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 331 to 360 publications on 572 in total

Evaluating variability and uncertainty separately in microbial quantitative risk assessment using two R packages

R. Pouillot, Marie Laure Delignette-Muller

International Journal of Food Microbiology . 142 : 330-340

Journal article

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Biogéographie Microbienne: mythe ou réalité ?

Nicolas Chemidlin Prévost-Bouré, Samuel Dequiedt, Nicolas N. Saby, Mélanie M. Lelievre, Claudy C. Jolivet, Dominique D. Arrouays...

Ecologie 2010 . : n.p.

Conference paper

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Online Reproducible Research: An Application to Multivariate Analysis of Bacterial DNA Fingerprint Data

J. Thioulouse, C. Valiente Moro, L. Zenner

The R Journal . 2 ( 1 ) : 44-52

Journal article

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Development of partial life-cycle experiments to assess the effects of endocrine disruptors on the freshwater gastropod Lymnaea stagnalis; a case-study with vinclozolin.

Virginie Ducrot, Mickaël Teixeira-Alves, Christelle Lopes, Marie Laure Delignette-Muller, Sandrine Charles, Laurent Lagadic

Ecotoxicology . 19 ( 7 ) : 1312-1321

DOI: 10.1007/s10646-010-0518-8

Journal article

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Continental-scale patterns of cecropia of phenology: evidence from herbarium specimen

Paul Camilo Zalamea, Patrick Heuret, François Munoz, C. E. Timothy Paine, Carolina Sarmiento, Daniel Sabatier...

Impacts of Global Change on Tropical Ecosystems - cross-cutting the Abiotic, Biotic and Human Spheres .

Poster

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A phylogenomic analysis of bacterial helix-turn-helix transcription factors

C. L. Santos, F. Tavares, J. Thioulouse, Philippe Normand

FEMS Microbiology Reviews . 33 ( 2 ) : 411-429

DOI: 10.1111/j.1574-6976.2008.00154.x

Journal article

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Distribution et déterminisme de la diversité des communautés de champignons telluriques à l'échelle de trois régions françaises

Nicolas Chemidlin Prévost-Bouré, Samuel S. Dequiedt, Rémy Doyen, Mélanie M. Lelievre, Claudy C. Jolivet, Manuel Martin...

4ème colloque de l'Association Francophone d'Ecologie Microbienne : le livre des résumés . : 91

Conference paper

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Controlled ectomycorrhization of an exotic legume tree species Acacia holosericea affects the structure of root nodule bacteria community and their symbiotic effectiveness on Faidherbia albida a native Sahelian Acacia

A. Faye, T. Krasova-Wabe, M. Thiao, J. Thioulouse, M. Neyra, Y. Prin...

Soil Biology and Biochemistry . 41(6) : 1245-1252

Journal article

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Biogeographical patterns of soil bacterial communities

Samuel Dequiedt, Jean Thioulouse, Claudy C. Jolivet, Nicolas N. Saby, Mélanie Lelièvre, Pierre-Alain Maron...

Environmental Microbiology Reports . 1 ( 4 ) : 251 - 255

DOI: 10.1111/j.1758-2229.2009.00040.x

Journal article

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Monitoring the Development of Nurse Plant Species to Improve the Performances of Reforestation Programs in Mediterranean Areas

R. Duponnois, M. Hafidi, J. Thioulouse, A. Galiana, L. Ouahmane, B. Dreyfus...

incollection . -- : 443-450

Journal article

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Aphylogenomic analysis of bacterial helix^turn^helix transcription factors

C.L. Santos, F. Tavares, J. Thioulouse, P. Normand

FEMS Microbiology Reviews . 33 : 411-429

Journal article

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DEBtox theory and matrix population models as helpful tools in understanding the interaction between toxic cyanobacteria and zooplankton

E. Billoir, A. da Silva Ferrão-Filho, Marie Laure Delignette-Muller, Sandrine Charles

Journal of Theoretical Biology . 258 : 380-388

Journal article

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Patterns biogéographiques de la diversité bactérienne des sols à l'échelle du territoire national

Samuel S. Dequiedt, Mélanie M. Lelievre, Claudy C. Jolivet, Manuel M. Martin, Nicolas N. Saby, Benoit B. Toutain...

