PhD in evolutionary biology: impact of adaptive introgression on genomes (M/W)

2 Sep 2023
Job Information

Organisation/Company

CNRS

Department

Centre d’écologie fonctionnelle et évolutive

Research Field

Biological sciences
Environmental science

Researcher Profile

First Stage Researcher (R1)

Country

France

Application Deadline

22 Sep 2023 – 23:59 (UTC)

Type of Contract

Temporary

Job Status

Full-time

Hours Per Week

35

Offer Starting Date

1 Dec 2023

Is the job funded through the EU Research Framework Programme?

Not funded by an EU programme

Is the Job related to staff position within a Research Infrastructure?

No

Offer Description

The thesis is part of a larger project financed by the ANR. It involves partners in other lab in Montpellier (CBGP, ISEM) and in Porto (Biopolis/CIBIO). Two PhD candidates are involved in the project.
One candidate has been hired already (co-supervision by CBGP and ISEM) and is devoted to i) assessing by simulations the methods that have been already published to detect adaptive introgression and to ii) develop a new method to detect and quantify the impact of adaptive introgression in genomes.
The second candidate will lead the main analysis of the project to quantify adaptive introgression in genomes sampled from 3 species of wall lizards in contrasted ecological conditions.
Sampling has been entirely done and we expect the whole genome sequences to be available when the PhD starts.

Scientific context
Adaptation by natural selection proceeds by favouring the genetic variants that are advantageous in a given environment. Mutation creates new variants (alleles) by modification of existing alleles while gene flow « recruits » genetic variation from other populations. Gene flow has long been considered to take place within species only but we now realize that it often occurs between species as well.
Gene flow between species may sound counterintuitive, as species are often defined as groups of individuals that are unable to interbreed successfully (e.g. Mayr 1942). Yet, it is now widely acknowledged that a significant amount of gene flow may take place without jeopardizing the speciation process (Mallet 2008, Pinho & Hey 2010), and some degree of hybridization between closely related species is indeed a widespread phenomenon (Mallet 2008, Arnold & Martin 2009). We still don’t know, however, how commonly gene flow effectively affects the genome of hybridizing species in the late stage of speciation, i.e. when species mostly behave as canonical biological species.
Such hybridization may in most cases be deleterious (i.e., lead to unfit offspring) or neutral but it may also be a source of adaptive genetic variation via the transfer of adaptations from the genome of one species to another, a phenomenon called “adaptive introgression” (Burke & Arnold 2001). Adaptive introgression has attracted much interest because of the possibility that adaptation may not only proceed by selection of new mutations, but also by recruitment of mutations that have already been tested by selection in another species. However, while there are a few prominent examples (see below), its overall importance for adaptation is still largely unknown.

Objectives
The PhD project will address the following questions: in a complex of closely related species (in the late stages of speciation, i.e. after the evolution of strongly differentiated genomes but before reproductive barriers are completely hermetic) i) how much of the genome is affected by introgression and ii) what proportion of introgression is adaptive?
The project combines whole-genome sequence data to quantify (adaptive) introgression with a direct ecological test of the adaptive introgression hypothesis to overcome some of the limitations inherent to the handling of the very large data sets generated by genomic approaches.
To perform the tests of adaptation, we will need to combine samples from several pairs of populations within each receiving species, each pair being composed of one population located in highly suitable climatic areas for the receiving species and the other from areas where climatic conditions are closer to the climatic niche of the donor species. Finding more candidate loci that have been subjected to introgression in areas that resemble more the climatic conditions of the “donor” species (the species where the introgressed loci have evolved) would be a clear evidence that adaptive introgression has helped these species adapt to local climatic conditions.

Skills
Master degree in evolutionary biology or related fields.
Niche modelling and sampling have all been completed and WGS data are expected to be available at the end of 2023. The PhD candidate will thus be expected to perform data analysis and writing only, starting from raw WGS data. A reference genome from the closely related Podarcis muralis is available to help with assembly and variant calling. Previous experience with bioinformatics or coding would thus be highly recommended.
The candidate is expected to work independently and to develop his own lines of research beside the necessary analysis of adaptive introgression. The ideal candidate should be highly motivated by questions in the genomics of speciation or adaptation and be able to master complex bioinformatic tools and population genomics methods.

Thesis organization
The thesis will be officially hosted at the GAIA Doctoral School of the University of Montpellier and based at CEFE (Centre d’Ecologie Fonctionnelle et Evolutive). The candidate will be co-supervised by Pierre-André Crochet (CEFE) and Pierre Boursot (ISEM)
The thesis is part of a larger ANR project (Introspec: Genomic consequences and evolutionary causes of introgression in the late stages of speciation) and the candidate will interact with other partners of this project. In particular the candidate will work in close collaboration with Jules Romieu (PhD candidate in CBGP/Montpellier who is developing a new method to quantify adaptive introgression from genomic data), Raphaël Leblois and Miguel Navascues (CBGP) and François Rousset (ISEM).

Requirements

Research Field

Biological sciences

Education Level

PhD or equivalent

Research Field

Environmental science

Education Level

PhD or equivalent

Languages

FRENCH

Level

Basic

Research Field

Biological sciences

Years of Research Experience

None

Research Field

Environmental science

Years of Research Experience

None

Additional Information

Website for additional job details

https://emploi.cnrs.fr/Offres/Doctorant/UMR5175-PIECRO-003/Default.aspx

Work Location(s)

Number of offers available

1

Company/Institute

Centre d’écologie fonctionnelle et évolutive

Country

France

City

MONTPELLIER

Where to apply

Website

https://emploi.cnrs.fr/Candidat/Offre/UMR5175-PIECRO-003/Candidater.aspx

Contact

City

MONTPELLIER

Website

http://www.cefe.cnrs.fr/

STATUS: EXPIRED