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 181 to 210 publications on 652 in total

Testing the Mantel statistic with a spatially‐constrained permutation procedure

Julie Crabot, Sylvie Clappe, Stéphane Dray, T. Datry

Methods in Ecology and Evolution . 10 ( 4 ) : 532-540

DOI: 10.1111/2041-210X.13141

Journal article

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Pollen limitation as a main driver of fruiting dynamics in oak populations

Marie-Claude Bel-Venner, David Fouchet, Aurélie Siberchicot, Vincent Boulanger, Thomas Caignard, Michel Thibaudon...

Ecology Letters . 22 ( 1 ) : 98-107

DOI: 10.1111/ele.13171

Journal article

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Importance de la variabilité intraspécifique de la polluosensibilité pour l’évaluation du risque ecotoxicologique basée sur l’approche SSD (Species Sensitivity Distribution)

Vincent Baillard, Laurine Malardier, Marie Laure Delignette-Muller, Eva Roubeau Dumont, Arnaud Elger, Agnes Bouchez...

38ème colloque de l’Association des Diatomistes de Langue Française (ADLaF) .

Conference paper

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Nine Quick Tips for Analyzing Network Data

Vincent Miele, Stephane S. Robin, Catherine Matias, Stéphane Dray

PLoS Computational Biology . 15 ( 12 ) : e1007434

DOI: 10.1371/journal.pcbi.1007434

Journal article

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Diversity indices for ecological networks: a unifying framework using Hill numbers

Marc Ohlmann, Vincent Miele, Stéphane Dray, Loic Chalmandrier, Louise O’connor, Wilfried Thuiller

Ecology Letters . 22 ( 4 ) : 737-747

DOI: 10.1111/ele.13221

Journal article

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Spatial analyses of multi-trophic terrestrial vertebrate assemblages in Europe

Joao Braga, Laura Pollock, Ceres Barros, Núria Galiana Ibañez, José Montoya, Dominique Gravel...

Global Ecology and Biogeography . 28 ( 11 ) : 1636-1648

DOI: 10.1111/geb.12981

Journal article

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Modelling of omics dose-response data for ecological risk assessment

Marie-Laure Delignette-Muller, F. Larras, E. Billoir, Aurélie Siberchicot, V. Baillard, Mechthild Schmitt-Jansen

Journées du GDR Ecologie Statistique (EcoStat) .

Conference paper

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New goodness-of-fit plots for censored data in the package fitdistrplus

Marie-Laure Delignette-Muller, Christophe Dutang, Aurélie Siberchicot

7ème rencontres R .

Conference paper

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Overview of GeoLifeCLEF 2018: location-based species recommendation

Christophe Botella, Pierre Bonnet, François Munoz, Pascal P. Monestiez, Alexis Joly

CLEF 2018 - Conference and Labs of the Evaluation Forum . 2125 ( 8 )

Conference paper

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Two dimensions define the variation of fine root traits across plant communities under the joint influence of ecological succession and annual mowing

Amandine Erktan, Catherine Roumet, Diane Bouchet, Alexia Stokes, Francois Pailler, François Munoz

Journal of Ecology . 106 ( 5 ) : 2031 - 2042

DOI: 10.1111/1365-2745.12953

Journal article

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A deep learning approach to Species Distribution Modelling

Christophe Botella, Alexis Joly, Pierre Bonnet, Pascal Monestiez, François Munoz

Multimedia Tools and Applications for Environmental & Biodiversity Informatics . 978-3-319-76444-3 : 169-199

DOI: 10.1007/978-3-319-76445-0_10

Book chapter

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What makes trait-abundance relationships when both environmental filtering and stochastic neutral dynamics are at play?

Jessy Loranger, Francois Munoz, Bill Shipley, Cyrille Violle

Oikos . 127 ( 12 ) : 1735-1745

DOI: 10.1111/oik.05398

Journal article

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Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids

Helena Bestová, Francois Munoz, Pavel Svoboda, Pavel Škaloud, Cyrille Violle

Oecologia . 186 ( 4 ) : 1017-1030

DOI: 10.1007/s00442-018-4074-x

Journal article

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ecolottery : Simulating and assessing community assembly with environmental filtering and neutral dynamics in R

Francois Munoz, Matthias Grenié, Pierre Denelle, Adrien Taudière, Fabien Laroche, Caroline Tucker...

Methods in Ecology and Evolution . 9 ( 3 ) : 693-703

DOI: 10.1111/2041-210X.12918

Journal article

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Functional rarity of coral reef fishes at the global scale: Hotspots and challenges for conservation

Matthias Grenié, David Mouillot, Sebastien Villeger, Pierre Denelle, Caroline M. Tucker, Francois Munoz...

