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 31 to 60 publications on 572 in total

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

Brian A Lerch, Akshata Rudrapatna, Nasser Rabi, Jonas Wickman, Thomas Koffel, Christopher A Klausmeier

Ecological monographs . 93 ( 4 )

DOI: 10.1002/ecm.1591

Journal article

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

Jonas Wickman, Thomas Koffel, Christopher A Klausmeier

The American Naturalist . 201 ( 4 ) : 501-522

DOI: 10.1086/723406

Journal article

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

Clément Car, André Gilles, Elen Goujon, Marie Laure Delignette-Muller, Luc Camoin, Sandrine Frelon...

BMC Biology . 21 ( 1 ) : 164

DOI: 10.1186/s12915-023-01659-2

Journal article

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

Elsa Coz, Eric Jouy, Géraldine Cazeau, Nathalie Jarrige, Claire Chauvin, Marie Laure Delignette-Muller

Preventive Veterinary Medicine . 213 : 105881

DOI: 10.1016/j.prevetmed.2023.105881

Journal article

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

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

DOI: 10.1101/2023.11.10.566512

Preprint

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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 : 24 p.

DOI: 10.1007/s10344-023-01742-7

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 - CB . 33 ( 6 ) : 1117-1124.e4

DOI: 10.1016/j.cub.2023.01.034

Journal article

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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

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

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

Journal article

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Quantifying the overall effect of biotic interactions on species distributions along environmental gradients

Marc Ohlmann, Catherine Matias, Giovanni Poggiato, Stéphane Dray, Wilfried Thuiller, Vincent Miele

Ecological Modelling . 483 : 110424

DOI: 10.1016/j.ecolmodel.2023.110424

Journal article

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Perfusion imaging in deep prostate cancer detection from mp-MRI: can we take advantage of it?

Audrey Duran, Gaspard Dussert, Carole Lartizien

19th IEEE International Symposium on Biomedical Imaging (ISBI) . : 1-5

DOI: 10.1109/ISBI52829.2022.9761616

Conference paper

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Learning to segment prostate cancer by aggressiveness from scribbles in bi-parametric MRI

Audrey Duran, Gaspard Dussert, Carole Lartizien

SPIE Medical Imaging 2022: Image Processing . : 178-184

DOI: 10.1117/12.2607502

Conference paper

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ProstAttention-Net: A deep attention model for prostate cancer segmentation by aggressiveness in MRI scans

Audrey Duran, Gaspard Dussert, Olivier Rouvière, Tristan Jaouen, Pierre-Marc Jodoin, Carole Lartizien

Medical Image Analysis . 77 : 102347

DOI: 10.1016/j.media.2021.102347

Journal article

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Disturbance‐driven alteration of patch connectivity determines local biodiversity recovery within metacommunities

Claire Jacquet, François Munoz, Núria Bonada, T. Datry, Jani Heino, Franck Jabot

Ecography . 2022 ( 12 )

DOI: 10.1111/ecog.06199

Journal article

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Very High Resolution Species Distribution Modeling Based on Remote Sensing Imagery: How to Capture Fine-Grained and Large-Scale Vegetation Ecology With Convolutional Neural Networks?

Benjamin Deneu, Alexis Joly, Pierre Bonnet, Maximilien Servajean, François Munoz

Frontiers in Plant Science . 13

DOI: 10.3389/fpls.2022.839279

Journal article

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Deep Species Distribution Modeling From Sentinel-2 Image Time-Series: A Global Scale Analysis on the Orchid Family

Joaquim Estopinan, Maximilien Servajean, Pierre Bonnet, François Munoz, Alexis Joly

Frontiers in Plant Science . 13 : 839327

DOI: 10.3389/fpls.2022.839327

Journal article

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How to evaluate and interpret the contribution of species turnover and interaction rewiring when comparing ecological networks?

