Directrice de recherche (DR1)

CEFE/CNRS
Campus du CNRS
1919, route de Mende
34293 Montpellier 5

E-mail : anne.charmantier[at]cefe.cnrs.fr

Thèmes de recherche: Evolution et génétique quantitative dans les populations naturelles; sénescence; sélection sexuelle.

Maitre de Conférences (EPHE)

CEFE/CNRS
Campus du CNRS
1919, route de Mende
34293 Montpellier 5

 tél : 33 (0)4 67 61 33 04
 fax: 33 (0)4 67 41 21 38

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 THEMES DE RECHERCHE

Mes thèmes de recherche concernent la phylogénie, la phylogéographie et l'évolution moléculaire à partir de l'analyse des séquences de gènes mitochondriaux et nucléaires. L’objectif est de répondre, à l’aide de l’outil moléculaire, à des questions de biodiversité et systématique évolutive à l’échelle des vertébrés (mammifères, amphibiens et reptiles). Je m’intéresse aussi à l’échelle temporelle (datations moléculaires) des différents niveaux de diversifications ce qui permet de confronter les inférences moléculaires avec les données morphologiques, paléontologiques et biogéographiques.

Directeur de recherche CNRS

CEFE/CNRS
Campus du CNRS
1919, route de Mende
34293 Montpellier 5

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A l’interface entre écologie fonctionnelle et écologie des communautés, je cherche à comprendre les causes de variation de la biodiversité, aussi bien à l’échelle locale que continentale, et l’effet de changements de la biodiversité sur la dynamique et le fonctionnement des écosystèmes.

Postdoctorant 

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Projet: effets du paysage sur la diversité génétique et les flux de gènes chez le Lièvre variable, le Lièvre d’Europe et le Lagopède alpin, dans les Alpes françaises.

Directeur de Recherche CNRS

luis-miguel.chevin[at]cefe.cnrs.fr

I am interested in adaptive evolution in response to changing environments: its ecological causes, phenotypic and genetic underpinnings, and demographic consequences. 

Directeur de Recherche / Senior scientist

I study the evolution of adaptive diversity, using colour patterns in butterflies as a model. In my group, we integrate many different approaches, including ecology, genetics, and modelling, to try and untangle how multiple factors influence the evolution and maintenance of diversity and polymorphisms.

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Directeur de Recherche au CNRS (DR2)

CEFE/CNRS
Campus du CNRS
1919, route de Mende
34293 Montpellier cedex 5

tél : +33 4 67 61 33 07
fax: +33 4 67 41 21 38

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Thématique de recherche

Je développe un travail d’écologie évolutive qui vise à analyser les traits d'histoire de vie chez les plantes (systèmes de reproduction, traits floraux, dispersion). L’accent est mis l'accent sur l'importance de la dynamique écologique (dynamique des métapopulations, démographie) comme un processus de sélection dans l'évolution contemporaine. Mon approche combine (1) Analyse des patrons d’adaptation et méthodes d’inférence des traits d’histoires de vie dans les métapopulations de plantes, en milieu naturel (2) élaboration de modèles formels en écologie évolutive (3) expérimentations et tests d’hypothèses en conditions contrôlées.

Most-clés :Métapopulation-traits d'histoire de vie-Ecologie évolutive théorique-dispersion-systèmes de reproduction-plasticité-Epigénétique

Chargée de Recherche, HDR

CEFE/CNRS
Campus du CNRS
1919, route de Mende
34293 Montpellier 5

Tél : +33/0 4 67 61 32 11

Stephanie.bedhomme[at]cefe.cnrs.fr

Bref CV

2018    : HDR, Université de Montpellier

2014-     : CRCN CNRS, CEFE

2012-13 : Postdoc at Bellvitge Biomedical Research Institute (IDIBELL, Barcelone, Spain)

2009-12 : Postdoc at the Molecular and Cellular Plant Biology Institute (IBMCP, Valence, Spain)

2007-09 : Teaching and researche assistant, Münster University (Allemagne)

2005-07 : Postdoc at Queen’s University (Kingston, Canada)

2000-04 : PhD in the Genetic and Evolution of Infectious Disease laboratory (IRD, Montpellier)

Current group members

Michael Finnegan

Jeanne Hamet

Méril Massot

Thèmes de recherches (english version below)

• Transfert horizontal de gène, résistance antibiotique et évolution post-transfert

Nous travaillons actuellement sur les règles de circulation des gènes par transfert horizontal. Le transfert horizontal est un mécanisme qui contribue fortement à l'évolution des génomes procaryotes mais tous les gènes ne sont pas dans tous les génomes. Il existe donc des facteurs qui favorisent ou limitent les transferts et les orientent. Les recherches que nous conduisons actuellement visent à étudier le rôle de ces facteurs à différentes échelles temporelles et spatiales. Nous nous intéressons en priorité, mais pas en exclusivité, aux transferts de gènes de résistance aux antibiotiques : les données et connaissance les concernant sont abondantes, la manipulation des pressions de sélection en laboratoire est aisée et nos résultats ont potentiellement des applications plus ou moins directes pour la gestion du problème de santé publique que représente la propagation des résistances antibiotiques.

Les questions auxquelles nous essayons de répondre actuellement sont :

• Quels sont les facteurs (écologie, pression de sélection, géographie…) qui déterminent les prévalences de gènes de résistances à l’échelle mondiale ?
• Quels sont les facteurs (partage de niche écologique, association à des éléments génétiques mobiles, similarité de contexte génomique, distance phylogénétique entre hôte) qui favorisent les transferts horizontaux ?
• L’usage de codons du gène transféré affecte-il la fonctionnalité de ce gène dans le génome récepteur ?
• Le transfert horizontal d’un gène peut-il entrainer une évolution compensatoire ?
• L’évolution post-transfert est-elle détectable à différentes échelles temporelles ?

Les approches utilisées sont la mesure de fitness de collections de mutants et de gènes, l'évolution expérimentale, la génomique bactérienne et la génomique comparative.

