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 181 to 210 publications on 572 in total

Sensitivity of community-level trait-environment relationships to data representativeness: a test for functional biogeography

Benjamin Borgy, Cyrille Violle, Philippe Choler, Eric Garnier, Jens Kattge, Jessy Loranger...

Global Ecology and Biogeography . 26 ( 6 ) : 729 - 739

DOI: 10.1111/geb.12573

Journal article

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funrar: An R package to characterize functional rarity

Matthias Grenié, Pierre Denelle, Caroline Tucker, François Munoz, Cyrille Violle

Diversity and Distributions . 23 ( 12 ) : 1365 - 1371

DOI: 10.1111/ddi.12629

Journal article

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Two disjunct Pleistocene populations and anisotropic postglacial expansion shaped the current genetic structure of the relict plant Amborella trichopoda

Rémi Tournebize, Stéphanie Manel, Yves Vigouroux, François Munoz, Alexandre de Kochko, Valérie Poncet

PLoS ONE . 12 ( 8 ) : e0183412

DOI: 10.1371/journal.pone.0183412

Journal article

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Plant community structure and nitrogen inputs modulate the climate signal on leaf traits

Benjamin Borgy, Cyrille Violle, Philippe Choler, Pierre Denelle, François Munoz, Jens Kattge...

Global Ecology and Biogeography . 26 ( 10 ) : 1138-1152

DOI: 10.1111/geb.12623

Journal article

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Numerical Modeling of Friction Stir (FSW) and Linear Friction (LFW) Welding Processes

Lionel Fourment, Antoine Potet, Sabrina Gastebois, Katia Mocellin

FSWP 2017 - 5th International Conference on Scientific and Technical Advances on Friction Stir Welding & Processing .

Conference paper

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New insights from niche theory on plant adaptation and ecosystem functioning

Thomas Koffel

Thesis

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Enseigner les recueil des données : explorer la variabilité biologique ... au chaud, dans une salle de cours

Anne-Béatrice Dufour, Jean R Lobry, Isabelle Amat

Statistique et Enseignement . 8 ( 2 ) : 79-85

Journal article

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Management 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

N. Benkhoua, M. Hafidi, W. Badri, Ezékiel Baudoin, Jean Thioulouse, Yves Prin...

Ecological Engineering . 101 : 130-136

DOI: 10.1016/j.ecoleng.2017.01.010

Journal article

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Increasing Spring temperature favors oak seed production in temperate areas

Thomas Caignard, Antoine Kremer, Cyril Firmat, Manuel Nicolas, Samuel Venner, Sylvain Delzon

EGU General Assembly 2017 . 19 : np

Poster

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Raisonner l'utilisation des légumineuses ligneuses pour réhabiliter des sols dégradés en milieu méditerranéen et tropical

Robin Duponnois, Jean Thioulouse, Ezekiel Baudoin, Christine Leroux, Antoine Galiana, Y Prin

Innovations Agronomiques . 60 : 125-131

DOI: 10.15454/1.5138523036590977E12

Journal article

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Response to Comment on "Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests

Marie Laure Delignette-Muller, P. Veber

Environmental Science and Technology . 51 : 8202-8203

DOI: 10.1021/acs.est.7b02548

Journal article

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Robust Fit of Toxicokinetic-Toxicodynamic Models Using Prior Knowledge Contained in the Design of Survival Toxicity Tests

Marie Laure Delignette-Muller, P. Ruiz, P. Veber

Environmental Science and Technology . 51 : 4038-4045

DOI: 10.1021/acs.est.6b05326

Journal article

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adegraphics: An S4 Lattice-Based Package for the Representation of Multivariate Data

Aurélie Siberchicot, A. Julien-Laferrière, Ab. Dufour, J. Thioulouse, S. Dray

The R Journal . 9 ( 2 ) : 198-212

DOI: 10.32614/RJ-2017-042

Journal article

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A critical issue in model-based inference for studying trait-based community assembly and a solution

Cajo J. F. ter Braak, P. Peres-Neto, Stéphane Dray

PeerJ . 5 : e2885

DOI: 10.7717/peerj.2885

Journal article

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Ecological networks to unravel the routes to horizontal transposon transfers

Samuel Venner, Vincent Miele, Christophe Terzian, Christian Biemont, Vincent Daubin, Cedric Feschotte...

