PROPOSITION POUR L`ORGANISATION D`UNE

Transcription

PROPOSITION POUR L'ORGANISATION
D’UNE CONFERENCE EN 2012
APPLICATION FOR THE ORGANIZATION
OF A CONFERENCE IN 2012
Dans le cas du renouvellement d’une conférence, le rapport de l’édition précédente doit être joint
(voir fichier "Rapport CJM 2007 Evolutionary Genomics.pdf")
TITRE DE LA CONFERENCE (en anglais et en français) :
TITLE OF THE CONFERENCE (in English and in French):
Theoretical and empirical advances in evolutionary genomics
Développements théoriques et empiriques en génomique évolutive
PRESIDENT - CHAIRPERSON: Juliette DE MEAUX
VICE-PRESIDENT - VICE-CHAIRPERSON: Xavier VEKEMANS
Avec la participation pour la rédaction de ce dossier de:
Guillaume ACHAZ, UPMC Paris 6
Laurent DURET, CNRS Lyon
Oscar GAGGIOTTI, Univ. Joseph Fourier Grenoble
Nicolas GALTIER, CNRS Montpellier
Lluis QUINTANA-MURCI, Institut Pasteur Paris
Olivier TENAILLON, INSERM Paris
Renaud VITALIS, INRA Montpellier
------------------------
A envoyer à - To be sent to: [email protected]
avant le 7 janvier 2011 - before January 7th, 2011
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PRESIDENT - CHAIRPERSON
Nom - Last name
DE MEAUX
Prénom - First name Juliette
Adresse professionnelle - Institution address
Plant Molecular Evolution
Institute for Evolution and Biodiversity
Münster University
Hüfferstr. 1
48149 Münster
ALLEMAGNE
Téléphone - Phone
+49 251 83 21 095
Télécopie – Fax
+49 251 83 24 668
Courrier électronique – [email protected]
(Veuillez joindre un bref curriculum vitae, un résumé succinct du programme de recherche et une liste
de vos principales publications et des conférences sur invitation des trois dernières années - 4 pages
maximum)
(Please, enclose a brief curriculum vitae, a summary of research programme and a list of your main
publications and invited lectures from the last three years - 4 pages maximum)
CV: voir Annexe A
VICE-PRESIDENT - VICE-CHAIRPERSON
Nom - Last name
VEKEMANS
Prénom - First name Xavier
Adresse professionnelle - Institute address
Laboratoire de Génétique et Evolution des Populations Végétales, FRE 3268
CNRS – Université Lille 1
Batiment SN2
Cité scientifique
59155 Villeneuve d'Ascq
Téléphone - Phone
03 20 43 67 53
Télécopie – Fax 03 20 43 69 79
Courrier électronique - E-mail [email protected]
(Veuillez joindre un bref curriculum vitae, un résumé succinct du programme de recherche et une liste
de vos principales publications et des conférences sur invitation des trois dernières années - 4 pages
maximum)
(Please, enclose a brief curriculum vitae, a summary of research programme and a list of your main
publications and invited lectures from the last three years - 4 pages maximum)
CV: voir Annexe B
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LISTE DES CONFERENCIERS PROPOSES (30 personnes maximum incluant Président et VicePrésident)
LIST OF PROPOSED LECTURERS (30 persons maximum including Chairperson and Vice-chairperson)
(Pour chaque conférencier, veuillez mentionner le nom, le prénom, l'adresse professionnelle et l'adresse mèl, le
thème de recherche et les références des trois principales publications des trois dernières années - For each
lecturer, please mention the last name, the first name, the institute address and e-mail, the research topic, and
the references of the three main publications from the last three years)
Dans le cas du renouvellement d’une de conférences, veuillez indiquer pour chaque conférencier s'il a participé
soit en tant que conférencier invité, soit en tant que participant sélectionné à la précédente conférence – In the
case of the renewal of a conference, for each lecturer, please indicate if he attented the previous conference as
an invited lecturer or as a selected participant.
Conférenciers non européens (7 à 8 personnes)
Non european lecturers (7 to 8 persons)
1. BUSTAMANTE Carlos (male, was not speaker or participant at CJM'07)
Address: Professor of Genetics, School of Medicine, Stanford University, USA
E-mail: [email protected]
Research topic:
He is actively involved in the analyses of genomewide data (including the 1000 genomes project) for
both demographic and selective inference. His research focuses on analyzing genome wide patterns of
variation within and between species to address fundamental questions in biology, anthropology, and
medicine. His group works on a variety of organisms and model systems ranging from humans and other
primates to domesticated plant and animals. Much of their research is at the interface of computational
biology, mathematical genetics, and evolutionary genomics
Three Publications:
Henn BM, Gravel S, Moreno-Estrada A, Acevedo-Acevedo S, Bustamante CD. Fine-scale population
structure and the era of next-generation sequencing. Hum Mol Genet. 2010 Oct 15;19(R2):R221-6.
Bryc K, Auton A, Nelson MR, Oksenberg JR, Hauser SL, Williams S, Froment A, Bodo JM, Wambebe
C, Tishkoff SA, Bustamante CD. Genome-wide patterns of population structure and admixture in
West Africans and African Americans. Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):786-91.
Auton A, Bryc K, Boyko AR, Lohmueller KE, Novembre J, Reynolds A, Indap A, Wright MH,
Degenhardt JD, Gutenkunst RN, King KS, Nelson MR, Bustamante CD. Global distribution of
genomic diversity underscores rich complex history of continental human populations. Genome Res.
2009 May;19(5):795-803.
2. EICHLER Evan (male, was not speaker or participant at CJM'07)
Address: Professor of Genome Sciences, Department of Genome Sciences, University of Washington,
USA
Research topic:
He is the worldwide expert in copy number of variation in the human genome, and involved in the
analyses of this type of variation in the 1000 genomes project. Genomic duplication followed by adaptive
mutation is considered one of the primary forces for evolution of new gene function. Duplicated
sequences are also dynamic regions of rapid structural change during the course of chromosome
evolution. The long-term goal of their research is to understand the evolution, pathology and
mechanism(s) of recent gene duplication and DNA transposition at the levels of the entire human
genome.
Three Publications:
Sudmant PH, Kitzman JO, Antonacci F, Alkan C, Malig M, Tsalenko A, Sampas N, Bruhn L, Shendure
J; 1000 Genomes Project, Eichler EE. Diversity of human copy number variation and multicopy
genes. Science. 2010 Oct 29;330(6004):641-6.
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Kidd JM, Graves T, Newman TL, Fulton R, Hayden HS, Malig M, Kallicki J, Kaul R, Wilson RK,
Eichler EE. A human genome structural variation sequencing resource reveals insights into
mutational mechanisms. Cell. 2010 Nov 24;143(5):837-47.
Alkan C, Kidd JM, Marques-Bonet T, Aksay G, Antonacci F, Hormozdiari F, Kitzman JO, Baker C,
Malig M, Mutlu O, Sahinalp SC, Gibbs RA, Eichler EE. Personalized copy number and segmental
duplication maps using next-generation sequencing. Nat Genet. 2009 Oct;41(10):1061-7. Epub 2009
Aug 30.
3. LANDRY Christian (male, was not speaker or participant at CJM'07)
Address: Département de Biologie, Institut de Biologie Intégrative et des Systèmes, Local 3106, Pavillon
Charles-Eugène-Marchand, 1030 Avenue de la Médecine, Université Laval, Québec G1V 0A6,
CANADA
Research topic:
Specialist of network evolution with a wet lab approach. He is investigating how genes interact with each
other, how these relationships influence their evolution and how functional linkages change during
evolution. In particular, he studies gene expression regulatory networks and protein-protein interaction
networks.
Three publications:
Landry CR Systems biology spins off a new model for the study of canalization. Trends Ecol Evol.
24:63-6 (2009)
Tarassov K, Messier V, Landry CR, Radinovic S, Serna Molina MM, Shames I, Malitskaya Y, Vogel J,
Bussey H, Michnick SW. An in vivo map of the yeast protein interactome. Science. 320:1465-70
(2008)
Landry CR, Lemos B, Rifkin SA, Dickinson WJ, Hartl DL. Genetic properties influencing the
evolvability of gene expression. Science. 317:118-21.(2007)
4. NOVEMBRE John (male, was not speaker or participant at CJM'07)
Address: Department of Ecology and Evolutionary Biology, University of California-Los Angeles 621
Charles E. Young Drive South, Box 951606, Los Angeles, CA 90095-1606, USA
Research topic:
Theoretical population genetics and statistical genetics. Specifically, projects focusing on developing
theory and statistical methods for analyzing genomic-scale population genetic data. Much of his work
investigates questions in evolutionary genetics, focusing on human evolutionary history and using data
from emerging genotyping and sequencing technologies.
Three publications:
Novembre J, Veeramah K, Tonjes A, Kovacs P, Stumvoll M. 2010. Genetic diversity of European
population isolates in the context of neighboring populations. American Journal of Physical
Anthropology: 179Novembre J, Di Rienzo A. 2009. Spatial patterns of variation due to natural selection in humans. Nature
Reviews Genetics 10: 745-55
Novembre J, Johnson T, Bryc K, Kutalik Z, Boyko AR, et al. 2008. Genes mirror geography within
Europe. Nature 456: 98-U5
5. PALSSON Bernhard (male, was not speaker or participant at CJM'07)
Address: Systems Biology Research Group, University of California San Diego, 9500 Gilman Drive,
Mail Code 0412, La Jolla CA 92093-0412, USA
Research topic:
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Specialist of systems biology, founded the Flux Balance analysis model, and uses experimental evolution
to validate his network predictions in terms of performance. (More than 20 publications per year in the
field)
Three publications:
Lewis NE, Hixson KK,…, and Palsson BØ. Omic data from evolved E. coli are consistent with
computed optimal growth from genome-scale models. Mol Syst Biol 6:390 (2010).
Hyduke DR and Palsson BØ. Towards genome-scale signalling network reconstructions Nature
Reviews Genetics 11:297-307 (2010)
Feist, A.M., Herrgard, M.J., Thiele, I., Reed, J.L., Palsson, B.Ø. Reconstruction of Biochemical
Networks in Microbial Organisms Nature Reviews Microbiology, 7(2)(2009).
6. PETROV Dmitri (male, was not speaker or participant at CJM'07)
Address : Department of Biology, Stanford University, 371 Serra St., CA 94305-5020 USA
E-mail : [email protected]
Research topic:
He is interested in a wide range of questions in molecular evolution and molecular population genetics.
He does theoretical, computational and experimental work to address these questions: How frequent is
adaptation? Does it generally involve mutations of small or large phenotypic effect? Does it tend to
involve new mutations or use standing variation? Are adaptive mutations typically coding or regulatory?