François Munoz

Peer Community In Ecology . : 100092

DOI: 10.24072/pci.ecology.100092

Other publication

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Using Partial Triadic Analysis (PTA) to Assess Spatiotemporal Variation in Water Quality

Noura Slimani, Eric Guilbert, David Sánchez-Fernández, Moncef Boumaïza, Malika Trabelsi-Ayadi, Kais Nahdi...

Recent Advances in Environmental Science from the Euro-Mediterranean and Surrounding Regions (4th Edition) . 978-3-031-51903-1 : 1063-1066

DOI: 10.1007/978-3-031-51904-8_231

Conference paper

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The morphological allometry of four closely related and coexisting insect species reveals adaptation to the mean and variability of the resource size

Emilie Fleurot, Samuel Venner, Pierre-François Pélisson, François Débias, M-C. Bel-Venner

Oecologia . 200 ( 1-2 ) : 159-168

DOI: 10.1007/s00442-022-05249-x

Journal article

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How public can public goods be? Environmental context shapes the evolutionary ecology of partially private goods

Brian A Lerch, Derek A Smith, Thomas Koffel, Sarah C Bagby, Karen C Abbott

PLoS Computational Biology . 18 ( 11 ) : e1010666

DOI: 10.1371/journal.pcbi.1010666

Journal article

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A general framework for species‐abundance distributions: Linking traits and dispersal to explain commonness and rarity

Thomas Koffel, Kaito Umemura, Elena Litchman, Christopher A Klausmeier

Ecology Letters . 25 ( 11 ) : 2359-2371

DOI: 10.1111/ele.14094

Journal article

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The global spectrum of plant form and function: enhanced species-level trait dataset

Sandra Díaz, Jens Kattge, Johannes Cornelissen, Ian Wright, Sandra Lavorel, Stéphane Dray...

Scientific Data . 9 ( 1 ) : 755

DOI: 10.1038/s41597-022-01774-9

Journal article

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Deep learning in veterinary medicine, an approach based on CNN to detect pulmonary abnormalities from lateral thoracic radiographs in cats

Léo Dumortier, Florent Guépin, Marie Laure Delignette-Muller, C. Boulocher, Thomas Grenier

Scientific Reports . 12 ( 1 ) : 11418

DOI: 10.1038/s41598-022-14993-2

Journal article

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Strain- and serotype-dependent affinity of Shiga toxin-producing Escherichia coli for bovine milk fat globules

A. Bagel, Marie Laure Delignette-Muller, Christelle Lopez, V. Michel, Delphine Thevenot-Sergentet, Thomas Douellou

Journal of Dairy Science . 105 ( 11 ) : 8688-8704

DOI: 10.3168/jds.2022-21840

Journal article

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Assessment of the French colistin action plan

Elsa Coz, Eric Jouy, Géraldine Cazeau, Nathalie Jarrige, Agnes Perrin-Guyomard, Anne Hemonic...

Third International Conference AACTING: Quantification, Benchmarking and Stewardship of Veterinary Antimicrobial Usage .

Poster

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Meta-transcriptomics reveals stress adaptation processes in microbial communities differing in exposure history

Floriane Larras, Elise Billoir, Stefan Lips, Stephan Schreiber, Philippe Veber, Marie Laure Delignette-Muller...

"Ecology and Evolution: New perspectives and societal challenges" SFE2-GfÖ-EEF joint meeting, International conference on ecological sciences .

Conference paper

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Mycobacterium tuberculosis genetic features associated with pulmonary tuberculosis severity

Charlotte Genestet, Guislaine Refrégier, Elisabeth Hodille, Rima Zein-Eddine, Adrien Le Meur, Fiona Hak...

International Journal of Infectious Diseases . 125 : 74-83

DOI: 10.1016/j.ijid.2022.10.026

Journal article

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Interpretation of the results of ELISA tests commercialized for the serological diagnosis of Coxiella burnetii infection in domestic ruminants: a user-friendly Shiny application based on latent class models in a Bayesian framework

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

31st WORLD BUIATRICS CONGRESS .

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...

31st World Buitatrics congress .

Conference paper

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