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 91 to 120 publications on 572 in total

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, Clément Claustre, David Abrial...

Veterinary Research . 52 ( 1 )

DOI: 10.1186/s13567-021-00926-w

Journal article

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Phenotypic and Transcriptomic Responses to Stress Differ According to Population Geography in an Invasive Species

Pierre Marin, Angelo Jaquet, Justine Picarle, Marie Fablet, Vincent Merel, Marie Laure Delignette-Muller...

Genome Biology and Evolution . 13 ( 9 ) : evab208

DOI: 10.1093/gbe/evab208

Journal article

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Overcoming the Spurious Groups Problem in Between-Group PCA

Jean Thioulouse, Sabrina Renaud, Anne-Béatrice Dufour, Stéphane Dray

Evolutionary Biology .

DOI: 10.1007/s11692-021-09550-0

Journal article

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Are human natal sex ratio differences across the world adaptive? A test of Fisher's principle

Mathieu Douhard, Stéphane Dray

Biology Letters . 17 ( 3 )

DOI: 10.1098/rsbl.2020.0620

Journal article

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Can citizen science analysis of camera trap data be used to study reproduction? Lessons from Snapshot Serengeti program

Lucie Thel, Simon Chamaillé-Jammes, Léa Keurinck, Maxime Catala, Craig Packer, Sarah E Huebner...

Wildlife Biology . 2021

DOI: 10.2981/wlb.00833

Journal article

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Evaluation, à l’aide de modèles à classes latentes, des performances diagnostic des tests ELISA commercialisés pour le diagnostic sérologique des infections par Coxiella burnetii chez les ruminants domestiques

T. Lurier, Elodie Rousset, Patrick Gasqui, Carole Sala, Clément Caustre, David Abrial...

17ème Rencontre des Microbiologistes du Pôle Clermontois .

Conference paper

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Revisiting animal photo-identification using deep metric learning and network analysis

Vincent Miele, Gaspard Dussert, Bruno Spataro, Simon Chamaillé-Jammes, Dominique Allainé, Christophe Bonenfant

Methods in Ecology and Evolution . 12 ( 5 ) : 863-873

DOI: 10.1111/2041-210X.13577

Journal article

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Rifampicin exposure reveals within-host Mycobacterium tuberculosis diversity in patients with delayed culture conversion

Charlotte Genestet, Elisabeth Hodille, Alexia Barbry, Jean-Luc Berland, Jonathan Hoffmann, Emilie Westeel...

PLoS Pathogens . 17 ( 6 ) : e1009643

DOI: 10.1371/journal.ppat.1009643

Journal article

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Long‐term high densities of African elephants clear the understorey and promote a new stable savanna woodland community

Nicolas Ferry, Stéphane Dray, Hervé Fritz, Audrey Ipavec, Benjamin Wigley, Tristan Charles‐dominique...

Journal of Vegetation Science . 32 ( 6 )

DOI: 10.1111/jvs.13101

Journal article

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Images, écologie et deep learning

Vincent Miele, Stéphane Dray, Olivier O. Gimenez

Regards sur la biodiversité .

Journal article

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Participation of LIRMM / Inria to the GeoLifeCLEF 2020 challenge

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

Preprint

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Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

Franck Jabot, Fabien Laroche, François Massol, Florent Arthaud, Julie Crabot, Maxime Dubart...

Ecology Letters . 23 ( 9 ) : 1330-1339

DOI: 10.1111/ele.13523

Journal article

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Ecological Specialization and Rarity of Arable Weeds: Insights from a Comprehensible Survey in France

François Munoz, Guillaume Fried, Laura Armengot, Bérenger Bourgeois, Vincent Bretagnolle, Joel J. Chadoeuf...

Plants . 9 ( 7 ) : 824

DOI: 10.3390/plants9070824

Journal article

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Weeds: Against the Rules?

Lucie Mahaut, Pierre-Olivier Cheptou, Guillaume Fried, François Munoz, Jonathan Storkey, François Vasseur...

Trends in Plant Science . 25 ( 11 ) : 1107-1116

DOI: 10.1016/j.tplants.2020.05.013

Journal article

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Bias in presence-only niche models related to sampling effort and species niches: Lessons for background point selection

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

PLoS ONE . 15 ( 5 ) : e0232078

DOI: 10.1371/journal.pone.0232078

Journal article

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Is prediction of species richness from stacked species distribution models biased by habitat saturation?

