Quantitative and Evolutionary Ecology of Communities Group

Members

Our research activities, focused on interspecific interactions (community ecology), aim to better understand the ecological and evolutionary processes structuring species assemblages and biodiversity at different temporal and spatial scales. Our team addresses these major issues using contrasting biological models (communities of large African mammals, insects, microbiota, plants) from 3 complementary angles:

  • Our work is strongly anchored in the conceptual framework of evolutionary biology by studying (i) the diversity of adaptive responses implemented by organisms to selective pressures in their environment, (ii) their consequences on population demography and ultimately (iii) the dynamics and composition of species communities.
  • Our research is closely linked to societal issues of biodiversity conservation and management by integrating both the functioning of socio-ecological systems and the context of climate change. We conduct experimental studies, manage and ensure the long-term monitoring of several community observation networks.
  • Methodological issues also occupy a central place in our team, with the development of new tools for statistical processing and modeling of ecological data. This activity leads to the development of methods and software that we develop and distribute freely.

 

Research programs

 

hwange

Functioning of African savanna communities

The Hwange LTSER (Long-Term Socio-Ecological Research site in Zimbabwe hosts a long-term interdisciplinary research program that focuses on the functioning of plant and animal communities within the Hwange National Park and the interactions between this protected area and humans living in its periphery. Based on this program, three axes are developed: (1) studying the population dynamics of elephants, exploring their impact and that of management policies on the socio-ecosystem functioning; (2) Understanding the extent to which interactions within and between trophic levels are sensitive to management actions (e.g. sport hunting, water management) and climate change; (3) Decoding human ecology and human-wildlife coexistence mechanisms towards integrated conservation and sustainable functioning of the socio-ecosystem. This research is complemented by more recent works in the Hluhluwe-iMfolozi Park and in the Madikwe reserve in South Africa, which focus on the role of environmental conditions on the hunting success of large African carnivores. We work in close collaboration with the IRL (International Research Lab) Rehabs.

Involved group members : Alice Bernard, Laura Lacomme, Aïssa Morin, Lisa Nicvert, Elie Pedarros, Yolan Richard, Marion Valeix*

 

Masting and the community dynamics of seed consumers

Masting is a reproductive strategy often encountered in perennial plants, characterized by fructifications highly fluctuating in time and being synchronized at the population level. The seeds produced that way constitute a pulsed resource with a strong impact on the eco-evolutionary dynamics of seed-consuming communities and forest regeneration. Our lack of knowledge of this system still impedes our understanding of the dynamics of temperate forest ecosystems and its future in the context of climate change. Our work carried out on oak forests aims to better understand (i) the proximal causes of masting, (ii) the mechanisms underlying the coexistence of species competing for such highly fluctuating resource and (iii) the co-evolution of consumer exploitation strategies for the fluctuating resource and forest tree fruiting strategies. On the basis of the results obtained, scenarii will be proposed on the future of forest regeneration under climate change, that may serve forest management.

Involved group members : Marie-Claude Bel-Venner*, Emilie Fleurot, Léa Keurinck, Jean Lobry, Samuel Venner

 

image_antibioresitance

The spread of antibiotic resistance genes in bacteria

Antibiotic resistance is recognized as one of the greatest current threats to human health, and the mobile genetic elements (MGEs) that circulate in bacterial populations and communities are the main vehicles. To understand the dynamics and diversity of MGEs in bacterial pangenomes and the emergence of antibiotic resistance genes, we propose to go beyond the framework of conventional genomics by considering pangenomes as complex ecological communities. In the Ab-One program, we mobilize the concepts and tools developed in community ecology based on an integrative approach (monitoring of bacterial populations/communities evolving in contrasting environments -One-Health approaches-, pan-genomic analyses, experimentation in molecular and cellular microbiology, mathematical modelling). This program is currently focused on the dynamics of MGEs in Acinetobacter baumannii, an antibiotic-resistant microorganism classified as a priority by the WHO. Other more general approaches will illustrate the relevance of this new conceptual framework to understand the dynamics and diversity of MGEs in bacterial pangenomes. This program, co-piloted by our team and a team from CIRI (Horigene) involves the participation of 9 organizations (6 from Lyon -LBBE, CIRI, MMSB, HCL, LEM, VetAgro Sup-, Institut Pasteur (Paris), LMGM (Toulouse ), Robert Koch Institute (Germany)).

