Quantitative and Evolutionary Ecology of Communities Group

Members

Delignette-Muller Marie-Laure

Professeure des universités

VetAgro-Sup

Tel: 33 04 72 43 27 56

Dray Stéphane

Directeur de recherche

CNRS

Tel: 33 04 72 43 27 57

Koffel Thomas

Maître de conférences

UCBL

Tel: 04 72 44 81 42

Lobry Jean

Professeur des universités

UCBL

Tel: 33 04 72 43 27 56

Thioulouse Jean

Directeur de recherche

CNRS

Tel: 33 04 72 43 27 56

Venner Marie-Claude

Maîtresse de conférences

UCBL

Tel: 33 04 72 43 29 02

Venner Samuel

Maître de conférences

UCBL

Tel: 33 04 72 43 29 02

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

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

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 121 to 150 publications on 572 in total

How does increasing mast seeding frequency affect population dynamics of seed consumers? Wild boar as a case study

Laura Touzot, Éliane Schermer, Samuel Venner, Sylvain S. Delzon, Cyril Rousset, Eric Baubet...

Ecological Applications . : 1-11

DOI: 10.1002/eap.2134

2020

Journal article

see the publication

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

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

2019

Conference paper

see the publication

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

2019

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

2019

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

2019

Journal article

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

SEFA 2019 Lyon .

2019

Conference paper

see the publication

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

2019

Journal article

see the publication

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

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

2018

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» .

2018

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

2018

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...

2018

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

2018

Journal article

see the publication

Members

Research programs

Functioning of African savanna communities

Masting and the community dynamics of seed consumers

The spread of antibiotic resistance genes in bacteria

Statistical analysis of ecological data

Publications

How does increasing mast seeding frequency affect population dynamics of seed consumers? Wild boar as a case study

Deep learning for species identification of modern and fossil rodent molars

Developmental variability channels mouse molar evolution

Investigating microbial associations from sequencing survey data with co-correspondence analysis

Can an herbivore affect where a top predator kills its prey by modifying woody vegetation structure?

Vaginal Tampon Colonization by Staphylococcus aureus in Healthy Women

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

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

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

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

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

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

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

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

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

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

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

Outils d'observation des boiteries

Testing the Mantel statistic with a spatially‐constrained permutation procedure

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

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

Nine Quick Tips for Analyzing Network Data

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

Spatial analyses of multi-trophic terrestrial vertebrate assemblages in Europe

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

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

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

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

Taxonomic and ecological database of trees of Western Ghats - TreeGhatsData

How teachers' attitudes on GMO relate to their environmental values

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