Matthias Grenié, Cyrille Violle, François Munoz

Ecological Indicators . 111 : 105970

DOI: 10.1016/j.ecolind.2019.105970

Journal article

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Growth trajectories, better than organ-level functional traits, reveal intraspecific response to environmental variation

François Munoz

Peer Community In Ecology . : 100041

DOI: 10.24072/pci.ecology.100041

Other publication

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Which traits make weeds more successful in maize crops? Insights from a three-decade monitoring in France

Guillaume Fried, Bruno Chauvel, François Munoz, Xavier Reboud

Plants . 9 ( 1 ) : 40

DOI: 10.3390/plants9010040

Journal article

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TRY plant trait database – enhanced coverage and open access

Jens Kattge, Gerhard Bonisch, Sandra Díaz, Sandra Lavorel, Iain Colin Prentice, Paul W. Leadley...

Global Change Biology . 26 ( 1 ) : 119-188

DOI: 10.1111/gcb.14904

Journal article

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Analyzing snapshot diversity patterns with the Neutral Theory can show functional groups’ effects on community assembly

Fabien Laroche, Cyrille Violle, Adrien Taudière, François Munoz

Ecology . 101 ( 4 ) : e02977

DOI: 10.1002/ecy.2977

Journal article

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Extinction–immigration dynamics lag behind environmental filtering in shaping the composition of tropical dry forests within a changing landscape

Grégoire Blanchard, Philippe Birnbaum, François Munoz

Ecography . 43 ( 6 ) : 869-881

DOI: 10.1111/ecog.04870

Journal article

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How citizen scientists contribute to monitor protected areas thanks to automatic plant identification tools

Pierre Bonnet, Alexis Joly, Jean-Michel Faton, Susan Brown, David Kimiti, Laura Mary...

Ecological Solutions and Evidence . 1 ( 2 )

DOI: 10.1002/2688-8319.12023

Journal article

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Resource manipulation through experimental defoliation has legacy effects on allocation to reproductive and vegetative organs in Quercus ilex

Iris Le Roncé, Maude Toïgo, Elia Dardevet, Samuel Venner, Jean-Marc Limousin, Isabelle Chuine

Annals of Botany . 126 ( 7 ) : 1165-1179

DOI: 10.1093/aob/mcaa137

Journal article

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Heterogeneity of water physico-chemical characteristics in artificially pumped waterholes: do African herbivores drink at the same locations and does it lead to interference competition?

Nicolas Ferry, Marion Cordonnier, Florence Hulot, Farisayi Dakwa, Lovelater Sebele, Stéphane Dray...

Journal of Arid Environments . 173 : 104014

DOI: 10.1016/j.jaridenv.2019.104014

Journal article

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A Speed-up Method for Numerical Simulations of Multi-strokes Cold Metallic Sheet Forming Processes

Anouar Krairi, Jalil Marmi, Sabrina Gastebois, Mark Veldhuis, Matthäus Kott

Procedia Manufacturing . 47 : 570 - 577

DOI: 10.1016/j.promfg.2020.04.173

Journal article

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Scarless Removal of Large Resistance Island AbaR Results in Antibiotic Susceptibility and Increased Natural Transformability in Acinetobacter baumannii

Anne-Sophie Godeux, Elin Svedholm, Agnese Lupo, Marisa Haenni, Samuel Venner, Maria-Halima Laaberki...

Antimicrobial Agents and Chemotherapy . 64 ( 10 ) : e00951

DOI: 10.1128/AAC.00951-20

Journal article

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A multi-omics concentration-response framework uncovers novel understanding of triclosan effects in the chlorophyte Scenedesmus vacuolatus

Floriane Larras, Elise Billoir, Stefan Scholz, Mika Tarkka, Tesfaye Wubet, Marie Laure Delignette-Muller...

Journal of Hazardous Materials . 397 : 122727

DOI: 10.1016/j.jhazmat.2020.122727

Journal article

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Surface water quality assessment in a semiarid Mediterranean region (Medjerda, Northern Tunisia) using partial triadic analysis

Noura Slimani, Juan José Jiménez, Eric Guilbert, Moncef Boumaiza, Jean Thioulouse

Environmental Science and Pollution Research .

DOI: 10.1007/s11356-020-09326-7

Journal article

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Bacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements

Gabriel Carvalho, David Fouchet, Gonché Danesh, Anne-Sophie Godeux, Maria-Halima Laaberki, Dominique Pontier...

mBio . 11 ( 2 ) : e02443-19

DOI: 10.1128/mbio.02443-19

Journal article

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