Quantitative and Evolutionary Ecology of Communities Group
Members
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Doctorante
UCBL
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/DelignetteMullerML.jpg?itok=GH9qFhky)
Professeure des universités
VetAgro-Sup
Tel: 33 04 72 43 27 56
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Directeur de recherche
CNRS
Tel: 33 04 72 43 27 57
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/DussertG.jpg?itok=yCLhwfo1)
Doctorant
UCBL
Tel: 04 72 44 81 42
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/FoxT.jpg?itok=G2ww7c9-)
Doctorant
CNRS
Tel: 04 72 44 81 42
Ingénieure de recherche CDD
CNRS
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/KeurinckL.jpg?itok=8SmHLl9E)
Doctorante
UCBL
Tel: 04 72 44 81 42
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/KoffelT_2023.jpg?itok=lUQOwbfK)
Maître de conférences
UCBL
Tel: 04 72 44 81 42
Stagiaire
UCBL
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/LacommeL.jpg?itok=SvPi2Z9X)
Doctorante
UCBL
Stagiaire
UCBL
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/LobryJ.jpg?itok=aN7vC2ra)
Professeur des universités
UCBL
Tel: 33 04 72 43 27 56
Stagiaire
UCBL
Stagiaire
UCBL
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/ThioulouseJ.jpg?itok=liIbI7-t)
Directeur de recherche
CNRS
Tel: 33 04 72 43 27 56
Doctorant
UCBL
Tel: 04 72 44 81 42
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__220x220__crop_main/public/media/directory_people/photo/VennerMC.jpg?itok=y5K8zAId)
Maîtresse de conférences
UCBL
Tel: 33 04 72 43 29 02
Maître de conférences
UCBL
Tel: 33 04 72 43 29 02
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__300x285__crop_main/public/media/images/eqeceng_0.png?itok=xMt9lxK2)
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](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__198x341__crop_main/public/media/images/hwange.png?itok=EAmSL9hs)
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*
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__320x240__crop_main/public/media/images/dispositif.jpg?itok=r-j_znfh)
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](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__320x240__crop_main/public/media/images/image_antibioresitance.png?itok=s8ho3Cge)
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*
![](https://lbbe.univ-lyon1.fr/sites/default/files/styles/img__198x370__crop_main/public/media/images/methode.png?itok=PJMRyNN6)
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 460 in total
Disentangling good from bad practices in the selection of spatial or phylogenetic eigenvectors
Ecography . 41 ( 10 ) : 1638-1649
DOI: 10.1111/ecog.03380
Journal article
see the publicationOptimizing the choice of a spatial weighting matrix in eigenvector-based methods
Ecology . 99 ( 10 ) : 2159-2166
DOI: 10.1002/ecy.2469
Journal article
see the publicationSimple parametric tests for trait–environment association
Journal of Vegetation Science . 29 ( 5 ) : 801-811
DOI: 10.1111/jvs.12666
Journal article
see the publicationSupervised Multiblock Analysis in R with the ade4 Package
Journal of Statistical Software . 86 ( 1 )
Journal article
see the publicationMOSAIC: a web-interface for statistical analyses in ecotoxicology
Environmental Science and Pollution Research . 25 ( 12 ) : 11295-11302
Journal article
see the publicationDRomics: A Turnkey Tool to Support the Use of the Dose–Response Framework for Omics Data in Ecological Risk Assessment
Environmental Science and Technology . 52 ( 24 ) : 14461-14468
Journal article
see the publicationAssessment of Ozone or Not-Treated Wastewater Ecotoxicity Using Mechanism-Based and Zebrafish Embryo Bioassays
Journal of Environmental Protection . 09 ( 04 ) : 325 - 346
Journal article
see the publicationIntegrating spatial and phylogenetic information in the fourth‐corner analysis to test trait–environment relationships
Ecology . 99 ( 12 ) : 2667-2674
DOI: 10.1002/ecy.2530
Journal article
see the publicationComplex ecological interactions of Staphylococcus aureus in tampons during menstruation
Scientific Reports . 8 ( 1 ) : 9942
Journal article
see the publicationBeyond neutrality: disentangling the effects of species sorting and spurious correlations in community analysis
Ecology . 99 ( 8 ) : 1737-1747
DOI: 10.1002/ecy.2376
Journal article
see the publicationAlgorithms and biplots for double constrained correspondence analysis
Environmental and Ecological Statistics . 25 ( 2 ) : 171-197
Journal article
see the publicationNumerical Modeling of Friction Stir (FSW) and Linear Friction (LFW) Welding Processes
FSWP 2017 - 5th International Conference on Scientific and Technical Advances on Friction Stir Welding & Processing .
Conference paper
see the publicationNew insights from niche theory on plant adaptation and ecosystem functioning
Thesis
see the publicationEnseigner les recueil des données : explorer la variabilité biologique ... au chaud, dans une salle de cours
Statistique et Enseignement . 8 ( 2 ) : 79-85
Journal article
see the publicationManagement of the mycorrhizal soil infectivity with Crotalaria ochroleuca, an indigenous wild legume in the tropics: Impacts on microbial functional diversity involved in phosphorus mobilization processes in a sahelian soil
Ecological Engineering . 101 : 130-136
Journal article
see the publicationIncreasing Spring temperature favors oak seed production in temperate areas
EGU General Assembly 2017 . 19 : np
Poster
see the publicationRaisonner l'utilisation des légumineuses ligneuses pour réhabiliter des sols dégradés en milieu méditerranéen et tropical
Innovations Agronomiques . 60 : 125-131
Journal article
see the publicationResponse to Comment on "Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests
Environmental Science and Technology . 51 : 8202-8203
Journal article
see the publicationRobust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests
Environmental Science and Technology . 51 : 4038-4045
Journal article
see the publicationadegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data
The R Journal . 9 ( 2 ) : 198-212
DOI: 10.32614/RJ-2017-042
Journal article
see the publicationA critical issue in model-based inference for studying trait-based community assembly and a solution
PeerJ . 5 : e2885
DOI: 10.7717/peerj.2885
Journal article
see the publicationEcological networks to unravel the routes to horizontal transposon transfers
PLoS Biology . 15 ( 2 ) : np
Journal article
see the publicationIncreasing spring temperatures favor oak seed production in temperate areas
Scientific Reports . 7 ( 1 ) : 1-8
Journal article
see the publicationThe use of STATICO and COSTATIS, two exploratory three-ways analysis methods: an application to the ecology of aquatic heteroptera in the Medjerda watershed (Tunisia)
Environmental and Ecological Statistics . 24 ( 2 ) : 269 - 295
Journal article
see the publicationEvolution microstructurale en soudage par friction malaxage - Application à la prédiction des propriétés mécaniques dans les tôles AA2024
‘La métallurgie, quel avenir !’ – Session ST1 : Procédés de fabrication innovants : Fabrication Voie Solide .
Conference paper
see the publicationCalibration of 3D ALE finite element model from experiments on friction stir welding of lap joints
ESAFORM 2016 . 1769 : 100006
DOI: 10.1063/1.4963500
Conference paper
see the publicationDéveloppement de l’assurance qualité officinale en Haute-Normandie en 2015
: 168
Geometrical envelopes: Extending graphical contemporary niche theory to communities and eco-evolutionary dynamics
Journal of Theoretical Biology . 407 : 271-289
Journal article
see the publicationFruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies
The American Naturalist . 188 ( 1 ) : 66-75
DOI: 10.1086/686684
Journal article
see the publication
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