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Auteur Cucherousset, J.; Villeger, S.
Titre Quantifying the multiple facets of isotopic diversity: New metrics for stable isotope ecology Type Article scientifique
Année 2015 Publication Revue Abrégée Ecological Indicators
Volume 56 Numéro Pages 152-160
Mots-Clés biodiversity; Bioindication; communities; diversity indices; food web; Populations; stable isotope analyses; Trophic diversity
Résumé Abstract

Stable isotope analyses have emerged as an insightful tool for ecologists, with quantitative methods being developed to analyse data at the population, community and food web levels. In parallel, functional ecologists have developed metrics to quantify the multiple facets of functional diversity in a n-dimensional space based on functional traits. Here, we transferred and adapted metrics developed by functional ecologists into a set of four isotopic diversity metrics (isotopic divergence, dispersion, evenness and uniqueness) complementary to the existing metrics. Specifically, these new metrics are mathematically independent of the number of organisms analysed and account for the abundance of organisms. They can also be calculated with more than two stable isotopes. In addition, we also provide a procedure for calculating the levels of isotopic overlap (similarity and turnover) between two groups of organisms. These metrics have been implemented into new functions in R made freely available to users and we illustrated their application using stable isotope values from a freshwater fish community. Transferring the framework developed initially for measuring functional diversity to stable isotope ecology will allow more efficient assessments of changes in the multiple facets of isotopic diversity following anthropogenic disturbances.
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ISSN 1470-160x ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1361
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Auteur Mérigot, B.; Frédou, F.L.; Viana, A.P.; Ferreira, B.P.; do Nascimento Costa Junior, E.; Beserra da Silva Júnior, C.A.; Frédou, T.
Titre Fish assemblages in tropical estuaries of northeast Brazil: A multi-component diversity approach Type Article scientifique
Année 2017 Publication Revue Abrégée Ocean & Coastal Management
Volume 143 Numéro Pages 175-183
Mots-Clés Diversity indices; Double principal coordinate analysis; ecosystem-based fisheries management; Estuaries; Fishes; monitoring; taxonomic diversity
Résumé Biodiversity in estuarine ecosystems suffers from the impact of environmental changes and human activities. This mainly involves changes in temperature, salinity, pollution, habitat degradation or loss and fishing activities. The diversity of species communities is traditionally assessed on the basis of their species richness and composition. However, there is growing interest in taking into account complementary components dealing with species differences (e.g. taxonomic relatedness). In spite of their social, ecological and economic importance, the diversity of tropical estuarine fish assemblages has rarely been monitored by means of a multi-component approach under different human pressure and environmental conditions. We analysed the diversity of exploited fish communities (both target and non-target species) sampled during scientific surveys within four estuarine complexes in the state of Pernambuco, Brazil: Itapissuma, Suape, Sirinhaém, and Rio Formoso. A total of 122 species were collected within 34 samples. Overall, diversity indices and species models fitting dominance-evenness profiles mainly revealed differences between assemblages from Itapissuma, being the largest estuary with wide areas of mangrove, and the other estuaries. While assemblages from Itapissuma generally encompassed more species and individuals than the other estuaries, species were more closely related from a taxonomic point of view. In addition, a Double Principal Coordinate Analysis (DPCoA) established a typology of assemblages, useful for management purposes, and linked to particular fish families: it highlighted differences between Itapissuma, Suape, Sirinhaém and Rio Formoso. This method combines matrices of species abundances and differences (here taxonomic distances according to the Linnean classification). It was particularly accurate with a first factorial plane explaining 73% of the total inertia, while only 17% was achieved by a traditional Principal Component Analysis (PCA). Overall, this study provides an assessment of the state of fish assemblage diversity in Pernambuco estuaries where contrasted human and environmental conditions occur. It underscores the accuracy of using a multi-component diversity approach, with a multivariate analysis that is not yet widely used, for monitoring the diversity of estuaries for ecosystem-based fisheries management purposes.
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Éditeur de collection Titre de collection The challenge of developing policies and management strategies under changing baselines and unbounded boundaries Titre de collection Abrégé
Volume de collection 143 Numéro de collection Edition
ISSN 0964-5691 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 2137
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Auteur Aubé, J.; Senin, P.; Pringault, O.; Bonin, P.; Deflandre, B.; Bouchez, O.; Bru, N.; Biritxinaga-Etchart, E.; Klopp, C.; Guyoneaud, R.; Goñi-Urriza, M.
Titre The impact of long-term hydrocarbon exposure on the structure, activity, and biogeochemical functioning of microbial mats Type Article scientifique
Année 2016 Publication Revue Abrégée Marine Pollution Bulletin
Volume 111 Numéro 1 Pages 115-125
Mots-Clés Biogeochemical functioning; diversity; Hydrocarbonoclastic bacteria; Microbial mats
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Volume de collection Numéro de collection Edition
ISSN 0025-326x ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2155
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Auteur Hillen, J.E.J.; Coscia, I.; Vandeputte, M.; Herten, K.; Hellemans, B.; Maroso, F.; Vergnet, A.; Allal, F.; Maes, G.E.; Volckaert, F.A.M.
Titre Estimates of genetic variability and inbreeding in experimentally selected populations of European sea bass Type Article scientifique
Année 2017 Publication Revue Abrégée Aquaculture
Volume 479 Numéro Pages 742-749
Mots-Clés Artificial selection; ddRAD; fish; genetic diversity; Genomics; Inbreeding
Résumé The aquaculture industry has increasingly aimed at improving economically important traits like growth, feed efficiency and resistance to infections. Artificial selection represents an important window of opportunity to significantly improve production. However, the pitfall is that selection will reduce genetic diversity and increase inbreeding in the farmed stocks. Genetic tools are very useful in this context as they provide accurate measures of genetic diversity together with many additional insights in the stock status and the selection process. In this study we assessed the level of genetic variability and relatedness over several generations of two lines of experimentally selected European sea bass (Dicentrarchus labrax L.). The first line was selected for growth over three generations and the second line for both high and low weight loss under a starvation regime over two generations. We used a genomic approach (2549 single nucleotide polymorphism markers derived from double digest restriction site associated DNA sequencing) in combination with eight microsatellites to estimate genetic variation, relatedness, effective population size and genetic differentiation across generations. Individual heterozygosity estimates indicated that the selected lines showed no significant reduction in diversity compared with wild populations. There was, however, a decreasing trend in allelic richness, suggesting the loss of low frequency alleles. We compared the estimates of effective population size from genetic markers with pedigree information and found good correspondence between methods. This study provides important insights in the genetic consequences of selective breeding and demonstrates the operational use of the latest genomic tools to estimate variability, inbreeding and at a later stage domestication and artificial selection.
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ISSN 0044-8486 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2183
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Auteur Cheng, L.; Blanchet, S.; Loot, G.; Villeger, S.; Zhang, T.; Lek, S.; Lek-Ang, S.; Li, Z.
Titre Temporal changes in the taxonomic and functional diversity of fish communities in shallow Chinese lakes: the effects of river–lake connections and aquaculture Type Article scientifique
Année 2014 Publication Revue Abrégée Aquatic Conservation: Marine and Freshwater Ecosystems
Volume 24 Numéro 1 Pages 23-34
Mots-Clés biodiversity loss; biotic homogenization; Functional richness; lakes; Yangtze River basin
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ISSN 1099-0755 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1160
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