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 448 in total

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

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

mBio .

DOI: 10.1128/mbio.02631-21

Journal article

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

Thomas Caignard, Antoine Kremer, Xavier Bouteiller, Julien Parmentier, Jean‐marc Louvet, Samuel Venner...

Functional Ecology . 35 ( 8 ) : 1745-1755

DOI: 10.1111/1365-2435.13830

Journal article

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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

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

Thibaut 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

Conference paper

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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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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...

Veterinary Research . 52 ( 1 )

DOI: 10.1186/s13567-021-00926-w

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

Mylène Hugoni, Naoise Nunan, Jean Thioulouse, Audrey Dubost, Danis Abrouk, Jean M F Martins...

Microbial ecology .

DOI: 10.1007/s00248-020-01660-0

Journal article

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An appraisal of graph embeddings for comparing trophic network architectures

Christophe Botella, Stéphane Dray, Catherine Matias, Vincent Miele, Wilfried Thuiller

Methods in Ecology and Evolution .

DOI: 10.1111/2041-210X.13738

Journal article

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

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

Preprint

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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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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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Images, écologie et deep learning

Vincent Miele, Stéphane Dray, Olivier O. Gimenez

Regards sur la biodiversité .

Journal article

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Climate Effects on Prey Vulnerability Modify Expectations of Predator Responses to Short- and Long-Term Climate Fluctuations

Aïssa Morin, Simon Chamaillé-Jammes, Marion Valeix

Frontiers in Ecology and Evolution . 8

DOI: 10.3389/fevo.2020.601202

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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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 )

DOI: 10.1128/AAC.00951-20

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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How does increasing mast seeding frequency affect population dynamics of seed consumers? Wild boar as a case study

Laura Touzot, Éliane Schermer, Samuel Venner, Sylvain S. Delzon, Cyril Rousset, Eric Baubet...

Ecological Applications . : 1-11

DOI: 10.1002/eap.2134

Journal article

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Developmental variability channels mouse molar evolution

Luke Hayden, Katerina Lochovska, Marie Sémon, Sabrina Renaud, Marie-Laure Delignette-Muller, Maurine Vilcot...

eLife .

DOI: 10.7554/eLife.50103

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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Vaginal Tampon Colonization by Staphylococcus aureus in Healthy Women

Myriam Chiaruzzi, Alexia Barbry, Anaëlle Muggeo, Anne Tristan, Isaline Jacquemond, Cedric Badiou...

Applied and Environmental Microbiology . 86 ( 18 ) : e01249-20

DOI: 10.1128/AEM.01249-20

Journal article

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Investigating microbial associations from sequencing survey data with co-correspondence analysis

Benjamin Alric, Cajo J.F. ter Braak, yves Desdevises, Hugo Lebredonchel, Stéphane Dray

Molecular Ecology Resources . 20 ( 2 ) : 468-480

DOI: 10.1111/1755-0998.13126

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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Can an herbivore affect where a top predator kills its prey by modifying woody vegetation structure?

Nicolas Ferry, Moreangels Mbizah, Andrew Loveridge, David Macdonald, Stéphane Dray, Hervé Fritz...

Oecologia . 192 ( 3 ) : 779-789

DOI: 10.1007/s00442-020-04617-9

Journal article

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Population responses of roe deer to the recolonization of the French Vercors by wolves

Malory Randon, Christophe Bonenfant, Jacques Michallet, Thierry Chevrier, Carole Toïgo, Jean-Michel Gaillard...

Population Ecology . 62 ( 2 )

DOI: 10.1002/1438-390X.12043

Journal article

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Disentangling the roles of bottom-up and top-down drivers in the trade-off between food acquisition and safety in prey with multiple predators

Olivier Pays, Pierrick Blanchard, Simon Chamaillé-Jammes, Marion Valeix, Andrew J Loveridge, David W Macdonald...

Functional Ecology .

DOI: 10.1111/1365-2435.13710

Journal article

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Disentangling the roles of bottom‐up and top‐down drivers in the trade‐off between food acquisition and safety in prey with multiple predators

Olivier Pays, Pierrick Blanchard, Simon Chamaillé-Jammes, Marion Valeix, Andrew Loveridge, David Macdonald...

Functional Ecology .

DOI: 10.1111/1365-2435.13710

Journal article

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Effect of ecological factors on fine‐scale patterns of social structure in African lions

Moreangels Mbizah, Damien Farine, Marion Valeix, Jane Hunt, David Macdonald, Andrew Loveridge

Journal of Animal Ecology . 89 ( 11 ) : 2665-2676

DOI: 10.1111/1365-2656.13334

Journal article

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Predator Effects on Herbivore Dynamics and Behavior - What Mechanisms Lead to Trophic Cascades in Savannas?

Simon Chamaillé-Jammes, Marion Valeix, Joris P. G. M. Cromsigt

Savanna woody plants and large herbivores .

Book chapter

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