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 151 to 180 publications on 645 in total

Vaginal Tampon Colonization by Staphylococcus aureus in Healthy Women

Myriam Chiaruzzi, Alexia Barbry, Anaëlle Muggeo, Anne Tristan, Isaline Jacquemond, Cedric Badiou...

Applied and Environmental Microbiology . 86 ( 18 ) : e01249-20

DOI: 10.1128/AEM.01249-20

Journal article

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Effect of interspecific competition on species sensitivity distribution models: Analysis of plant responses to chemical stress

Vincent Baillard, Cécile Sulmon, Anne-Kristel Bittebiere, Cendrine Mony, Ivan Couée, Gwenola Gouesbet...

Ecotoxicology and Environmental Safety . 200 : 110722

DOI: 10.1016/j.ecoenv.2020.110722

Journal article

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Utilisation de DRomics pour modéliser les données omiques de type dose-réponse dans le cadre de l’appréciation du risque environnemental

Marie-Laure Delignette-Muller, F. Larras, Elise Billoir, Aurélie Siberchicot, Mechthild Schmitt-Jansen

SEFA (Société d’Ecotoxicologie Fondamentale et Appliquée) .

Conference paper

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Some issues about the design of preclinical trials

Marie-Laure Delignette-Muller

Séminaire Celphedia (Création, ELevage, PHEnotypage, DIstribution et Archivage d'organismes modèles) .

Conference paper

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DRomics: an R tool for modelling omics dose-response data

Marie-Laure Delignette-Muller, Floriane Larras, Elise Billoir, Aurélie Siberchicot, Mechthild Schmitt-Jansen

Congrès useR! .

Poster

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Comparison of the effect of alfaxalone VS medetomidine and ketamine for induction of anaesthesia in Trachemys scripta sp. undergoing sterilisation

L. Gantner, Karine Portier, Marie-Laure Delignette-Muller, B. Quintard

Joint Leibniz-IZW/EAZWV/ECZM Zoo and Wildlife Health Conference .

Conference paper

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Combination of prior distributions elicited from expert opinions previous to Bayesian inference. Application to personalized medicine

A. Loubert, Muriel Rabilloud, Marie-Laure Delignette-Muller, Fabien Subtil

Bayes 2019 (Bayesian Biostatistics conference) .

Conference paper

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Regional rainfall and local topography jointly drive tree community assembly in lowland tropical forests of New Caledonia

Grégoire Blanchard, François Munoz, Thomas Ibanez, Vanessa Hequet, Hervé Vandrot, Jérémy Girardi...

Journal of Vegetation Science . 30 ( 5 ) : 845-856

DOI: 10.1111/jvs.12781

Journal article

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Population dynamics in a structured habitat

Estelle Pitard, François Munoz

Les Dossiers d'Agropolis International . 23 : 38-38

Journal article

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Functional biogeography of dietary strategies in birds

Jean-Yves Barnagaud, Nathan Mazet, Francois Munoz, Matthias Grenié, Pierre Denelle, Mar Sobral...

Global Ecology and Biogeography . 28 ( 7 ) : 1004-1017

DOI: 10.1111/geb.12910

Journal article

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Disentangling the processes driving tree community assembly in a tropical biodiversity hotspot (New Caledonia)

Robin Pouteau, Francois Munoz, Philippe Birnbaum

Journal of Biogeography . 46 ( 4 ) : 796-806

DOI: 10.1111/jbi.13535

Journal article

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Distinguishing the signatures of local environmental filtering and regional trait range limits in the study of trait–environment relationships

Pierre Denelle, Cyrille Violle, Francois Munoz

Oikos . 128 ( 7 ) : 960-971

DOI: 10.1111/oik.05851

Journal article

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A new multi-species method to correct for sampling bias in presence only niche models, and its application to Pl@ntNet citizen science data in France

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

ESA 2019 - Annual Meeting of the Ecological Society of America .

Conference paper

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Deterministic processes drive functional and phylogenetic temporal changes of woody species in temperate forests in Northeast China

Shuai Fang, François Munoz, Ji Ye, Fei Lin, Zuoqiang Yuan, Xu Kuang...

Annals of Forest Science . 76 ( 2 ) : 42

DOI: 10.1007/s13595-019-0830-2

Journal article

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Phylogenetic diversity in the Western Ghats biodiversity hotspot reflects environmental filtering and past niche diversification of trees

Ruksan Bose, B.R. Ramesh, Raphaël Pélissier, François Munoz

Journal of Biogeography . 46 ( 1 ) : 145-157

DOI: 10.1111/jbi.13464

Journal article

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What makes a weed a weed? A large-scale evaluation of arable weeds through a functional lens

Bérenger Bourgeois, François Munoz, Guillaume Fried, Lucie Mahaut, Laura Armengot, Pierre Denelle...

American Journal of Botany . 106 ( 1 ) : 90-100

DOI: 10.1002/ajb2.1213

Journal article

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Assessment of diagnostic tests in the absence of a gold standard: a Bayesian approach simultaneously using latent class and mixture models for the diagnosis of bovine dictyocaulosis

Thibaut Lurier, Marie-Anne Arcangioli, Gilles Bourgoin, Marie Laure Delignette-Muller

BAYES2019 Lyon: Bayesian Biostatistics .

Conference paper

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Microbial cross-feeding promotes multiple stable states and species coexistence, but also susceptibility to cheaters

Zepeng Sun, Thomas Koffel, Simon Stump, Ghjuvan Micaelu Grimaud, Christopher Klausmeier

Journal of Theoretical Biology . 465 : 63-77

DOI: 10.1016/j.jtbi.2019.01.009

Journal article

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Assessing potential surrogates of macroinvertebrate diversity in North-African Mediterranean aquatic ecosystems

Noura Slimani, David Sánchez-Fernández, Eric Guilbert, Moncef Boumaiza, Simone Guareschi, Jean Thioulouse

Ecological Indicators . 101 : 324-329

DOI: 10.1016/j.ecolind.2019.01.017

Journal article

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Flower phenology as a disruptor of the fruiting dynamics in temperate oak species

Éliane Schermer, Marie-Claude Bel-Venner, Jean-Michel Gaillard, Stéphane Dray, Vincent Boulanger, Iris Le Roncé...

New Phytologist . 225 ( 3 ) : 1181-1192

DOI: 10.1111/nph.16224

Journal article

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Approche de Modélisation Hiérarchique pour la Description de l'Effet de la Compétition Interspécifique sur la Tolérance Chimique d'Herbacées

Vincent Baillard, Marie Laure Delignette-Muller, Cécile Sulmon, Anne‐kristel Bittebière, Cendrine Mony, Simon Devin...

SEFA 2019 Lyon .

Conference paper

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Phenotypic plasticity in the invasive pest Drosophila suzukii: activity rhythms and gene expression in response to temperature

Christophe Plantamp, Hélène Henri, Thibault Andrieux, Corinne Régis, Gladys Mialdea, Stéphane Dray...

Journal of Experimental Biology . 222 : jeb199398

DOI: 10.1242/jeb.199398

Journal article

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Outils d'observation des boiteries

Valentin Poulain, Luc Mounier, Marie Laure Delignette-Muller, Dorothee Ledoux

Journées Nationales des Groupements Techniques Vétérinaires (JNGTV) . : np

Poster

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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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