• Propagation des hypermutateurs dans les populations bactériennes

Les hypermutateurs sont des génotypes bactériens dont le taux de mutation ponctuel est plus élevé (10 à 1000 fois) que dans le reste de l’espèce. Des modèles théoriques prédisent qu’ils ont un avantage et se propagent dans les populations qui se trouvent loin de leur optimum adaptatif. En effet, dans cette situation, la proportion de mutations avantageuses parmi toutes les mutations générées est plus importante ; les hypermutateurs ont donc un avantage transitoire en augmentant à l’approvisionnement en mutation avantageuse puis ils augmentent en fréquence en raison de la liaison génétique entre le déterminant génétique de l’hypermutation et la mutation avantageuse générée. Les conditions de propagation des hypermutateurs ont été étudiées par des approches théoriques et par des approches expérimentales qui mettent en compétition un hypermutateur avec son ancêtre mais il existe très peu d’approches expérimentales où l’apparition et la propagation d’hypermutateurs a été suivie dans plusieurs conditions environnementales. Nous avons mis en place un dispositif d’évolution expérimentale qui permet de faire cela pour les conditions environnementales suivantes : doses subinhibitrices de gentamicine et forte salinité.

Dans le cadre de cette approche, nous posons les questions suivantes :

• La probabilité et la vitesse de propagation des hypermutateurs dépend-elle du type de stress et de la largeur de la base génétique d’adaptation à ce stress ?
• Comment déterminer la nature et la base génétique de l’adaptation par une approche « évoluer et reséquencer » ?
• L’évolution en présence de concentrations subinhibitrices de gentamicine conduit-elle à des niveaux élevés de résistance ?
• Quel est le rôle de l’hétérogénéité de taux de mutation le long du génome dans l’évolution parallèle entre populations indépendante ?

• Pollution microplastique, bactéries pathogènes et résistance antibiotique.

Les plastiques, en usage ou après usage, se dégradent et libèrent dans leur environnement immédiat des nano- et microparticules. Ces particules sont transportées à longue distance par l’eau ou l’air, peuvent pénétrer dans tous les organismes vivants et représentent un danger direct pour la santé humaine, animale et végétale. Ces particules peuvent également se convertir en support pour la formation de biofilm qui peuvent contenir des espèces bactériennes pathogènes pour certaines espèces animales et/ou pour les humains. Nous nous intéressons au rôle potentiel des micro-plastiques comme vecteur de pathogènes en utilisant Vibrio anguillarum comme modèle bactérien et des microparticules de polystyrène, polypropylène et polyéthylène téréphtalate.

Dans ce contexte scientifique, nous posons les questions suivantes :

• Quelle est la variabilité intraspécifique d’adhérence de anguillarum aux microparticules de plastique ? Peut-on identifier les déterminants génétiques de cette adhérence ?
• Quelles sont les espèces bactériennes composant les biofilms sur les microparticules ? Comment cette composition varie-t-elle au cours des saisons et au travers des environnements marins ou côtier ?
• Les biofilms associés aux microplastiques présentent-ils une surreprésentation de certaines espèces ou de certains gènes (résistance aux antibiotiques par exemple) par rapport au microbiote environnant ?
• La composition des biofilms associés aux microplastiques affecte-t-elle l’adhésion de la bactérie pathogène anguillarum?
• Les biofilms associés aux microplastiques sont-ils des points chauds de transfert horizontal ?

Mots clés:

transfert horizontal de gène, résistance aux antibiotiques, effet en fitness de la variation synonyme, usage des codons, évolution expérimentale, génomique bactérienne, biofilms, pollution microplastique.

Research topics

• Horizontal gene transfer, antibiotic resistance and post-transfer evolution

We are currently working on the horizontal transfer traffic rules. Horizontal transfer is a mechanism that strongly contributes to the evolution of prokaryotic genomes but all genes are not found in all genomes. There are therefore factors that promote or limit transfers and direct them. Our current research aims to study the role of these factors at different temporal and spatial scales. We are primarily, but not exclusively, interested in the transfer of antibiotic resistance genes: data and knowledge about them are abundant, the manipulation of selection pressures in the laboratory is easy, and our results have potentially more or less direct applications for the management of the public health problem represented by the spread of antibiotic resistance.

The questions we are currently trying to answer are:

- What are the factors (ecology, selection pressure, geography...) that determine the prevalences of resistance genes on a global scale?

• - What are the factors (ecological niche sharing, association with mobile genetic elements, genomic context similarity, phylogenetic distance between hosts) that favor horizontal transfers?
• - Does codon usage of the transferred gene affect the functionality of that gene in the recipient genome?
• - Can horizontal transfer of a gene lead to compensatory evolution?
• - Is post-transfer evolution detectable at different time scales?

The approaches used are fitness measurement of mutant and gene collections, experimental evolution, bacterial genomics and comparative genomics.

• Propagation of hypermutators in bacterial populations

Hypermutators are bacterial genotypes with a higher point mutation rate (10 to 1000 times) than the rest of the species. Theoretical models predict that they have an advantage and spread in populations that are far from their adaptive optimum. This is because in this situation, the proportion of advantageous mutations among all generated mutations is greater; thus, hypermutators have a transient advantage by increasing in supply of advantageous mutation and then increase in frequency due to the genetic linkage between the genetic determinant of the hypermutation and the generated advantageous mutation. The conditions of hypermutator propagation have been studied by theoretical approaches and by experimental approaches that put a hypermutator in competition with its ancestor but there are very few experimental approaches where the appearance and propagation of hypermutators has been followed under several environmental conditions. We have set up an experimental evolutionary setup that does this for the following environmental conditions: subinhibitory doses of gentamicin and high salinity.

In this approach, we ask the following questions:

• Does the probability and rate of hypermutator spread depend on the type of stress and the width of the genetic basis for adaptation to that stress?
• How can the nature and genetic basis of adaptation be determined by an "evolve and resequence" approach?
• Does evolution in the presence of subinhibitory concentrations of gentamicin lead to high levels of resistance?
• What is the role of mutation rate heterogeneity along the genome in parallel evolution between independent populations?

