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 652 in total

Improved testing of species traits-environment relationships in the fourth-corner problem

C. Terbraak, A. Cormont, Stéphane Dray

Ecology . 93 : 1525--1526

DOI: 10.1890/12-0126.1

Journal article

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Spatial processes driving soil microbial community assembly on a wide scale

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

4. International Congress Eurosoil 2012 - Soil Science for the Benefit of Mankind and Environment .

Conference paper

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A handbook for uncovering the complete energetic budget in insects: the van Handel's method (1985) revisited

Vincent Foray, Pierre-François Pelisson, Marie-Claude Bel-Venner, Emmanuel Desouhant, Samuel Venner, Frédéric Menu...

Physiological Entomology . 37 ( 3 ) : 295-302

DOI: 10.1111/j.1365-3032.2012.00831.x

Journal article

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Comparison of bioassays with different exposure time patterns: The added value of dynamic modelling in predictive ecotoxicology

Elise Billoir, Hélène Delhaye, Carole Forfait-Dubuc, Bernard Clément, Gaëlle Triffault-Bouchet, Sandrine Charles...

Ecotoxicology and Environmental Safety . 75 : 80-86

DOI: 10.1016/j.ecoenv.2011.08.006

Journal article

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Fitting a lognormal distribution to enumeration and absence/presence data

Natalie N. Commeau, Éric É. Parent, Marie Laure Delignette-Muller, Marie Cornu

International Journal of Food Microbiology . 155 ( 3 ) : 146 - 152

DOI: 10.1016/j.ijfoodmicro.2012.01.023

Journal article

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Modeling of Clostridium perfringens vegetative cell inactivation in beef-in-sauce products: A meta-analysis using mixed linear models

S. Jaloustre, Laurent Guillier, E. Morelli, V. Noël, Marie Laure Delignette-Muller

International Journal of Food Microbiology . 154 : 44-51

Journal article

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Survival data analyses in ecotoxicology: critical effect concentrations, methods and models. What should we use?

Carole Forfait-Dubuc, Sandrine Charles, Elise Billoir, Marie-Laure Delignette-Muller

Ecotoxicology . 21 : 1072--1083

DOI: 10.1007/s10646-012-0860-0

Journal article

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Analyse de (K+1) tableaux avec le logiciel ade4. Application en épidémiologie.

Stéphanie Bougeard, Stéphane Dray

1ères Rencontres R .

Conference paper

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Visualisation de données multivariées: réimplémentation des fonctionnalités graphiques de la librairie ade4

Alice Julien-Laferriere, Stéphane Dray

1ères Rencontres R .

Conference paper

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How to measure and test phylogenetic signal

Tamara Münkemüller, S. Lavergne, B. Bzeznik, Stéphane Dray, T. Jombart, K. Schiffers...

Methods in Ecology and Evolution . 3 : 743-756

DOI: 10.1111/j.2041-210X.2012.00196.x

Journal article

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The Harttiini (Siluriformes, Loricariidae) from the Guianas: a multi-table approach to assess their diversity, evolution, and distribution

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

Cybium : Revue Internationale d’Ichtyologie . 36 ( 1 ) : 115-161

DOI: 10.26028/cybium/2012-361-010

Journal article

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Community ecology in the age of multivariate multiscale spatial analysis

S. Dray, R. Pelissier, P. Couteron, M. -J. Fortin, P. Legendre, P. R. Peres-Neto...

Ecological monographs . 82 ( 3 ) : 257 - 275

DOI: 10.1890/11-1183.1

Journal article

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Equation or algorithm: differences and choosing between them

Cédric Gaucherel, Sèverine Bérard, François Munoz

Acta Biotheoretica . 59 ( 1 ) : 67-79

DOI: 10.1007/s10441-010-9119-4

Journal article

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How does herbivory affect individuals and populations of the perennial herb Paeonia officinalis ?

Émilie Andrieu, Max Debussche, François Munoz, John D. Thompson

Flora . 206 ( 6 ) : 544-549

DOI: 10.1016/j.flora.2010.10.001

Journal article

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Continental-scale patterns of Cecropia reproductive phenology: evidence from herbarium specimens

Paul-Camilo Zalamea, François Munoz, Pablo R. Stevenson, C. E. Timothy Paine, Carolina Sarmiento, Daniel Sabatier...