How frequent are population or environment-specific versus whole-species adaptations? What effect does
recurrent adaptation has on patterns of neutral variation? Is the Neutral Theory dead?
Three publications:
Hershberg, R. and D.A. Petrov.(2010). Evidence that mutation is universally biased towards AT in
bacteria. PLoS Genetics, 6(9): e1001115
Karasov, T., Messer, P., and D.A. Petrov. (2010). Evidence that adaptation in Drosophila is not limited
by mutation at single sites. PLoS Genetics, 6(6): e1000924.
González, J., Lenkov, K., Lipatov, M., Macpherson, J.M., and D.A. Petrov.(2008). High rate of recent
TE-induced adaptations in Drosophila melanogaster. PLoS Biology 6(10): e251.
7- SCHMITT Johanna (female, was not speaker or participant at CJM'07)
Address : Brown University, Providence, RI, USA
Research topic:
Adaptive evolution of developmental, physiological, and life history traits in natural plant populations.
The Schmitt lab uses quantitative genetics, QTL mapping, and association studies of candidate loci to
examine the genomics of natural variation in ecologically important traits. Natural selection on these
traits and the loci underlying them is measured in the field by experimentally manipulating environments,
phenotypes, and genotypes. A major research objective is to elucidate the genetic and ecological
mechanisms of adaptation to seasonal and geographic variation in climate.
Three Publications :
Stinchcombe JR. Weinig C. Heath KD. Brock MT. Schmitt J. Polymorphic genes of major effect:
consequences for variation, selection and evolution in Arabidopsis thaliana. Genetics. 182(3):911-22,
2009.
Wilczek AM. Roe JL. Knapp MC. Cooper MD. Lopez-Gallego C. Martin LJ. Muir CD. Sim S. Walker
A. Anderson J. Egan JF. Moyers BT. Petipas R. Giakountis A. Charbit E. Coupland G. Welch SM.
Schmitt J. Effects of genetic perturbation on seasonal life history plasticity. Science. 323(5916):9304, 2009.
Korves TM. Schmid KJ. Caicedo AL. Mays C. Stinchcombe JR. Purugganan MD. Schmitt J. Fitness
effects associated with the major flowering time gene FRIGIDA in Arabidopsis thaliana in the field.
American Naturalist. 169(5):E141-57, 2007.
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8- WITTKOPP Trisha (Patricia) (female, was not speaker or participant at CJM'07)
Address: University of Michigan, 1061 Natural Science Building, 830 North University Avenue, Ann
Arbor, Michigan 48109-1048
Research topic:
She investigates the genetic, developmental, and population-level processes by which new phenotypes
evolve. She focuses on the molecular mechanisms by which gene expression is regulated and evolves.
Complex networks that regulate gene expression complicate the identification of specific nucleotides
responsible for expression differences. The basic properties of regulatory mutations are investigated and
the frequency of cis - and trans - changes between pairs of species separated for different amounts of time
are compared. To better understand the relationship between expression divergence, Drosophila
pigmentation is used as a model system for understanding the genetic basis of phenotypic evolution.
Three Publications:
Wittkopp, P.J. (2010). Variable transcription factor binding: a mechanism of evolutionary change. PLoS
Biology, 8, e1000342.
Wittkopp, P.J., E.E. Stewart, A.H. Neidert, B.K. Haerum, L.L. Arnold, E. M. Thompson, G. SmithWinberry, and L. Shefner (2009). Intraspecific polymorphism to interspecific divergence: genetics of
pigmentation in Drosophila. Science 326, 540-544.
Wittkopp, P.J., B.K. Haerum, and A. Clark (2008) Genetic basis of regulatory variation within and
between Drosophila species, Nature Genetics, 40, 346-50
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Conférenciers européens non français (9 à 11 personnes, incluant le Président ou le Vice-Président)
Non french european lecturers (9 to 11 persons, including the Chairperson or the Vice-Chairperson)
1. BELDADE Patricia (female, was not speaker but participated to CJM'07)
Address: Evolutionary Biology, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE
Leiden, THE NETHERLANDS
Research interests :
Her work focuses on the colour patterns on the wings of Bicyclus anynana butterflies to address key
issues in Evolutionary Developmental Biology. Butterfly wing patterns are ideally suited to study the
reciprocal interactions between evolutionary and developmental processes (evo-devo) that shape
morphological variation. They are visually compelling products of selection, often with a clear adaptive
value, and are also amenable to a detailed developmental characterization at different levels, including
genomics .Her lab is also interested in the Evolutionary Genetics and Genomics analysis in non-model
systems.
Three publications:
Saenko SV, French V, Brakefield PM, Beldade P. 2008. Conserved developmental processes and the
formation of evolutionary novelties: examples from butterfly wings. Phil. Trans. R. Soc. BBiological Sciences 363: 1549-1555.
Beldade P, Saenko SV, Pul N, et al. 2009. A Gene-Based Linkage Map for Bicyclus anynana Butterflies
Allows for a Comprehensive Analysis of Synteny with the Lepidopteran Reference Genome. Plos
Genetics 5, e1000366.
Wittkopp PJ, Beldade P. 2009. Development and evolution of insect pigmentation: Genetic mechanisms
and the potential consequences of pleiotropy. Sem. In Cell & Developmental Biology 20: 65-71.
2. DONNELLY Peter (male, was not speaker or participant at CJM'07)
Address: Professor of Statistical Science, Wellcome Trust Centre for Human Genetics, Roosevelt
Drive, Oxford OX3 1BN,UNITED KINGDOM
Research topic:
He is the director of the Wellcome Trust Centre for Human Genetics, and a pioneer of the application of
coalescence theory in population genetics. His area of expertise is in stochastic modelling, applications of
probability and statistics in genetics, gene mapping, early human evolution, population genetics,
measure-valued diffusions, and statistical issues in DNA profiling.
Three publications:
Wellcome Trust Case Control Consortium, Craddock N, Hurles ME, Cardin N, […], Donnelly P (2010)
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared
controls. Nature, 7289 : 713-720
Donnelly P (2008) Progress and challenges in genome-wide association studies in humans. Nature
Insight 456: 728-731
Chaix R, Cao C, Donnelly P (2008) Is mate choice in humans MHC-dependent? PLoS Genetics 4:
e1000184
3. EXCOFFIER Laurent (male, was vice-president of CJM'07)
Address: Computational and Molecular Population Genetics, Institute of Ecology and Evolution,
University of Bern, 6 Baltzerstrasse, CH-3012 Bern, SWITZERLAND
Research topic:
He is developing computational methods to understand evolutionary processes at the population and
species level, for instance to study how past climatic and environmental changes have influenced the
pattern of genetic diversity of a given species, or to detect evidence of local adaptations from genomic
information. He has studied the effect of complex demography on the molecular genetic diversity of a
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species, for instance such as after a spatial expansion in a heterogeneous environment. He is also
involved in the development and the application of approximate Bayesian computations (ABC) methods
Three publications:
Ray N, Wegmann D, Fagundes NJR, Wang S, Ruiz-Linares A & Excoffier L (2010) A statistical
evaluation of models for the initial settlement of the American continent emphasizes the importance
of gene flow with Asia. Molecular Biology and Evolution 27: 337-345
Excoffier L, Foll M & Petit RJ (2009) Genetic Consequences of Range Expansions. Annual Review in
Ecology, Evolution, and Systematics 40: 481-501
Fagundes N J R, Ray N, Beaumont M, Neuenschwander S, Salzano F M, Bonatto S L & Excoffier L
(2007) Statistical evaluation of alternative models of human evolution. Proceedings of the National
Academy of Sciences USA 104: 17614-17619
4. GORDO Isabel (female, was not speaker or participant at CJM'07)
Address: Instituto Gulbenkian de Ciencia, Portugal
Research interests: Her lab is interested in combining both theoretical and empirical work with the aim at
understanding the major forces that shape variation in natural populations. E. coli is used as a model
organism to test theoretical predictions about the evolution of mutation rates and the genetics of
adaptation. Other topics of current work are: generation of diversity in germinal centers and antigenic
diversity in parasites.
Three publications:
Trindade S, Sousa A, Xavier KB, Dionisio F, Ferreira MG, Gordo I 2009. Positive Epistasis Drives the
Acquisition of Multidrug Resistance. Plos Genetics 5: e1000578.
Perfeito L, L. Fernandes, C. Mota and I. Gordo (2007) Adaptive Mutations in Bacteria: High Rate and
Small Effects. Science 317(5839):813-5.
Combadão J , Dionisio F., Campos. PRA and I. Gordo (2007) Small-word networks decrease the speed
of Muller's ratchet Genetical Research 89(1):7-18
5. KAESSMANN Henrik (male, was not speaker or participant at CJM'07)
Address: Center for Integrative Genomics, Genopode, University of Lausanne, CH-1015 Lausanne,
SWITZERLAND
Research topic:
He uses bioinformatics analyses to study the functional evolution of mammalian genes (e.g., emergence
of new genes and their functions; the origin and evolution of mammalian sex chromosomes) on the basis
of publicly available genomic data as well as data generated by the wet lab unit of his group (e.g., largescale transcriptome data obtained using next generation sequencing technologies). His work on
transcriptomics aims at investigating the evolution of gene expression levels, alternative splicing,
microRNAs and their expression, dosage compensation, and germ cell transcriptomes.
Three publications:
Henrichsen, C. N., Vinckenbosch, N., Zollner, S., Chaignat, E., Pradervand, S., Schutz, F., Ruedi, M.,
*Kaessmann, H., and *Reymond, A. (2009) Segmental copy number variation shapes tissue
transcriptomes. Nat. Genet. 41: 424-429
Kaessmann, H., Vinckenbosch, N., and Long, M.: RNA-based gene duplication: mechanistic and
evolutionary insights. (2009) Nat. Rev. Genet. 10: 19-31.
Brawand, D., Wahli, W. and Kaessmann, H. (2008) Loss of egg yolk genes in mammals and the origin
of lactation and placentation. PLoS Biol. 3: e63.
6. Mc LYSAGHT Aoife (female, was not speaker or participant at CJM'07)
Address: Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, IRELAND
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Research topic:
She is conducting molecular evolution research through bioinformatics methods. The current focus of her
research is on the origin and evolution of new genes and gene loss. She is examining these phenomena in
two widely different groups of organisms: vertebrates and poxviruses. She is studying genomic sequence
available from many vertebrates in order to examine the phylogenetic distribution of genes present in
each vertebrate lineage and to examine the molecular evolution of genes that have been gained recently in
the vertebrate lineage. Poxviruses have simple genomes amenable to analysis and are therefore a useful
system to study. The properties of the origin and evolution of new genes in poxviruses are expected to be
different from the properties in vertebrate genomes both because of the comparative simplicity of
poxvirus genomes, and also because of the differences in their life cycle.