• Microplastic pollution, pathogenic bacteria and antibiotic resistance.

Plastics, in use or after use, degrade and release nano- and micro-particles into their immediate environment. These particles are transported over long distances by water or air, can penetrate all living organisms and represent a direct danger for human, animal and plant health. These particles can also become a surface where biofilm forms which may contain bacterial species pathogenic to certain animal species and/or humans. We are interested in the potential role of micro-plastics as pathogen vectors using Vibrio anguillarum as a bacterial model and polystyrene, polypropylene and polyethylene terephthalate microparticles.

In this scientific context, we ask the following questions:

• What is the intraspecific variability of anguillarum adherence to plastic microparticles? Can we identify the genetic determinants of this adhesion?
• What are the bacterial species composing biofilms on microparticles? How does this composition vary over the seasons and across marine or coastal environments?
• Do microplastic-associated biofilms show an over-representation of certain species or genes (e.g. antibiotic resistance) relative to the surrounding microbiota?
• Does the composition of microplastic-associated biofilms affect the adhesion of the pathogenic bacterium anguillarum?
• Are microplastic-associated biofilms hotspots for horizontal transfer?

Key words:

Horizontal gene transfer, antibiotic resistance, fitness effect of synonymous variation, codon usage, experimental evolution, bacterial genomics, biofilms, microplastic pollution.

Publications

• Finnegan M., Hamet J., Desmarais E. and Bedhomme S. (2023) Following the Dynamics of Structural Variants in Experimentally Evolved Populations. J. Vis. Exp. (192), e64709, doi:10.3791/64709.
• Pradier L. and Bedhomme S. (2023) Ecology, more than antibiotics consumption, is the major predictor for the global distribution of aminoglycoside-modifying enzymes. eLife 12:e77015. doi:10.7554/eLife.77015.
• Callens M., Rose C.J., Finnegan M., Gatchitch F., Simon L., Hamet, J., Pradier, L., Dubois, M-P. and Bedhomme, S. (2023) Hypermutator emergence in experimental Escherichia coli populations is stress-type dependent. Evolution Letters, 7: 252–261. doi:10.1093/evlett/qrad019.
• Callens M., Scornavacca C. and Bedhomme S. (2021) Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa. Microbial Genomics, 7:000587. doi: 10.1099/mgen.0.000587.
• Pradier L., Tissot T., Fiston-Lavier A-S. and Bedhomme S. (2021) PlasForest: a homology-based random forest classifier for plasmid detection in genomic datasets. BMC Bioinformatics, 22: 349. doi: 10.1186/s12859-021-04270-w.
• Callens M., Pradier L., Finnegan M., Rose C.J. and Bedhomme S. (2021) Read between the lines: Diversity of non-translational selection pressures on local codon usage. Genome Biology and Evolution, evab097. doi:10.1093/gbe/evab097.
• Bedhomme S., Amorós-Moya D., Valero L.M., Bonifaci N., Pujana M-A. and Bravo I.G. (2019) Evolutionary changes after translational challenges imposed by horizontal gene transfer. Genome Biology and Evolution, 11:814–831. doi:10.1093/gbe/evz031.
• Bedhomme S., Perez-Pantoja D. and Bravo I.G. (2017) Plasmid and clonal interference during post-horizontal gene transfer evolution. Molecular Ecology, 26: 1832-1847. doi:10.1111/mec.14056.
• Mengual-Chuliá B., Bedhomme, S., Lafforgue, G., Elena, S.F., Bravo, I.G. (2016) Assessing parallel gene histories in viral genomes. BMC Evolutionary Biology 16:32.
• Félez-Sánchez M., Trösemeier J-H., Bedhomme S., González-Bravo M-I, Kamp C. and Bravo I.G. (2015) Cancer, warts or asymptomatic infections: clinical presentation matches codon usage preferences in human papillomaviruses. Genome Biology and Evolution, 7:2117–2135.
• Bedhomme S., Hillung, J. and Elena S.F. (2015). Emerging viruses: why they are not jacks of all trades? Current Opinion in Virology10:1–6.
• Larcombe S.D., Bedhomme S., Garnier S., Cellier-Holzem E., Faivre B. and Sorci G. (2013) Social interactions modulate the virulence of avian malaria infection. International Journal of Parasitology43: 861-867.
• Bedhomme S., Lafforgue G. and Elena S.F. (2013) Genotypic but not phenotypic historical contingency revealed by viral experimental evolution. BMC Evolutionary Biology13:46.
• Bedhomme, S.,Lafforgue, G. and Elena S.F. (2012) Multihost experimental evolution of a plant RNA virus reveals local adaptation and host specific mutations. Molecular Biology and Evolution29:1481–1492.
• Bedhomme, S., Chippindale, A.K., Prasad, N.G, Delcourt, M., Abbott, J.K., Mallet, M.A. and Rundle, H.D. (2011) Male-limited evolution suggests no extant intralocus sexual conflict over the sexually dimorphic cuticular hydrocarbons of Drosophila melanogaster. Journal of Genetics90: 443-452.
• Jiang, P.P., Bedhomme, S., Prasad, N.G. and Chippindale, A.K. (2011) Sperm competition and mate harm unresponsive to male-limited selection in Drosophila: An evolving genetic architecture under domestication. Evolution65: 2448-2460.
• Bedhomme, S. and Elena, S.F. (2011) Virus infection suppresses Nicotiana benthamianaadaptive phenotypic plasticity. PLoS ONE 6: e17275.
• Elena, S.F.,Bedhomme, S., Carrasco, P., Cuevas, J.M., de la Iglesia, F., Lafforgue,G., Lalić, J., Pròsper, A., Tromas, N. and Zwart, M.P. (2011) The evolutionary genetics of emerging plant RNA viruses. Molecular Plant-Microbe Interactions24: 287–293.
• Abbott, J.K., Bedhomme, S. and Chippindale A.K. (2010) Sexual conflict in wing size and shape inDrosophila melanogaster. Journal of Evolutionary Biology 23: 1989-1997.
• Amoros-Moya, D., Bedhomme, S., Hermann, M. and Bravo, I.G. (2010) Evolution in regulatory regions rapidly compensates the cost of non-optimal codon usage. Molecular Biology and Evolution 27: 2141–2151.
• Bedhomme, S., Bernasconi, G., Koene, J.M., Lankinen, A.,Arathi, H.S., Michiels, N.K. and Anthes, N. (2009) How does breeding system variation modulate sexual antagonism? Biology Letters5: 717-720.
• Michalakis, Y., Bedhomme, S., Biron, D.G., Rivero, A., Sidobre, C. and Agnew, P. (2008) Virulence and resistance in a mosquito – microsporidium interaction. Evolutionary applications1: 49-56.
• Bedhomme, S., Prasad, N.G., Jiang, P.P., Chippindale, A.K. (2008) Reproductive Behaviour Evolves Rapidly When Intralocus Sexual Conflict Is Removed. PLoS ONE3: e2187.
• Kwan, L., Bedhomme, S., Prasad, N.G. and Chippindale, A.K. (2008) Sexual conflict and environmental change: tradeoffs within and between the sexes during the evolution of desiccation resistance. Journal of Genetics87: 383–394.
• Rivero, A., Agnew, P., Bedhomme, S., Sidobre, C. and Michalakis, Y. (2007) Resource depletion in Aedes aegyptimosquitoes infected by the microsporidia Vavraia culicis. Parasitology 134: 1355-1362.
• Prasad, N.G., Bedhomme, S., Day, T. and Chippindale, A.K. (2007) An evolutionary cost of separate genders revealed by male-limited evolution. American Naturalist169: 29–37.
• Prasad, N.G. and Bedhomme, S. (2006) Sexual conflict in plants. Journal of Genetics85: 161-165.
• Bedhomme, S., Agnew, P., Sidobre, C., Vital P.O. Y. and Michalakis, Y. (2005) Prevalence-dependent costs of parasite virulence.PLoS Biology 3: e262.
• Bedhomme, S., Agnew, P., Sidobre, C. and Michalakis, Y. (2005) Pollution by conspecifics as a component of intraspecific competition among Aedes aegyptiEcological Entomology 30: 1-7.
• Agnew, P., Berticat, C., Bedhomme, S., Sidobre, C. and Michalakis, Y. (2004) Parasitism increases and decreases the costs of insecticide resistance in mosquitoes. Evolution58: 579-586.
• Bedhomme, S., Agnew, P., Sidobre, C. and Michalakis, Y. (2004) Virulence reaction norms across a food gradient. Proceedings of the Royal Society of London B271: 739-744.
• Bedhomme, S., Agnew, P., Sidobre, C. and Michalakis, Y. (2003) Sex-specific reaction norms to intraspecific larval competition in the mosquito Aedes aegypti. Journal of Evolutionary Biology16: 721-730.
• Agnew, P., Bedhomme, S., Haussy, C. and Michalakis, Y. (1999). Age and size at maturity of the mosquito Culex pipiens infected by the microsporidian parasite Vavraia culicis. Proceedings of the Royal Society of London B 266: 947-952.

