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 241 to 270 publications on 572 in total

How root traits are modified in secondary succession gradient along roadsides ?

Amandine Erktan, Alexia Stokes, Catherine Roumet, Diane Bouchet, Yogan Monnier, Francois Pailler...

BES and SFE Joint Annual Meeting . : np

Conference paper

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Designing ‘trait-based null model’ approaches to investigate community assembly mechanisms

Rémi Perronne, Benjamin Borgy, Xavier Reboud, François Munoz, Sabrina Gaba

BES and SFE Joint Annual Meeting 2014 . : np

Conference paper

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Modification des traits racinaires le long d’une succession secondaire sur des talus routiers: implications dans la dynamique des communautés et la protection des sols contre l’érosion

Amandine Erktan, Alexia Stokes, Catherine Roumet, Yves Caraglio, Christophe Jourdan, Diane Bouchet...

Ecoveg 10 . : np

Poster

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Procesos ecológicos a múltiples escalas que afectan a las dinámicas de comunidades de plantas en los humedales altoandinos de Bolivia - Multi-scale ecological processes driving plant community dynamics in high-elevation peatlands of Bolivia

François Munoz, Fabien Anthelme, Valérie Raevel

Ecologia en Bolivia . 49 ( 3 ) : 104-120

Journal article

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Characterizing the phylogenetic tree community structure of a protected tropical rain forest area in Cameroon

Stéphanie Manel, Thomas L. P. Couvreur, François Munoz, Pierre Couteron, Olivier Hardy, Bonaventure Sonke

PLoS ONE . 9 : e98920

DOI: 10.1371/journal.pone.0098920

Journal article

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Modélisation microstructurale de la précipitation en soudage par friction malaxage Application à l’alliage d’aluminium 2024 (CM-13-639)

Valentine Legrand, Sabrina Gastebois, Gildas Guillemot, Charles-André Gandin, Lionel Fourment

Matériaux 2014, 13 - Procédés d’assemblage ~ 9ème Journée Nationale du Soudage .

Conference paper

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Determining the instar of a weevil larva (Coleoptera: Curculionidae) using a parsimonious method

A. Merville, A. Vallier, Samuel Venner, A. Siberchicot, D. Fouchet, A. Heddi...

European Journal of Entomology . 111 ( 4 ) : 567-573

DOI: 10.14411/eje.2014.056

Journal article

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Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation.

Stéphane Dray, Philippe Choler, Sylvain Dolédec, Pedro R. Peres-Neto, Sandrine Pavoine, Cajo J. F. ter Braak

Ecology . 95 ( 1 ) : 14-21

DOI: 10.1890/13-0196.1

Journal article

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Similar Processes but Different Environmental Filters for Soil Bacterial and Fungal Community Composition Turnover on a Broad Spatial Scale

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

PLoS ONE . 9 ( 11 ) : 1-11

DOI: 10.1371/journal.pone.0111667

Journal article

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Statistical handling of reproduction data for exposure-response modeling

Marie Laure Delignette-Muller, Christelle Lopes, Philippe Veber, Sandrine Charles

Environmental Science and Technology . 48 : 7544-51

DOI: 10.1021/es502009r

Journal article

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Spatially constrained clustering of ecological networks

Vincent Miele, Franck Picard, S. Dray

Methods in Ecology and Evolution . 5 ( 8 ) : 771-779

DOI: 10.1111/2041-210X.12208

Journal article

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Analysing a pair of tables : coinertia analysis and duality diagrams

Stéphane Dray

Visualization and Verbalization of Data . 978-1-4665-8980-3 : 289-300

Book chapter

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Statistical ecology comes of age

Olivier Gimenez, Stephen T. Buckland, Byron J.T. Morgan, Nicolas Bez, Sophie Bertrand, Rémi Choquet...

Biology Letters . 10 ( 20140698 ) : np

DOI: 10.1098/rsbl.2014.0698

Journal article

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Functional analysis of normalized difference vegetation index curves reveals overwinter mule deer survival is driven by both spring and autumn phenology

M. A. Hurley, M. Hebblewhite, Jean-Michel Gaillard, Stéphane Dray, K. A. Taylor, W. K. Smith...

Philosophical Transactions of the Royal Society B: Biological Sciences . 369 ( 1643 ) : 20130196

DOI: 10.1098/rstb.2013.0196

Journal article

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Ectomycorrhizal fungi on the early colonizing shrub Sarcolaena oblongifolia F. facilitate the establishment of an endemic tree Uapaca bojeri L. in Madagascarian highland forests

H. Ramanankierana, R. Baohanta, H. Randriambanona, Y Prin, N. Rakotoarimanga, E. Baudoin...

International Journal of Ecology and Ecosolution . 1 : 1-15

Journal article

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Development and validation of an OECD reproductive toxicity test guideline with the pond snail Lymnaea stagnalis (Mollusca, Gastropoda)

Virginie Ducrot, Clare Askem, Didier Azam, Denise Brettschneider, Rebecca Brown, Sandrine Charles...

