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Auteur Teixido, N.; Gambi, M.C.; Parravacini, V.; Kroeker, K.; Micheli, F.; Villeger, S.; Ballesteros, E. doi  openurl
  Titre Functional biodiversity loss along natural CO2 gradients Type Article scientifique
  Année 2018 Publication Revue Abrégée Nat. Commun.  
  Volume 9 Numéro Pages 5149  
  Mots-Clés carbon; community; consequences; diversity; fish; impact; ocean acidification; redundancy; reveals; vulnerability  
  Résumé The effects of environmental change on biodiversity are still poorly understood. In particular, the consequences of shifts in species composition for marine ecosystem function are largely unknown. Here we assess the loss of functional diversity, i.e. the range of species biological traits, in benthic marine communities exposed to ocean acidification (OA) by using natural CO2 vent systems. We found that functional richness is greatly reduced with acidification, and that functional loss is more pronounced than the corresponding decrease in taxonomic diversity. In acidified conditions, most organisms accounted for a few functional entities (i.e. unique combination of functional traits), resulting in low functional redundancy. These results suggest that functional richness is not buffered by functional redundancy under OA, even in highly diverse assemblages, such as rocky benthic communities.  
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  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 2041-1723 ISBN Médium  
  Région Expédition Conférence  
  Notes Approuvé pas de  
  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2477  
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Auteur Villon, S.; Mouillot, D.; Chaumont, M.; Darling, E.S.; Subsol, G.; Claverie, T.; Villeger, S. doi  openurl
  Titre A Deep learning method for accurate and fast identification of coral reef fishes in underwater images Type Article scientifique
  Année 2018 Publication Revue Abrégée Ecol. Inform.  
  Volume 48 Numéro Pages 238-244  
  Mots-Clés Automated identification; Convolutional neural network; density; Machine learning; Marine fishes; neural-networks; system; temperate; Underwater pictures; video stations; visual census; vulnerability  
  Résumé Identifying and counting fish individuals on photos and videos is a crucial task to cost-effectively monitor marine biodiversity, yet it remains difficult and time-consuming. In this paper, we present a method to assist the identification of fish species on underwater images, and we compare our model performances to human ability in terms of speed and accuracy. We first tested the performance of a convolutional neural network (CNN) trained with different photographic databases while accounting for different post-processing decision rules to identify 20 fish species. Finally, we compared the performance of species identification of our best CNN model with that of humans on a test database of 1197 fish images representing nine species. The best CNN was the one trained with 900,000 images including (i) whole fish bodies, (ii) partial fish bodies and (iii) the environment (e.g. reef bottom or water). The rate of correct identification was 94.9%, greater than the rate of correct identification by humans (89.3%). The CNN was also able to identify fish individuals partially hidden behind corals or behind other fish and was more effective than humans to identify fish on smallest or blurry images while humans were better to identify fish individuals in unusual positions (e.g. twisted body). On average, each identification by our best CNN using a common hardware took 0.06 s. Deep Learning methods can thus perform efficient fish identification on underwater images and offer promises to build-up new video-based protocols for monitoring fish biodiversity cheaply and effectively.  