Book chapter:

• Bataillon, T., Bedhomme, S., Dillmann, C., Gaba, S., Gallet, R., Guidot, A., Goldringer, I., Jasmin, J-N., Kaltz, O., Méry, F., Nidelet, T., Reboud, X., Schneider, D., Sicard, D. and Spor, A. 2015. Evolution expérimentale. In F. Thomas, T. Lefèvre et M. Raymond (Eds), Biologie Evolutive, De Boeck, collection LMD, France, 617-646.
• Bedhomme, S. and Chippindale A.K. (2007) Irreconcilable differences: When sexual dimorphism fails to resolve sexual conflict (pp 185-194). In: Sex, Size and Gender Roles: Evolutionary studies of sexual size dimorphism. DJ Fairbairnm WU Blanckenhorn et T Székely editors. Oxford University Press, Oxford.

Directeur de Recherche CNRS

CEFE
Campus du CNRS
1919, route de Mende
34293 Montpellier 5
Tél : +33/0 4 67 61 32 91
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@Th_Lenormand

My principal area of research is Evolutionary genetics and evolutionary ecology. I have a broad expertise in evolutionary biology, genetics and ecology.

I have been working on adaptation and mutation, local adaptation, evolution of genetic systems (sex, recombination, sex chromosomes), evolution of gene duplicates, speciation, genetic conflicts, dispersal, biotic interactions (parasites, microbiota), statistics and fitness measures. I have been working with many empirical systems (vertebrates, insects, crustaceans, fungi, plants, helminths, bacteria), in the lab and in the field.

Currently, my scientific activity rests on three axes: first I do theoretical work (theoretical population genetics, statistics, and bioinformatics development). I am particularly interested currently on the evolution of gene expression (on sex chromosomes or in asexuals). Second, I work on small crustaceans Artemia and Daphnia. I’m particularly interested currently on sex-asex transitions, biotic interactions and adaptation to temperature. Third, I do experimental evolution on E. coli. I'm particularly interested on testing fitness landscape models, adaptation to different doses of antibiotics, and coevolution of species coexisting by frequency dependence.

Research interests by keywords
adaptation, local adaptation, migration, speciation, (sex) chromosomes, clines, sex, parthenogenesis, meiosis, recombination, epistasis, dominance, mutations, resistance, duplications, modifiers, mating systems, sexual conflicts, parasites, microbiota.

Brief CV

Deputy director CEFE

Research director CNRS (DR1)
HDR (2007)
Ph.D Evolutionary Biology (1998)

ERC "advanced grant" (2023)
Radcliffe Fellow, Harvard Univ. (2017-2018)
ERC "starting grant" (2007)
Theodosius Dobzhansky Prize (Society for the Study of Evolution), 2000
Young Investigator Prize (American Society of Naturalists), 2000

ResearchGate, GoogleScholar,  AcademicTree

	Editor2012 - 2015
	Associate editor2005 - 2008
	Associate editor2004 - 2011
	Associate editor2003 - 2007
	Associate editor2023 -...

