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Auteur Carteron, A.; Jeanmougin, M.; Leprieur, F.; Spatharis, S.
Titre Assessing the efficiency of clustering algorithms and goodness-of-fit measures using phytoplankton field data Type Article scientifique
Année 2012 Publication Revue Abrégée Ecol. Inform.
Volume 9 Numéro Pages 64-68
Mots-Clés 2-norm; Beta diversity; Cophenetic correlation coefficient; Dendrogram; Upgma; Ward's algorithm; beta-diversity; blooms; classification; communities; cophenetic correlation; environment; forest; functional diversity; som
Résumé Investigation of patterns in beta diversity has received increased attention over the last years particularly in light of new ecological theories such as the metapopulation paradigm and metacommunity theory. Traditionally, beta diversity patterns can be described by cluster analysis (i.e. dendrograms) that enables the classification of samples. Clustering algorithms define the structure of dendrograms, consequently assessing their performance is crucial. A common, although not always appropriate approach for assessing algorithm suitability is the cophenetic correlation coefficient c. Alternatively the 2-norm has been recently proposed as an increasingly informative method for evaluating the distortion engendered by clustering algorithms. In the present work, the 2-norm is applied for the first time on field data and is compared with the cophenetic correlation coefficient using a set of 105 pairwise combinations of 7 clustering methods (e.g. UPGMA) and 15 (dis)similarity/distance indices (e.g. Jaccard index). In contrast to the 2-norm, cophenetic correlation coefficient does not provide a clear indication on the efficiency of the clustering algorithms for all combinations. The two approaches were not always in agreement in the choice of the most faithful algorithm. Additionally, the 2-norm revealed that UPGMA is the most efficient clustering algorithm and Ward's the least. The present results suggest that goodness-of-fit measures such as the 2-norm should be applied prior to clustering analyses for reliable beta diversity measures. (C) 2012 Elsevier B.V. All rights reserved.
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ISSN 1574-9541 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 457
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Auteur Mazel, F.; Guilhaumon, F.; Mouquet, N.; Devictor, V.; Gravel, D.; Renaud, J.; Cianciaruso, M.V.; Loyola, R.; Diniz, J.A.F.; Mouillot, D.; Thuiller, W.
Titre Multifaceted diversity-area relationships reveal global hotspots of mammalian species, trait and lineage diversity Type Article scientifique
Année 2014 Publication Revue Abrégée Global Ecology and Biogeography
Volume 23 Numéro 8 Pages 836-847
Mots-Clés Conservation biogeography; Hill's numbers; biodiversity hotspots; congruent; conservation priorities; diversity indices; ecoregions; endemism; evolutionary; functional diversity-area; histories; mammals; phylogenetic diversity; phylogenetic diversity-area; relationship; richness gradients; spatial-patterns; species-area relationship
Résumé Aim To define biome-scale hotspots of phylogenetic and functional mammalian biodiversity (PD and FD, respectively) and compare them with 'classical' hotspots based on species richness (SR) alone. Location Global. Methods SR, PD and FD were computed for 782 terrestrial ecoregions using the distribution ranges of 4616 mammalian species. We used a set of comprehensive diversity indices unified by a recent framework incorporating the relative species coverage in each ecoregion. We built large-scale multifaceted diversity-area relationships to rank ecoregions according to their levels of biodiversity while accounting for the effect of area on each facet of diversity. Finally we defined hotspots as the top-ranked ecoregions. Results While ignoring relative species coverage led to a fairly good congruence between biome-scale top ranked SR, PD and FD hotspots, ecoregions harbouring a rich and abundantly represented evolutionary history and FD did not match with the top-ranked ecoregions defined by SR. More importantly PD and FD hotspots showed important spatial mismatches. We also found that FD and PD generally reached their maximum values faster than SR as a function of area. Main conclusions The fact that PD/FD reach their maximum value faster than SR could suggest that the two former facets might be less vulnerable to habitat loss than the latter. While this point is expected, it is the first time that it has been quantified at a global scale and should have important consequences for conservation. Incorporating relative species coverage into the delineation of multifaceted hotspots of diversity led to weak congruence between SR, PD and FD hotspots. This means that maximizing species number may fail to preserve those nodes (in the phylogenetic or functional tree) that are relatively abundant in the ecoregion. As a consequence it may be of prime importance to adopt a multifaceted biodiversity perspective to inform conservation strategies at a global scale.
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ISSN 1466-822x ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 722
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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.