Involved group members : Stéphane Dray, Rémi Tuffet, Samuel Venner*

 

Statistical analysis of ecological data

Understanding the structure and dynamics of species assemblages, and the processes behind them, requires collecting data that are becoming increasingly complex owing to the sophisticated technological developments made available for their acquisition (e.g. GPS, loggers, satellite imagery, molecular data). We are developing new methods for analysing such data, that provide new insights into the ecological processes at work in communities. Multivariate analysis methods allow the analysis of spatial structures, accounting for various information on species (functional traits, morphology, phylogeny), the spatio-temporal variation of species-environment relationships or the multifaceted perception of the protected human-environment relationship. We also model multi-'omics' dose-response data within communities in order to better understand the Adverse Outcome Pathway (AOP) and to better appreciate the risks to the environment. These methodological innovations are made available to the scientific community through the development, distribution and maintenance of software (libraries for the R language: ade4, adegraphics, adephylo, ade4TkGUI, nlstools, fitdistrplus, DRomics, seqinr).

Involved group members: Marie Laure Delignette-Muller, Stéphane Dray*, Jean Lobry, Jean Thioulouse.

Publications

Display of 361 to 390 publications on 572 in total

Ecomic - RMQs : Cartographie de la diversité microbienne des sols à l'échelle de la France

Samuel S. Dequiedt, Mélanie M. Lelievre, Claudy C. Jolivet, Dominique D. Arrouays, Nicolas N. Saby, Jean J. Thioulouse...

4ème Colloque de l'Association Francophone d'Ecologie Microbienne (AFEM) . : 1 p.

Conference paper

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Diversité des communautés microbiennes telluriques à l'échelle du territoire national

Samuel S. Dequiedt, Mélanie M. Lelievre, Claudy C. Jolivet, Manuel Martin, Nicolas Saby, Dominique Arrouays...

Journées d'Etude des Sols . : 151-152

Conference paper

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Rhizosphere microbiota interfers with plant-plant interactions

A. Sanon, Z. N. Andrianjaka, Y. Prin, R. Bally, J. Thioulouse, G. Comte...

Plant and Soil . ( 321 ) : 259-278

DOI: 10.1007/s11104-009-0010-5

Journal article

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Multivariate analysis of the spatial patterns of 8 trace elements using the French soil monitoring network data

N.P.A. Saby, J. Thioulouse, C. Jolivet, C. Ratié, Line Boulonne, A. Bispo...

Science of the Total Environment . 407 : 5644-5652

Journal article

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Responses of Pinus halepensis growth soil microbial catabolic functions and phosphate-solubilizing bacteria after rock phosphate amendment and ectomycorrhizal inoculation

L. Ouahmane, J.C. Revel, M. Hafidi, J. Thioulouse, Y. Prin, A. Galiana...

Plant and Soil . 320 (1-2) : 169-179

Journal article

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Responses of Pinus halepensis growth, soil microbial catabolic functions and phosphate-solubilizing bacteria after rock phosphate amendment and ectomycorrhizal inoculation.

L. Ouahmane, J.C. Revel, M. Hafidi, J. Thioulouse, Y. Prin, A. Galiana...

Plant and Soil . 320 : 169-179

DOI: 10.1007/s11104-008-9882-z

Journal article

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Multivariate analysis of the spatial patterns of 8 trace elements using the French soil monitoring network data

Nicolas N. Saby, J. Thioulouse, Claudy C. Jolivet, Céline Ratié, Line Boulonne, Antonio Bispo...

Science of the Total Environment . 407 : 5644–5652

DOI: 10.1016/j.scitotenv.2009.07.002

Journal article

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Beta diversity in spatially implicit neutral models: a new way to assess species migration.

François Munoz, Pierre Couteron, B. R. Ramesh

The American Naturalist . 172 ( 1 ) : 116-27

DOI: 10.1086/587842

Journal article

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Equation against Al-gorithm : Which differences and which one to choose ?

Cedric Gaucherel, François Munoz, Severine Berard

European conference on Computing And Philosophy E-CAP 2008 .

Conference paper

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Organisation spatiale de la diversité des arbres des forêts tropicales aux échelles régionales : enjeux méthodologiques et application dans les Ghâts occidentaux de l’Inde

Raphaël Pélissier, Narayanan Ayyappan, Champak Reddy Beeravolu, K. Belna, S. Ramalingam, B.R. Ramesh...

: p. 149-163

Report

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The exotic legume tree species Acacia holosericea alters microbial soil functionalities and the structure of the arbuscular mycorrhizal community

P. Remigi, A. Faye, A. Kane, M. Deruaz, J. Thioulouse, M. Cissoko...

Applied and Environmental Microbiology . 74 : 1485-1493

Journal article

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Unexpected male choosiness for mates in a spider

Marie-Claude Bel-Venner, S. Dray, Dominique Allainé, F. Menu, Samuel Venner

Proceedings of the Royal Society B: Biological Sciences . 275 : 77-82

Journal article

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Use of the library fitdistrplus to specify distribution from non-censored or censored data

Marie Laure Delignette-Muller, Régis Pouillot, Jean-Baptiste Denis

Report

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On the number of principal components: A test of dimensionality based on measurements of similarity between matrices

S. Dray

Computational Statistics and Data Analysis . 52 : 2228-2237

Journal article

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Serotyping of Toxoplasma gondii: striking homogeneous pattern between symptomatic and asymptomatic infections within Europe and South America.

