  
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Auteur Brandt, M.; Trouche, B.; Henry, N.; Liautard-Haag, C.; Maignien, L.; de Vargas, C.; Wincker, P.; Poulain, J.; Zeppilli, D.; Arnaud-Haond, S. doi  openurl
  Titre An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities Type Article scientifique
  Année 2020 Publication Revue Abrégée Front. Mar. Sci.  
  Volume 7 Numéro Pages (down) 234  
  Mots-Clés benthic ecology; biomonitoring; deep-sea biodiversity; diversity; environmental metabarcoding; extracellular dna; extracellular DNA; extraction; foraminifera; impacts; method testing; preservation; RNA versus DNA; sediments; taxa  
  Résumé The abyssal seafloor covers more than 50% of planet Earth and is a large reservoir of still mostly undescribed biodiversity. It is increasingly targeted by resource-extraction industries and yet is drastically understudied. In such remote and hard-to-access ecosystems, environmental DNA (eDNA) metabarcoding is a useful and efficient tool for studying biodiversity and implementing environmental impact assessments. Yet, eDNA analysis outcomes may be biased toward describing past rather than present communities as sediments contain both contemporary and ancient DNA. Using commercially available kits, we investigated the impacts of five molecular processing methods on eDNA metabarcoding biodiversity inventories targeting prokaryotes (16S), unicellular eukaryotes (18S-V4), and metazoans (18S-V1, COI). As the size distribution of ancient DNA is skewed toward small fragments, we evaluated the effect of removing short DNA fragments via size selection and ethanol reconcentration using eDNA extracted from 10 g of sediment at five deep-sea sites. We also compare communities revealed by eDNA and environmental RNA (eRNA) co-extracted from similar to 2 g of sediment at the same sites. Results show that removing short DNA fragments does not affect alpha and beta diversity estimates in any of the biological compartments investigated. Results also confirm doubts regarding the possibility to better describe live communities using eRNA. With ribosomal loci, eRNA, while resolving similar spatial patterns than co-extracted eDNA, resulted in significantly higher richness estimates, supporting hypotheses of increased persistence of ribosomal RNA (rRNA) in the environment and unmeasured bias due to overabundance of rRNA and RNA release. With the mitochondrial locus, eRNA detected lower metazoan richness and resolved fewer spatial patterns than co-extracted eDNA, reflecting high messenger RNA lability. Results also highlight the importance of using large amounts of sediment (>= 10 g) for accurately surveying eukaryotic diversity. We conclude that eDNA should be favored over eRNA for logistically realistic, repeatable, and reliable surveys and confirm that large sediment samples (>= 10 g) deliver more complete and accurate assessments of benthic eukaryotic biodiversity and that increasing the number of biological rather than technical replicates is important to infer robust ecological patterns.  
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  ISSN ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2791  
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