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 151 to 180 publications on 572 in total

Species distribution modeling based on the automated identification of citizen observations

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

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

2018

Journal article

see the publication

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

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

2018

Book

see the publication

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

2018

Journal article

see the publication

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

2018

Journal article

see the publication

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

2018

Journal article

see the publication

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

2018

Journal article

see the publication

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

Functional Ecology and Environment .

2017

Poster

see the publication

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

2017

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

2017

Journal article

see the publication

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

2017

Journal article

see the publication

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

2017

Conference paper

see the publication

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

2017

Conference paper

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

Species distribution modeling based on the automated identification of citizen observations

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

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

Plant Strategies along Resource Gradients

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

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

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

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

Diagnosis of bovine dictyocaulosis by bronchoalveolar lavage technique: A comparative study using a Bayesian approach

Disentangling good from bad practices in the selection of spatial or phylogenetic eigenvectors

Optimizing the choice of a spatial weighting matrix in eigenvector-based methods

Simple parametric tests for trait–environment association

Supervised Multiblock Analysis in R with the ade4 Package

MOSAIC: a web-interface for statistical analyses in ecotoxicology

DRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment

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

Multivariate Analysis of Ecological Data with ade4

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

Complex ecological interactions of Staphylococcus aureus in tampons during menstruation

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

Algorithms and biplots for double constrained correspondence analysis

Caractère fonctionnelle des plantes adventices : comparaison avec les espèces prairiales

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

What makes a weed a weed ? Towards a functional characterization

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

Functional Rarity: The Ecology of Outliers

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

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

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

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

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