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 211 to 240 publications on 645 in total

Assessment of Ozone or Not-Treated Wastewater Ecotoxicity Using Mechanism-Based and Zebrafish Embryo Bioassays

Adriana Wigh, Selim Ait-Aissa, Nicolas Creusot, Hugo Terrisse, Marie Laure Delignette-Muller, Alexandre Bergé...

Journal of Environmental Protection . 09 ( 04 ) : 325 - 346

DOI: 10.4236/jep.2018.94022

Journal article

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Multivariate Analysis of Ecological Data with ade4

Jean Thioulouse, Stéphane Dray, Anne-Béatrice Dufour, Aurélie Siberchicot, Thibaut Jombart, Sandrine Pavoine

DOI: 10.1007/978-1-4939-8850-1

Book

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Integrating spatial and phylogenetic information in the fourth‐corner analysis to test trait–environment relationships

Joao Braga, Cajo J.F. ter Braak, Wilfried Thuiller, Stéphane Dray

Ecology . 99 ( 12 ) : 2667-2674

DOI: 10.1002/ecy.2530

Journal article

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Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

Isaline Jacquemond, Anaëlle Muggeo, Gery Lamblin, Anne Tristan, Yves Gillet, Pierre Adrien Bolze...

Scientific Reports . 8 ( 1 ) : 9942

DOI: 10.1038/s41598-018-28116-3

Journal article

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Beyond neutrality: disentangling the effects of species sorting and spurious correlations in community analysis

Sylvie Clappe, Stéphane Dray, Pedro Peres-Neto

Ecology . 99 ( 8 ) : 1737-1747

DOI: 10.1002/ecy.2376

Journal article

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Algorithms and biplots for double constrained correspondence analysis

Cajo J.F. ter Braak, Petr Šmilauer, Stéphane Dray

Environmental and Ecological Statistics . 25 ( 2 ) : 171-197

DOI: 10.1007/s10651-017-0395-x

Journal article

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Database Of Weeds In Cultivation Fields Of France And Uk, With Ecological And Biogeographical Information

François Munoz, Guillaume Fried, Laura Armengot, Bérenger Bourgeois, Vincent V. Bretagnolle, Joel J. Chadoeuf...

DOI: 10.5281/zenodo.1112342

Other publication

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Caractère fonctionnelle des plantes adventices : comparaison avec les espèces prairiales

Béranger Bourgeois, François Munoz, Guillaume Fried, Sabrina Gaba, Lucie Mahaut, Pierre Denelle...

Journée "Approche fonctionnelle pour la gestion des espèces adventices et de la flore des linéaires non cultivés » .

Conference paper

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A Common Toolbox to Understand, Monitor or Manage Rarity? A Response to Carmona et al.

Cyrille Violle, Wilfried Thuiller, Nicolas Mouquet, François Munoz, Nathan J.B. Kraft, Marc W. Cadotte...

Trends in Ecology & Evolution . 32 ( 12 ) : 891-893

DOI: 10.1016/j.tree.2017.10.001

Journal article

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What makes a weed a weed ? Towards a functional characterization

Bérenger Bourgeois, Pierre Denelle, François Munoz, Guillaume Fried, Sabrina Gaba, Jonathan Storkey...

"Functional Ecology and Environment" Conference .

DOI: 10.13140/RG.2.2.36807.60321

Conference paper

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Studying community assembly using the trait-based null model approach: synthesis and main results on grassland communities

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

Functional Ecology and Environment .

Poster

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Functional Rarity: The Ecology of Outliers

Cyrille Violle, Wilfried Thuiller, Nicolas Mouquet, François Munoz, Nathan J.B. Kraft, Marc Cadotte...

Trends in Ecology & Evolution . 32 ( 5 ) : 356 - 367

DOI: 10.1016/j.tree.2017.02.002

Journal article

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Mowing influences community-level variation in resource-use strategies and flowering phenology along an ecological succession on Mediterranean road slopes

Diane C. Bouchet, Pierre-Olivier Cheptou, François Munoz

Applied Vegetation Science . 20 ( 3 ) : 376 - 387

DOI: 10.1111/avsc.12311

Journal article

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How to design trait-based analyses of community assembly mechanisms: insights and guidelines from a literature review

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

Perspectives in Plant Ecology, Evolution and Systematics . 25 : 29-44

DOI: 10.1016/j.ppees.2017.01.004

Journal article

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Dynamics of tree diversity in undisturbed Evergreen forest at Uppangala, Central Western Ghats

Narayanan Ayyappan, B.R. Ramesh, Soupramanien Aravajy, S. Ramalingam, N. Barathan, Selvaraj Jeyakumar...