Interested to join the lab?

If you're interested in the research topics mentioned above, or related ones, do not hesitate to contact me to discuss possible internships, PhDs, or postdocs.

Preprints

Houtain A, A Derzelle, M Lliros, B Hespeels, E Nicolas, P Simion, J Virgo, A-C Heuskin, T Lenormand, B Hallet, K Van Doninck.Transgenerational chromosome repair in the asexual bdelloid rotifer Adineta vaga. bioRxiv

Recent papers

Lenormand T, Roze D. 2024 Can mechanistic constraints on recombination reestablishment explain the long-term maintenance of degenerate sex chromosomes? Peer Community Journal 4.

Molinier C, Lenormand T, Haag C. 2023. No recombination suppression in asexually produced males of Daphnia pulex. Evolution, qpad114

Boyer L, R Jabbour-Zahab, P Joncour, S Glémin, CR Haag, T Lenormand. 2023. Asexual male production by ZW recombination in Artemia parthenogenetica. Evolution 77: 1-12

Laroche F, Lenormand T. 2023. The genetic architecture of local adaptation in a cline. Peer Community Journal 3.

Lenormand T, Roze D. 2022. Y recombination arrest and degeneration in the absence of sexual dimorphism. Science, 375:663-666.

Muyle A, Marais GAB, Bačovský V, Hobza R, Lenormand T. 2022. Dosage compensation evolution in plants: theories, controversies and mechanisms. Philosophical Transactions B 377: 20210222

Pais-Costa AJ, Lievens EJ, Redón S, Sánchez MI, Jabbour-Zahab R, Joncour P, Van Hoa N, Van Stappen G, Lenormand T. 2022. Phenotypic but no genetic adaptation in zooplankton 24 years after an abrupt +10°C climate change. Evolution Letters 6:284-294.

Rode NO, Jabbour-Zahab R, Boyer L, Flaven É, Hontoria F, Van Stappen G, Haag C, Lenormand T. 2022. The origin of asexual brine shrimps. Am. Nat. 200: E52-E76.

Boyer L, R Zahab, M Mosna, C Haag, T Lenormand. 2021. Not so clonal asexuals: unraveling the secret sex life of Artemia parthenogenetica. Evolution Letters 5:164-174.

Bestová H, Segrestin J, von Schwartzenberg K, Škaloud P, Lenormand T, Violle C. 2021. Biological scaling in green algae: the role of cell size and geometry. Scientific Reports 11: 1-9.

Simion P, Narayan J, Houtain A, Derzelle A, Baudry L, Nicolas E,... and Van Doninck K. 2021. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga. Science advances 7: eabg4216.

Lenormand, T., Fyon, F., Sun, E., & Roze, D. 2020. Sex chromosome degeneration by regulatory evolution. Current Biology 30: 3001-3006.

Lievens EJP, Y Michalakis, T Lenormand. 2020. Trait-specific trade-offs prevent niche expansion in two parasites. Recommended by PCI Evol Biol. JEB 33:1704-1714.

Harmand N, V Federico, T Hindre, T Lenormand. 2019. Non-linear frequency-dependent selection promotes long-term coexistence between bacteria species. Ecology Letters 22, 1192-1202

Lievens EJP, Rode NO, Landes J, Segard A, Jabbour-Zahab R, Michalakis Y, Lenormand T. 2019. Long-term prevalence data reveals spillover dynamics in a multi-host (Artemia), multi-parasite (Microsporidia) community. International Journal for Parasitology, 49, 471-480.

Selected publications by topics

Adaptation and mutation effects

Bourguet, D., T. Lenormand, T. Guillemaud, V. Marcel, D. Fournier, and M. Raymond. 1997. Variation of dominance of newly arisen adaptive genes. Genetics 147:1225-1234.

Chevin L.-M., G. Martin, T. Lenormand. 2010. Fisher’s model and the genomics of adaptation: restricted pleiotropy, heterogeneous mutation and parallel evolution. Evolution 64: 3213-3231PDF

Gallet R., Latour Y., Bradley H., and T. Lenormand. 2014. The dynamics of niche evolution upon abrupt environmental change. Evolution 68:1257-1269

Gallet R, Violle C, Fromin N, Jabbour-Zahab R, Enquist B, Lenormand T. 2017. The evolution of bacterial cell size: the internal diffusion-constraint hypothesis. ISME J. 11:1559-156

Harmand N, Gallet R, Jabbour-Zahab R, Martin G, Lenormand T. 2016. Fisher’s geometrical model and the mutational patterns of antibiotic resistance across dose gradients. Evolution 71:23-37.

Harmand N, Gallet R, Martin G, Lenormand T. 2018. Evolution of bacteria specialization along an antibiotic dose gradient.Evol.Let. in press.

Jasmin J.-N., Lenormand T. 2016. Accelerating mutational load is not due to synergistic epistasis or mutator alleles in mutation accumulation lines of yeast. Genetics DOI 115.182774

Labbé, P., Sidos, N., Raymond, M., and Lenormand, T., 2009. Resistance Gene Replacement in the Mosquito Culex pipiens: Fitness Estimation from Long Term Cline Series. Genetics 182:303-312PDF

Lenormand, T., D. Roze, F. Rousset. 2009. Stochasticity in evolution. Trends in Ecology & Evolution. 24: 157-165.PDF

Lenormand T, Chevin LMC, Bataillon T. 2016. Parallel evolution : what does it (not) tell us and why is it (still) interesting? [Book chapter, in Chance in Evolution Ramsey G & C Pence Eds, Univ. Chicago Press]. 

Lenormand, Nougué O, Jabbour-Zahab R, Arnaud F, Dezileau L, Chevin L.-M and Sánchez M. 2017 Resurrection Ecology in Artemia. Evol Appl. 11:76-87

Lenormand T, Harmand N, Gallet R. Cost of resistance: an unreasonably expensive concept. bioRxiv.

Manna F., Martin G., and T. Lenormand. 2011. Fitness landscape: an alternative theory for the dominance of mutations. Genetics 189:923-937.PDF.

