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Marcon, E.; Herault, B. |
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Title |
Decomposing phylodiversity |
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Journal Article |
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2015 |
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Methods in Ecology and Evolution |
Abbreviated Journal |
Methods in Ecology and Evolution |
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6 |
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3 |
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333-339 |
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Biodiversity; Entropy; Functional diversity; Phylogenetic diversity |
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Measuring functional or phylogenetic diversity is the object of an active literature. The main issues to address are relating measures to a clear conceptual framework, allowing unavoidable estimation-bias correction and decomposing diversity along spatial scales. We provide a general mathematical framework to decompose measures of species-neutral, phylogenetic or functional diversity into α and β components. We first unify the definitions of phylogenetic and functional entropy and diversity as a generalization of HCDT entropy and Hill numbers when an ultrametric tree is considered. We then derive the decomposition of diversity. We propose a bias correction of the estimates allowing meaningful computation from real, often undersampled communities. Entropy can be transformed into true diversity, that is an effective number of species or communities. Estimators of α- and β-entropy, phylogenetic and functional entropy are provided. Proper definition and estimation of diversity is the first step towards better understanding its underlying ecological and evolutionary mechanisms. © 2015 British Ecological Society. |
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Cirad, UMR EcoFoG, BP 709Kourou, French Guiana |
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Export Date: 31 March 2015 |
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EcoFoG @ webmaster @ |
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590 |
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Pavoine, S.; Marcon, E.; Ricotta, C. |
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‘Equivalent numbers’ for species, phylogenetic or functional diversity in a nested hierarchy of multiple scales |
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Journal Article |
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2016 |
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Methods in Ecology and Evolution |
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Methods in Ecology and Evolution |
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7 |
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10 |
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1152-1163 |
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alpha diversity; beta diversity; biodiversity; community ecology; community phylogenetics; diversity apportionment; gamma diversity; quadratic entropy |
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Many recent studies have searched to integrate species’ functions and phylogenies in the measurement of biodiversity. To obtain easily interpretable measures, some researchers recommended diversity indices expressed in terms of equivalent numbers of species: the number of equally likely and maximally dissimilar species needed to produce the given value of diversity. Then, biodiversity is often calculated at three scales: within communities (α diversity), among communities (β diversity) and in a region (γ diversity). These three scales are, however, insufficient to tackle the organization of biodiversity in space because, for most organisms, there is a nested hierarchy of multiple scales characterized by different patterns and processes, from the small neighbourhood to the biosphere. We developed methodologies for analysing species, functional, taxonomic or phylogenetic diversity in a hierarchy of multiple scales using equivalent numbers of species. As an example, we analysed the taxonomic and functional diversity of macroinvertebrate assemblages in the Loire River, France, at four levels: within sites (α diversity), among sites within geological regions (β1 diversity), among geological regions (β2 diversity) and at the river scale (γ diversity). The new hierarchical approaches of biodiversity revealed very low differences among sites within regions and among regions in terms of taxonomy and functional traits (size and diet), despite moderate, significant species turnover among geological regions. We compare our framework with those other authors have developed. We argue that different definitions of α, β, γ diversities are used in the literature reflecting different points of view on biodiversity. We make recommendations on how to normalize functional (or phylogenetic) dissimilarities among species to render sites and regions comparable, and discuss the pros and cons of our approach. The hierarchical approaches of biodiversity in terms of ‘equivalent numbers’ respond to current demands to obtain intuitive, easily interpretable components of biodiversity. The approaches we propose go beyond current developments by considering a hierarchy of spatial scales and unbalanced sampling design. They will provide powerful tools to detect the ecological and evolutionary processes that act differently at different scales. © 2016 The Authors. Methods in Ecology and Evolution © 2016 British Ecological Society |
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Department of Environmental Biology, University of Rome ‘La Sapienza’, Piazzale Aldo Moro 5, Rome, Italy |
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Export Date: 20 October 2016 |
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EcoFoG @ webmaster @ |
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697 |
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Gargallo-Garriga, Albert ; Sardans, Jordi ; Alrefaei, Abdulwahed Fahad ; Klem, Karel ; Fuchslueger, Lucia ; Ramirez-Rojas, Irène ; Donald, Julian ; Leroy, Celine ; Van Langenhove, Leandro ; Verbruggen, Erik ; Janssens, Ivan A. ; Urban, Otmar ; Penuelas, Josep |
