UMR CNRS 5558 - LBBE "Biométrie et Biologie Évolutive" UCB Lyon 1 - Bât. Grégor Mendel 43 bd du 11 novembre 1918 69622 VILLEURBANNE cedex
- Research interests I am an 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. 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). 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 used coalescence simulations to explore possible evolutionary models in order to estimate the parameters describing demographic, reproductive and selective events associated with their colonization (Haudry et al. 2011). At the University of Toronto, I worked on a project of comparative genomics of nine Brassicaceae species. Part of the project consisted 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 (Haudry et al. in prep.). Using both interspecific conservation across orthologous bases and intraspecific polymorphism distribution, we found that at least 17% of the Arabidopsis thaliana genome is under selection, with nearly one-quarter of the sequence under selection lying outside of coding regions (in over 90,000 identified conserved noncoding sequences). Overall, this study highlight both similarities and several key differences between the regulatory DNA of plants and other species (Haudry et al. 2013). Since I am working in Lyon, I developped new projects in regards with genome size evolution and transposable elements dynamics (See current projects and job opportunities).
- Projets de Recherche
- For prospective students and postdocs
Whether I advertise an open position below or not, I always welcome enquiries about possible research projects, from students and postdocs alike. There are always interesting things to do, so please do not hesitate to send me an email with your research interest and current situation.