Modeling the Amplification of Transposable Elements During Geographic Expansions
Scientific Context
Transposable elements are DNA sequences found in the genomes of nearly all living organisms, capable of moving and multiplying within the genome. Often regarded as genomic parasites, transposable elements are mutagenic and their activity is likely costly; however, they may also give rise to genetic variants that are potentially useful for adaptation. Transposable elements are highly diverse, and their number varies greatly across genomes. The reasons behind their unequal distribution among species are poorly understood; they likely involve differences in the mechanisms regulating transposition, but also the recent history—and particularly the demography—of different species.
Species’ ranges change over time. Invasive alien species, such as the tiger mosquito or the Asian hornet, which were unknown in our regions until recently, are striking examples. However, it is now well known that most of the flora and fauna surrounding us have also undergone considerable changes in distribution in the recent past: during the last glacial maximum, most temperate European species were confined to the southern peninsulas of the continent. From these glacial refuges, they recolonized northern Europe as the climate warmed (from around 15,000 years ago), undergoing significant geographic expansions.
Geographic expansions are characterized by particular demographic patterns: successive bottlenecks (sharp reductions in population size) occur at the expansion front. These bottlenecks lead to strong genetic drift, which may promote the proliferation of deleterious mutations and thus of transposable elements within frontier populations. Colonizing new habitats also requires genetic adaptation, potentially involving the rapid fixation of new variants. These conditions also seem favorable for the accumulation of transposable elements; however, there are currently no formal models in population genetics and genomics that provide a solid theoretical foundation for this hypothesis.
Objectives
The goal of this internship is to study, using numerical simulations, the process of accumulation of transposable elements in the colonization wave of a species undergoing geographic expansion. The project is based on an already available individual-based simulation software, which will be used in an explicitly spatial context where available habitats are gradually colonized by migrants from already established populations. The internship will address the following questions: do the simulations confirm an increase in the number of transposable element copies at the range margin? What are the effects of the model parameters (transposition rate, migration rate, population size) on this accumulation? Over what time span and geographic distance can this accumulation be detected?
Profile
We are looking for a student with a strong background in population genetics and genomics, with an interest in theoretical questions. As the simulation software (C++) is already available, the internship will not involve software development per se, although code adaptation or optimization may be considered. Proficiency with computational tools (R / Python / Unix) will be appreciated. The internship will last for 6 months, ideally from January to June 2026.
Host Laboratories
The internship will be co-supervised by Arnaud Le Rouzic (Research Scientist, CNRS, EGCE, IDEEV, Université Paris-Saclay) and Matthieu Boulesteix (Lecturer, Université Lyon I). The student may be based either in Gif-sur-Yvette or in Lyon.
Contact:
Arnaud Le Rouzic, arnaud.le-rouzic@universite-paris-saclay.fr
Matthieu Boulesteix, matthieu.boulesteix@univ-lyon1.fr
Literature
On the topic:
Dolgin, E. S., & Charlesworth, B. (2008). The effects of recombination rate on the distribution and abundance of transposable elements. Genetics, 178(4), 2169-2177.
Excoffier, L., & Ray, N. (2008). Surfing during population expansions promotes genetic revolutions and structuration. Trends in ecology & evolution, 23(7), 347-351.
Hallatschek, O., & Nelson, D. R. (2008). Gene surfing in expanding populations. Theoretical population biology, 73(1), 158-170.
Peischl, S., Dupanloup, I., Kirkpatrick, M., & Excoffier, L. (2013). On the accumulation of deleterious mutations during range expansions. Molecular Ecology, 22(24), 5972-5982. https://doi.org/10.1111/mec.12524
From the host labs:
Le Rouzic, A., & Capy, P. (2005). The first steps of transposable elements invasion: parasitic strategy vs. genetic drift. Genetics, 169(2), 1033-1043.
Mérel, V., Gibert, P., Buch, I., Rodriguez Rada, V., Estoup, A., Gautier, M., Fablet, M., Boulesteix, M., & Vieira, C. (2021). The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions. Molecular biology and evolution, 38(10), 4252-4267.
Tomar, S. S., Hua-Van, A., & Le Rouzic, A. (2023). A population genetics theory for piRNA-regulated transposable elements. Theoretical Population Biology, 150, 1-13.
Le Rouzic, A., & Hua-Van, A. (2024). Genome Invasion Dynamics. Transposable Elements and Genome Evolution, 175-191.