Manna F., Gallet R., Martin G., and T. Lenormand. 2012. The high throughput yeast deletion fitness data and the theories of dominance. JEB, 25:892-903.PDF.

Martin, G., and T. Lenormand. 2006. A general multivariate extension of Fisher's geometrical model and the distribution of mutation fitness effects across species. Evolution 60:893-907. AwardedFisher Prize 2007, Best PhD paper published in Evolution in 2006.PDF

Martin, G., and T. Lenormand. 2006. The fitness effect of mutations in stressful environments: a survey in the light of fitness landscape models. Evolution 60:2413-2427.PDF

Martin, G., S.F. Elena and T. Lenormand. 2007. Distributions of epistasis in microbes fit predictions from a fitness landscape model. Nature Genetics 39:555-560.PDF

Martin, G., and T. Lenormand. 2008. The distribution of beneficial and fixed mutation fitness effects close to an optimum. Genetics. 179: 907-916.PDF

Martin, G., and T. Lenormand. 2015. The fitness effect of mutations across environments: Fisher's geometric model with multiple optima.Evolution 69:1433-1447 

Nougué O, Svendsen N, Zahab R, Lenormand T, Chevin LM. 2016. The ontogeny of tolerance curves : habitat quality versus acclimation in a stressful environment.J. Anim. Ecol. Doi 10.1111/1365-2656.12572.

Pais-Costa AJ, Lievens EJ, Redón S, Sánchez MI, Jabbour-Zahab R, Joncour P, Van Hoa N, Van Stappen G, Lenormand T. 2022. Phenotypic but no genetic adaptation in zooplankton 24 years after an abrupt +10°C climate change. Evolution Letters 6:284-294.

Local adaptation

Alberto F., S. N. Aitken, R. Alía, S. C. González-Martínez, H. Hänninen, A. Kremer, F. Lefèvre, T. Lenormand, S. Yeaman, R. Whetten, O. Savolainen. 2013. Potential for evolutionary responses to climate change - evidence from tree populations. Global Change Biology doi: 10.1111/gcb.12181.

Debarre F., Lenormand, T. and Gandon S. Evolutionary epidemiology of drug-resistance in space. 2009. PLoS Comp. Biol. 5:e1000337.PDF

Debarre F.,and T. Lenormand. 2011.Distance-limited dispersal promotes coexistence at habitat boundaries: reconsidering the competitive exclusion principle. Ecology Letters, 14: 260-266PDF

Epinat, G., and T. Lenormand. 2009. The evolution of assortative mating and selfing with in- and outbreeding depression. Evolution. 63: 2047-2060.PDF

Gallet R, Latour Y, Hughes B S, Lenormand T. 2014. The dynamics of niche evolution upon abrupt environmental change. Evolution 68: 1257-1269

Guillemaud, T., T. Lenormand, D. Bourguet, C. Chevillon, N. Pasteur, and M. Raymond. 1998. Evolution of resistance in Culex pipiens: Allele replacement and changing environment. Evolution 52:443-453.

Labbe, P., T. Lenormand, and M. Raymond. 2005. On the worldwide spread of an insecticide resistance gene: a role for local selection. Journal of Evolutionary Biology 18:1471-1484.PDF

Laroche F, Lenormand T. 2023. The genetic architecture of local adaptation in a cline. Peer Community Journal 3.

Lenormand, T. 2002. Gene flow and the limits to natural selection. Trends in Ecology & Evolution 17:183-189.PDF

Lenormand, T., D. Bourguet, T. Guillemaud, and M. Raymond. 1999. Tracking the evolution of insecticide resistance in the mosquito Culex pipiens. Nature 400:861-864.PDF

Lenormand, T., and M. Raymond. 1998. Resistance management: the stable zone strategy. Proceedings of the Royal Society of London Series B-Biological Sciences 265:1985-1990.PDF

Lenormand, T., and M. Raymond. 2000. Analysis of clines with variable selection and variable migration. American Naturalist 155:70-82.PDF

Milesi P, Lenormand T., Lagneau C, Weill M, Labbé P. 2016. Relating Fitness to Long-term Environmental Variations in natura.Molecular Ecoloy 25:5483-5499.

Gene duplication evolution

Labbe, P., A. Berthomieu, C. Berticat, H. Alout, M. Raymond, T. Lenormand, and M. Weill. 2007. Independent duplications of the acetylcholinesterase gene conferring insecticide resistance in the mosquito Culex pipiens. Molecular Biology and Evolution 24:1056-1067. PDF

Lenormand, T., T. Guillemaud, D. Bourguet, and M. Raymond. 1998. Appearance and sweep of a gene duplication: Adaptive response and potential for new functions in the mosquito Culex pipiens. Evolution 52:1705-1712. PDF

Labbé P., Milesi P., Yébakima A., Weill M., and T. Lenormand. 2014. Gene dosage effects on fitness in recent adaptive duplications : ace-1 in the mosquito Culex pipiens. Evolution 68: 2092-2101

Labbe, P., C. Berticat, A. Berthomieu, S. Unal, C. Bernard, M. Weill and T. Lenormand. 2007. Forty years of erratic insecticide resistance evolution in the mosquito Culex pipiens. PLoS Genetics, 3:e205. PDF

Milesi P, Weill M, Lenormand T., Labbé P. 2017. Heterogeneous gene duplications can be adaptive because they permanently associate overdominant alleles.Evolution Letters,1:169-180.

Sex, recombination, sex chromosomes, life cycles

Boyer L, R Jabbour-Zahab, P Joncour, S Glémin, CR Haag, T Lenormand. 2023. Asexual male production by ZW recombination in Artemia parthenogenetica. Evolution 77: 1-12

Boyer L, R Zahab, M Mosna, C Haag, T Lenormand. 2021. Not so clonal asexuals: unraveling the secret sex life of Artemia parthenogenetica. Evolution Letters 5:164-174.

Doums C, P Chifflet-Belle, T Lenormand, R Boulay, I Villalta. 2023. A putatively new ant species from the Cataglyphis cursor group displays low levels of polyandry with standard sexual reproduction. Insectes Sociaux 70: 439-450.

