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 61 to 90 publications on 572 in total

Interbacterial Transfer of Carbapenem Resistance and Large Antibiotic Resistance Islands by Natural Transformation in Pathogenic Acinetobacter

Anne-Sophie Godeux, Elin Svedholm, Samuel Barreto, Anaïs Potron, Samuel Venner, Xavier Charpentier...

mBio . 13 ( 1 ) : e02631-21

DOI: 10.1128/mbio.02631-21

2022

Journal article

see the publication

Unravelling the environmental correlates influencing the seasonal biodiversity of aquatic Heteropteran assemblages in northern Africa

Noura Slimani, Eric Guilbert, James White, Matthew Hill, Paul Wood, Moncef Boumaïza...

Limnologica . : 126021

DOI: 10.1016/j.limno.2022.126021

2022

Journal article

see the publication

Editorial: Advances in Statistical Ecology: New Methods and Software

Gilles Guillot, Ali Arab, Janine Bärbel Illian, Stéphane Dray

Frontiers in Ecology and Evolution . 9

DOI: 10.3389/fevo.2021.828919

2022

Journal article

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Interpretation of the results of Q fever ELISA tests in domestic ruminants : a user-friendly Shiny appli-cation based on latent class models in a Bayesian framework

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

ESCCAR International congress on Rickettsiae and 9th Meeting of the European Society for Chlamydia Research (ESCR) .

2022

Conference paper

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Evaluation using latent class models of the diagnostic performances of three ELISA tests commercialized for the serological diagnosis of Coxiella burnetii infection in domestic ruminants

Thibaut Lurier, Elodie Rousset, Patrick Gasqui, Carole Sala, Clément Claustre, David Abrial...

ESCCAR International congress on Rickettsiae and 9th Meeting of the European Society for Chlamydia Research (ESCR) . : #231

2022

Poster

see the publication

Charlotte Genestet, Elisabeth Hodille, François Massol, Guislaine Refrégier, Alexia Barbry, Emilie Westeel...

DOI: 10.1101/2021.04.07.438754

2021

Preprint

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How does interspecific competition modify the response of grass plants against herbicide treatment? A hierarchical concentration-response approach

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

Science of the Total Environment . 778 : 146108

DOI: 10.1016/j.scitotenv.2021.146108

2021

Journal article

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Evaluation using latent class models of the diagnostic performances of three ELISA tests commercialized for the serological diagnosis of Coxiella burnetii infection in domestic ruminants

T. Lurier, Elodie Rousset, Patrick Gasqui, Carole Sala, Eric Morignat, Clément Claustre...

Gemeinsamen Arbeitstagung der Nationalen Referenzlabore Chlamydiose, Q-Fieber, Paratuberkulose und Tuberkulose der Rinder - Online-Tagung veranstaltet . : 17 slides

2021

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

Interbacterial Transfer of Carbapenem Resistance and Large Antibiotic Resistance Islands by Natural Transformation in Pathogenic Acinetobacter

Unravelling the environmental correlates influencing the seasonal biodiversity of aquatic Heteropteran assemblages in northern Africa

Editorial: Advances in Statistical Ecology: New Methods and Software

Interpretation of the results of Q fever ELISA tests in domestic ruminants : a user-friendly Shiny appli-cation based on latent class models in a Bayesian framework

Evaluation using latent class models of the diagnostic performances of three ELISA tests commercialized for the serological diagnosis of Coxiella burnetii infection in domestic ruminants

Coxiella burnetii within- and between-herd true seroprevalence assessment in domestic ruminants in France accounting for diagnostic uncertainty with latent class

An appraisal of graph embeddings for comparing trophic network architectures

Genetic and species‐level biodiversity patterns are linked by demography and ecological opportunity

When more competitors means less harvested resource

Pl@ntNet, ten years of automatic plant identification and monitoring

The dimensionality and structure of species trait spaces

Drivers of tree community assembly during tropical forest post-fire succession in anthropogenic savannas

Unveiling ecological assembly rules from commonalities in trait distributions

Imprints of Past Habitat Area Reduction on Extant Taxonomic, Functional, and Phylogenetic Composition

Convolutional neural networks improve species distribution modelling by capturing the spatial structure of the environment

Functional biogeography of weeds reveals how anthropogenic management blurs trait–climate relationships

Jointly estimating spatial sampling effort and habitat suitability for multiple species from opportunistic presence‐only data

How Do Deep Convolutional SDM Trained on Satellite Images Unravel Vegetation Ecology ?

Designing sampling protocols for plant-pollinator interactions - timing, meteorology, flowering variations and failed captures matter

Do ecological specialization and functional traits explain the abundance–frequency relationship? Arable weeds as a case study

Canopy and understory tree guilds respond differently to the environment in an Indian rainforest

Small-Scale Variability in Bacterial Community Structure in Different Soil Types

Resource Competition and Host Feedbacks Underlie Regime Shifts in Gut Microbiota

From competition to facilitation and mutualism: a general theory of the niche

Determinants of genetic diversity and species richness of North American amphibians

Counter‐gradient variation of reproductive effort in a widely distributed temperate oak Quercus petraea

Water Quality Shapes Freshwater Macroinvertebrate Communities in Northern Tunisia

Within-host genetic micro-diversity of Mycobacterium tuberculosis and the link with tuberculosis disease features

How does interspecific competition modify the response of grass plants against herbicide treatment? A hierarchical concentration-response approach

Evaluation using latent class models of the diagnostic performances of three ELISA tests commercialized for the serological diagnosis of Coxiella burnetii infection in domestic ruminants

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