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 31 to 60 publications on 652 in total

Deep dive into the chronic toxicity of tyre particle mixtures and their leachates

Paul Boisseaux, Cassandra Rauert, Pradeep Dewapriya, Marie Laure Delignette-Muller, Robyn Barrett, Lee Durndell...

Journal of Hazardous Materials . 466 : 133580

DOI: 10.1016/j.jhazmat.2024.133580

2024

Journal article

see the publication

Modeling HepaRG metabolome responses to pyrrolizidine alkaloid exposure for insight into points of departure and modes of action

Estelle Dubreil, Keyvin Darney, Marie Laure Delignette-Muller, Audrey Barranger, Sylvie Huet, Kevin Hogeveen...

Journal of Hazardous Materials . 474 : 134721

DOI: 10.1016/j.jhazmat.2024.134721

2024

Journal article

see the publication

Development, feeding, and sex shape the relative quantity of the nutritional obligatory symbiont Wolbachia in bed bugs

Marius Poulain, Elodie Rosinski, Hélène Henri, Séverine Balmand, Marie Laure Delignette-Muller, Abdelaziz Heddi...

Frontiers in Microbiology . 15 : 1386458

DOI: 10.3389/fmicb.2024.1386458

2024

Journal article

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

T. Lurier, Florence Ayral, Carole Sala, Kristel Gache, Marie Laure Delignette-Muller, Elsa Jourdain...

SBED Conference 2024: Insights in Action .

2024

Poster

see the publication

Harmonisation of the diagnostic performances of ELISA tests for C. burnetii antibodies in ruminants: optimal positivity thresholds and performance reassessment

Laureline Rivière, Elodie Rousset, Elsa Jourdain, Marie Laure Delignette-Muller, T. Lurier

SBED Conference 2024: Insights in Action .

2024

Poster

see the publication

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...

SBED Conference 2024: Insights in Action .

2024

Conference paper

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Using the multivariate Hawkes process to study interactions between multiple species from camera trap data

Lisa Nicvert, Sophie Donnet, Mark Keith, Mike Peel, Michael J Somers, Lourens H Swanepoel...

Gaspard Dussert, Simon Chamaillé-Jammes, Stéphane Dray, Vincent Miele

DOI: 10.1101/2023.11.10.566512

2023

Preprint

see the publication

The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images

Noa Rigoudy, Gaspard Dussert, Abdelbaki Benyoub, Aurélien Besnard, Carole Birck, Jérome Boyer...

European Journal of Wildlife Research . 69 ( 6 ) : 113

DOI: 10.1007/s10344-023-01742-7

2023

Journal article

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Oak masting drivers vary between populations depending on their climatic environments

Emilie Fleurot, Jean R Lobry, Vincent Boulanger, François Débias, Camille Mermet-Bouvier, Thomas Caignard...

Current Biology . 33 ( 6 ) : 1117-1124.e4

DOI: 10.1016/j.cub.2023.01.034

2023

Journal article

see the publication

The CV is dead, long live the CV !

Jean R Lobry, Marie‐claude Bel‐venner, Michał Bogdziewicz, Andrew Hacket‐pain, Samuel Venner

Methods in Ecology and Evolution .

DOI: 10.1111/2041-210X.14197

2023

Journal article

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DRomics, a workflow to exploit dose-response omics data in ecotoxicology

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

Peer Community Journal . 3 : e90

DOI: 10.24072/pcjournal.325

2023

Journal article

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PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

Aurore Comte, Théo Tricou, Eric Tannier, Julien Joseph, Aurélie Siberchicot, Simon Penel...

Molecular Biology and Evolution . 40 ( 11 ) : msad234

DOI: 10.1093/molbev/msad234

2023

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

Deep dive into the chronic toxicity of tyre particle mixtures and their leachates

Modeling HepaRG metabolome responses to pyrrolizidine alkaloid exposure for insight into points of departure and modes of action

Development, feeding, and sex shape the relative quantity of the nutritional obligatory symbiont Wolbachia in bed bugs

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

Harmonisation of the diagnostic performances of ELISA tests for C. burnetii antibodies in ruminants: optimal positivity thresholds and performance reassessment

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.

Using the multivariate Hawkes process to study interactions between multiple species from camera trap data

Résistance à la colistine chez le porc - des mesures de maîtrise efficaces

seqinr: Biological Sequences Retrieval and Analysis

adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

phylter: Detect and Remove Outliers in Phylogenomics Datasets

Projections climatiques CMIP6 à l’échelle du sud-ouest de la Côte d’Ivoire : évolution des contraintes thermo-pluviométriques pour les principaux agrosystèmes associant cacao, hévéa, palmier à huile et manioc

Object-based characterization of vegetation heterogeneity with sentinel images proves efficient in a highly human-influenced National Park of Côte d’Ivoire

The functional trait distinctiveness of plant species is scale dependent

Synergizing Digital, Biological, and Participatory Sciences for Global Plant Species Identification: Enabling access to a worldwide identification service

The ecological causes of functional distinctiveness in communities

Avoid, tolerate, or escape? Native vegetation responses to invasion vary between functional groups

Links to rare climates do not translate into distinct traits for island endemics

Revisiting extinction debt through the lens of multitrophic networks and meta‐ecosystems

Dissecting fine root diameter distribution at the community level captures root morphological diversity

Connecting local and regional scales with stochastic metacommunity models: Competition, ecological drift, and dispersal

A Theoretical Framework for Trait-Based Eco-Evolutionary Dynamics: Population Structure, Intraspecific Variation, and Community Assembly

Population transcriptogenomics highlights impaired metabolism and small population sizes in tree frogs living in the Chernobyl Exclusion Zone

Evolution of the proportion of colistin-resistant isolates in animal clinical Escherichia coli over time - A hierarchical mixture model approach

Beyond accuracy : score calibration in deep learning models for camera trap image sequences

The DeepFaune initiative: a collaborative effort towards the automatic identification of European fauna in camera trap images

Oak masting drivers vary between populations depending on their climatic environments

The CV is dead, long live the CV !

DRomics, a workflow to exploit dose-response omics data in ecotoxicology

PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

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