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Tree Species and Epiphyte Taxa Determine the “Metabolomic niche” of Canopy Suspended Soils in a Species-Rich Lowland Tropical Rainforest |
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2021 |
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Metabolites |
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11 |
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11 |
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Bacteria, Canopy soils, Epiphyte, French Guiana, Metabolomics |
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Tropical forests are biodiversity hotspots, but it is not well understood how this diversity is structured and maintained. One hypothesis rests on the generation of a range of metabolic niches, with varied composition, supporting a high species diversity. Characterizing soil metabolomes can reveal fine-scale differences in composition and potentially help explain variation across these habitats. In particular, little is known about canopy soils, which are unique habitats that are likely to be sources of additional biodiversity and biogeochemical cycling in tropical forests. We studied the effects of diverse tree species and epiphytes on soil metabolomic profiles of forest floor and canopy suspended soils in a French Guianese rainforest. We found that the metabolomic profiles of canopy suspended soils were distinct from those of forest floor soils, differing between epiphyte-associated and non-epiphyte suspended soils, and the metabolomic profiles of suspended soils varied with host tree species, regardless of association with epiphyte. Thus, tree species is a key driver of rainforest suspended soil metabolomics. We found greater abundance of metabolites in suspended soils, particularly in groups associated with plants, such as phenolic compounds, and with metabolic pathways related to amino acids, nucleotides, and energy metabolism, due to the greater relative proportion of tree and epiphyte organic material derived from litter and root exudates, indicating a strong legacy of parent biological material. Our study provides evidence for the role of tree and epiphyte species in canopy soil metabolomic composition and in maintaining the high levels of soil metabolome diversity in this tropical rainforest. It is likely that a wide array of canopy microsite-level environmental conditions, which reflect interactions between trees and epiphytes, increase the microscale diversity in suspended soil metabolomes |
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MDPI |
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1041 |
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Houel, E.; Gonzalez, G.; Bessière, J.-M.; Odonne, G.; Eparvier, V.; Deharo, E.; Stien, D. |
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Therapeutic switching: From antidermatophytic essential oils to new leishmanicidal products |
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2015 |
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Memorias do Inst. Oswaldo Cruz |
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110 |
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1 |
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106-113 |
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Antifungal agents; Antiparasitic agents; Leishmania; Peritoneal macrophages – sesquiterpenes; Therapeutic switching |
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This study examined whether the antidermatophytic activity of essential oils (EOs) can be used as an indicator for the discovery of active natural products against Leishmania amazonensis. The aerial parts of seven plants were hydrodistilled. Using broth microdilution techniques, the obtained EOs were tested against three strains of dermatophytes (Trichophyton mentagrophytes, Microsporum gypseum and Microsporum canis). To compare the EOs antifungal and antiparasitic effects, the EOs activities against axenic amastigotes of L. amazonensis were concurrently evaluated. For the most promising EOs, their antileishmanial activities against parasites infecting peritoneal macrophages of BALB/c mice were measured. The most interesting antifungal candidates were the EOs from Cymbopogon citratus, Otacanthus azureus and Protium heptaphyllum, whereas O. azureus, Piper hispidum and P. heptaphyllum EOs exhibited the lowest 50% inhibitory concentration (IC50) values against axenic amastigotes, thus revealing a certain correspondence between both activities. The P. hispidum EO was identified as the most promising product in the results from the infected macrophages model (IC50: 4.7 μg/mL, safety index: 8). The most abundant compounds found in this EO were sesquiterpenes, notably curzerene and furanodiene. Eventually, the evaluation of the antidermatophytic activity of EOs appears to be an efficient method for identifying new potential drugs for the treatment of L. amazonensis. |
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Export Date: 17 March 2015 |
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587 |
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Campillo, F.; Rakotozafy, R.; Rossi, V. |
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Parallel and interacting Markov chain Monte Carlo algorithm |
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2009 |
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Mathematics and Computers in Simulation |
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Math. Comput. Simul. |
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79 |
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12 |
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3424-3433 |
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Markov chain Monte Carlo method; Interacting chains; Hidden Markov model |
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In many situations it is important to be able to propose N independent realizations of a given distribution law. We propose a strategy for making N parallel Monte Carlo Markov chains (MCMC) interact in order to get an approximation of an independent N-sample of a given target law. In this method each individual chain proposes candidates for all other chains. We prove that the set of interacting chains is itself a MCMC method for the product of N target measures. Compared to independent parallel chains this method is more time consuming. but we show through examples that it possesses many advantages. This approach is applied to a biomass evolution model. (C) 2009 IMACS. Published by Elsevier B.V. All rights reserved. |
