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 211 to 240 publications on 572 in total

Calibration of 3D ALE finite element model from experiments on friction stir welding of lap joints

Lionel Fourment, Sabrina Gastebois, Laurent Dubourg

ESAFORM 2016 . 1769 : 100006

DOI: 10.1063/1.4963500

Conference paper

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Geometrical envelopes: Extending graphical contemporary niche theory to communities and eco-evolutionary dynamics

Thomas Koffel, Tanguy Daufresne, François Massol, Christopher A. Klausmeier

Journal of Theoretical Biology . 407 : 271-289

DOI: 10.1016/j.jtbi.2016.07.026

Journal article

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Fruiting Strategies of Perennial Plants: A Resource Budget Model to Couple Mast Seeding to Pollination Efficiency and Resource Allocation Strategies

Samuel Venner, A. Siberchicot, P.F. Pélisson, E. Schermer, Marie-Claude Bel-Venner, M. Nicolas...

The American Naturalist . 188 ( 1 ) : 66-75

DOI: 10.1086/686684

Journal article

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Molecular phylogeny of the highly diversified catfish subfamily Loricariinae (Siluriformes, Loricariidae) reveals incongruences with morphological classification

R. Covain, S. Fisch-Muller, C. Oliveira, J. H. Mol, J. I. Montoya-Burgos, Stéphane Dray

Molecular Phylogenetics and Evolution . 94 : 492-517

DOI: 10.1016/j.ympev.2015.10.018

Journal article

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Interspecific interference competition at the resource patch scale: do large herbivores spatially avoid elephants while accessing water?

Nicolas Ferry, Stéphane Dray, Hervé Fritz, Marion Valeix

Journal of Animal Ecology . 85 ( 6 ) : 1574-1585

DOI: 10.1111/1365-2656.12582

Journal article

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Impact of Wheat/Faba Bean Mixed Cropping or Rotation Systems on Soil Microbial Functionalities

Sanâa Wahbi, Yves Prin, Jean Thioulouse, Hervé Sanguin, Ezékiel Baudoin, Tasnime Maghraoui...

Frontiers in Plant Science . 7 : 1364

DOI: 10.3389/fpls.2016.01364

Journal article

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Spatial Distribution of a Large Herbivore Community at Waterholes: An Assessment of Its Stability over Years in Hwange National Park, Zimbabwe

Simon Chamaillé-Jammes, Anaïs Charbonnel, Stéphane Dray, H. Madzikanda, H. Fritz

PLoS ONE . 11 : e0153639

DOI: 10.1371/journal.pone.0153639

Journal article

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The global spectrum of plant form and function

S. Diaz, J. Kattge, J. H. Cornelissen, I. J. Wright, S. Lavorel, Stéphane Dray...

Nature . 529 ( 7585 ) : 167-71

DOI: 10.1038/nature16489

Journal article

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Addressing ecological effects of radiation on populations and ecosystems to improve protection of the environment against radiation: Agreed statements from a Consensus Symposium

F. Brechignac, D. Oughton, C. Mays, L. Barnthouse, J. C. Beasley, A. Bonisoli-Alquati...

Journal of Environmental Radioactivity . 158-159 : 21-29

DOI: 10.1016/j.jenvrad.2016.03.021

Journal article

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Occurrence of Stenotrophomonas maltophilia in agricultural soils and antibiotic resistance properties

Amélie Deredjian, Nolwenn Alliot, Laurine Blanchard, Elisabeth Brothier, Makram Anane, Philippe Cambier...

Research in Microbiology . 167 ( 4 ) : 313-324

DOI: 10.1016/j.resmic.2016.01.001

Journal article

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Bacterial community structure at the microscale in two different soils

Rory Michelland, Jean Thioulouse, Martina Kyselková, Geneviève Grundmann

Microbial ecology . 72 ( 3 ) : 717-724

DOI: 10.1007/s00248-016-0810-0

Journal article

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Analysis of hemocytes in Lymnaea stagnalis: Characterization and effects of repeated hemolymph collections

Paul Boisseaux, Marie Laure Delignette-Muller, Khédidja Abbaci, Hélène Thomas, Jeanne Garric

Fish and Shellfish Immunology . 57 : 116-126

DOI: 10.1016/j.fsi.2016.08.007

Journal article

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Recommendations for the analysis of hemocyte-related immunocompetent oxidative activity in the freshwater snail Lymnaea stagnalis

P. Boisseaux, P. Noury, Marie Laure Delignette-Muller, H. Thomas, J. Garric

Journal of Xenobiotics . 6 : 25-27

DOI: 10.4081/xeno.2016.6585

Journal article

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Everything is NOT everywhere: network and trait-based approaches to microbial communities

Helena Bestová, François Munoz, Pavel Svoboda, Pavel Škaloud, Cyrille Violle

Annual Meeting BES .