Stéphane Morisset, François Peyron, Jean R Lobry, Justus Garweg, Josette Ferrandiz, Karine Musset...

Microbes and Infection . 10 ( 7 ) : 742-7

DOI: 10.1016/j.micinf.2008.04.001

Journal article

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Quantitative risk assessment for Escherichia coli O157:H7 in frozen ground beef patties consumed by young children in French households

Marie Laure Delignette-Muller, M. Cornu

International Journal of Food Microbiology . 128 : 77-84

Journal article

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Persistence of Shiga toxin-producing Escherichia coli O26 in various manure-amended soil types

B. Fremaux, C. Prigent-Combaret, Marie Laure Delignette-Muller, B. Mallen, M. Dothal, A. Gleizal...

Journal of Applied Microbiology . 104 : 296-304

DOI: 10.1111/j.1365-2672.2007.03532.x

Journal article

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From W.S. Gosset`s pieces of card (1908) to R software : analysing Macdonell`s dataset of 3000 criminals

Anne-Béatrice Dufour, J.R. Lobry

Biométrie Humaine et Anthropologie - revue de la Société de biométrie humaine . 26 : 33-39

Journal article

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An agent-based model for predicting the prevalence of Trypanosoma cruzi I and II in their host and vector populations

H. Devillers, J.R. Lobry, F. Menu

Journal of Theoretical Biology . 255 : 307-315

Journal article

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Spatial ordination of vegetation data using a generalization of Wartenberg's multivariate spatial correlation

S. Dray, S. Saïd, F. Débias

Journal of Vegetation Science . 19 : 45-56

Journal article

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Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes

R. Covain, S. Dray, S. Fisch-Muller, J.I. Montoya-Burgos

Molecular Phylogenetics and Evolution . 46 : 986-1002

Journal article

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Analyzing or explaining beta diversity ? comment

R. Pelissier, P. Couteron, S. Dray

Ecology . 89 : 3227-3232

Journal article

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Testing the species traits-environment relationships : the fourth-corner problem revisited

S. Dray, P. Legendre

Ecology . 89 : 3400-3412

Journal article

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Microbial-biogeography of France by the use of molecular tools applied to the French soil quality monitoring network (RMQS)

Lionel Ranjard, Samuel S. Dequiedt, Mélanie M. Lelievre, Claudy C. Jolivet, Nicolas N. Saby, Manuel M. Martin...

Eurosoil 2008 Book of Abstracts . : 59-60

Conference paper

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Bacterial taxa associated with the hematophagous mite Dermanyssus gallinae detected by 16S rRNA PCR amplification and TTGE fingerprinting

Claire Valiente Moro, Jean Thioulouse, Claude Chauve, Philippe Normand, Lionel Zenner

Research in Microbiology . 160 ( 1 ) : 63-70

DOI: 10.1016/j.resmic.2008.10.006

Journal article

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A bayesian approach to analyse ecotoxicological data

Elise Billoir, Marie Laure Delignette-Muller, Alexandre R.R. Pery, Sandrine Charles

Environmental Science and Technology . 42 ( 23 ) : 8978-8984

DOI: 10.1021/es801418x

Journal article

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Les conceptions d'enseignants du primaire et du secondaire sur le déterminisme biologique de la personnalité humaine dans 12 pays d’Europe, d'Afrique et du Moyen Orient.

Jérémy Castéra, François Munoz, Pierre Clement

Congrès international AREF 2007 (Actualité de la Recherche en Education et en Formation) .

Conference paper

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Le projet ECOMIC-RMQS ou comment faire de la microbiogéographie à l'échelle de la France

Samuel S. Dequiedt, Mélanie M. Lelievre, Claudy C. Jolivet, Manuel Martin, Nicolas Saby, Dominique Arrouays...

Journées d'animations scientifiques des ORE ACBB . : n.p.

Conference paper

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Arbuscular mycorrhizas and ectomycorrhizas of Uapaca bojeri L. (Euphorbiaceae): sporophore diversity patterns of root colonization and effects on seedling growth and soil microbial catabolic diversity

N. Ramanankierana, M. Ducousso, N. Rakotoarimanga, Y. Prin, J. Thioulouse, E. Randrianjohany...

Mycorrhiza . 17 : 195-208

Journal article

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Soil functional diversity and P solubilization from rock phosphate after inoculation whith native or allochtonous arbuscular mycorrhizal fungi

L. Ouahmane, Jean Thioulouse, M. Hafidi, Yves Prin, Marc Ducousso, Antoine Galiana...

Forest Ecology and Management . 241 ( 1-3 ) : 200-208

DOI: 10.1016/j.foreco.2007.01.015

Journal article

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