Three publications:
Makino, T., and McLysaght, A. (2010). Ohnologs in the human genome are dosage balanced and
frequently associated with disease Proc Natl Acad Sci U S A. 19(10):1752-9
Knowles, D.G., and McLysaght, A. (2009). Recent de novo origin of human protein-coding genes
Genome Research 19(10):1752-9
McLysaght, A. (2008). Evolutionary steps of sex chromosomes are reflected in retrogenes. Trends in
Genetics 24(10):478-481
7. Mc VEAN Gilean (male, was invited speaker at CJM'07)
Address: Department of Statistics, University of Oxford, 1 South Parks Road, Oxford 0X1 3TG,
UNITED KINGDOM
Research topic:
He is the leader of the statistical analsyes of the 1000 genomes project. His research covers several areas
in evolutionary biology and population genetics, combining both theoretical work and empirical analyses.
Of particular interest is the analysis of recombination from population genetic data, the relationship
between linkage disequilibrium and properties of the underlying genealogy, and methods for inferring
genealogical history from DNA sequence data.
Three publications:
1000 Genomes Project Consortium, Durbin RM, Abecasis GR, Altshuler DL, Auton A, Brooks LD,
Durbin RM, Gibbs RA, Hurles ME, McVean GA. A map of human genome variation from
population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.
International HapMap 3 Consortium. Integrating common and rare genetic variation in diverse human
populations. Nature. 2010 Sep 2;467(7311):52-8.
Myers S, Freeman C, Auton A, Donnelly P, McVean G. A common sequence motif associated with
recombination hot spots and genome instability in humans. Nat Genet. 2008 Sep;40(9):1124-9.
8. NORDBORG Magnus (male, was not speaker or participant at CJM'07)
Address: Gregor Mendel Institute of Molecular Plant Biology, Dr. Bohr-Gasse 3, 1030 Vienna,
AUSTRIA
Research topic: Scientific director of the Gregor Mendel Institute, Vienna. The central theme of the
Nordborg group is the genetic basis of adaptation. A combination of empirical and theoretical approaches
from population genetics and related areas, such as statistical genetics and molecular evolution, are used.
Empirical research focuses on Arabidopsis thaliana but the group works on a wide range of organisms,
including primates.
Three publications:
Li Y, Huang Y, Bergelson J, Nordborg M, Borevitz JO (2010) Association mapping of local climatesensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci USA 107 : 21199-21204
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Atwell S, Huang YS, Vilhálmsson BJ, Willems G, Horton M, Li Y, Meng D, Platt A, Tarone A, Hu TT,
Jiang R, Muliyati NW, Zhang X, Amer MA, Baxter I, Brachi B, Chory J, Dean C, Debieu M, de
Meaux J, Ecker JR, Faure N, Kniskern JM, Jones JDG, Michael T, Nemri A, Roux F, Salt DE, Tang
C, Todesco M, Traw MB, Weigel D, Marjoram P, Borevitz J, Bergelson J, Nordborg M (2010)
Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465:
627-631
Nordborg M, Weigel D (2008) Next-generation genetics in plants. Nature 456: 720-723
9. PAPP Balazs (male, was not speaker or participant at CJM'07)
Address: Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences,
Szeged, Temesvári krt. 62, H-6701, HUNGARY.
Research topic:
He is developing novel computational methods to analyze functional genomic datasets and to automate
scientific discovery in the fields of systems biology and drug discovery. His research focuses on:
understanding genetic interaction networks; automated refinement of metabolic network models;
automated discovery of optimal antimicrobial drug combinations
Three publications:
Costanzo M, et al The genetic landscape of a cell. Science. 327425-31 (2010)
Kovács K, Hurst LD, Papp B. Stochasticity in protein levels drives colinearity of gene order in metabolic
operons of Escherichia coli. PLoS Biol. 7:e1000115. (2009)
Notebaart RA, Teusink B, Siezen RJ, Papp B. Co-regulation of metabolic genes is better explained by
flux coupling than by network distance. PLoS Comput Biol. 4:e26 (2008).
10. WEIGEL Detlef (male, was not speaker or participant at CJM'07)
Address: Department of Molecular Biology, Max Planck Institute for Developmental Biology,
Spemannstrasse 37-39, D-72076 Tübingen, Germany.
Research topic:
The majority of the Weigel's group investigates genetic diversity, which is being studied on several
different levels. In addition to forward genetic analyses of wild Arabidopsis thaliana strains, he is
examining sequence variation and its impact on a spectrum of phenotypes, including hybrid performance,
on a whole-genome, whole-species scale. Such studies benefit tremendously from knowledge about the
genomes of other species, and he has taken the lead in assembling genome sequences for several A.
thaliana relatives. Second-generation sequencing is playing a major role. The department has been at the
forefront of developing bioinformatic methods for the analysis of Illumina (Solexa) data, and has been
using these for a range of applications, from sequencing A. thaliana strains to mapping of transcription
factor binding sites and one-step mutation identification.
Three publications:
Laubinger S, Zeller G, Henz SR,..., and Weigel D. Global effects of the small RNA biogenesis machinery
on the Arabidopsis thaliana transcriptome. 2010. PNAS 107:17466-17473.
Ossowski, S, Schneeberger, K, Lucas-Lledo, JI, Warthmann, N, Clark, RM, Shaw, RG, Weigel, D, and
Lynch, M (2010). Science, 327(5961):92-94.
Todesco, M, Balasubramanian, S, Hu, TT, Traw, MB, Horton, M, Epple, P, Kuhns, C, Sureshkumar, S,
Schwartz, C, Lanz, C, Laitinen, RAE, Huang, Y, Chory, J, Lipka, V, Borevitz, JO, Dangl, JL,
Bergelson, J, Nordborg, M, and Weigel, D (2010). Natural allelic variation underlying a major fitness
trade-off in Arabidopsis thaliana. Nature, 465(7298):632-6.
11. DE MEAUX Juliette - President of the conference
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Conférenciers français (9 à 11 personnes, incluant le Président ou le Vice-Président)
French lecturers (9 to 11 persons, including the Chairperson or the Vice-Chairperson)
1. BLUM Michael (male, was not speaker but participated to CJM'07)
Address: Laboratoire TIMC, Domaine de la Merci, Faculté de Médecine, 38706 La Tronche
E-mail: michael.blum.imag.fr
Research topic:
Statistical genetics, Bayesian statistics and Approximate Bayesian Computation for making inferences
about human evolutionary genetics and in particular inferring demographic history based on populationgenetic data
Three publications:
Blum M.G.B., M. Jakobsson. (2011) Deep divergences of human gene trees and models of human
origins. Molecular Biology and Evolution, Advance Access, doi:10.1093/molbev/msq265
Blum M.G.B. (2010) Approximate Bayesian Computation: a nonparametric perspective. Journal of the
American Statistical Association, 105: 1178-1187
Blum M.G.B., V-C Tran. (2010) HIV with contact tracing: a case study in Approximate Bayesian
Computation. Biostatistics, 11: 644-660
2. CARBONE Alessandra (female, was not speaker or participant at CJM'07)
Address: Génomique Analytique, Laboratoire de Génomique des Microorganismes, FRE3214, CNRS Université Pierre et Marie Curie, 15, rue de l'École de Médecine, 75006 Paris
Research topic:
Combinatorial and Statistical Methods in Molecular Biology (Mathematical analysis of networks);
Algorithms in Computational Biology; DNA Nanotechnologies and DNA Tiling; Proof Theory and
Complexity Theory; Graph Theory; Finite Automata and Symbolic Dynamics
Three publications:
Mathelier A, Carbone A. Chromosomal periodicity and positional networks of genes in Escherichia coli.
Mol Syst Biol. 11;6:366. (2010)
S.Engelen, L.A.Trojan, S.Sacquin-Mora, R.Lavery, A.Carbone, JET: detection and analysis of protein
interfaces based on evolution, PLoS Computational Biology, 5(1): e1000267, 1--17, (2009)
Baussand J, Carbone A. A combinatorial approach to detect coevolved amino acid networks in protein
families of variable divergence. PLoS Comput Biol.;5(9):e1000488 (2009)
3. DURET Laurent (male, was invited speaker at CJM'07)
Address: Laboratoire Biométrie et Biologie Evolutive, UMR CNRS 5558, Université Lyon 1, 43 Bld du
11 Novembre 1918, 69622 Villeurbanne
Research topic:
He is using comparative genomic approaches to study processes of genomic evolution. His work has
focused on the evolutionary consequences of whole genome duplications, and on the effect of biased
gene conversion as an important evolutionary process impacting genomic landscapes. He has produced
many bioinformatic tools and databases used by the evolutionary genomics community.
Three publications:
Gout J-F, Kahn D, Duret L (2010). The Relationship among Gene Expression the Evolution of Gene
Dosage and the Rate of Protein Evolution, PLoS Genetics, vol. 6(5) pp.1-9.
Duret L, Galtier N (2009). Biased Gene Conversion and the Evolution of Mammalian Genomic
Landscapes, Annual Review of Genomics and Human Genetics, vol. 10 pp.285-311.
Duret L (2009). Mutation Patterns in the Human Genome:More Variable Than Expected, PLoS Biology,
vol. 7(2) e1000028: pp.803-806
11
4. DUTHEIL Julien (male, was not speaker or participant at CJM'07)
Address: Institut des Sciences de l’Evolution de Montpellier, Université Montpellier 2, CC 065, Place
Eugène Bataillon, 34095 Montpellier
Research topic:
Models for genome analysis using a population genetics perspective. Applications of Hidden Markov
Models to infer population genetics parameters like speciation time or ancestral population sizes. Also
models and statistic methods to infer past demographic and selective events.
Three publications:
Dutheil JY, Ganapathy G, Hobolth A, Mailund T, Uyenoyama MK, Schierup MH. (2009) Ancestral
population genomics: the coalescent hidden Markov model approach. Genetics 183:259-74.
Dutheil JY, Jossinet F, Westhof E. (2010) Base pairing constraints drive structural epistasis in ribosomal
RNA sequences. Mol Biol Evol 27:1868-76.
Dutheil J. (2008) Detecting site-specific biochemical constraints through substitution mapping. J Mol
Evol. 67:257-65.
5. GLÉMIN Sylvain (male, was not speaker or participant at CJM'07)
Address: Institut des Sciences de l'Evolution. CC64, Université Montpellier II, Place Eugène Bataillon,
34095 Montpellier
Research topic:
Theoretical population genetics; Molecular evolution and evolutionary genomics; Genomic consequences
of mating system evolution; Occurrence and consequences of GC-Biased gene conversion; Genetic and
genomic of plant domestication; Determinant of mitochondrial DNA evolutionary rates.