Conference paper

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Vegetation ecology meets ecosystem science: Permanent grasslands as a functional biogeography case study

Cyrille Violle, Philippe Choler, Benjamin Borgy, Eric Garnier, Bernard Amiaud, Guilhem Debarros...

Science of the Total Environment . 534 ( 15 november 2015 ) : 43--51

DOI: 10.1016/j.scitotenv.2015.03.141

Journal article

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Microstructural evolution during friction stir welding on AA2024 aluminium alloys - Application to the prediction of the mechanical properties

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

11th International Seminar ‘Numerical Analysis of Weldability’ . : 497-513

Conference paper

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Simulation numérique du soudage FSW à l'aide d'une formulation ALE

Sabrina Gastebois

Thesis

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Modeling of Microstructural Evolution during Friction Stir Welding Applied to AA2024 Aluminum Alloys to Predict the Weld Mechanical Properties

Valentine Legrand, Sabrina Gastebois, Gildas Guillemot, Charles-André Gandin, Lionel Fourment, Rousse Jean-Jacques...

2015 TMS Annual Meeting & Exhibition .

Conference paper

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Field Application of the Mycorrhizal Fungus Rhizophagus irregularis Increases the Yield of Wheat Crop and Affects Soil Microbial Functionalities

S. Wahbi, Y. Prin, T. Maghraoui, H. Sanguin, Jean Thioulouse, K. Oufdou...

American Journal of Plant Sciences . 06 : 3205-3215

DOI: 10.4236/ajps.2015.619312

Journal article

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fitdistrplus : An R Package for Fitting Distributions

Marie Laure Delignette-Muller, Christophe Dutang

Journal of Statistical Software . 64 ( 4 )

DOI: 10.18637/jss.v064.i04

Journal article

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Considering external information to improve the phylogenetic comparison of microbial communities: a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA)

Stéphane Dray, Sandrine Pavoine, Daniel Aguirre De Carcer

Molecular Ecology Resources . 15 ( 2 ) : 242-9

DOI: 10.1111/1755-0998.12300

Journal article

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Generating spatially constrained null models for irregularly spaced data using Moran spectral randomization methods

H. H. Wagner, Stéphane Dray

Methods in Ecology and Evolution . 6 : 1169-1178

DOI: 10.1111/2041-210x.12407

Journal article

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Revisiting the link between breeding effort and oxidative balance through field evaluation of two sympatric sibling insect species

Benjamin Rey, Pierre-François Pélisson, Marie-Claude Bel-Venner, Yann Voituron, Samuel Venner

Evolution - International Journal of Organic Evolution . 69 ( 3 ) : 815–822

DOI: 10.1111/evo.12586

Journal article

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Constructing Time-Resolved Species Sensitivity Distributions Using a Hierarchical Toxico-Dynamic Model

Guillaume Kon Kam King, Marie Laure Delignette-Muller, Ben J. Kefford, Christophe Piscart, Sandrine Charles

Environmental Science and Technology . 49 ( 20 ) : 12465-12473

DOI: 10.1021/acs.est.5b02142

Journal article

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A Toolbox for Nonlinear Regression in R: The Package nistools

F. Baty, C. Ritz, Sandrine Charles, M. Brutsche, Jean-Pierre Flandrois, Marie Laure Delignette-Muller

Journal of Statistical Software . 66 : 1-21

Journal article

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Potentialities of ecological engineering strategy based on native arbuscular mycorrhizal community for improving afforestation programs with carob trees in degraded environments

N. Manaut, H. Sanguin, L. Ouahmane, M. Bressan, Jean Thioulouse, E. Baudoin...

Ecological Engineering . 79 : 113-119

Journal article

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Soil Organic Matter Quality, Structure and Activity of the Denitrifiers Community as Influenced by Decaying Mulched Crop Residues

A. Dieng, E. Baudoin, Jean Thioulouse, D. Brunet, J. Toucet, Sn. Sylla...

Applied Ecology and Environmental Research . 13 : 655-675

Journal article

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MOSAIC_SSD: A new web tool for species sensitivity distribution to include censored data by maximum likelihood

Guillaume Kon Kam King, Philippe Veber, Sandrine Charles, Marie Laure Delignette-Muller

Ecotoxicology and Environmental Safety . 33 ( 9 ) : 2133 - 2139

DOI: 10.1002/etc.2644

Journal article

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Hierarchical modelling of species sensitivity distribution: development and application to the case of diatoms exposed to several herbicides

Guillaume Kon Kam King, Floriane Larras, Sandrine Charles, Marie Laure Delignette-Muller

Ecotoxicology and Environmental Safety . 114 : 212-221

DOI: 10.1016/j.ecoenv.2015.01.022

Journal article

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