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  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 1574-9541 ISBN Médium  
  Région Expédition Conférence  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2475  
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Auteur Chiarello, M.; Auguet, J.-C.; Bettarel, Y.; Bouvier, C.; Claverie, T.; Graham, N.A.J.; Rieuvilleneuve, F.; Sucre, E.; Bouvier, T.; Villeger, S. doi  openurl
  Titre Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet Type Article scientifique
  Année 2018 Publication Revue Abrégée Microbiome  
  Volume 6 Numéro Pages 147  
  Mots-Clés bacterial communities; divergence; diversity; evolution; insights; life-history; Microbiota; mucus; patterns; Phylogenetic diversity; Phylogenetic signal; Phylosymbiosis; sequence data; Teleost; Tropical; vulnerability  
  Résumé Background: The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health of their host While such microbiomes have been deeply examined in marine invertebrates such as corals and sponges, the microbiomes living on marine vertebrates have received less attention. Specifically, the diversity of these microbiomes, their variability among species, and their drivers are still mostly unknown, especially among the fish species living on coral reefs that contribute to key ecosystem services while they are increasingly affected by human activities. Here, we investigated these knowledge gaps analyzing the skin microbiome of 138 fish individuals belonging to 44 coral reef fish species living in the same area. Results: Prokaryotic communities living on the skin of coral reef fishes are highly diverse, with on average more than 600 OTUs per fish, and differ from planktonic microbes. Skin microbiomes varied between fish individual and species, and interspecific differences were slightly coupled to the phylogenetic affiliation of the host and its ecological traits. Conclusions: These results highlight that coral reef biodiversity is greater than previously appreciated, since the high diversity of macro-organisms supports a highly diversified microbial community. This suggest that beyond the loss of coral reefs-associated macroscopic species, anthropic activities on coral reefs could also lead to a loss of still unexplored host-associated microbial diversity, which urgently needs to be assessed.  
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  Volume de collection Numéro de collection Edition  
  ISSN 2049-2618 ISBN Médium  
  Région Expédition Conférence  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 2421  
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Auteur D'agata, S.; Mouillot, D.; Wantiez, L.; Friedlander, A.M.; Kulbicki, M.; Vigliola, L. doi  openurl
  Titre Marine reserves lag behind wilderness in the conservation of key functional roles Type Article scientifique
  Année 2016 Publication Revue Abrégée Nat. Commun.  
  Volume 7 Numéro Pages 12000  
  Mots-Clés biodiversity; coral-reef fishes; diversity indexes; ecosystem; new-caledonia; population-density; protected areas; species richness; visual-census; vulnerability  
  Résumé Although marine reserves represent one of the most effective management responses to human impacts, their capacity to sustain the same diversity of species, functional roles and biomass of reef fishes as wilderness areas remains questionable, in particular in regions with deep and long-lasting human footprints. Here we show that fish functional diversity and biomass of top predators are significantly higher on coral reefs located at more than 20 h travel time from the main market compared with even the oldest (38 years old), largest (17,500 ha) and most restrictive (no entry) marine reserve in New Caledonia (South-Western Pacific). We further demonstrate that wilderness areas support unique ecological values with no equivalency as one gets closer to humans, even in large and well-managed marine reserves. Wilderness areas may therefore serve as benchmarks for management effectiveness and act as the last refuges for the most vulnerable functional roles.  
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  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 2041-1723 ISBN Médium  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1625  
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Auteur Mouillot, D.; Parravicini, V.; Bellwood, D.R.; Leprieur, F.; Huang, D.; Cowman, P.F.; Albouy, C.; Hughes, T.P.; Thuiller, W.; Guilhaumon, F. doi  openurl
  Titre Global marine protected areas do not secure the evolutionary history of tropical corals and fishes Type Article scientifique
  Année 2016 Publication Revue Abrégée Nat. Commun.  
  Volume 7 Numéro Pages 10359  
  Mots-Clés Biodiversity; conservation; extinction risk; functional diversity; management; patterns; phylogenetic diversity; reef fisheries; species richness; vulnerability  
  Résumé Although coral reefs support the largest concentrations of marine biodiversity worldwide, the extent to which the global system of marine-protected areas (MPAs) represents individual species and the breadth of evolutionary history across the Tree of Life has never been quantified. Here we show that only 5.7% of scleractinian coral species and 21.7% of labrid fish species reach the minimum protection target of 10% of their geographic ranges within MPAs. We also estimate that the current global MPA system secures only 1.7% of the Tree of Life for corals, and 17.6% for fishes. Regionally, the Atlantic and Eastern Pacific show the greatest deficit of protection for corals while for fishes this deficit is located primarily in the Western Indian Ocean and in the Central Pacific. Our results call for a global coordinated expansion of current conservation efforts to fully secure the Tree of Life on coral reefs.  
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  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 2041-1723 ISBN Médium  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1506  
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