Although Sylvain Glémin belongs to the same laboratory as Julien Dutheil, their expertise are very
different, and they are invited to give presentation in two distinct session: session "Theoretical population
genomics" for Julien Dutheil who is developing new methods of inference of population genetic
parameters from genomic data; session "Evolutionary genomics" for Sylvain Glémin who is producing
and analyzing large sets of genomic data to compare the relative effects of different processes on
genomic evolution.
Three publications:
S. Glémin. 2010. Surprising fitness consequences of GC-biased gene conversion : I. Mutation load and
inbreeding depression. Genetics 185:939-959
J. Escobar, A. Cenci, J. Bolognini, A. Haudry, S. Laurent, J. David and S. Glémin. 2010. An integrated
test of the dead-end hypothesis of selfing evolution in Triticeae (Poaceae). Evolution 64(10):2855-72.
Nabholz, B., J. F. Mauffrey, E. Bazin, N. Galtier, and S. Glémin. 2008. Determination of mitochondrial
genetic diversity in mammals. Genetics 178:351-361
6. HEYER Evelyne (female, was invited speaker at CJM'07)
Address: UMR 7206 Eco-anthropologie, Equipe "génétique des populations humaines", MNHN, CP 139,
57 rue Cuvier, 75231 Paris Cedex 05
Research topic:
She is working in the field of Human Evolutionary genetics with a special focus in Human population
genetics. She focuses on three topics: peopling history; detecting and estimating natural selection;
evaluating the importance of social behaviour and their transmission in the evolution of the Human
species. Among other projects she is investigating populations from Central Asia, collecting DNA
samples, linguistic data and performing ethnological surveys. Using these data she investigates the
population history of the region, the impact of social organization on genetic diversity, the genetic
linguistic distances and the adaptation to diet (NAT2, Lactase Persistency, Diabetes Type II).
Three publications:
12
Ségurel L., Martínez-Cruz B., Quintana-Murci L., Balaresque P., Georges M., Hegay T., Aldashev A.,
Nasyrova F., Jobling M. A., Heyer E. Sex-specific genetic structure and social organization in
Central Asia : insights from a multi-locus study. et al PLoS Genetics 4, 9 (2008)
Heyer E, Quintana-Murci L . 2009. Evolutionary genetics as a tool to target genes involved in
phenotypes of medical relevance. Evolutionary Applications 2: 71-80.
Heyer E, Balaresque P, Jobling MA, et al. 2009. Genetic diversity and the emergence of ethnic groups in
Central Asia. BMC Genetics 10: 49.
7. LOUDET Olivier (male, was not speaker or participant at CJM'07)
Address: Plant Breeding and Genetics Unit, INRA Versailles, Route de Saint Cyr 78000 Versailles.
Research topic:
Our group is involved in understanding the genetic basis of adaptation and response to abiotic stress in
Arabidopsis thaliana. In that purpose we are mostly using natural variation as a source of biodiversity to
find new genes and new alleles controlling shoot and root growth under drought and osmotic stress
conditions. Recently we have also initiated projects to pinpoint natural variation for cis-acting
transcriptional regulation using a combination of eQTL fine-mapping and allelic expression assay.
Three publications:
Vlad D., Rappaport F., Simon M., Loudet O. (2010) Gene transposition causing natural variation for
growth in Arabidopsis thaliana. PLoS Genetics 6(5): e1000945
Bikard D., Patel D., Le Metté C., Giorgi V., Camilleri C., Bennett M.J., Loudet O. (2009) Divergent
evolution of duplicate genes leads to genetic incompatibilities within A. thaliana Science 323: 623626
Loudet O., Saliba-Colombani V., Camilleri C., Calenge F., Gaudon V., Koprivova A., North K.A.,
Kopriva S., Daniel-Vedele F. (2007) Natural variation for sulfate content in Arabidopsis is highly
controlled by APR2. Nature Genetics 39: 896-900
8. QUINTANA-MURCI Lluis (male, was invited speaker at CJM'07)
Address: UP Human Evolutionary Genetics, CNRS URA3012, Institut Pasteur, 25, rue du Dr. Roux,
75724 Paris 15.
Research topic:
His research is focused on understanding how natural selection, human demography and lifestyle have
shaped the patterns of diversity of the human genome in different populations worldwide. In particular,
he is interested in exploring how infectious diseases have exerted selective pressures on human genes
involved in immunity and host defence in order to unmask immunological mechanisms that have been
critical for our past and present survival. To this end, his laboratory combines molecular and population
genetics approaches with computational modelling, often working closely to theoretical population
geneticists, immunologists, epidemiological geneticists as well as anthropologists.
Three publications:
Barreiro, L.B., Ben-Ali, M., Quach H, Laval G, Patin E, Pickrell J, Bouchier C, Tichit M, Neyrolles O,
Gicquel B, Kidd JR, Kidd KK, Alcaïs A, Ragimbeau J, Pellegrini S, Abel L, Casanova JL, QuintanaMurci L. (2009). Evolutionary Dynamics of Human Toll-Like Receptors and their Different
Contributions to Host Defense. PLoS Genet 5(7):e1000562.
Patin, E., Laval, G., Barreiro, L. B., Salas, A., Semino, O., Santachiara-Benerecetti, S., Kidd, K. K.,
Kidd, J. R., Van der Veen, L., Hombert, J. M., Gessain, A., Froment, A., Bahuchet, S., Heyer, E. and
Quintana-Murci, L. (2009). Inferring the demographic history of african farmers and pygmy huntergatherers using a multilocus resequencing data set. PLoS Genet 5(4):e1000448.
Quintana-Murci, L., Quach, H., Harmant, C., Luca, F., Massonnet, B., Patin, E., Sica, L., MouguiamaDaouda, P., Comas, D., Tzur, S., Balanovsky, O., Kidd, K. K., Kidd, J. R., van der Veen, L.,
Hombert, J. M., Gessain, A., Verdu, P., Froment, A., Bahuchet, S., Heyer, E., Dausset, J., Salas, A.
and Behar, D. M. (2008). Maternal traces of deep common ancestry and asymmetric gene flow
13
between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc Natl Acad Sci U S A 105, 15961601.
9. ROCHA Eduardo (male, was not speaker or participant at CJM'07)
Address: Microbial Evolutionary Genomics group, Institut Pasteur, 25 rue Dr Roux, 75724 Paris.
Research topic:
His scientific activities are centered on the bioinformatics and biostatistics analysis of genomes, at the
crossroads of molecular evolution, population genetics, evolutionary ecology and molecular genetics. He
is focussing on three major questions: 1) How and why are genomes organized? 2) How are such
organizational features evolving in face of the extensive genome dynamics? 3) What are the roles of
mobile elements in the trade-offs between organization and dynamics?
Three publications:
Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EPC (2009) Horizontal Gene Transfer
of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence. Curr Biol 19:168391.
Vieira-Silva S, Rocha EPC (2009) The Systemic Imprint of Growth Rates and its Uses in Ecological
(Meta)genomics. Plos Genet 6:e1000808.
Rocha EP (2008) The organization of the bacterial genome. Annu Rev Genet 42:211-33.
10. TENAILLON Olivier (male, was not speaker but participated to CJM'07)
Address: INSERM U722, 16 rue Henri Huchard, 75018 Paris.
Research topic:
He is a population geneticist and microbiologist who uses experimental evolution, theoretical modelling
and molecular evolution to study microbial evolution. His current research is on the evolution of genome
architecture and complexity, using Escherichia coli as a model organism.
Three publications:
Tenaillon O, Skurnik D, Picard B, et al. 2010. The population genetics of commensal Escherichia coli.
Nature Rev. Microbiol. 8: 207-217.
