Theoretical Biology¶
I was recruited in 2018 at the Laboratoire Génome et Développement des Plantes (LGDP, UMR-5096, UPVD/CNRS/IRD, Perpignan) to develop interdisciplinary research about population dynamics including a genomic aspects within the team of Theoretical Biology.
Transposable Elements¶
Genomes are primarily composed of genes and transposable elements (TEs), often referred to as jumping genes. TEs have the ability to move or replicate within the genome. Once regarded as genomic parasites of little interest or even as harmful components, it is now well established that their insertions can play important roles in genome function and evolution. The team has developed a theoretical model to describe TE dynamics under asexual reproduction by fixing dsitribution of TEs in population of genomes [FLO20]. I developped an agent-based model to explore how TEs evolve in populations reproducing asexually by fitting their distributions [ROS25a]. Unlike classical population genetics models, which predict rapid elimination of TEs or host extinction, our models reveal that TE populations can persist over long timescales when host genomes show high variability in TE content. Importantly, TE silencing further enhances this persistence. These results provide theoretical insights consistent with empirical observations in bdelloid rotifers, offering a new perspective on the long-term dynamics of selfish genetic elements.
Parasites of chestnut trees¶
My research also focuses on the infestation of chestnut trees by the gall wasp (Dryocosmus kuriphilus, Hymenoptera). I designed a novel methodology based on graph analysis to identify both vulnerable and high-risk areas within forests, using the spatial distribution of chestnut trees as a predictor [ROS25b]. Understanding how trees are distributed across the landscape provides a valuable tool to anticipate potential invasions and to design more effective management strategies.
References
Flores-Ferrer, A. et al. The ecology of the genome and the dynamics of the biological dark matter. Journal of Theoretical Biology 518, 110641 (2021).
Rosalie, M., El Baidouri, M. & Gourbière, S. Modelling the dynamics of transposable elements in genomes under asexual reproduction using agent-based model. bioRxiv (2025). doi:10.1101/2025.09.28.679026. Algorithms implemented in python are available on GitHub and plots, data and video are available on Zenodo
Rosalie, M., Zitoun, J.-L., Casteigts, A. & Gourbière, S. Modelling parasite invasion with graph: Dryocosmus kuriphilus a threat for Castanea sativa. HAL preprint (2025). https://hal.science/hal-05267084v1. Code, data and plots are available on Zenodo