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 1 to 30 publications on 576 in total

19. Colistin resistance in pigs – assessing the effectiveness of mitigation measures

Claire Chauvin, Elsa Coz, Eric Jouy, Marie-Laure Delignette-Muller, Agnès Perrin-Guyomard, Xavier Sauzea...

Animal. Science proceedings . 15 ( 4 ) : 268-269

DOI: 10.1016/j.anscip.2024.06.183

Journal article

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Reconciling Pollen Limitation Theories: Insights From Temperate Oak Masting

Emilie Fleurot, Léa Keurinck, Vincent Boulanger, François Debias, Nicolas Delpierre, Sylvain Delzon...

Ecology Letters . 27 ( 11 ) : e70009

DOI: 10.1111/ele.70009

Journal article

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Genomics unveils country-to-country transmission between animal hospitals of a multidrug-resistant and sequence type 2 Acinetobacter baumannii clone

Amédée André, Julie Plantade, Isabelle Durieux, Pauline Durieu, Anne-Sophie Godeux, Maxence Decellieres...

Microbial Genomics . 10 ( 10 )

DOI: 10.1099/mgen.0.001292

Journal article

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Trait matching without traits: using correspondence analysis to analyze the latent structure of interaction networks

Lisa Nicvert, Hervé Fritz, Stéphane Dray

DOI: 10.1101/2024.10.22.619454

Preprint

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Manipulation of natural transformation by AbaR-type islands promotes fixation of antibiotic resistance in Acinetobacter baumannii

Rémi Tuffet, Gabriel Carvalho, Anne-Sophie Godeux, Fanny Mazzamurro, Eduardo P C Rocha, Maria-Halima Laaberki...

Proceedings of the National Academy of Sciences of the United States of America . 121 ( 39 ) : e2409843121

DOI: 10.1073/pnas.2409843121

Journal article

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Zero-shot animal behavior classification with vision-language foundation models

Gaspard Dussert, Vincent Miele, Colin van Reeth, Anne Delestrade, Stéphane Dray, Simon Chamaillé-Jammes

DOI: 10.1101/2024.04.05.588078

Preprint

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Evolutionary ecology of masting: mechanisms, models, and climate change

Michal Bogdziewicz, Dave Kelly, Davide Ascoli, Thomas Caignard, Francesco Chianucci, Elizabeth Crone...

Trends in Ecology & Evolution . 39 ( 9 ) : 851-862

DOI: 10.1016/j.tree.2024.05.006

Journal article

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Intransitive stability collapses under the influence of dominant competitors

Laure Gallien, Maude Charlie Cavaliere, Marie Charlotte Grange, François Munoz, Tamara Münkemüller

The American Naturalist . 204 ( 1 ) : E1-E10

DOI: 10.1086/730297

Journal article

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Being confident in confidence scores: calibration in deep learning models for camera trap image sequences

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

Remote Sensing in Ecology and Conservation .

DOI: 10.1002/rse2.412

Journal article

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Response of a carnivore community to water management in a semi-arid savanna

Aïssa Morin, Olivier Gimenez, Lara L Sousa, Justin Seymour-Smith, Holly O'Donnell, Marie-Laure Delignette-Muller...

Biological Conservation . 299 : 110777

DOI: 10.1016/j.biocon.2024.110777

Journal article

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ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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

Software

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Community ionomics reveals a diversity of mineral nutrition in a species‐rich shrubland on infertile soil

Juliette Hocedez, Karine Gotty, Vanessa Hequet, Sandrine Chay, Audrey Léopold, Stéphane Dray...

Journal of Vegetation Science . 35 ( 5 ) : e13301

DOI: 10.1111/jvs.13301

Journal article

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Why incorporate plant architecture into trait-based ecology?

Marilyne Laurans, François Munoz, Tristan Charles-Dominique, Patrick Heuret, Claire Fortunel, Sandrine Isnard...

Trends in Ecology & Evolution . 39 ( 6 ) : 524-536

DOI: 10.1016/j.tree.2023.11.011

Journal article

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Mapping global orchid assemblages with deep learning provides novel conservation insights

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

Ecological Informatics . 81 : 102627

DOI: 10.1016/j.ecoinf.2024.102627

Journal article

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New Automatic Identification Tools: An Aid for Botanists and Nature Managers ?

François Munoz, Pierre Bonnet

Linking with Nature in the Digital Age: Volume 1 - Communication, Environment, Science and Society SET . 9781786308580 ( 1 ) : 161-175

DOI: 10.1002/9781394297580.ch9

Book chapter

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Refocusing the microbial rare biosphere concept through a functional lens

Elena Litchman, Sébastien Villéger, Zinger Lucie, Jean-Christophe Auguet, Wilfried Thuiller, François Munoz...

Trends in Ecology & Evolution .

DOI: 10.1016/j.tree.2024.06.005

Journal article

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The three‐species problem: Incorporating competitive asymmetry and intransitivity in modern coexistence theory

Ravi Ranjan, Thomas Koffel, Christopher A Klausmeier

Ecology Letters . 27

DOI: 10.1111/ele.14426

Journal article

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Insights on the effect of mega-carcass abundance on the population dynamics of a facultative scavenger predator and its prey

Mellina Sidous, Sarah Cubaynes, Olivier Gimenez, Nolwenn Drouet-Hoguet, Stéphane Dray, Loïc Bollache...

Peer Community Journal . 4 : e53

DOI: 10.24072/pci.ecology.100594

Journal article

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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

Journal article

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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

Journal article

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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

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 .

Poster

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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 .

Poster

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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...

SBED Conference 2024: Insights in Action .

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...

Ecology . 105 ( 4 ) : e4237

DOI: 10.1002/ecy.4237

Journal article

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

Claire Chauvin, Elsa Coz, Eric Jouy, Marie Laure Delignette-Muller, Agnes Perrin-Guyomard, Xavier Sauzea...

56. Journées de la Recherche Porcine . 56 : 81-82

Conference paper

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

Pierre Bonnet, Antoine Affouard, Jean-Christophe Lombardo, Mathias Chouet, Hugo Gresse, Vanessa Hequet...

Biodiversity Information Science and Standards . 7 : e112545

DOI: 10.3897/biss.7.112545

Journal article

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The ecological causes of functional distinctiveness in communities

François Munoz, Christopher A Klausmeier, Pierre Gaüzère, Gaurav Kandlikar, Elena Litchman, Nicolas Mouquet...

Ecology Letters . 26 ( 8 ) : 1452-1465

DOI: 10.1111/ele.14265

Journal article

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

Marie Charlotte Grange, François Munoz, Marco Moretti, Sylvain Varona-Y-Varona, Julien Renaud, Marie-Pascale Colace...

Biological Invasions . 25 ( 5 ) : 1387-1401

DOI: 10.1007/s10530-022-02983-4

Journal article

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