Alan Moses' Computational Biology Lab

Annabelle Haudry

Postdoctoral fellow

Department of Ecology and Evolutionary Biology
University of Toronto
25 Willcocks Street
Toronto, M5S 3B2, Ontario, Canada
Phone: +1 416 978-5563

Research Interests

I am a Postdoctoral Fellow at the University of Toronto, working with Alan Moses and Stephen Wright on a project of molecular evolution in Brassicaceae.

I am a plant evolutionary geneticist, particularly interested in questions such as how neutral forces and natural selection are interacting to drive gene and genome evolution and population diversity patterns. I am really interested in how identifying these interactions at the molecular level and how interpret DNA sequence signatures in regards of population or species evolutionary history.

Key words: domestication, mating system, recombination, GC content, polymorphism, selection, demography, biased gene conversion, regulatory sequences.

My personal area of expertise is the use of population genetics and molecular evolution theories to test competing evolutionary hypotheses in order to explain the observed pattern of genetic diversity in empirical data. For this purpose, I've developed bioinformatics skills in complement to by evolutionary biology background. So far, I investigated demographic and selective impact in association with the domestication of wheat (Haudry et al. 2007, Berard et al. 2009) and genomic consequences of the shift to selfing (Haudry et al. 2008, Escobar et al. 2010, Foxe et al. 2010 and few others coming soon).

During my phD, I studied how molecular evolution was affected by variations in effective population size due to demographic and selective events in the plant family of the Triticeae. First, I found evidence for strong bottlenecks associated with the domestication of wheat: genetic diversity of cultivated forms was 3 to 6 times lower compared to the wild ancestors. Second, my results revealed that a neutral process associated with recombination enriched the genome in GC content and reduced selection efficiency in outcrossing plants.

At the University of Glasgow, I worked on the evolutionary history of natural populations of North American Arabidopsis lyrata. Breakdown of self-incompatibility and both selfing and outcrossing mating systems have been found in these populations. I worked in the genetic characterisation of their genetic diversity, structuration and estimated respective impact of (i) the breakdown of self-incompatibility and (ii) the shift to selfing on their genetic variation. I am currently using coalescence simulations to explore possible evolutionary models in order to estimate the parameters describing demographic, reproductive and selective events associated with their colonization.

At the University of Toronto, I'm working on a project of comparative genomics of six species of Brassicaceae. Part of the project consist in investigating the evolution of the selective patterns of regulatory sequences as it's now recognized that gene expression is a major determinant of the functioning of organizations and an important substrate for evolution. This work sould provide a new light on the evolution of noncoding sequences and their role in the transitions of mating systems.

Short CV

2010-present     Postdoctoral Fellow at the University of Toronto (Canada) in Alan Moses and in Stephen Wright's lab, Department of Ecology and Evolutionary Biology. Evolution of Regulatory Sequences in Brassicaceae.
2008-2010            Postdoctoral Fellow at the University of Glasgow (UK) in Barbara Mable's lab, Division of Ecology & Evolutionary Biology. Evolution of Self-incompatibility in Brassicaceae.
2007-2008            Postdoctoral Research and Teaching Assistant of Biology at the University of Montpellier II, Department of Biology and Ecology.
2004-2008            PhD. How domestication and mating system affect diversity and molecular evolution in Triticeae species? Pr Jacques David and Dr Sylvain Glémin.
    2004                   Research postgraduate degree Ressources Phytogénétiques et Interactions biologiques at the University of Montpellier. Sequence polymorphism sheds light on wheat domestication. Pr Jacques David.
    2003                   Master degree in Population and Ecosystem Biology at the University of Montpellier.
                                Genetic diversity in a wild population of Manihot esculenta. Pr Doyle Mc Key.
                                Genetic variability and structure in Santalum insulare. Dr Jean-Marc Bouvet .