Gros PA, Le Nagard K. and Tenaillon O. The Evolution of Epistasis and Its Links With Genetic
Robustness, Complexity and Drift in a Phenotypic Model of Adaptation. Genetics 182 :277-293
(2009)
Touchon et al Organised genome dynamics in the Escherichia coli species results in highly diverse
adaptive paths. PLoS Genet. 5: e1000344.(2009)
11. VEKEMANS Xavier - Vice-President of the conference
14
NOMBRE DE PARTICIPANTS ENVISAGE :
NUMBER OF PARTICIPANTS EXPECTED :
115
PRINCIPAUX LABORATOIRE FRANCAIS ET EUROPEENS INTERESSES PAR LE SUJET DE LA
CONFERENCE (indiquer le nom et l'adresse complète de chaque laboratoire)
MAIN FRENCH AND EUROPEAN LABORATORIES INTERESTED IN THE TOPIC OF THE
CONFERENCE (with indication of a contact name, the name and full postal address of each laboratory)
(Adresses complètes fournies dans le fichier Excel " Interested_labs_Evolutionary Genomics.xlsx")
Laboratory
Institution
City
Country
FRE CNRS 3355 Biologie Integrative
des Organismes Marins
UMR INRA 077 Pathologie végétale
PaVé
UMR INRA Biodiversité, gènes et
communautés BIOGECO
UMR CNRS INRA 8120 Génétique
végétale du Moulon
UPR9034 Laboratoire Evolution,
Génomes et Spéciation LEGS
UMR CNRS 5163 Adaptation et
Pathogénie des Microorganismes
UMR CNRS 5553 Laboratoire
d'écologie alpine LECA
UMR INRA 1313 Génétique Animale et
Biologie Intégrative
UR INRA 1077 Mathématique,
Informatique & Génome
UMR CNRS 5525 TIMC-IMAG
CNRS-UPMC Paris 6
Banyuls-sur-Mer
France
INRA-Université Angers-INHP Beaucouze
Agrocampus Ouest
INRA-Université de Bordeaux Cestas
1
CNRS-INRA
Gif-sur-Yvette
France
CNRS Gif
Gif-sur-Yvette
France
CNRS-Université Joseph
Fourier Grenoble
Fourier Grenoble
INRA-AgroParisTech
Grenoble
France
Grenoble
France
Jouy-en-Josas
France
INRA Jouy-en-Josas
Jouy-en-Josas
France
La Tronche
France
Maugio
France
Montferrier-sur-Lez
France
Montpellier
France
Montpellier
France
Orsay
France
Paris
France
Orsay
France
Paris 05
France
Paris 05
France
Paris 05
France
Paris 05
France
Paris 05
France
Fourier Grenoble
UMR INRA 1097 Diversité et Adaptation INRA-Université de
des Plantes Cultivées DIA-PC
Montpellier 2 - IRD Montpellier Supagro
UMR INRA Centre de Biologie pour la
INRA-IRD-CIRAD- Montpellier
Gestion des Populations CBGP
Supagro
UMR CNRS 5175 Centre d'écologie
CNRS Montpellier
fonctionnelle et évolutive CEFE
UMR CNRS 5554 Institut des Sciences CNRS-Université Montpellier
de l'Evolution Montpellier ISEM
2
UMR CNRS 8621 Institut de Génétique CNRS-Université Paris-sud
et Microbiologie IGM
UMR 7205 Organisation, structure et
CNRS-MNHN
évolution de la biodiversité
UMR CNRS 8079 Ecologie,
CNRS-Université Paris-sud
Systématique et Evolution ESE
CNRS UMR8197 Institut de Biologie de CNRS-Ecole Normale
l'Ecole Normale Supérieure
Supérieure
UMR 7205 Organisation, structure et
CNRS-MNHN
évolution de la biodiversité
UMR CNRS 7206 Eco-anthropologie et CNRS-MNHN-Université
Ethnobiologie
Paris 7
UMR CNRS 7625 Ecologie et Evolution CNRS-UPMC Paris 6-Ecole
Normale supérieure
UMR7138 Systématique, Adaptation,
CNRS-UPMC Paris 6-MNHN-
France
France
15
Evolution SAE
URA 2171 Génétique moléculaire des
levures
URA CNRS 3012 Hôtes, vecteurs et
agents infectieux: biologie et dynamique
USC INRA 2019 Biologie et
Pathogénécités fongiques
U722 INSERM Ecologie et évolution
des microorganismes
FRE Biologie et Ecologie tropicale et
méditerranéenne
USR 3278 Centre de Recherches
Insulaires et Observatoire de
l'Environnement (CRIOBE)
UMR CNRS 6553 Ecosystèmes
Biodiversité Evolution ECOBIO
UMR CNRS 7144 Adaptation et
Diversité en Milieu Marin
UMR CNRS 5554 Institut des Sciences
de l'Evolution Montpellier ISEM
FRE 2960 Anthropologie moléculaire et
Imagerie de synthèse
UMR CNRS 5174 Evolution et diversité
biologique EDB
UR INRA Biologie et gestion des
risques en agriculture - Champignons
pathogènes des plantes
FRE CNRS 3268 Génétique et
Evolution des populations végétales
GEPV
UMR CNRS 5558 Biométrie et biologie
évolutive LBBE
IRD
CNRS-Institut Pasteur-UPMC
Paris 15
France
CNRS-Institut Pasteur
Paris 15
France
Institut Pasteur-INRA
Paris 15
France
INSERM-Université Paris 7
Paris 18
France
CNRS-Université de
Perpignan
CNRS-EPHE
Perpignan
France
Perpignan
France
CNRS-Université de Rennes
1
CNRS-UPMC Paris 6 Station
Biologique Roscoff
CNRS-Université Montpellier
II
CNRS-Université Paul
Sabatier Toulouse III
CNRS-Université Paul
Sabatier Toulouse III
INRA-AgroParisTech
Rennes
France
Roscoff
France
Sète
France
Toulouse
France
Toulouse
France
Versailles
France
CNRS-Université Lille 1
Villeneuve d'Ascq
France
CNRS-Université Claude
Bernard Lyon 1
Villeurbanne
France
Gregor Mendel Institute of Molecular
Plant Biology GMI
Institute of Population Genetics
Bioinformatics Research Center,
Institute of Biology
Metapopulation Research Group
Institute of Evolution and Biodiversity
Institut fuer Genetik
University of Cologne
MPI Tübingen
MPI Plön
Austria
Wien
University of Veterinary
Medicine Vienna
Aarhus University
University of Helsinki
Wilhelminienne University
Münster
Heinrich-Heine Universitaet
Duesseldorf
Institute for Theoretical Physics
Max Planck Institute for
Developmental Biology
Max-Planck-Institut für
Evolutionsbiologie
Heinrich-Heine Universitaet
Duesseldorf
LMU München
Institut für Informatik
Department of Evolutionary Biology
Laboratory for Zoology and Evolutionary
Biology
University of Konstanz
University of Dublin, Trinity
Smurfit Institute of Genetics
College
Instituto de Biologia Molecular e Celular Universidade do Porto
Wien
Austria
Aarhus
Helsinki
Denmark
Finland
Münster
Germany
Duesseldorf
Köln
Germany
Germany
Tübingen
Germany
Ploen
Germany
Duesseldorf
Planegg-Martinsried
Germany
Germany
Konstanz
Germany
Dublin 2
Porto
Ireland
Portugal
16
Center of Forest Research, INIA
Departament de Genètica
Dept of Ecology and Genetics,
Evolutionary Biology Centre
Institut d'Ecologie et d'Evolution
Laboratory of Anthropology, Genetics
and Peopling history
Institute of Plant Biology
Institute of Integrative Biology
Evolutionary Biology
Institute for Biodiversity and Ecosystem
Dynamics
Biology and Environmental Science
School of Animal and Microbial
Sciences
Department of Plant Sciences
Institute of Evolutionary Biology
Instituto Nacional de
Investigación y Tecnología
Agraria y Alimentaria
Universitat de Barcelona
Madrid
Barcelona
Spain
Spain
Uppsala University
Bern University
Uppsala
Bern
Sweden
Switzerland
Université de Genève
University of Zurich
ETH Zurich
Institute of Biology, Leiden
University
Genève 4
Zurich
Zurich
University of Amsterdam
University of Sussex
Amsterdam
Brighton
Switzerland
Switzerland
Switzerland
The
Netherlands
the
Netherlands
UK
University of Reading
University of Oxford
School of Biological Sciences
The University of Edinburgh
Reading
Oxford
UK
UK
Edinburgh
UK
Leiden
17
SUGGESTIONS DE DATES DE LA CONFERENCE:
DATES SUGGESTED FOR THE MEETING:
(Faire trois propositions réparties sur 3 mois différents - Make three propositions spread over three months)
1. Du samedi 5 au mercredi 9 mai 2012
2. Du mercredi 9 au dimanche 13 mai 2012
3. Du samedi 29 septembre au mercredi 3 octobre 2012
EXPOSE SUR LES THEMES DEVELOPPES AU COURS DE LA CONFERENCE (5 pages maximum)
ET MOTS-CLÉS (une dizaine environ)
DESCRIPTION OF THE TOPICS TO BE DEALT WITH DURING THE MEETING (5 pages maximum)
AND KEY WORDS (about 10)
Key words: Evolutionary genomics, population genomics, next generation sequencers,
molecular evolution, systems biology, experimental evolution, evolutionary inference,
ecological genomics, adaptive evolution, evolutionary novelties.
1. Background
Recent seminal advances in high-throughput sequencing technologies now empower
comparative molecular genetics approaches to an unprecedented degree. This technological
advance is about to revolutionize biology as a whole. However, taking full advantage of this
novel potential to understand genome organization and diversity requires the development of
a solid evolutionary scaffold, calling upon the theoretical and empirical expertise of
population geneticists and molecular evolutionists. The French scientific community of
evolutionary biologists has a strong reputation in these fields and several research groups
conduct high-level research in empirical evolutionary genomics. However, the speed at which
some countries are pushing forward the use of high-throughput sequencing technologies
makes the competition very strong. We propose to organize a Jacques Monod Conference that
will highlight the French expertise in this field, foster novel international collaborations as
well as trans-disciplinary exchanges with mathematicians and molecular geneticists, with the
aim of better understanding the processes of genome evolution.
The conference will be devoted to the presentation of theoretical and empirical advances in
the field of evolutionary genomics. Evolutionary genomics is a discipline that compares
whole genomes with the aim of describing the diversity of life, and deciphering the
evolutionary processes that shape functional and structural patterns of genomic organization.
Traditionally, evolutionary genomic studies are concentrated on inter-specific comparisons of
genomes. Although embedded within evolutionary genomics, population genomics focuses
specifically on the comparative analysis of multiple genomes within species. It is a discipline
devoted to characterizing the population genetic processes influencing genomic variation
between individuals and populations, and their adaptation to environmental stressors. The
disciplines of population and evolutionary genomics both combine theoretical and empirical
approaches, with the aim of describing patterns of genomic variation between individuals and
species, and of developing models of genomic evolution that integrate the effects of
evolutionary processes such as mutation, recombination, genetic drift, genetic exchange, and
natural selection.
18
The French community of population genomics is structured around a large GDR funded by
CNRS in 1999, GDR 1928 (http://gepv.univ-lille1.fr/GDR1928/acc.htm) "Génomique des
populations et génomique évolutive", that comprises 33 research teams with a wide diversity
of biological models (from microorganisms to plants and animals including humans) covering
a diversity of life histories (diversity of reproductive modes, of population structure, and of
function within ecosystems), and a diversity of approaches (bioinformatic and statistical
analyses of genomic data, modelling, experimental evolution approaches). The GDR
community experienced the release of the single genome projects in model organisms, and
their impact (in the so-called "post-genomic era") on evolutionary and population genomics.
The first Jacques Monod Conference on "Evolutionary Genomics" was organized in 2007 by
Michel Veuille, former director of this GDR, at a time of maturation of this post-genomic era,
and also at the time of flourishing of single genome projects in non-model organisms. The
conference was an immense success, with many leading scientists in the field present and
enjoying the conference set-up. It also acted as a boost for the French community with several
new research teams joining after the conference the activities of the GDR 1928.
Jacques Monod Conference on "Evolutionary Genomics" in 2007, Roscoff
2. Themes developed in the proposed programme
Since this CJM in 2007, evolutionary genomics and population genomics have witnessed a
tremendous development in relation to the technological revolution of sequencing approaches
(next generation sequencers), leading to the massive production of data from new genomes
(non-model organisms), but also from re-sequencing of whole genomes and transcriptomes.
The production, analyses and interpretation of these massive amounts of data constitute
major challenges to our scientific community, but also open new areas of theoretical and
experimental developments, in particular as trans-disciplinary projects with
mathematicians and molecular geneticists. We are convinced that the set-up of a new
Jacques Monod conference on evolutionary genomics and population genomics is timely, and
we have chosen five major topics in this field that are either emerging ones, or topics
that have experienced major developments since the previous CJM in 2007, and selected
invited speakers from the international leaders in these fields.
The first topic (session "Towards a fine-grained map of genetic variation in model
organisms") will examine the contribution made by genome-wide data to the field of
population genomics in model organisms. Over the last few years, our knowledge on the
allelic architecture of genomes, its different types of genomic diversity and the extent to
which such diversity varies at the population level has witnessed an exponential growth in a
handful of model organisms, including humans. Today, millions of single nucleotide
19
polymorphisms (SNPs) as well as copy number polymorphisms (CNPs) have been genotyped
in multiple human populations (eg HapMap Consortium Phase III). More recently, complete
human genomes of individuals from different ethnic backgrounds have been completed by
different laboratories, and the results of the pilot phase of the 1000 genomes project, designed
to develop and compare different strategies for genome-wide sequencing with highthroughput platforms, have been released. All these population genetics efforts are
contributing to the increased understanding of past human demography and adaptation and
encourage deeper interrogation of genomic variation and its role in human diseases. These
studies serve as a first step towards a high-resolution landscape of human genetic variation. In
plants, comparable steps have been made in Arabidopsis thaliana, and next-generation
sequencing technologies now allow the sequencing of genomes with single base resolution.