Biological Conservation . 226 : 288-299

DOI: 10.1016/j.biocon.2018.08.011

Journal article

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Pollen limitation as a main driver of fruiting dynamics in oak populations

Éliane Schermer, Marie‐claude Bel‐venner, David Fouchet, Aurélie Siberchicot, Vincent Boulanger, Thomas Caignard...

Ecology Letters . 22 ( 1 ) : 98-107

DOI: 10.1111/ele.13171

Journal article

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How to implement functional responses of migroalgae in risk assessment processing ?

F. Larras, E. Billoir, S. Schloz, Marie-Laure Delignette-Muller, M. Schmitt-Jansen

Congrès européen de la SETAC «Science and Technology for Environmental Protection» .

Conference paper

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Defining simple toxicity values (EC, BMD) is not so simple

E. Billoir, F. Larras, V. Baillard, S. Devin, M. Schmitt-Jansen, Marie-Laure Delignette-Muller

Congrès européen de la SETAC «Science and Technology for Environmental Protection» .

Poster

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Multiple facets of rarity among rain forest trees in the Western Ghats of India

Priya Davidar, François Munoz, Jean-Philippe Puyravaud, D Mohandass, V.S Ramachandran

Biological Conservation . 228 : 110-119

DOI: 10.1016/j.biocon.2018.10.014

Journal article

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Taxonomic and ecological database of trees of Western Ghats - TreeGhatsData

Valérie Raevel, Narayanan Ayyappan, Natesan Balachandran, Soupramanien Aravajy, N. Barathan, B.R. Ramesh...

Preprint

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How teachers' attitudes on GMO relate to their environmental values

Jérémy Castéra, Pierre Clément, François Munoz, Franz Bogner

Journal of Environmental Psychology . 57 : 1-9

DOI: 10.1016/j.jenvp.2018.04.002

Journal article

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Species distribution modeling based on the automated identification of citizen observations

Christophe Botella, Alexis Joly, Pierre Bonnet, Pascal P. Monestiez, François Munoz

Applications in Plant Sciences . 6 ( 2 ) : 1-11

DOI: 10.1002/aps3.1029

Journal article

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Cushion-plant protection determines guild-dependent plant strategies in high-elevation peatlands of the Cordillera Real, Bolivian Andes

Valérie Raevel, Fabien Anthelme, Rosa Isela Meneses, François Munoz

Perspectives in Plant Ecology, Evolution and Systematics . 30 : 103-114

DOI: 10.1016/j.ppees.2017.09.006

Journal article

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Impact of currently marketed tampons and menstrual cups on Staphylococcus aureus growth and TSST-1 production in vitro

Louis Nonfoux, Myriam Chiaruzzi, Cédric Badiou, Jessica Baude, Anne Tristan, Jean Thioulouse...

Applied and Environmental Microbiology . 84 ( 12 )

DOI: 10.1128/AEM.00351-18

Journal article

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Plant Strategies along Resource Gradients

Thomas Koffel, Tanguy Daufresne, François Massol, Christopher Klausmeier

The American Naturalist . 192 ( 3 ) : 360 - 378

DOI: 10.1086/698600

Journal article

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Facilitation- versus competition-driven succession: the key role of resource-ratio

Thomas Koffel, Simon Boudsocq, Nicolas Loeuille, Tanguy Daufresne

Ecology Letters . 21 ( 7 ) : 1010-1021

DOI: 10.1111/ele.12966

Journal article

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The ground plot counting method: A valid and reliable assessment tool for quantifying seed production in temperate oak forests?

Laura Touzot, Marie-Claude Bel-Venner, Marlène Gamelon, Stefano Focardi, Marlène Gamelon, François Débias...

Forest Ecology and Management . 430 : 143-149

DOI: 10.1016/j.foreco.2018.07.061

Journal article

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The ground plot counting method: A valid and reliable assessment tool for quantifying seed production in temperate oak forests?

Laura Touzot, Marie-Claude Bel-Venner, Marlène Gamelon, Stefano Focardi, Vincent Boulanger, Francois Débias...

Forest Ecology and Management . 430 : 143-149

DOI: 10.1016/j.foreco.2018.07.061

Journal article

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Evaluation de méthodes diagnostiques en l’absence de gold standard sur la base de variables binaires et continues : intérêt de l'approche bayésienne

T. Lurier, Marie Laure Delignette-Muller, Elsa Jourdain, Florence Ayral

Journée AppliBUGS . : 38 slides

Conference paper

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