Fyon F, Lenormand T. 2018. Cis-regulator runaway and divergence in asexuals. Evolution 10.1111/evo.13424

Haag C, Theodosiou L, Zahab R, Lenormand T. 2017. Low recombination rates in sexual species and sex-asex transitions Phil. Trans. Roy. Soc. B. DOI: 10.1098/rstb. 2016-0461

Lenormand T, Roze D. 2024 Can mechanistic constraints on recombination reestablishment explain the long-term maintenance of degenerate sex chromosomes? Peer Community Journal 4.

Lenormand T, Roze D. 2022. Y recombination arrest and degeneration in the absence of sexual dimorphism. Science, 375:663-666.

Lenormand T, Engelstädter J, Johnston SE, Wijnker E, Haag CR. 2016. Evolutionary mysteries in meiosis. Phil. Trans. Roy. Soc. B, Doi 10.1098/rstb.2016.0001. alsohereon BiorXiv

Lenormand, T. 2003. The evolution of sex dimorphism in recombination. Genetics 163:811-822.PDF

Lenormand, T., and S. P. Otto. 2000. The evolution of recombination in a heterogeneous environment. Genetics 156:423-438.PDF

Lenormand, T., and J. Dutheil. 2005. Recombination difference between sexes: A role for haploid selection.PLoS Biology 3:396-403. PDF 

Lenormand T, Roze D, Cheptou P-O, Maurice S. 2010. L'évolution du sexe: un carrefour pour la biologie évolutive. in Biologie évolutive. M. Raymond, F. Thomas, T. Lefèvre, Eds. DeBoeck.
Everything you ever wanted to know about sex, but in French

Lievens EJP, Henriques GJB, Michalakis Y, Lenormand T. 2016. Maladaptive sex ratio adjustment in the invasive brine shrimp Artemia franciscana. Curr Biol. 26:1463–1467

Martin, G., S. P. Otto, and T. Lenormand. 2006. Selection for recombination in structured populations. Genetics 172:593-609.PDF

Molinier C, Lenormand T, Haag C. 2023. No recombination suppression in asexually produced males of Daphnia pulex. Evolution, qpad114

Mollion M, Ehlers BK, Figuet E, Santoni S, Lenormand T, Maurice S, Galtier N, Bataillon T. 2017. Patterns of genome-wide nucleotide diversity in the gynodioecious plant Thymus vulgaris are compatible with recent sweeps of cytoplasmic genes. Genome biology and evolution 10:239-248

Muyle A, Marais GAB, Bačovský V, Hobza R, Lenormand T. 2022. Dosage compensation evolution in plants: theories, controversies and mechanisms. Philosophical Transactions B 377: 20210222

Nougué O, Flaven E, Jabbour-Zahab R, Rode N O, Dubois M-P, Lenormand T. 2015. Characterization of nine new polymorphic microsatellite markers in Artemia parthenogenetica. Biochemical Systematics and Ecology 58, 59-63

Nougué O, Rode NO, Jabbour Zahab R, Ségard A, Chevin LMC, Haag C, Lenormand T. 2015. Automixis in Artemia: solving a century old controversy. J. Evol. Biol. 28:2337-2348

Otto, S. P., and T. Lenormand. 2002. Resolving the paradox of sex and recombination. Nature Reviews Genetics 3:252-261.PDF

Rescan M, Lenormand T, Roze D. 2016. Interaction between genetic and ecological effects on the evolution of life cycles. American Naturalist 187: 19-34

Rode NO, Jabbour-Zahab R, Boyer L, Flaven É, Hontoria F, Van Stappen G, Haag C, Lenormand T. 2022. The origin of asexual brine shrimps. Am. Nat. 200: E52-E76.

Roze, D., and T. Lenormand. 2005. Self-fertilization and the evolution of recombination. Genetics 170:841-857.PDF

Henry, P. Y., L. Vimond, T. Lenormand, and P. Jarne. 2006. Is delayed selfing adjusted to chemical cues of density in the freshwater snail Physa acuta? Oikos 112:448-455.PDF

Svendsen N, Reisser CMO, Dukić M, Thuillier V, Ségard A, Liautard-Haag C, Fasel D, Hürlimann E, Lenormand T, Galimov Y and Haag CR. 2015. Uncovering Cryptic Asexuality in Daphnia magnaby RAD-Sequencing. Genetics 201:1143-1155

Speciation

Bierne, N., T. Lenormand, F. Bonhomme, and P. David. 2002. Deleterious mutations in a hybrid zone: can mutational load decrease the barrier to gene flow? Genetical Research 80:197-204.PDF

Chevin, L.-M., Decorzent G., T. Lenormand. 2014. Niche dimensionality and the genetics of ecological speciation. Evolution 68:1244-1256

Fel-Clair, F., J. Catalan, T. Lenormand, and J. Britton-Davidian. 1998. Centromeric incompatibilities in the hybrid zone between house mouse subspecies from Denmark: Evidence from patterns of NOR activity. Evolution 52:592-603.

Fel-Clair, F., T. Lenormand, J. Catalan, J. Grobert, A. Orth, P. Boursot, M. C. Viroux, and J. BrittonDavidian. 1996. Genomic incompatibilities in the hybrid zone between house mice in Denmark: Evidence from steep and non-coincident chromosomal clines for Robertsonian fusions. Genetical Research 67:123-134.