                                Haudry A, Zha HG, Stift M, Mable BK. Disentangling the effects of breakdown of self-incompatibility and transition to selfing in North-American Arabidopsis lyrata. In press in Molecular Evolution.
    2010                   Foxe JP, Stift M, Tedder A, Haudry A, Wright SI, Mable BK. Reconstructing origins of loss of self-incompatibility and selfing in North American Arabidopsis lyrata: a population genetic context. Evolution. 64 (12): 3495-3510. pdf
                                Escobar JS, Cenci A, Bolognini J, Haudry A, Laurent S, David JL, Glémin S. An integrative test of the dead-end hypothesis of selfing evolution in Triticeae (Poaceae). Evolution. 64 (10): 2855-2872. pdf
    2009                   Bérard A, Le Paslier M-C, Dardevet M, Exbrayat-Vinson F, Bonnin I, Cenci A, Haudry A, Brunel D, Ravel C. High throughput SNP genotyping in wheat (Triticum spp.). Plant Biotechnol J. 7(4):364-374. pdf
    2008                   Haudry A, Cenci A, Guilhaumon C, Paux E, Poirier S, Santoni S, David J, Glémin S. Mating system and recombination affect molecular evolution in four Triticeae species. Genet. Res. 90:97-109. pdf
    2007                   Haudry A, Cenci A, Ravel C, Bataillon T, Brunel D, Poncet C, Hochu I, Poirier S, Santoni S, Glémin S, David J. Grinding up wheat: a massive loss of nucleotide diversity since domestication. Mol. Biol. Evol. 24:1506-1517. pdf
                                Haudry A.PhD thesis. Influence de la domestication et du système de reproduction sur la diversité et l`évolution des genes chez les Triticeae. PhD thesis Université Montpellier II Sciences et Techniques du Languedoc. pdf
    2006                   Bataillon T, Chantret N, Cenci A, Gautier M-F, Joudrier P, Haudry A, Muller M-H, Poncet C, Prosperi J-M, Ronfort J, Roumet P, Santoni S, Thuillet A-C, David J. Impacts d'événements démographiques et sélectifs sur la diversité des plantes cultivées : apports de l'analyse du polymorphisme allié à la théorie de la coalescence. Les actes du BRG vol.6, p. 243-257. pdf
                                Seguin M, Attard A, Bataillon T, Billot C, Cenci A, Chantret N, Courtois B, David J, Deu M, El Azhari N, Glaszmann JC, Glemin S, Haudry A, Le Guen V, Maynadier M, Pomies V, Ronfort J, Tsitrone A, Weber C. Analyse et prédiction des patrons de déséquilibre de liaison dans les collections de ressources génétiques de plantes pérennes ou annuelles, autogames ou allogames. Les actes du BRG vol.6, p. 57-74. pdf

Grants and Fellowships

    2010                   BBSRC ISIS grant to visit Stephen Wright at the University of Toronto (4 months): £3,100.
    2009                   Scottish Bioinformatics Forum Sponsorship (SBF): £2,600.
                                Ecology and Evolutionary Biology Research Theme (University of Glasgow): £1,000.
                                Roberts funding award (University of Glasgow): £500.
    2008                   Roberts funding award (University of Glasgow): £420.
    2004                   PhD Fellowship from the Ministry of Research (MRT): €43,200.
                                Competitively awarded PhD teaching funding from CIES Montpellier: €16,500.


2009-2010            Teaching Assistant in Perl workshop at the University of Glasgow: see details of the course on the BioPhyloPop Group webpage .
                                Lecture in Meeting on Mathematical Modelling at the University of Glasgow on Gene Genealogies & Coalescence Theory: see presentation .
                                Computer lab on DNA sequences analysis and detection of selection at the University of Glasgow.
2007-2008            Postdoctoral Teaching Assistant at the University of Montpellier II
                                Biology and Genetics 80 hours (bachelor deree)
                                Plant biology 33 hours (bachelor degree)
2004-2007            PhD Teaching Assistant at the University of Montpellier II
                                Plant biology 125 hours (bachelor degree)
                                Molecular Biology and Evolution 59 hours (bachelor and master degrees)
                                Population Genetics 47 hours (master degree)
                                Genetics 42 hours (bachelor degree)
                                Biostatistics 3 hours (master degree)

When I`m not in front of my computer, I love...

  walking around in Toronto (Kensington market, China town, Korea town, Queen street, Toronto Island...)
  travelling (Caribbean Islands, Europe, Philippines, La reunion, Canada)
  diving (PADI Advanced Open Water Diver)
  photography see a sample of my shots.

Alan Moses' Lab, Copyright 2009.