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[Rossi, Vivien] CIRAD, Res Unit, Montpellier, France, Email: Fabien.Campillo@inria.fr |
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ELSEVIER SCIENCE BV |
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0378-4754 |
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ISI:000269289100006 |
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EcoFoG @ eric.marcon @ |
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197 |
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Mathieu, A.; Letort, V.; Cournède, P.H.; Zhang, B.G.; Heuret, P.; De Reffye, P. |
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Oscillations in functional structural plant growth models |
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2012 |
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Mathematical Modelling of Natural Phenomena |
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7 |
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6 |
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47-66 |
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Cecropia trees; Cucumber plant; Dynamic system of plant growth; Functional-structural plant models; GreenLab |
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The dynamic model of plant growth GreenLab describes plant architecture and functional growth at the level of individual organs. Structural development is controlled by formal grammars and empirical equations compute the amount of biomass produced by the plant, and its partitioning among the growing organs, such as leaves, stems and fruits. The number of organs initiated at each time step depends on the trophic state of the plant, which is evaluated by the ratio of biomass available in plant to the demand of all the organs. The control of the plant organogenesis by this variable induces oscillations in the simulated plant behaviour. The mathematical framework of the GreenLab model allows to compute the conditions for the generation of oscillations and the value of the period according to the set of parameters. Two case-studies are presented, corresponding to emergence of oscillations associated to fructification and branching. Similar alternating patterns are commonly reported by botanists. In this article, two examples were selected: alternate patterns of fruits in cucumber plants and alternate appearances of branches in Cecropia trees. The model was calibrated from experimental data collected on these plants. It shows that a simple feedback hypothesis of trophic control on plant structure allows the emergence of cyclic patterns corresponding to the observed ones. © EDP Sciences, 2012. |
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CIRAD, UMR AMAP, Montpellier, France |
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Export Date: 27 December 2012; Source: Scopus |
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452 |
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Petit, M.; Denis, T.; Rux, O.; Richard-Hansen, C.; Berzins, R. |
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Estimating jaguar (Panthera onca) density in a preserved coastal area of French Guiana |
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2018 |
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Mammalia |
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Mammalia |
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82 |
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2 |
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188-192 |
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camera trapping; density; French Guiana; home range; Panthera onca; spatially explicit capture recapture |
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Knowledge of the jaguar population is needed in French Guiana that faces an increase of human-jaguar conflicts. We carried out a camera trap survey to assess jaguar local density and home range size in a preserved coastal area of French Guiana. We ran spatially explicit capture recapture (SECR) models. In our model, the scale parameter σ, that is linked to the home range size, was larger for males (σ=3.87±0.59 SE km) than for females (σ=2.33±0.30 SE km). The assessed jaguar density was 3.22±0.87 SE ind. 100 km â '2, which should be considered as an optimal density in a French Guiana coastal area. |
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Office National de la Chasse et de la Faune Sauvage, Campus Agronomique, BP316, Kourou Cedex, French Guiana |
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Export Date: 7 May 2018 |
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803 |
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Leba, L.-J.; Musset, L.; Pelleau, S.; Estevez, Y.; Birer, C.; Briolant, S.; Witkowski, B.; Ménard, D.; Delves, M.J.; Legrand, E.; Duplais, C.; Popovici, J. |
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Use of Plasmodium falciparum culture-adapted field isolates for in vitro exflagellation-blocking assay |
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2015 |
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Malaria Journal |
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Malaria Journal |
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14 |
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234 |
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Background: A major requirement for malaria elimination is the development of transmission-blocking interventions. In vitro transmission-blocking bioassays currently mostly rely on the use of very few Plasmodium falciparum reference laboratory strains isolated decades ago. To fill a piece of the gap between laboratory experimental models and natural systems, the purpose of this work was to determine if culture-adapted field isolates of P. falciparum are suitable for in vitro transmission-blocking bioassays targeting functional maturity of male gametocytes: exflagellation. Methods: Plasmodium falciparum isolates were adapted to in vitro culture before being used for in vitro gametocyte production. Maturation was assessed by microscopic observation of gametocyte morphology over time of culture and the functional viability of male gametocytes was assessed by microscopic counting of exflagellating gametocytes. Suitability for in vitro exflagellation-blocking bioassays was determined using dihydroartemisinin and methylene blue. Results: In vitro gametocyte production was achieved using two isolates from French Guiana and two isolates from Cambodia. Functional maturity of male gametocytes was assessed by exflagellation observations and all four isolates could be used in exflagellation-blocking bioassays with adequate response to methylene blue and dihydroartemisinin. Conclusion: This work shows that in vitro culture-adapted P. falciparum field isolates of different genetic background, from South America and Southeast Asia, can successfully be used for bioassays targeting the male gametocyte to gamete transition, exflagellation. © 2015 Leba et al. |