Regulatory Toxicology and Pharmacology . 70 ( 3 ) : 605-614

DOI: 10.1016/j.yrtph.2014.09.004

Journal article

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Managing Mediterranean nurse plants-mediated effects on soil microbial functions to improve rock phosphate solubilization processes and early growth of Cupressus atlantica G

M. Hafidi, L. Ouahmane, J. Thioulouse, H. Sanguin, A. Boumezzough, Y. Prin...

Ecological Engineering . 57 : 57--64

DOI: 10.1016/j.ecoleng.2013.04.006

Journal article

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Native plant resources to optimize the performances of forest rehabilitation in Mediterranean and tropical environment: some examples of nursing plant species that improve the soil mycorrhizal potential

R. Duponnois, H. Ramanankierana, M. Hafidi, R. Baohanta, E. Baudoin, Jean Thioulouse...

Comptes Rendus. Biologies . 336 : 265-272

DOI: 10.1016/j.crvi.2013.04.015

Journal article

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L'introduction d'acacias australiens pour réhabiliter des écosystèmes dégradés est-elle dépourvue de risques environnementaux ?

R. Duponnois, E. Baudoin, H. Sanguin, Jean Thioulouse, C. Le Roux, E. Tournier...

Bois et Forêts des Tropiques . 318 : 59-65

Journal article

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A new process to promote the use of controlled mycorrhization practice in forest nurseries

L. Ndoye, A. Soumaré, Ec. Agbangba, J. Thioulouse, A. Galiana, Y. Prin...

African Journal of Agricultural Research . 8 : 308--316

DOI: 10.5897/AJAR12.1642

Journal article

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Simulation 3D du soudage par frottement malaxage (FSW) à l'aide d'une formulation Arbitrairement Lagrangienne ou Eulérienne (ALE)

Sabrina Gastebois, Lionel Fourment

CSMA 2013 - 11ème colloque national en calcul des structures .

Conference paper

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Two-component Bose gases with one-body and two-body couplings

Samuel Lellouch, Tung-Lam Dao, Thomas Koffel, Laurent Sanchez-Palencia

Physical Review A : Atomic, molecular, and optical physics [1990-2015] . 88 : 063646

DOI: 10.1103/PhysRevA.88.063646

Journal article

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Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity.

L. Ranjard, S. Dequiedt, Nicolas Chemidlin Prévost-Bouré, J. Thioulouse, N. P. A. Saby, M. Lelievre...

Nature Communications . 4 : 1434

DOI: 10.1038/ncomms2431

Journal article

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Méthodes d'analyse multivariée pour l'étude de l'influence de la mycorhizosphère sur la structure et le fonctionnement des communautés bactériennes du sol

Jean Thioulouse, H. Sanguin, Yves Prin, Robin Duponnois

Des champignons symbiotiques contre la désertification. Ecosystèmes mediterranéens, tropicaux et insulaires . 978-2-7099-1949-4 : 474-508

Book chapter

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From Income to Capital Breeding: When Diversified Strategies Sustain Species Coexistence

Pierre-François Pelisson, Marie-Claude Bel-Venner, David Giron, Frédéric Menu, Samuel Venner

PLoS ONE . 8 ( 9 ) : e76086

DOI: 10.1371/journal.pone.0076086

Journal article

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A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients

N. Mason, F. de Bello, D. Mouillot, S. Pavoine, S. Dray

Journal of Vegetation Science . 24 : 794--806

DOI: 10.1111/jvs.12013

Journal article

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Ecologie prédictive & changement planétaire

Frédéric Austerlitz, Michael Blum, Sarah Calba, Jérôme Chave, Marc Choisy, Audrey Coreau...

Prospective de l'Institut écologie & environnement du CNRS . hors s\'{e}rie : 9-44

Book chapter

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Endosymbiont diversity among sibling weevil species competing for the same resource

Adrien Merville, Samuel Venner, Hélène Henri, Agnès Vallier, Frédéric Menu, Fabrice Vavre...

BMC Evolutionary Biology . 13 : 28

DOI: 10.1186/1471-2148-13-28

Journal article

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Conference Report: Deuxièmes Rencontres R

Aurélie Siberchicot, S. Dray

The R Journal . 5/2 : 164--165

Journal article

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