PhD position (M/F): Prevalence, mechanisms and genomic targets of balancing selection, and interactions with structural variants in Coelopa flies

Job Description

Thesis Subject

Balancing selection refers to any form of natural selection that maintains genetic diversity within a population, in contrast to positive and negative selection, which lead to a decrease in diversity over time. The best-known mechanisms of balancing selection are heterozygote advantage (the fitness of heterozygotes is higher than that of homozygotes), frequency-dependent selection (fitness depends on the rarity of the allele in the population), and fluctuating selection (fitness varies over time and/or space). We do not yet know precisely the importance and relative prevalence of these mechanisms in explaining the (phenotypic and genetic) diversity observed in nature. Recently, empirical studies (phenotypic studies or genome-wide scans) have suggested that balancing selection likely plays a greater role in species adaptation than previously estimated. Indeed, it underlies the maintenance of numerous polymorphisms (sometimes in the form of structural variants) that control complex adaptive phenotypes (such as migratory behavior or reproductive systems) in many taxa. Multiple variants involved in immunity, olfaction, and host-parasite coevolution constitute other putative targets of balancing selection (operating through frequency-dependent and fluctuating selection mechanisms). However, the genomic signatures of balancing selection (e.g., increased diversity and coalescence time of variants, and decreased divergence) are highly sensitive to alignment errors, which can lead to false positives. The availability of high-coverage long-read sequencing that we have today therefore presents an interesting opportunity to address this limitation and better estimate the prevalence of balancing selection based on genomic data. At the same time, long-read data also provide access to structural variants (insertions, deletions, inversions, etc.) and thus allow us to directly assess whether these variants are preferentially targeted by balancing selection, as suggested by certain theoretical studies. In this thesis project, we propose to study the genomic targets, mechanisms, and prevalence of balancing selection at the intra- and interspecific levels, focusing on several non-model taxa. More specifically, the project will involve i) constructing and implementing a workflow to detect balancing selection using a combination of short-read and long-read sequencing data, ii) studying the mechanisms and genomic targets of balancing selection in flies of the genus Coelopa, particularly in relation to structural variants, and iii) estimating the prevalence of balancing selection relative to other taxa with similar demographic and ecological characteristics.

The PhD candidate should have a master degree in evolutionary biology with previous expertise in bioinformatics. Earlier experience with programming in R and/or bash is preferred. The PhD candidate should be comfortable speaking and writing in English.

Your Work Environment

The PhD will be co-supervised by Laure Ségurel, a population geneticist who focuses in particular on adaptive dynamics—such as balancing selection—using empirical approaches, and Claire Mérot, a researcher in evolutionary genomics, who works notably on the Coelopa fly model system and has extensive expertise in the analysis of structural variants. The two co-advisors will oversee the thesis as a whole, provide guidance on data analysis, and assist with the interpretation of results. The Laboratory of Biometry and Evolutionary Biology (LBBE) in Lyon, where this thesis will be conducted, is highly diverse and the Bioinformatics, Phylogeny and Evolutionary Genomics Group (BPGE) encompasses a range of expertise in evolutionary genomics, from phylogenetics to population genomics, bioinformatics, and modeling. The PhD student will receive regular guidance through weekly meetings with their thesis advisor, as well as informal daily discussions as needed.
In addition, the team holds weekly meetings (including research presentations and a journal club), and PhD students are encouraged to present their work at these sessions. Finally, a monitoring committee including specialists in evolutionary genomics will be established to ensure the thesis progresses smoothly.
Some of the genomic data needed for the successful completion of this project have already been obtained and will be available from the start of the dissertation. The remaining data is currently being acquired through an ANR grant led by Laure Ségurel and awarded in 2026 in collaboration with Claire Mérot (ECOBIO, Rennes) and Violaine Llaurens (CIRB, Paris). The student will have a suitable work environment and access to the LBBE-PRABI computing cluster. The PhD student will be integrated into the ANR project team and will benefit from associated national and international collaborations. He or she will be invited to spend time in Rennes to foster interactions with ECOBIO.
Our added benefits:
• A stimulating working environment alongside research staff
• Professional support with in-house training at the laboratory
• The option to work from home
• A staff canteen offering lunch at an affordable price.
• Partial reimbursement of travel costs (75%) + a sustainable mobility allowance of up to €300 per year
• A site accessible by public transport (Tram T1, T4 and T6, and buses)
• 44 days' annual leave per year
• Supplementary health and welfare cover

Compensation and benefits

Compensation

2300 € gross monthly

Annual leave and RTT

44 jours

Remote Working practice and compensation

Pratique et indemnisation du TT

Transport

Prise en charge à 75% du coût et forfait mobilité durable jusqu’à 300€

About the offer

About the CNRS

The CNRS is a major player in fundamental research on a global scale. The CNRS is the only French organization active in all scientific fields. Its unique position as a multi-specialist allows it to bring together different disciplines to address the most important challenges of the contemporary world, in connection with the actors of change.

CNRS

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