Évolution des Génomes, des populations et des espèces : données et Modèles

Modeling the impact of facultative reproduction on genome composition

SCIENTIFIC CONTEXT

GC-biased gene conversion (gBGC) is a recombination-associated mechanism that favors the
transmission of G and C bases over A and T bases. It can be measured in obligately sexual species, but
also in facultatively sexual species such as yeast, where it has been detected at recombination
hotspots. In all cases, gBGC leaves a genomic footprint that resembles that of positive selection in
favor of G/C bases.
However, its role in the long-term evolution of genomes in facultatively sexual species is still poorly
understood, and it remains unclear whether facultative reproduction tends to reinforce or, on the
contrary, limit its genomic impact.
This internship is part of the ANR RECAF project, which investigates the effect of facultative
reproduction on genome composition. A postdoctoral researcher in the project is studying purifying
selection in this context; the intern will in parallel develop the part dedicated to gBGC.

RESEARCH PROPOSAL/OBJECTIVES

The intern will set up population genetics simulations to explore how the frequency of sexual
reproduction (α) influences the strength and efficiency of gBGC.

• Assess whether a lower frequency of sexual reproduction reduces or alters its evolutionary
  impact,
• Consolidate knowledge in population genetics,
• Prepare the transition to the PhD, where a dedicated mathematical model will be developed
  and compared with both simulation results and real (genomic) data.
  

Description of data

Only simulations will be conducted at this stage.

Technical skills required:

• Setting up a reproducible analysis pipeline (Snakemake or, at minimum, Bash),
• Result visualization (Python, R).

Methodologies

Become familiar with the simulation software SLiM and the use of a computing cluster (Slurm):

• Build simple models simulating neutral mutations, mutations under selection, and mutations subject to gBGC,
• Vary key parameters (population size, mutation rate, recombination rate, frequency of sex) and analyze their impact,
• Present and discuss the results with the team (critical analysis in relation to the literature).

Réferences

• Lesecque, Y, Mouchiroud, D, Duret, L (2013) GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance Mol Biol Evol doi : 10.1093/molbev/mst056
• Ollivier L, Charlesworth B, Pouyet F (2025) Beyond recombination: Exploring the impact of meiotic frequency on genome-wide genetic diversity. PLoS Genet doi :10.1371/journal.pgen.1011798
• BC Haller, PL Ralph, PW Messer (2025). SLiM 5: Eco-evolutionary simulations across multiple chromosomes and full genomes. bioRxiv.

Lieu du stage

Laboratoire interdisciplinaire des sciences du numérique → team website : https://www.lisn.upsaclay.fr/recherche/departements-et-equipes/science-des-donnees/bioinfo-2/