Mots-Clés
recombinaison
génétique des populations
levure
analyse de données
démographie
sélection
Description
Comparative population genomics of yeast populations: demography and signatures of facultative sexual reproduction
Introduction and Scientific context
Sexual reproduction has a major impact on genome evolution by promoting recombination and
affecting the efficiency of natural selection. However, many organisms, including several microbial
eukaryotes, do not reproduce exclusively sexually. They alternate between sexual and asexual
phases, with potentially large consequences for the evolution of their genomes.
The budding yeast Saccharomyces cerevisiae is a particularly interesting model to study the
evolutionary consequences of facultative sexual reproduction. Although yeast is often considered
as a predominantly selfing species, recent population genomic studies have revealed a much more
complex picture, with high levels of genetic diversity and contrasted population histories. Whether
natural yeast populations differ in their reproductive strategies, and how these differences have
shaped their genomes, remains largely unknown.
A recent population genomic study performed in our laboratory analysed more than 3,500 whole-
genome sequences of natural S. cerevisiae isolates and identified 38 genetically differentiated
populations. Among these, approximately 1,600 strains belong to non-admixed populations,
providing a unique framework to compare the evolutionary history and genomic characteristics of
distinct yeast lineages.
This internship is part of the ANR RECAF project, which aims to understand how facultative
sexual reproduction influences genome evolution. Mélodie Bastian, one of the internship
supervisors, is currently a postdoc funded by the ANR RECAF. Her work involves simulating the
evolution of yeast populations in the context of linked selection, recessive mutations, and
facultative sex. This to characterize the mechanisms that influence the observed diversity. Mélodie
and the intern will work together on the same dataset.
Research proposal/objectives
Although all yeast populations belong to the same species, they display substantial differences in
genetic diversity, genome structure and evolutionary history. The origin of this variation remains
poorly understood. Several processes may contribute to these differences, including demographic
history, natural selection, linked selection and variation in reproductive strategies. The main
objective of this internship is to understand the evolutionary processes responsible for the
contrasted patterns of genomic diversity observed among natural populations of S. cerevisiae.
Using the 38 genetically differentiated populations identified from a dataset of more than 3,500
yeast genomes, the student will investigate which evolutionary factors best explain variation in
genomic diversity among populations.
The main questions addressed during the internship will be:
- Why do natural yeast populations exhibit different levels of genomic diversity and to what extent
can these differences be explained by demographic history?
- Do differences in reproductive strategies, including variation in the frequency of sexual
reproduction, contribute to shaping population genomic patterns?
- Are populations with contrasted reproductive regimes characterized by different signatures of
recombination and linked selection?
The student will combine comparative population genomic analyses with demographic inference
approaches to disentangle the contribution of population history and evolutionary processes
shaping genome diversity. The final objective will be to identify how reproductive strategies
contribute to the maintenance of genetic diversity and to the long-term evolution of yeast genomes.
Description of the data
The internship will rely on an unpublished whole-genome dataset comprising 3,570 natural isolates
of S. cerevisiae from diverse ecological and anthropogenic environments. Population genomic
analyses performed in our laboratory have identified 38 genetically differentiated populations
among these strains. Approximately 1,600 strains belong to non-admixed populations and will
constitute the main dataset for comparative analyses during the internship.
The student will have access to variant data for unadmixed strains; population assignments based
on genome-wide genetic structure; phylogenetic information describing relationships among
populations and available biological metadata, including strain origin and ecological information.
Expected skills and techniques
The student will combine approaches from population genetics, computational genomics and
evolutionary biology to compare natural yeast populations. The main analyses will include
characterization of genome-wide patterns of genetic diversity across populations; inference of
demographic parameters to account for the impact of population history; integration of genomic
and biological information to identify factors associated with differences in genome diversity.
The student will develop reproducible computational workflows and analyse a large-scale genomic
dataset using Python for data analysis and visualization; Linux environment and high-performance
computing resources (SLURM); Bash and workflow management tools (e.g. Snakemake) for
reproducible analyses.