Permanent staff

Current research

I am currently developing my own research on the population genomics of transposable elements, and the application of population genomics tools to conservation. I am currently working on the date palm (Phoenix dactylifera), a keystone crop of oasis agrosystems.

I recently obtained funding from the French National Research Agency (ANR) and will soon recruit a PhD student (September 2024) and a post-doctoral researcher (starting January 2025). I am also looking for a Masters student starting in January 2024 (with the option to continue for a PhD). Contact me (yann.bourgeois@ird.fr) if interested! Below is a summary of the ANR project:

The interaction between transposable elements (TEs) and their hosts is one of the most intricate co-evolutionary processes found in nature. Quantifying how TEs impact their host's fitness has practical relevance in relation to real-world applications, such as understanding the molecular bases of selected phenotypes, or assessing mutational load in crops (so-called "cost of domestication"). The following project will focus on the impact of TEs on the host's fitness, using the date palm (Phoenix dactylifera) as a model. This crop is of major economic and social importance in the Middle East and Northern Africa, and its consumption keeps rising every year. However, it is also threatened by more frequent droughts and increasing salinity due to climate change. A precise characterization of its genetic diversity is therefore essential to understand the adaptability of this species to growing environmental pressures. The project will use genomic data to examine the role of polymorphic TEs in selection and differentiation of date palm varieties across the species range. It will revolve around two questions: What is the distribution of TEs fitness effects in date palms? Can this distribution be predicted from functional genomic features such as gene regulatory networks? We will develop and apply new methods in population genomics to estimate the fraction of advantageous and harmful polymorphic TEs. We will compare results with de novo functional annotations of chromatin organization and regulatory networks to draw a comprehensive view of TEs' impact on a keystone perennial species of agronomic interest for both developed and developing countries.

Past research

I am a molecular ecologist/evolutionary biologist/population geneticist, interested in understanding how selection acts on polymorphism and speciation in natural populations, by combining genetics and genomics with the study of environmental variations and ecology. My thesis in Toulouse dealt with the genetic bases of color variations in an endemic bird from Réunion island, Zosterops borbonicus. I used multiple approaches such as classical population genetics, candidate genes studies, RAD-sequencing, but also GIS and niche modelling. After a post-doc in Dieter Ebert's team at Basel University my interests now include the genetics of host-parasite interactions. I also collaborated on various projects such as the study of evolutionary radiations on archipelagoes in Tetragnatha spiders, museomics of Crowned pigeons from New Guinea (Goura), or evolution of the Foudia genus in the Mascarenes.