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Department of Life Sciences, Imperial College, London, United Kingdom |
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Export Date: 16 July 2015 |
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612 |
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Talaga, S.; Petitclerc, F.; Carrias, J.-F.; Dezerald, O.; Leroy, C.; Céréghino, R.; Dejean, A. |
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Environmental drivers of community diversity in a neotropical urban landscape: a multi-scale analysis |
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2017 |
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Landscape Ecology |
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Landscape Ecology |
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32 |
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9 |
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1805-1818 |
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Aquatic metacommunity; Landscape ecology; Mosquitoes; Neotropics; Scale dependency; Tank bromeliads; Urban ecology |
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Context: Many aquatic communities are linked by the aerial dispersal of multiple, interacting species and are thus structured by processes occurring in both the aquatic and terrestrial compartments of the ecosystem. Objectives: To evaluate the environmental factors shaping the aquatic macroinvertebrate communities associated with tank bromeliads in an urban landscape. Methods: Thirty-two bromeliads were georeferenced to assess the spatial distribution of the aquatic meta-habitat in one city. The relative influence of the aquatic and terrestrial habitats on the structure of macroinvertebrate communities was analyzed at four spatial scales (radius = 10, 30, 50, and 70 m) using redundancy analyses. Results: We sorted 18,352 aquatic macroinvertebrates into 29 taxa. Water volume and the amount of organic matter explained a significant part of the taxa variance, regardless of spatial scale. The remaining variance was explained by the meta-habitat size (i.e., the water volume for all of the bromeliads within a given surface area), the distance to the nearest building at small scales, and the surface area of buildings plus ground cover at larger scales. At small scales, the meta-habitat size influenced the two most frequent mosquito species in opposite ways, suggesting spatial competition and coexistence. Greater vegetation cover favored the presence of a top predator. Conclusions: The size of the meta-habitat and urban landscape characteristics influence the structure of aquatic communities in tank bromeliads, including mosquito larval abundance. Modifications to this landscape will affect both the terrestrial and aquatic compartments of the urban ecosystem, offering prospects for mosquito management during urban planning. © 2017, Springer Science+Business Media B.V. |
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IRD; UMR AMAP (botAnique et Modélisation de l’Architecture des Plantes et des végétations), Boulevard de la Lironde, TA A‐51/PS2, Montpellier Cedex 5, France |
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Perz, S.G.; Qiu, Y.; Xia, Y.; Southworth, J.; Sun, J.; Marsik, M.; Rocha, K.; Passos, V.; Rojas, D.; Alarcón, G.; Barnes, G.; Baraloto, C. |
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Trans-boundary infrastructure and land cover change: Highway paving and community-level deforestation in a tri-national frontier in the Amazon |
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2013 |
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Land Use Policy |
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34 |
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27-41 |
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Amazon; Brazil, Peru; Globalization; Infrastructure; Land |
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Economic globalization manifests in landscapes through regional integration initiatives involving trans-boundary infrastructure. While the relationships of roads, accessibility and land cover are well-understood, they have rarely been considered across borders in national frontier regions. We therefore pursue an analysis of infrastructure connectivity and land cover change in the tri-national frontier of the southwestern Amazon where Bolivia, Brazil and Peru meet, and where the Inter-Oceanic Highway has recently been paved. We integrate satellite, survey, climate and other data for a sample of rural communities that differ in terms of highway paving across the tri-national frontier. We employ a suite of explanatory variables tied to road paving and other factors that vary both across and within the three sides of the frontier in order to model their importance for deforestation. A multivariate analysis of non-forest land cover during 2005-2010 confirms the importance of paving status and travel times, as well as land tenure and other factors. These findings indicate that integration affects land cover, but does not eliminate the effects of other factors that vary across the frontier, which bears implications for the study of globalization, trans-boundary infrastructure, environmental governance and land cover change. © 2013 Elsevier Ltd. |
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Department of Biology, University of Florida, Gainesville, FL 32611, United States |
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Export Date: 14 March 2013; Source: Scopus |
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EcoFoG @ webmaster @ |
Serial |
475 |
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