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 271 to 300 publications on 572 in total

Functional traits reveal processes driving natural afforestation at large spatial scales

N. W. Mason, S. K. Wiser, S. J. Richardson, M. J. Thorsen, R. J. Holdaway, S. Dray...

PLoS ONE . 8 : e75219

DOI: 10.1371/journal.pone.0075219

Journal article

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Reciprocal modulation of internal and external factors determines individual movements

J. Martin, B. Van Moorter, E. Revilla, P. Blanchard, S. Dray, Py. Quenette...

Journal of Animal Ecology . 82 : 290--300

DOI: 10.1111/j.1365-2656.2012.02038.x

Journal article

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Does local habitat fragmentation affect large-scale distributions? The case of a specialist grassland bird

L. Reino, P. Beja, Mb. Araújo, S. Dray, P. Segurado, R. Heikkinen

Diversity and Distributions . 19 : 423--432

DOI: 10.1111/ddi.12019

Journal article

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The exotic legume tree species, Acacia mearnsii, alters microbial soil functionalities and the early development of a native tree species, Quercus suber, in North Africa

I. Boudiaf, E. Baudoin, H. Sanguin, A. Beddiar, Jean Thioulouse, A. Galiana...

Soil Biology and Biochemistry . 65 : 172--179

Journal article

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Ectomycorrhizal diversity enhances growth and nitrogen fixation of Acacia mangium seedlings

N. Diagne, J. Thioulouse, H. Sanguin, Y. Prin, T. Krasova-Wade, S. Sylla...

Soil Biology and Biochemistry . 57 : 468-476

DOI: 10.1016/j.soilbio.2012.08.030

Journal article

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Australian acacia introduction to rehabilitate degraded ecosystems is it free of environmental risks?

Robin Duponnois, Ezekiel Baudoin, Hervé Sanguin, Jean Thioulouse, Christine Le Roux, Estelle Tournier...

Bois et Forêts des Tropiques . 318 ( 4 ) : 59-65

Journal article

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Ecophylogenetics: advances and perspectives

Nicolas Mouquet, Vincent Devictor, Christine N. Meynard, François Munoz, Louis-Félix Bersier, Jérôme Chave...

Biological Reviews . 87 ( 4 ) : 769-785

DOI: 10.1111/j.1469-185X.2012.00224.x

Journal article

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Multivariate analyses in soil microbial ecology: a new paradigm

Jean Thioulouse, Y. Prin, R. Duponnois

Environmental and Ecological Statistics . 19 ( 4 ) : 499--520

DOI: 10.1007/s10651-012-0198-z

Journal article

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Response of native soil microbial functions to the controlled mycorrhization of an exotic tree legume, Acacia holosericea in a Sahelian ecosystem

A. Bilgo, Sk. Sangare, Jean Thioulouse, Y Prin, V. Hien, A. Galiana...

Mycorrhiza . 22 ( 3 ) : 175--187

DOI: 10.1007/s00572-011-0390-2

Journal article

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Restoring native forest ecosystems after exotic tree plantation in Madagascar: combination of the local ectotrophic species Leptolena bojeriana and Uapaca bojeri mitigates the negative influence of the exotic species Eucalyptus camaldulensis and Pinus pat

R. Baohanta, Jean Thioulouse, H. Ramanankierana, Y. Prin, R. Rasolomampianina, E. Baudoin...

Biological Invasions . 14 ( 11 ) : 2407--2421

DOI: 10.1007/s10530-012-0238-5

Journal article

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Putative endosymbiont-mediated coexistence of weevil sibling species competing with each other

Adrien Merville, Samuel Venner, H. Henri, Agnès Vallier, F. Menu, F. Vavre...

7. International Symbiosis Society (ISS) Congress "The earth’s vast symbiosphere" .

Poster

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Contrasted breeding strategies in four sympatric sibling insect species: when a proovigenic and capital breeder copes with a stochastic environment

Pierre-François Pelisson, Marie-Claude Bel-Venner, Benjamin Rey, Lorraine Burgevin, François Martineau, François Fourel...

Functional Ecology . 26 ( 1 ) : 198-206

DOI: 10.1111/j.1365-2435.2011.01925.x

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

DOI: 10.1016/j.ijfoodmicro.2011.12.013

Journal article

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What to do with NOECS/NOELS - prohibition or innovation?

Dr Fox, Elise Billoir, S. Charles, Marie-Laure Delignette-Muller, C. Lopes

Integr Environ Assess Manag . 8 : 764--766

DOI: 10.1002/ieam.1350

Journal article

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Assessing species and community functional responses to environmental gradients: which multivariate methods?

M. Kleyer, Stéphane Dray, F. de Bello, J. Leps, Jr. Pakeman, B. Strauss...

Journal of Vegetation Science . 23 : 805--821

DOI: 10.1111/j.1654-1103.2012.01402.x

Journal article

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Disentangling plant trait responses to livestock grazing from spatio-temporal variation: the partial RLQ approach

D. Wesuls, J. Oldeland, S. Dray

Journal of Vegetation Science . 23 : 98-113

Journal article

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Predator-prey spatial game as a tool to understand the effects of protected areas on harvester-wildlife interactions

V. Tolon, J. Martin, Stéphane Dray, A. Loison, C. Fischer, E. Baubet

Ecological Applications . 22 : 648-657

DOI: 10.1890/11-0422.1

Journal article

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Assessing the effects of spatial contingency and environmental filtering on metacommunity phylogenetics

P-R. Peres-Neto, M-A. Leibold, Stéphane Dray

Ecology . 93 : S14-S30

DOI: 10.1890/11-0494.1

Journal article

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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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