Congrès AFEM (Association Francophone pour l'Ecologie Microbienne . : n.p.

Conference paper

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

Nicolas Chemidlin Prévost-Bouré, Samuel Dequiedt, Jean Thioulouse, Claudy C. Jolivet, Nicolas N. Saby, Mélanie M. Lelievre...

BAGECO10 .

Conference paper

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Prédiction des propriétés du sol à l’échelle nationale à partir des données du RMQS : Exemple des Éléments Trace Métalliques

Nicolas N. Saby, Claudy C. Jolivet, Line Boulonne, Céline Ratié, Ben P. Marchant, R. Murray Lark...

10. Journées d'Etude des Sols .

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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ECOMIC-RMQS : biogéographie microbienne à l’échelle de la France. Etat d’avancement et premiers résultats

Samuel Dequiedt, Maud Lelièvre, Claudy C. Jolivet, Nicolas N. Saby, Manuel Pascal Martin, J. Thioulouse...

Étude et Gestion des Sols . 16 ( 3-4 ) : 219-231

Journal article

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Ecophysiological attributes of adult overwintering in insects: insights from a field study of the nut weevil, Curculio nucum

Marie-Claude Bel-Venner, Nathalie Mondy, Florent Arthaud, Julien Marandet, David Giron, Samuel Venner...

Physiological Entomology . 34 : 61-70

DOI: 10.1111/j.1365-3032.2008.00652.x

Journal article

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Les Harttiini (Siluriformes, Loricariidae) des Guyanes : phylogénie et évolution des formes ou variation sur un même thème

Raphaël Covain, Sonia Fisch-Muller, Juan Montoya-Burgos, Jan Mol, Pierre-Yves Le Bail, Stéphane Dray

4. Rencontres de l'Ichtyologie en France .

Conference paper

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Dynamics of transposable elements:towards a community ecology of the genome

Samuel Venner, C. Feschotte, C. Biémont

Trends in Genetics . 25(7) : 317-323

Journal article

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DEBtox theory and matrix population models as helpful tools in understanding the interaction between toxic cyanobacteria and zooplankton

Elise Billoir, Aloysio da Silva Ferrão-Filho, Marie Laure Delignette-Muller, Sandrine Charles

Journal of Theoretical Biology . 258 ( 3 ) : 380

DOI: 10.1016/j.jtbi.2008.07.029

Journal article

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ReBaStaBa: handling Bayesian networks with R

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

The R User Conference 2009 .

Conference paper

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Fitting parametric distributions using R : the fitdistrplus package

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

The 5th R useR conference Agrocampus Ouest . : 47

Conference paper

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Quantitative Risk Assessment of Listeria monocytogenes in French cold-smoked Salmon: II. Risk Characterization

Regis Pouillot, Véronique Goulet, Marie Laure Delignette-Muller, Aurélie Mahé, Marie Cornu

Risk Analysis . 29 ( 6 ) : 806-819

DOI: 10.1111/j.1539-6924.2008.01200.x

Journal article

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Fate of acid-resistant and non-acid resistant Shiga toxin-producing Escherichia coli strains in experimentally contaminated French fermented raw meat sausages

M-P. Montet, S. Christieans, D. Thevenot, V. Coppet, S. Ganet, Marie Laure Delignette-Muller...

International Journal of Food Microbiology . 129(3) : 264-270

Journal article

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Finding essential scales of spatial variation in ecological data: a multivariate approach

T. Jombart, S. Dray, Anne-Béatrice Dufour

Ecography . 32(1) : 161-168

Journal article

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The concept of animals trajectories from a data analysis perspective

Clément Calenge, S. Dray, Manuela Royer-Carenzi

Ecological Informatics . 4 ( 1 ) : 34-41

DOI: 10.1016/j.ecoinf.2008.10.002

Journal article

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Responding to spatial and temporal variations in predation risk: space use of a game species in a changing landsape of fear

Vincent Tolon, Stéphane Dray, Anne Loison, Achim Zeileis, Claude Fischer, Eric Baubet

Canadian Journal of Zoology . 87 : 1129-1137

DOI: 10.1139/Z09-101

Journal article

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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 Arrouays, Nicolas Saby, Jean Thioulouse...

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

Conference paper

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