Proceedings of the Royal Society B: Biological Sciences . 278 ( 1717 ) : 2437-2445

DOI: 10.1098/rspb.2010.2259

Journal article

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Large trends in French topsoil characteristics are revealed by spatially constrained multivariate analysis

D. Arrouays, N.P.A. Saby, Jean Thioulouse, C. Jolivet, Line Boulonne, C. Ratié

Geoderma . 161 : 107-114

DOI: 10.1016/j.geoderma.2010.12.002

Journal article

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Diversity, Geographic Distribution, and Habitat-Specific Variations of Microbiota in Natural Populations of the Chicken Mite, Dermanyssus gallinae

C. Valiente-Moro, J. Thioulouse, C. Chauve, Lionel Zenner

Journal of Medical Entomology . 48 ( 4 ) : 788-796

DOI: 10.1603/ME10113

Journal article

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Nurse shrubs increased the early growth of Cupressus seedling by enhancing belowground mutualism ans doil microbial activity

R. Duponnois, L. Ouahmane, A. Kane, Jean Thioulouse, M. Hafidi, A. Boumezzough...

Soil Biology and Biochemistry . 43 ( 10 ) : 2160-2168

DOI: 10.1016/j.soilbio.2011.06.020

Journal article

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Biogeographical patterns of soil molecular microbial biomass as influenced by soil characteristics and management

S. Dequiedt, Nicolas P. A. Saby, M. Lelievre, C. Jolivet, J. Thioulouse, B. Toutain...

Global Ecology and Biogeography . 20 : 641-652

DOI: 10.1111/j.1466-8238.2010.00628.x

Journal article

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SIMULTANEOUS ANALYSIS OF A SEQUENCE OF PAIRED ECOLOGICAL TABLES: A COMPARISON OF SEVERAL METHODS

J. Thioulouse

Annals of Applied Statistics . 5 ( 4 ) : 2300-2325

DOI: 10.1214/10-AOAS372

Journal article

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Bayesian modelling of daphnid responses to time-varying cadmium exposure in laboratory aquatic microcosms

Elise Billoir, Hélène Delhaye, Bernard Clément, Marie Laure Delignette-Muller, Sandrine Charles

Ecotoxicology and Environmental Safety . 74 ( 4 ) : 693-702

DOI: 10.1016/j.ecoenv.2010.10.023

Journal article

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The importance of incorporating age and sex when backcalculating length in bullhead Cottus gobio

J. Kielbassa, Sandrine Charles, Marie Laure Delignette-Muller

Journal of Fish Biology . 78 : 1492-1507

DOI: 10.1111/j.1095-8649.2011.02956.x

Journal article

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The Nile monitor (Varanus niloticus; Squamata: Varanidae) as a sentinel species for lead and cadmium contamination in sub-Saharan wetlands.

A. Ciliberti, P. Berny, Marie Laure Delignette-Muller, V. de Buffrénil

Science of the Total Environment . 409 : 4735-4745

Journal article

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Bayesian modeling of Clostridium perfringens growth in beef-in-sauce products

S. Jaloustre, M. Cornu, E. Morelli, C. Noël, Marie Laure Delignette-Muller

Food Microbiology . 28 : 311-320

DOI: 10.1016/j.fm.2010.04.002

Journal article

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Estimating the Number of Contributors to Forensic DNA Mixtures: Does Maximum Likelihood Perform Better Than Maximum Allele Count?

Hinda Haned, Laurent Pène, J.R. Lobry, Anne-Béatrice Dufour, D. Pontier

Journal of Forensic Sciences . 56 ( 1 ) : 23-28

DOI: 10.1111/j.1556-4029.2010.01550.x

Journal article

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Biogeography of soil microbial communities: a review and a description of the ongoing french national initiative

Lionel Ranjard, Samuel Dequiedt, Claudy Jolivet, Nicolas Saby, Jean Thioulouse, Jérôme Harmand...

Sustainable Agriculture Volume 2 . 978-94-007-0393-3 : 857-865

DOI: 10.1007/978-94-007-0394-0_37

Book chapter

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How can ecological status be summarized for an operational Pressures/States model ?

N. Lalande, Flavie Cernesson, Stéphane Dray, M.G. Tournoud, T. Tormos, Pascal Kosuth

EGU (European Geosciences Union) General Assembly 2011 . : 1

Poster

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Relationships between species feeding traits and environmental conditions in fish communities: a three-matrix approach

A. Brind'Amour, D. Boisclair, Stéphane Dray, P. Legendre

Ecological Applications . 21 ( 2 ) : 363-377

DOI: 10.1890/09-2178.1

Journal article

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Identification at the larval stage of four Curculio species coexisting on oak trees using PCR-RFLP

P-F. Pelisson, H. Henri, Marie-Claude Bel-Venner, R. Allemand, A. Merville, F. Menu...

Entomologia Experimentalis et Applicata . 138 : 77-82

DOI: 10.1111/j.1570-7458.2010.01077.x

Journal article

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Coexistence of Insect Species competing for a pulsed resource: toward a unified theory of biodiversity in fluctuating environments

Samuel Venner, P-F. Pelisson, Marie-Claude Bel-Venner, F. Debias, Etienne Rajon, F. Menu

PLoS ONE . 6 ( 3 ) : e18039

DOI: 10.1371/journal.pone.0018039

Journal article

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