PLoS Biology . 15 ( 2 ) : np

DOI: 10.1371/journal.pbio.2001536

Journal article

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Increasing spring temperatures favor oak seed production in temperate areas

Thomas Caignard, Antoine Kremer, Cyril Firmat, Manuel Nicolas, Samuel Venner, Sylvain Delzon

Scientific Reports . 7 ( 1 ) : 1-8

DOI: 10.1038/s41598-017-09172-7

Journal article

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The use of STATICO and COSTATIS, two exploratory three-ways analysis methods: an application to the ecology of aquatic heteroptera in the Medjerda watershed (Tunisia)

Noura Slimani, Eric Guilbert, Foued El Ayni, Amel Jrad, Moncef Boumaiza, Jean Thioulouse

Environmental and Ecological Statistics . 24 ( 2 ) : 269 - 295

DOI: 10.1007/s10651-017-0370-6

Journal article

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Using the past to predict the future: the case of French Mediterranean orchids

Bertrand Schatz, Hélène Vogt-Schilb,, François Munoz, Philippe Geniez, Laetitia Hugot, Roger Pradel...

The Mediterranean Region under Climate Change: A scientific update . 978-2-7099-2219-7 : p. 377-386

Book chapter

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The DISCO-WEED project : disentangling the role of anthropic DISturbances and eCOlogical processes on WEED community assembly

Sabrina Gaba, Bérenger Bourgeois, Laura Armengot, Florent Bonneu, Vincent Bretagnolle, Joel Chadoeuf...

Sfécologie-2016, International Conference of Ecological Sciences . : np

Poster

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Stabilisation of soil aggregates along a plant community succession: indirect positive effects of root biomass and root diameter diversity

Amandine Erktan, Catherine Roumet, Francois Pailler, Yves Le Bissonnais, François Munoz, Alexia Stokes

Sfécologie-2016, International Conference of Ecological Sciences . : np

Conference paper

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Plant diversity loss forces shift in ecological strategies for wild bees - Insights from historical time series at a country-wide scale

Floriane Jacquemin, Cyrille Violle, François Munoz, Adrien Taudière, Pierre Rasmont, Mireille Dufrene

Sfécologie-2016, International Conference of Ecological Sciences . : np

Conference paper

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Ecological, biogeographical and evolutionary drivers of tree rarity in Indian rainforests

Priya Davidar, François Munoz, Puyravaud Jean-Philippe, Mohandass D, Ramachandran V.S

5th International EcoSummit Congress "EcoSummit 2016 - Ecological Sustainability: Engineering Change .

Conference paper

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Understanding plant community successional dynamics: Exploring the role of fine root morphological heterogeneity

Amandine Erktan, Catherine Roumet, Alexia Stokes, François Munoz

EcoSummit 2016, The 5th International EcoSummit Congress on Ecological Sustainability: Engineering Change .

Conference paper

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Influence of long-term biogeography and evolution on current patterns of rarity: consequence for conservation strategies

Régis Tournebize, François Munoz

The 5th International EcoSummit Congress on Ecological Sustainability: Engineering Change (EcoSummit 2016) .

Conference paper

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Cushion plants in high-elevation peatlands of Andes determines the functional and taxonomic composition of associated plant communities under intense herbivory and abiotic stress

Valérie Raevel, Fabien Anthelme, François Munoz

EcoSummit 2016, The 5th International EcoSummit Congress on Ecological Sustainability: Engineering Change .

Conference paper

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Into the functional ecology of ectomycorrhizal communities: environmental filtering of enzymatic activities

Pierre-Emmanuel Courty, François Munoz, Stéven Criquet, Marc-André Selosse, Myriam Duchemin, Claude Plassard...

Journal of Applied Ecology . 13 ( 8 ) : 1585-1598

DOI: 10.1111/1365-2745.12633

Journal article

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Growth rings in tropical trees: role of functional traits, environment, and phylogeny

Cheryl D. Nath, François Munoz, Raphaël Pélissier, David F. R. P. Burslem, Gowrappan Muthusankar

Trees - Structure and Function .

DOI: 10.1007/s00468-016-1442-1

Journal article

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Dynamics of trace element accumulation at the plant communauty level along mediterranean roadside secondary succession

Aliaksandr Kolbas, Amandine Erktan, Alexia Stokes, Diane Bouchet, Yogan Monnier, Francois Pailler...

10th ISEB conference . : np

Conference paper

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CSR ecological strategies and plant mating systems: outcrossing increases with competitiveness but stress-tolerance is related to mixed mating

François Munoz, Cyrille Violle, Pierre-Olivier Cheptou

Oikos . 125 ( 9 ) : 1296-1303

DOI: 10.1111/oik.02328

Journal article

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Evolution microstructurale en soudage par friction malaxage - Application à la prédiction des propriétés mécaniques dans les tôles AA2024

Valentine Legrand, Sabrina Gastebois, Gildas Guillemot, Michel Bellet, Lionel Fourment, Charles-André Gandin

‘La métallurgie, quel avenir !’ – Session ST1 : Procédés de fabrication innovants : Fabrication Voie Solide .

Conference paper

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