This session will therefore include contributions from several major model organisms in
genomics.
The second topic (session "Theoretical population genomics") is devoted to recent
developments in methods of evolutionary inference from molecular data. Indeed, the
development of molecular biology techniques in the last 20 years, has allowed increasing
tremendously the body of data available to study genetic polymorphisms at the population
level, leading to a new cross-disciplinary field between population genetics and genomics,
referred to as “population genomics”. Along with this burst of genomic data, the population
genetics “toolbox” has considerably improved in recent years, principally by means of the
increasing use of advanced statistical techniques relying on maximum-likelihood or Bayesian
approaches. These model-based and computationally demanding methods make a much better
use of the information contained in polymorphism data. They also allow the consideration of
complex demographic scenarios and the estimation of demographic parameters from genetic
polymorphism data. These methodological advances were made possible by the combination
of two major theoretical developments: (i) coalescent theory (Kingman 1982), which offers a
probabilistic model for gene genealogies under a large number of demographic models; (ii)
Monte Carlo methods such as importance sampling (IS), Monte Carlo Markov chains
(MCMC) and, more recently, approximate Bayesian computation methods (ABC). Although
quite successful, these two methodological approaches are currently being challenged by the
enormous quantities of data generated by Next Generation Sequencing techniques and a
renewed interest in making inferences about selection and local adaptation. In order to
address this new challenge, theoretical population geneticists have brought back to the fore
two somewhat old techniques, namely forward-in-time simulations and multivariate analysis.
The first one allows the consideration of a wider range of selection models than coalescent
simulations and can easily be incorporated into ABC approaches. The second provides a fast
and efficient exploration of huge data sets, something that MCMC-based techniques cannot
do. All these techniques, both old and new, in combination with NGS technologies, are
revolutionizing the field of genetic polymorphism data analyses and will continue do so for
many years to come.
The third topic (session "Evolutionary genomics") deals with the insight gained from
comparative genomic approaches in the study of processes of molecular evolution. Despite
the enormous, and rapidly increasing, size of publicly available genomic data sets, many
aspects relevant to the content and dynamics of genomes are still mysterious. The adaptive
impact of gene gain, gene loss and gene duplication, the relationship between gene expression
and evolution, the influence of selfish elements on genome dynamics, the role of
chromosomal rearrangements, of population size, of molecular drive, are still debated, and
sometimes controversial. We need to decipher the processes of molecular evolution, and
discriminate between the many evolutionary forces (mutation, selection, genetic drift,
20
recombination) that shape genomes in the long run. This is a prerequisite to correct
interpretation of genomic landscapes, and appropriate usage of genes and genomes for
functional purposes. This session will provide the opportunity to discuss these issues in
various taxonomic groups (plants, animals, bacteria), at distinct time scales (from withinspecies polymorphism up to LUCA), with the goal of reaching a synthesis of recent research
on this vast but central topic.
The fourth topic (session "Evolutionary systems biology ") concerns an emerging field at the
intersection between molecular and evolutionary genomics. The development of high
throughput technologies has shifted the analysis of the cellular machinery from a single gene
approach to that of integrated networks. The reconstruction of networks (protein-protein
interaction networks, regulation networks, metabolic networks,…) constitutes the primary
focus of the discipline called system biology; the goal being to build a comprehensive in
silico genotype to phenotype map. Yet, as the phenotype of an organism defines its fitness,
any such map is subject to the action of natural selection, therefore their present state informs
us about the past encountered evolutionary pressures. The phenotype to genotype map also
informs us about the evolvability of the organisms, or how it can face novel challenges.
Therefore a new "evolutionary system biology" approach has emerged in the recent years. It
focuses on network properties in terms of epistasis and robustness, as well as in term of
performance and optimization under selection. It seeks to make inferences on network
topological stability and conducts comparative analyses of networks across species.
Furthermore, this new discipline sets up artificial models to understand how observed
network properties emerge during evolution. The aim of this session will be to highlight the
diversity of these approaches, and how they can be used to understand genome evolution and
diversity within species.
The fifth topic (session "The ecological genetics of molecular systems controlling complex
phenotypes") will specifically highlight recent progress made in the elucidation of the
molecular basis of adaptive innovations in natural environment. In fact, patterns of nucleotide
variation within and between species are molded by the complex interaction of stochastic and
deterministic factors, and those can be transitory or pertain over extended periods of time.
This, in turn, creates complex signals that are difficult to ascertain. In many model species,
however, the take-off of genomic information has occurred along with the development of
efficient molecular and genetic tools that considerably accelerate the dissection of the
molecular basis of natural variation. In the last decades, the associated study of nucleotide
and functional variation has begun to unravel the molecular bases of an increasing number of
adaptive changes, covering aspects of development, life-history, morphology or behavior.
They combine population genetics inferences with molecular studies of functional variation.
Recently, the field performance of phenotypic variance has begun to be monitored, providing
novel insights into the role of environmental variation in shaping both phenotypic and
molecular evolution. This approach is beginning to be complemented by novel approaches in
ecological genomics, drawing the geographical landscape of species or eco-system variation.
This session will concentrate on the best characterized examples of adaptive molecular
changes and highlight the diversity of genomic settings in which molecular novelties find
ecological success. The goal of this session will be to contribute a novel and synthetic view
on the molecular processes by which complex phenotypes evolve to maximize fitness. For
this, it will bring together contributors from the fields of ecological genetics, molecular
genetics of natural variation and evolutionary genetics, who, by focusing on specific traits of
ecological relevance, make use of the wealth of genomic information and, in return,
illuminate our understanding of adaptation.
21
These sessions will contain both invited and contributed talks. They also will be
complemented by an "open session" that will only include contributed talks that cannot fit
into one of these selected topics. Additionally three speakers will be invited to give more
general presentations on selected topics in evolutionary genomics.
As a total there are 30 invited speakers (including the President and Vice-President), 8 of
which are female (27%), and 8 of which (27%) that attended to the previous conference (but
not all of them were speaker).
Other recent related congresses and Jacques Monod conferences
As stated above, a previous Jacques Monod conference on evolutionary genomics was
organized in 2007. This was headed by Michel VEUILLE, at that time director of the GDR
1928, and the Vice-President was Laurent EXCOFFIER, from Bern University (Switzerland).
At the end of the conference, Laurent EXCOFFIER was nominated as the President for a
forthcoming second edition of the conference, and Xavier VEKEMANS was nominated as
the Vice-President. For personal reasons, Laurent EXCOFFIER has recently declined the task
of organizing the second edition of the conference, but Juliette DE MEAUX, formerly group
leader at the Max Planck Institute of Cologne, but now Professor at the University of Münster
(Germany), has accepted to take the lead. As stated above, the field has grown considerably
in a few years, and the scientific challenges are important. As compared to the programme of
the previous Jacques Monod conference (with only 8 invited speakers that attended the
previous conference), the proposed programme is more ambitious in terms of the interdisciplinarity, with among others, invited specialists in systems biology.
The laboratory LBBE (UMR CNRS 5558) from Lyon (member of the GDR 1928) organized
the annual meeting of the Society for Molecular Biology and Evolution in July 2010. This
congress hosted more than 1000 participants and was a great success. The topics of
Evolutionary genomics and Population genomics were well represented in the organized
symposia, and this constituted a great opportunity to highlight the contribution of the French
community, and for the young French researchers to attend presentations from the leading
international teams. A Jacques Monod conference would be the opportunity to foster
discussions and collaborations with a selected set of top scientists in the field.
A Jacques Monod conference will hold in 2011 on the topic "Integrative ecological
genomics". This conference is willing to foster the link between the empirical molecular
biology and genomic community on one side, and the ecological community, on the other
side. In contrast our proposed conference is focusing on the link between theoretical and
empirical communities of molecular geneticists on one side, and the theoretical and empirical
communities of evolutionary biology, population genetics, and molecular evolution, on the
other side. These two conferences are clearly complementary.