Paper presented at the Fourth Indian Biodiversity Congress (IBC 2017) . : 293

Conference paper

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Wood and leaf strategies in a low-elevation rainforest of Western Ghats

François Munoz, Sylvain Schmitt, Valérie Raevel, Maxime Réjou-Méchain, Narayanan Ayyappan, Natesan Balachandran...

Paper presented at the Fourth Indian Biodiversity Congress (IBC 2017), 10-12 March 2017, Pondicherry University, Puducherry, India . : p. 38

Conference paper

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Sensitivity of community-level trait-environment relationships to data representativeness: a test for functional biogeography

Benjamin Borgy, Cyrille Violle, Philippe Choler, Éric Garnier, Jens Kattge, Jessy Loranger...

Global Ecology and Biogeography . 26 ( 6 ) : 729 - 739

DOI: 10.1111/geb.12573

Journal article

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funrar: An R package to characterize functional rarity

Matthias Grenié, Pierre Denelle, Caroline Tucker, François Munoz, Cyrille Violle

Diversity and Distributions . 23 ( 12 ) : 1365 - 1371

DOI: 10.1111/ddi.12629

Journal article

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Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda

Rémi Tournebize, Stéphanie Manel, Yves Vigouroux, François Munoz, Alexandre de Kochko, Valérie Poncet

PLoS ONE . 12 ( 8 ) : e0183412

DOI: 10.1371/journal.pone.0183412

Journal article

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Plant community structure and nitrogen inputs modulate the climate signal on leaf traits

Benjamin Borgy, Cyrille Violle, Philippe Choler, Pierre Denelle, François Munoz, Jens Kattge...

Global Ecology and Biogeography . 26 ( 10 ) : 1138-1152

DOI: 10.1111/geb.12623

Journal article

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Numerical Modeling of Friction Stir (FSW) and Linear Friction (LFW) Welding Processes

Lionel Fourment, Antoine Potet, Sabrina Gastebois, Katia Mocellin

FSWP 2017 - 5th International Conference on Scientific and Technical Advances on Friction Stir Welding & Processing .

Conference paper

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New insights from niche theory on plant adaptation and ecosystem functioning

Thomas Koffel

Thesis

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Enseigner les recueil des données : explorer la variabilité biologique ... au chaud, dans une salle de cours

Anne-Béatrice Dufour, Jean R Lobry, Isabelle Amat

Statistique et Enseignement . 8 ( 2 ) : 79-85

Journal article

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Management of the mycorrhizal soil infectivity with Crotalaria ochroleuca, an indigenous wild legume in the tropics: Impacts on microbial functional diversity involved in phosphorus mobilization processes in a sahelian soil

N. Benkhoua, M. Hafidi, W. Badri, Ezékiel Baudoin, Jean Thioulouse, Yves Prin...

Ecological Engineering . 101 : 130-136

DOI: 10.1016/j.ecoleng.2017.01.010

Journal article

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Increasing Spring temperature favors oak seed production in temperate areas

Thomas Caignard, Antoine Kremer, Cyril Firmat, Manuel Nicolas, Samuel Venner, Sylvain Delzon

EGU General Assembly 2017 . 19 : np

Poster

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Raisonner l'utilisation des légumineuses ligneuses pour réhabiliter des sols dégradés en milieu méditerranéen et tropical

Robin Duponnois, Jean Thioulouse, Ezekiel Baudoin, Christine Leroux, Antoine Galiana, Y Prin

Innovations Agronomiques . 60 : 125-131

DOI: 10.15454/1.5138523036590977E12

Journal article

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Response to Comment on "Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests

Marie Laure Delignette-Muller, P. Veber

Environmental Science and Technology . 51 : 8202-8203

DOI: 10.1021/acs.est.7b02548

Journal article

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Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests

Marie Laure Delignette-Muller, P. Ruiz, P. Veber

Environmental Science and Technology . 51 : 4038-4045

DOI: 10.1021/acs.est.6b05326

Journal article

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adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data

Aurélie Siberchicot, A. Julien-Laferrière, Ab. Dufour, J. Thioulouse, S. Dray

The R Journal . 9 ( 2 ) : 198-212

DOI: 10.32614/RJ-2017-042

Journal article

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A critical issue in model-based inference for studying trait-based community assembly and a solution

Cajo J. F. ter Braak, P. Peres-Neto, Stéphane Dray

PeerJ . 5 : e2885

DOI: 10.7717/peerj.2885

Journal article

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