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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ISSN 2041-1723 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1506
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Auteur Mouton, T.L.; Matheson, F.E.; Stephenson, F.; Champion, P.D.; Wadhwa, S.; Hamer, M.P.; Catlin, A.; Riis, T.
Titre Environmental filtering of native and non-native stream macrophyte assemblages by habitat disturbances in an agricultural landscape Type Article scientifique
Année 2019 Publication Revue Abrégée Sci. Total Environ.
Volume 659 Numéro Pages 1370-1381
Mots-Clés Agricultural impacts; classification; ecological impacts; eutrophication; Functional diversity; functional diversity measures; Functional traits; land-use; management; metaanalysis; Non-native flora; restoration; RLQ and fourth-corner analyses; species traits; trait responses
Résumé Understanding how inter-specific variation in functional traits affects native and non-native species responses to stream disturbances, is necessary to inform management strategies, providing tools for biomonitoring, conservation and restoration. This study used a functional trait approach to characterise the responses of macrophyte assemblages to reach-scale disturbances (measured by lack of riparian shading, altered hydromorphology and eutrophication), from 97 wadeable stream sites in an agriculturally impacted region of New Zealand. To determine whether macrophyte assemblages differed due to disturbances, we examined multidimensional assemblage functional structure in relation to eleven functional traits and further related two functional diversity indices (entropy and originality) to disturbances. Macrophyte assemblages showed distinct patterns in response to disturbances, with riparian shading and hydromorphological conditions being the strongest variables shaping macrophyte functional structure. In the multidimensional space, most of the non-native species were associatedwith disturbed conditions. These species had traits allowing faster colonisation rates (higher number of reproductive organs and larger root-rhizome system) and superior competitive abilities for resources (tall and dense canopy, heterophylly and greater preferences for light and nitrogen). In addition, lack of riparian shading increased the abundance of functionally distinct species (i.e. entropy), and eutrophication resulted in the growth of functionally unique species (i.e. originality). We demonstrated that stream reach-scale habitat disturbances were associated to a dominance of more productive species, equating to a greater abundance of non-native species. This, can result in a displacement of native species, habitat alterations, and changes to higher trophic level assemblages. Our results suggests that reachscale management efforts such as the conservation and restoration of riparian vegetation that provides substantial shading and hydromorphologically diverse in-stream habitat, would have beneficial direct and indirect effects on ecosystem functioning, and contribute to the mitigation of land-use impacts. (C) 2018 Published by Elsevier B.V.
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ISSN 0048-9697 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2571
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Auteur Benedetti, F.; Ayata, S.-D.; Irisson, J.-O.; Adloff, F.; Guilhaumon, F.
Titre Climate change may have minor impact on zooplankton functional diversity in the Mediterranean Sea Type Article scientifique
Année 2019 Publication Revue Abrégée Divers. Distrib.
Volume 25 Numéro 4 Pages 568-581
Mots-Clés biogeography; calanus-helgolandicus; climate change; communities; conservation; fish assemblages; framework; functional diversity; future; marine biodiversity; Mediterranean Sea; niche modelling; null model; ocean; trait; zooplankton
Résumé Aim To assess the impact of climate change on the functional diversity of marine zooplankton communities. Location The Mediterranean Sea. Methods We used the functional traits and geographic distributions of 106 copepod species to estimate the zooplankton functional diversity of Mediterranean surface assemblages for the 1965-1994 and 2069-2098 periods. Multiple environmental niche models were trained at the global scale to project the species habitat suitability in the Mediterranean Sea and assess their sensitivity to climate change predicted by several scenarios. Simultaneously, the species traits were used to compute a functional dendrogram from which we identified seven functional groups and estimated functional diversity through Faith's index. We compared the measured functional diversity to the one originated from null models to test if changes in functional diversity were solely driven by changes in species richness. Results All but three of the 106 species presented range contractions of varying intensity. A relatively low decrease of species richness (-7.42 on average) is predicted for 97% of the basin, with higher losses in the eastern regions. Relative sensitivity to climate change is not clustered in functional space and does not significantly vary across the seven copepod functional groups defined. Changes in functional diversity follow the same pattern and are not different from those that can be expected from changes in richness alone. Main conclusions Climate change is not expected to alter copepod functional traits distribution in the Mediterranean Sea, as the most and the least sensitive species are functionally redundant. Such redundancy should buffer the loss of ecosystem functions in Mediterranean zooplankton assemblages induced by climate change. Because the most negatively impacted species are affiliated to temperate regimes and share Atlantic biogeographic origins, our results are in line with the hypothesis of increasingly more tropical Mediterranean communities.
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ISSN 1366-9516 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2582
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