22
PROJET DE PROGRAMME détaillé le plus possible, incluant au moins deux sessions de 'posters' et une
après-midi libre
DRAFT PROGRAMME detailed as much as possible, including at least two poster sessions and a free
afternoon
Day 1
15:30-20:00
19:00-20:00
Arrival, registration and poster installation
DINNER (Buffet)
Opening session
20:00-20:15
J DE MEAUX (Germany) and X VEKEMANS (F) Opening and welcome
20:15-21:00
I GORDO (Portugal)
keynote lecture 1
21:00-21:45
E HEYER (F)
keynote lecture 2
Day 2 POPULATION GENOMICS
Session 1 TOWARDS A FINE-GRAINED MAP OF GENETIC VARIATION IN MODEL ORGANISMS
09:00-09:30
C BUSTAMANTE (USA)
09:30-10:00
G Mc VEAN (UK)
10:00-10:30
D WEIGEL (Germany)
10:30-11:00
Coffee break
11:00-11:30
E EICHLER (USA)
11:30-12:00
L QUINTANA-MURCI (F)
12:00-12:15
contributed talk 1
12:15-12:30
contributed talk 2
12:30-12:45
contributed talk 3
12:45-13:00
general discussion
13:00-14:30
LUNCH
Session 2 THEORETICAL POPULATION GENOMICS
14:30-15:00
J NOVEMBRE (USA)
15:00-15:30
P DONNELLY (UK)
15:30-16:00
J DUTHEIL (F)
16:00-16:30
Coffee break
16:30-17:00
M. NORDBORG (Austria)
17:00-17:30
M BLUM (F)
17:30-17:45
contributed talk 1
17:45-18:00
contributed talk 2
18:00-18:15
contributed talk 3
18:15-18:30
general discussion
19:00-20:30
20:30-22:00
DINNER
POSTER SESSION 1
Day 3
Session 3 EVOLUTIONARY GENOMICS
09:00-09:30
D PETROV (USA)
09:30-10:00
A Mc LYSAGHT (Ireland)
10:00-10:30
E ROCHA (F)
10:30-11:00
Coffee break
11:00-11:30
H KAESSMANN (Switzerland)
11:30-12:00
S GLEMIN (F)
12:00-12:15
contributed talk 1
12:15-12:30
contributed talk 2
12:30-12:45
contributed talk 3
12:45-13:00
general discussion
13:00-15:00
15:00-
POSTER SESSION 2 and LUNCH (buffet froid)
BOAT TRIP
DINNER in local restaurants
23
Day 4 FROM MOLECULAR BIOLOGY TO POPULATION GENETICS
Session 4 EVOLUTIONARY SYSTEMS BIOLOGY
09:00-09:30
B PALSSON (USA)
09:30-10:00
B PAPP (Hungary)
10:00-10:30
O TENAILLON (F)
10:30-11:00
Coffee break
11:00-11:30
C LANDRY (Canada)
11:30-12:00
A CARBONE (F)
12:00-12:15
contributed talk 1
12:15-12:30
contributed talk 2
12:30-12:45
contributed talk 3
12:45-13:00
general discussion
13:00-14:30
LUNCH
Session 5 THE ECOLOGICAL GENETICS OF MOLECULAR SYSTEMS CONTROLLING
COMPLEX PHENOTYPES
14:30-15:00
15:00-15:30
15:30-16:00
16:00-17:30
17:30-18:00
18:00-18:30
18:30-18:45
18:45-19:00
19:00-19:15
19:15-19:30
T WITTKOPP (USA)
J DE MEAUX (Germany)
O LOUDET (F)
Coffee break and POSTER SESSION 3
J SCHMITT (USA)
P BELDADE (The Netherlands)
contributed talk 1
contributed talk 2
contributed talk 3
general discussion
20:00-
CONFERENCE DINNER
Day 5
09:00-09:40
09:40-10:10
10:10-10:30
10:30-11:00
L EXCOFFIER (Switzerland) keynote lecture 3
L DURET (F)
X VEKEMANS (F)
Coffee break
Session 6 OPEN SESSION
11:00-11:15
contributed talk 1
11:15-11:30
contributed talk 2
11:30-11:45
contributed talk 3
11:45-12:00
contributed talk 4
12:00-12:30
FINAL GENERAL DISCUSSION
24
BUDGET PREVISIONNEL ET CONCOURS FINANCIERS SOLLICITES
PROVISIONAL BUDGET AND FINANCIAL SUPPORTS SOLICITED
Voir également fichier excel attaché ("Budget Roscoff_Evolutionary Genomics.xlsx")
C.N.R.S. Conférence Jacques Monod
Theoretical and empirical advances in evolutionary
genomics
Roscoff - 2011
nombre de
personnes
nombre de
prestations
montant en
euros
- Non européens (entre 1000 et 1500 Euros)
8
---
1 200.00
9 600.00
- Européens (entre 500 et 750 euros)
11
---
600.00
6 600.00
- Français (entre 200 et 350 Euros)
11
---
240.00
2 640.00
Séjour des conférenciers invités
30
---
390.00
11 700.00
Séjour des participants sélectionnés
85
---
390.00
33 150.00
Pauses café
115
6
2.50
1 725.00
- salle de conférence (journée)
---
3
290.00
870.00
- salle de conférence (demi-journée)
---
1
190.00
190.00
- salle posters (journée)
---
3
100.00
300.00
- salle posters (demi-journée)
---
1
50.00
50.00
Transferts aéroport/gare - Roscoff
---
1
900.00
900.00
Annonces, reprographie
---
1
500.00
500.00
Excursion Ile de Batz
75
6.00
450.00
Recettes *
Dépenses
Voyage des conférenciers invités
Location de salles
Droits d'inscription des participants sélectionnés, incluant les frais
de séjour
- Etudiants en thèse
25
---
250.00
5 225.75
- Non étudiants (y compris post-docs)
475.00
23 829.43
60
---
Financements
- C.N.R.S. - INSB et INEE **
---
30 000.00
30 000.00
GDR CNRS 1928
---
5 000.00
4 180.60
SFB 680
---
2 500.00
2 090.30
Sponsors privés: Roche, Perkin Elmer,
Illumina
- indiquer le nom du sponsor
---
4 000.00
3 344.48
---
0.00
- indiquer le nom du sponsor
---
0.00
Total
68 670.57
68 675.00
25
Annex A: CV Juliette de MEAUX
Prof. Dr. Juliette de Meaux
Plant Molecular Evolution
Hüfferstr. 1
48149 Münster
e mail: [email protected]; [email protected]
Tel: +49(0)251 83 21 095
Current position
Since April 2010
Full Professor for Plant Molecular Evolution
University of Münster, Germany.
Research summary
Our research seeks to reconstruct the recent history of adaptive molecular variation in the weedy
annual and model plant species Arabidopsis thaliana. We are especially interested in the accurate
characterization of adaptively relevant variation. Our ultimate goal is to understand the molecular
basis of adaptation in plants. For this, we are taking both trait-specific and genomic approaches.
Our research seeks to reconstruct the recent history of adaptive molecular variation in the weedy
annual and model plant species Arabidopsis thaliana. We are especially interested in the accurate
characterization of adaptively relevant variation. This is the necessary path to illuminate our
understanding of the molecular basis of adaptation in plants.
We have begun with the assessment of the evolutionary history of various genes involved in traits of
proven or suspected adaptive relevance. This first approach proved very successful and we identified
a handful of loci with intriguing patterns of diversity. We are now in the process of elucidating the
details of functional and historical aspects of their evolution. We use a range of approaches and apply
the highest standards of both molecular and evolutionary biology (e.g. population genetics, candidate
gene analysis, association genetics, landscape genetics, transgenics, QTL mapping, Near-Isogenic
Lines (NILs), functional assays, fitness assays).
In addition to that, we are taking genomic approach to characterize the evolution of non-coding
regulatory DNA. We are analyzing patterns of both nucleotide and functional diversity throughout the
non-coding part of the genome.
Previous positions
September 2005- March 2010
Junior Research Group Leader
Population genetics & Evolution Group
Max Planck Institute of Plant Breeding Research, Cologne, Germany
February 2002 – August 2005
Max Planck Institute of Chemical Ecology, Jena, Germany
Postdoctoral research scientist; Advisor: Dr. T. Mitchell-Olds
26
Education
PhD in Plant Pathology (January 2002), University of Orsay and Institut National Agronomique, Paris,
France .Thesis: Molecular Polymorphism for resistance in wild populations of common bean,
Phaseolus vulgaris. Advisor: Prof. Claire Neema
University of Orsay and Ecole Normale Supérieure, Paris, France. Preparation for and admission to
the “Agrégation de Sciences Naturelles” (July 1998).
University of Lyon I Claude Bernard and University of Jussieu Paris VI, France.
Licence, maîtrise and DEA “Biology, Diversity and Adaptation of Cultivated Species” (Sept. 1997).
University of Lyon II Louis Lumière, France.
Licence « History of Art and Archeology » (June 1995).
Admission in the “Ecole Normale Supérieure in Lyon”(July 1993).
Scholarships and Funding
2010: Board member SPP1529 “Adaptomics” Funding Decision April 2010.
2010-2014: 235 200 Euro granted by DFG (Deutsche Forschungsgemeinschaft) within the framework
SFB680 The molecular basis of evolutionary innovations.
2006-2010: 235 200 Euro granted by DFG (Deutsche Forschungsgemeinschaft) within the framework
SFB680 The molecular basis of evolutionary innovations.
2002-2005: PostDoc Scholarship from the Max Planck Gesellschaft.
Fall 2001: Short term Assistant Professor Position in University of Orsay.
1998 – 2001: Allocation Couplée, Graduate and Teaching Assistant scholarship.
1993 – 1998: ENS funded student.
PhD Advisor
Marilyne Debieu, Comprehensive analysis of life-cycle variation in Arabidopsis thaliana at phenotypic
and genomic levels. Jan. 2006 - March 2010
Madlen Vetter, Evolution of flagellin perception in Arabidopsis thaliana and its relatives, Jan. 2007June 2010
Ilkka Kronholm, Genetics of local adaptation in Arabidopsis thaliana – seed dormancy as a case
study. Oct. 2006 - June 2010
Selected peer reviewed publications
Arabidopsis thaliana Leaf Form Evolved via Loss of KNOX Expression in Leaves in Association with a
Selective Sweep. P. Piazza, C. D. Bailey, M. Cartolano, J. Krieger, J. Cao, S. Ossowski, K.
Schneeberger, F. He, J. de Meaux, N. Hall, N. MacLeod, D. Filatov, A. Hay and M. Tsiantis (2010).
Current Biology 20, 1–6, DOI 10.1016/j.cub.2010.11.037
Natural variation at Strubbelig Receptor Kinase 3 drives immune triggered incompatibilities between
A. thaliana accessions. R. Alcázar, A. V. García, I. Kronholm, J. de Meaux, M. Koornneef, J. E. Parker
and M. Reymond (2010). Nature Genetics 42, 1135–1139.
Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred
lines. S. Atwell, Y. Huang, B. Vilhj´almsson, G. Willems, M. Horton, D. Meng, A. Platt, A. Tarone, R.
Jiang, Y. Li, W. Muliati, M. Ali Amer, I. Baxter, B. Brachi, Joanne Chory, Caroline Dean, Marilyne
Debieu, J.de Meaux, J. Ecker, N. Faure, J. Iskern, J. D. G. Jones, T. Michael, A. Nemri, F. Roux, D.
27
Salt, C. Tang, B. Traw, D. Weigel, J. Borevitz, J. Bergelson, M. Nordborg. Nature, 2010 Vol. 465
(7298): 627:631
Adaptation at different rates of environmental change. S. Collins and J. de Meaux, (2009) Evolution,
63 (11) : 2952-2965.
Structurally different alleles of the ath- MIR824 microRNA precursor are maintained at high frequency
in Arabidopsis thaliana. J. de Meaux, J.Y. Hu, U. Tartler and U. Goebel (2008) Proc. Nat. Acad.
Sci.105(26): 8994–8999 .
Evolution of Chalcone Synthase cis-regulation in genus Arabidopsis. J. de Meaux, A. Pop and T.
Mitchell-Olds (2006) Genetics, 174 (4): 2181-2202.
Allele-specific assay reveals functional variation in the Arabidopsis thaliana chalcone synthase
promoter region that is compatible with neutral evolution. J. de Meaux, U Goebel, A. Pop and T.
Mitchell-Olds. (2005) Plant Cell ,17, 676-690.
Invited seminars
Asymmetric distribution of cis-regulatory differences between Arabidopsis genomes, Arabidopsis trinational meeting, Salzburg, Austria, Sept. 2010.
Cis-regulatory (epi) divergence between Arabidopsis specie, EED 2010, Paris France, July 2010.
Maintenance of Allelic Polymorphism in miRNA824 processing, ENS Ulm, Paris, France, June 2010.
Maintenance of Allelic Polymorphism in miRNA824 processing, 2nd Moscow International Meeting on
Molecular Phylogenetics, Russia, May 2010.
Molecular underpinnings of life-history evolution in Arabidopsis thaliana, Duke University, NC, USA,
March 2010.
