Post-Doc: Development of a new method to study the distribution of the effect sizes of QTL

Organisation/Company Ecoles Pratique des Hautes Etudes - PSL

Research Field Biological sciences » Biodiversity

Researcher Profile Recognised Researcher (R2) Established Researcher (R3)

Country France

Application Deadline 14 May 2025 - 22:00 (Europe/Paris)

Type of Contract Temporary

Job Status Full-time

Hours Per Week 35

Offer Starting Date 16 Sep 2024

Is the job funded through the EU Research Framework Programme? Horizon Europe - ERC

Reference Number 101114976

Is the Job related to staff position within a Research Infrastructure? No

Offer Description

We offer a 2-years position, working as post-doctoral fellow to improve our ability to study the genetic architecture of complex traits, by developing a new method to study the distribution of the effect sizes of Quantitative Trait Loci (QTL). The job will be mostly computational, based on statistical modelling and development, as well as assessing the performance of the method using simulated data. The candidate will work for the École Pratique des Hautes Études (PSL University), joining Pierre de Villemereuil’s team, at the Institute for Systematics, Evolution, Biodiversity (ISYEB), located within the Muséum National d’Histoire Naturelle (MNHN) in Paris. This position is funded as part of the EvoGenArch ERC Starting Grant. The position starts on 2024-09-16.

Scientific Context

Most traits of ecological and evolutionary relevance are complex traits, i.e. influenced by a large number of loci (named Quantitative Trait Loci, or QTL) in the genomes. The features of the QTL are often referred to as the genetic architecture of the trait. One of the most important collective features to characterise such architecture is the distribution of the effect sizes (i.e. the phenotypic impact of replacing one allele for the other) of QTL. Current methods allowing for the study of such distribution of effect sizes make the same core assumption: all QTL are a subset of the genetic markers (generally SNPs) available in the genome. However, QTL should come in all possible varieties of genetic variants. This distinction between markers and QTL is generally not problematic if the aim is to locate a region of interest in the genome or perform genomic predictions. However, if the goal is to infer the distribution of effect sizes from an evolutionary perspective, this distinction between markers and QTL becomes highly important. Indeed, if many, or most, markers are only linked to causal QTL, then the amount of linkage disequilibrium between each QTL and the markers will distort the inferred distribution of effect sizes. If we want to have a chance to empirically test the evolutionary predictions from the theoretical models, it is thus necessary to develop new methods that are focused on the inference of the distribution of QTL. The aim of this post-doctoral project is thus to develop such a new method, using the relation between linkage disequilibrium among markers nearby a QTL and the trait variance each of them “explain,” which is linked to the effect size of the QTL.

Responsibilities

Under the supervision of Pierre de Villemereuil, in remote collaboration with Olivier François and Bertrand Servin, the candidate will:

1. Develop the statistical method (including implementation, either as a package or as compiled software) to infer the distribution of the effect sizes of QTL, using phenotypic and genomic data on a set of individuals. As a first approach, the method will follow the principles described in the EvoGenArch project, but the candidate will be at full liberty to put forward original ideas relevant to the project aim.
2. Test the performance of the method, compared to existing state-of-the-art methods that do not distinguish between markers and QTL, using phenotypic and genomic data simulated according to a set of scenarios.
3. Empirically test the relevance of the new method by re-analysing a published dataset.

Pierre de Villemereuil’s research focuses on the genetics of adaptation, trying to understand how the levels of the genotype, phenotype, and environment interact to drive evolution in wild populations, notably in response to anthropic pressures. A combination of evolutionary ecology, quantitative genetics, population genomics, and statistical modelling is necessary to unveil the patterns and processes of adaptation in the wild. The Institute for Systematics, Evolution, Biodiversity (ISYEB), located in the beautiful Jardin des Plantes of the Muséum National d’Histoire Naturelle in Paris, is one of the largest labs studying evolution in the city. ISYEB hosts worldwide leading science in evolution, systematics, phylogeny, genomics, and ecology.

Where to Apply

E-mail pierre.devillemereuil@ephe.psl.eu

Requirements

Research Field Biological sciences » Biodiversity

Education Level PhD or equivalent

Research Field Biological sciences » Biology

Education Level PhD or equivalent

Research Field Biological sciences » Biological engineering

Education Level PhD or equivalent

Skills/Qualifications

1. PhD in statistical genetics, genomics, bioinformatics, or related fields.
2. Track record of research activity and academic output (publications, conference communications, etc.).
3. Demonstrated ability to work as part of a scientific team, take on research tasks.
4. Experience in and interest for statistical genetics and/or statistical development.
5. Technical skills in a programming language, preferably compiled, as well as a data analysis language (R/Python/Julia...) are a requirement.
6. Background in even basic quantitative genetics will be highly appreciated.

Languages ENGLISH Level Good

Additional Information

Selection process

Please send (1) a CV/résumé; (2) a short (max. 2 pages) letter of application highlighting past research experience and accomplishment, your fit to the profile, and your motivation for the position; and (3) a letter of recommendation or contact details of past supervisors (PhD or Post-doc) to the address pierre.devillemereuil@ephe.psl.eu. Selected candidates will be auditioned by a committee of two to three persons, including the PI, starting from May 15th, for as long as the position is not filled. Candidates are not discriminated against based on their gender, ethnicity, or sexual orientation; please all feel welcome to apply!

Work Location(s)

Number of offers available 1

Company/Institute Institute for Systematics, Evolution, Biodiversity (ISYEB UMR 7205), Muséum National d'Histoire Naturelle

Country France

City Paris

Postal Code 75005

Street 12, rue Buffon

Geofield