Ganem, G, C. Litel, and T. Lenormand. 2008. Variation in mate preference across a house mouse hybrid zone. Heredity. 6:594-601PDF

Gay, L., P. Crochet, D. Bell, and T. Lenormand. 2008. Comparing genetic and phenotypic clines in hybrid zones: a window on tension zone models. Evolution 62: 2789-2806PDF

Lenormand T. 2012. From local adaptation to speciation: specialization and reinforcement. International Journal of Ecology. Ecological speciation (special issue) article ID 508458.PDF

Lenormand, T., F. FelClair, K. Manolakou, P. Alibert, and J. BrittonDavidian. 1997. Chromosomal transmission bias in laboratory hybrids between wild strains of the two European subspecies of house mice.Genetics 147:1279-1287. PDF

Dispersal

Billiard, S., and T. Lenormand. 2005. Evolution of migration under kin selection and local adaptation. Evolution 59:13-23. PDF

Lenormand, T., T. Guillemaud, D. Bourguet, and M. Raymond. 1998. Evaluating gene flow using selected markers: A case study. Genetics 149:1383-1392. PDF

Rieux A, Lenormand T., Carlier J., de Lapeyre de Bellaire L., Ravigne V. 2013 Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen.Ecology Letters 16 :721-730

Genetic conflicts

Autran D, Baroux C, Raissig MT, Lenormand T, Wittig M, Grob S, Steimer A, Barann M, Klostermeir UC, Leblanc O, Vielle-Calzada JP, Rosenstiel P, Grimanelli D, Grossniklaus U. 2011. Maternal epigenetic pathways control parental contributions to Arabidopsisearly embryogenesis. Cell 145: 707-719.PDF

Cailleau A., P.-O. Cheptou, T. Lenormand. 2010. Ploidy and the evolution of endosperm of flowering plants. Genetics 184:439-453.PDF

Cailleau A, Grimanelli D, Cheptou P-O, Lenormand T. 2018. Dividing a maternal pie among half-sibs: genetic conflicts and the control of resource allocation to seeds in maize. Am. Nat. 192: 577-592

Fyon F., Cailleau A., Lenormand T. 2015. Enhancer runaway and the Evolution of diploid gene expression.PLoS Genet. DOI 10.1371/journal.pgen.1005665.

Rode N., Charmantier A., Lenormand T. 2011. Male-female coevolution in the wild : evidence from a time series in Artemia franciscana. Evolution 65:2881-2892.PDF
On the web See a great summary by Carl Zimmerhere or in Wiredhere.

Biotic interactions

Ehlers B., David P., Damgaard C.F., Lenormand T. 2016. Competitor relatedness, indirect soil effects, and plant co-existence. Journal of Ecology 104: 1134-1135

Gallet, R., T. Lenormand and I.-N. Wang, 2012 Phenotypic stochasticity prevents lytic bacteriophage population from extinction during bacterial stationary phase. Evolution 66: 3485-3494.PDF

Lievens EJP, Rode NO, Landes J, Segard A, Jabbour-Zahab R, Michalakis Y, Lenormand T. 2018. Long-term prevalence data reveals spillover dynamics in a multi-host (Artemia), multi-parasite (Microsporidia) community. International Journal for Parasitology 49, 471-480.

Lievens EJP, Perreau JMA, Agnew P, Michalakis Y, Lenormand T. 2018. Decomposing parasite fitness in a two-host, two-parasite system reveals the underpinnings of parasite specialization. bioRxiv 256974.

Nougué O, Gallet R, Chevin LMC, Lenormand T. 2015. Niche Limits of Symbiotic Gut Microbiota Constrain the Salinity Tolerance of Brine Shrimp. American Naturalist 186:390-403
Microbiota impact the niche and an extended definition of realized niches

Rode N.O., Lievens EJP, Flaven E., Segard A., Jabbour-Zahab R., Sanchez M, Lenormand T. 2013. Why join groups? Lessons from parasite-manipulated Artemia. Ecology Letters 16:493-501.PDF
On the web:Parasites Make Their Hosts Sociable So They Get Eaten. Ed Yong's National Geographic Blog

Rode N.O., Landes J., Lievens E.J.P., Flaven E., Segard A., Jabbour-Zahab R., Michalakis Y., Agnew P., Vivares C., Lenormand T. 2013. Cytological, molecular and life cycle characterization of Anostracospora rigaudi n. g., n. sp. and Enterocytospora artemiae n. g., n. sp., two new microsporidian parasites infecting gut tissues of the brine shrimp Artemia.Parasitology 140:1168-1185 

Sánchez M.I., N.O. Rode, E. Flaven, S. Redón, F. Amat, G.P. Vasileva, T. Lenormand. 2012. Differential susceptibility to parasites of invasive and native species of Artemia living in sympatry: consequences for the invasion of A. franciscana in the Mediterranean Region. Biological Invasion, 14:1819-1829.PDF

Sanchez M., Pons I., Martinez-Haro M., Taggart M.A., Lenormand T., Green A. 2016. When parasites are good for health: cestode parasitism increases resistance to arsenic in brine shrimps. PLoS Pathogens DOIe1005459

Vasileva G.P., Redon S., Amat F., Nikolov P.N., Sanchez M., Lenormand T., Georgiev B.B. 2009 Records of cysticercoids of Fimbriarioides tadornae (Maksimova, 1976) and Branchiopodataenia gvozdevi (Maksimova, 1988) (Cyclophyllidea, Hymenolepididae) from brine shrimps at the Mediterraneancoasts of Spain and France, with a key to cestodes from Artemia spp. from the Western Mediterranean.Acta Parasitologica 54: 143-150. PDF

Fitness

Gallet R., Cooper T., Elena S.F., T. Lenormand. 2012. Measuring selection coefficients below 10-3 : method, questions and prospects. Genetics, 190:175-186.PDF
Over 150 millions phenotypes scored, one of the most precise measure of selection ever made and the questions it raises

Gimenez O., R. Covas, C. Brown, M. Anderson, M. Bomberger Brown, and T. Lenormand. 2006. Nonparametric estimation of natural selection on a quantitative trait using capture-mark-recapture data. Evolution 60:460-466.PDF

Gimenez O., Gregoire A., Lenormand T. 2009. Estimating and visualizing fitness surfaces using mark-recapture data.Evolution. 63: 3097-3105. 

Lenormand T, Rode NO, Chevin LMC, Rousset F. 2016. Valeur sélective: définitions, enjeux et mesures. in Biologie évolutive 2nd edition. M. Raymond, F. Thomas, T. Lefèvre, Eds. DeBoeck.
Everything you ever wanted to know about fitness, but in French

Download CFit : a stand-alone package to fit clines

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