Molecular underpinnings of life-history evolution in Arabidopsis thaliana, Brown University, RI, USA,
March 2010.
Natural variation in the light of evolution: Adaptation in Arabidopsis thaliana, University of Toronto,
Canada, March 2010.
Functional evolution in Arabidopsis thaliana, University of Chicago, Il USA, March 2010.
Molecular underpinnings of life-history evolution in Arabidopsis thaliana, University of Jena, Germany,
Jan. 2010.
Polymorphism at the miR824 precursor: cause and consequences of a balanced polymorphism, Paris,
France Nov. 2009.
Molecular underpinnings of life-history evolution in Arabidopsis thaliana, Versailles, France, Oct. 2009.
Molecular underpinnings of life-history evolution in Arabidopsis thaliana, Zürich, Switzerland, Sept.
2009.
Evolution of flagellin sensing in Arabidopsis thaliana and its relatives, Obergurgl, Austria, ESF
Conference, April 2009.
Regulatory evolution and adaptation in Arabidopsis thaliana, University of Lausanne, Switzerland,
May. 2009.
Regulatory evolution in Arabidopsis thaliana and its relatives. University of Muenster, Germany. Jan.
2009.
Uppsala University, Uppsala, Sweden. Polymorphisms of ecological relevance: seed dormancy in
Arabidopsis thaliana. Dec. 2007.
University of Barcelona, Spain. Nucleotide and structural variation at miRNA-encoding loci in
Arabidopsis thaliana. Nov. 2007.
28
Institut Jean Claude Bourgin INRA Versailles, France. Molecular basis of genetic adaptation in
Arabidopsis thaliana. April 2007.
Max Planck Institute for Developmental Biology, Tübingen, Germany. The molecular basis of genetic
adaptation in Arabidopsis thaliana: Ongoing research projects. April 2007.
VIB Ghent, Belgium. Ongoing research projects investigating the molecular basis of genetic
adaptation in Arabidopsis thaliana.Feb. 2007.
Language skills
French: mother tongue
English, Spanish and German: written and spoken
Italian: spoken
Personal data
Date of birth: Feb. 28th 1974
Family status: Married – Three children
Hobbies: Cinema, Piano, Literature
29
Annex B: CV Xavier VEKEMANS
I. General information
Born in 1963 at Antwerpen, Belgium.
Father of 3 children
Tél.: 03 20 43 67 53; Fax. : 03 20 43 69 79
Mail: [email protected]
II. Current functions
Professeur 1ère classe, Université Lille 1
Laboratoire de Génétique et Evolution des Populations Végétales (GEPV) FRE CNRS 3268
Directeur GDR CNRS 1928, Génomique des populations et génomique évolutive
III. Previous positions
1994-2002
Assistant Professor, Faculté des Sciences, Université Libre de Bruxelles, Belgium.
1992-1994
Postdoctoral research, University of California, Berkeley, Department of Integrative
Biology, Advisor: Prof. M. Slatkin.
IV. Education
1987-1992
PhD Sciences Agronomiques, Université Libre de Bruxelles, Belgium
1982-1986
Master in Agronomy, Université Libre de Bruxelles, Belgium
V. Research summary
I am an evolutionary biologist and my overall field of research is plant population genetics and
genomics and their applications to conservation biology. I have been mostly involved in the study of
evolutionary implications of mating systems in plants and of the effect of gene dispersal in plants on
spatial genetic structure. My research projects involved both theoretical modelling, mostly using
numerical simulations, and empirical investigations using genetic markers and nucleotide sequences.
Recently I focused my research projects on the population genetics and molecular evolution of the
self-incompatibility system in Arabidopsis halleri, a close relative to A. thaliana. Me and my
collaborators have been investigating the signature of balancing selection on the self-incompatibility
locus at different levels: (1) within a population between successive generations; (2) among
populations; (3) among closely related species; (4) at the nucleotide sequence level looking at patterns
of nucleotide diversity across the gene; and (5) at the genomic level looking at hitchhiking effects on
nearby genes. Currently we are investigating the genomic structure and diversity in the nonrecombining region flanking the self-incompatibility locus, which shows properties similar to Y
chromosomes. I am also involved in population genomic studies aiming at inferring the historical
context of the speciation between A. halleri and A. lyrata , specifically testing the hypothesis of a role
of adaptation to heavy-metal tolerance in A. halleri in the speciation process.
VI. Selected peer reviewed publications (since 2008)
Vekemans X. 2010. What's good for you may be good for me: evidence for adaptive introgression of
multiple traits in plants. New Phytologist, 187: 6-9.
V. Castric, J. Bechsgaard, R. Nourredine, S. Grenier, MH Schierup, & X. Vekemans, 2010 :
"Intrahaplotype polymorphism reveals intragenic recombination at a sporophytic selfincompatibility locus", Molecular Biology and Evolution, 27: 11-20.
V. Llaurens, S. Billiard, V. Castric & X. Vekemans, 2009 Evolution of dominance in sporophytic
self-incompatibility systems: I. Genetic load and co-evolution of levels of dominance in pollen and
pistil", Evolution, 63: 2427-37.
V. Castric, J. Bechsgaard, MH. Schierup & X. Vekemans, 2008 : "Repeated adaptive introgression at
a gene under multiallelic balancing selection", Plos Genetics, 4(8): e1000168.
30
M. Hasselmann, X. Vekemans, J. Pflugfelder, N. Koeniger, G. Koeniger, S. Tingek & M. Beye, 2008:
"Evidence for convergent nucleotide evolution and high allelic turnover rates at the complementary
sex determiner (csd) gene of western and Asian honey bees". Molecular Biology and Evolution,
25:696-708.
M.H. Schierup & X. Vekemans, 2008: "Genomic consequences of selection on self-incompatibility
genes". Current Opinion in Plant Biology, 11:116-122.
M.V. Ruggiero, B. Jacquemin, V. Castric & X. Vekemans, 2008: "Hitch-hiking to a locus under
balancing selection: high sequence diversity and low population subdivision at the S-locus
genomic region in Arabidopsis halleri". Genetics Research, 90: 37-46.
VII. Invited seminars (since 2008)
June 2010: Oxford University, Department of Plant Sciences (UK). Seminar on "Population
genomics of the sister species Arabidopsis halleri and A. lyrata: signature of selection in the S-locus
region and evolution of heavy-metal tolerance".
February 2010: ETH Zurich, Institute of Integrative Biology (Switzerland). Seminar on "Patterns of
genetic structure among populations and species in the self-incompatibility locus genomic region in
the genus Arabidopsis".
February 2010: Institute Gregor Mendel, Vienna, Austria. Seminar on "Genomic signature of strong
balancing selection in the self-incompatibility (S-locus) region in the genus Arabidopsis".
May 2009: ESF Congen meeting in Trondheim (Norway). Seminar on "The conservation genetics
of self-incompatible plant species: assessing the S-Allee effect in Biscutella neustriaca".
March 2008: Laboratoire Evolution, Génomes et Spéciation, CNRS, Gif-sur-Yvette. Seminar
entitled: "Différenciation interspécifique dans une région génomique soumise à sélection balancée:
exemple du locus d'auto-incompatibilité dans le genre Arabidopsis".
VIII. Scholarships and Funding
2007-2010: ANR Programme Blanc, as a Principal Investigator, project SELMULTILOC " The
effect of selection at multiple loci on molecular polymorphism within a chromosomal region" (130
k€ ).
2007-2010: ANR Programme Biodiversité, project TRANSBIODIV, coordinatrice Marie-Louise
Cariou, CNRS Gif-sur-Yvette, intitulé: "Neutral and functional trans-specific biodiversity" (170
k€)
2007-2008: CNRS ATIP-Plus, Départements Sciences du Vivant et EDD. (30 k€).
2006-2007: Engagement du Génoscope pour séquençage de 23 Mb (13 clones BAC de 150 kb avec
un recouvrement de 12x). Intitulé du projet: " How did the transition to selfing in Arabidopsis
thaliana affect the local genomic environment of the self-incompatibility locus ?". Porteur du
projet: V. Castric.
2003-2005: ARCir grant "Emerging teams" from Région Nord-Pas de Calais :"Impact de la sélection
naturelle sur le polymorphisme moléculaire et les interactions génomiques chez les végétaux :
étude du locus d’auto-incompatibilité chez Arabidopsis halleri et de son influence sur le
polymorphisme moléculaire aux régions chromosomiques voisines". (153 k€).
2003-2006. ATIP grant, CNRS, Project " Evolution des locus d'auto-incompatibilité chez les
végétaux supérieurs aux échelles macro et micro-évolutives: Arabidopsis halleri comme espèce
modèle à auto-incompatibilité sporophytique". (135 k€).
IX. PhD Advisor
31
Camille Roux, "Effets de la sélection naturelle et de l'histoire démographique sur les patrons de
polymorphisme nucléaire - Comparaisons interspécifiques chez Arabidopsis halleri et A. lyrata
entre le fond génomique et deux régions cibles de la sélection" defended in December 2010
Jean-Baptiste Leducq, "Système de reproduction, dispersion et succès reproducteurs chez une espèce
végétale menacée - exemple de Biscutella neustriaca (Brassicaceae), une espèce autoincompatible et micro endémique", defended in January 2010
Violaine Llaurens, " Mise en évidence des forces évolutives agissant au locus d'auto-incompatibilité
chez Arabidopsis halleri ", defended in December 2008
Four other PhD theses at Université Libre de Bruxelles (1997-2003)
X. Referee
Foreign research agencies: FWF Austria (2009); SATW, Switzerland (2009); FWO, Flanders-B
(2004, 2005, 2009); SNSF, Switzerland (2008); Leverhulme Trust, UK (2003); IBMC, Universidade
do Porto (2009); University of Minnesota (2008)
French research agencies: ANR Blanc (2009, 2010); ANR Jeunes Chercheurs (2006, 2010); ANR
6ème extinction (2009); ANR OGM (2005); ANR BIOSYS (2006); INRA EFPA, projets innovants
(2010); INRA DARESE - création jeune équipe (2009); Ministère de l'Enseignement Supérieur et de
la Recherche, primes PES (2009, 2010); EPHE (2009, 2010); AERES (2010); …
PhD thesis jurys: 51 thesis jurys among which 20 as "rapporteur"
HDR jurys: 17 HDR jurys among which 14 as "rapporteur"
XI. Scientific Societies
Member of the SMBE (Society of Molecular Biology and Evolution) and of the ESEB (European
Society of Evolutionary Biology; member of the scientific board of ESEB from 2001 to 2005 and
Executive Vice-President of ESEB from 2005 to 2007).
32

PROPOSITION POUR L`ORGANISATION D`UNE

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