PhD thesis M/F+ : Eco-Evolutionary Genomics of the French Antarctic Southern Territories (TAAF) Fauna in Response to the H5N1 Influenza Virus.

Job Description

Thesis Subject

PhD thesis: Eco-Evolutionary Genomics of the French Antarctic Southern Territories (TAAF) Fauna in Response to the H5N1 Influenza Virus.

Since late 2022, the highly pathogenic avian influenza virus H5N1 (subclade 2.3.4.4b) has caused catastrophic mortality in birds and marine mammals. In October 2024, this epizootic reached the French Antarctic Southern Territories (TAAF), causing exceptional mortality in three remarkable species: the southern elephant seal (Mirounga leonina), the king penguin (Aptenodytes patagonicus), and the wandering albatross (Diomedea exulans). These species have been subject to demographic, ecological, and epidemiological monitoring for decades by teams from the Biological Research Centre of Chizé (CEBC) and the Centre for Functional and Evolutionary Ecology (CEFE), in cooperation with the French Polar Institute Paul-Émile Victor (IPEV). However, they have been little or never studied from genetic and molecular perspectives. The H5N1 epidemic in the TAAF raises questions about the demo-genetic impact of the epizootic on bird and mammal populations, the genetic determinants of virus resilience/vulnerability, particularly regarding genes involved in immune responses, and the risk that certain species could facilitate virus pre-adaptation to humans.
This thesis is part of a MITI Santé inter-institutional CNRS initiative (Ecology & Environment – Biology) and aims to exploit the complementarity between population genomics, phylogenomics, molecular and functional evolution, and molecular virology to (i) characterize the impact of the H5N1 epizootic on TAAF populations, and (ii) identify the genetic determinants of intra- and inter-species differences in virus vulnerability/resistance. The thesis will be organized into four complementary work packages:
1. Pre-epizootic genetic diversity status. Establish a historical reference for genetic diversity predating the epizootic through whole genome analysis of 20 individuals per species. Bioinformatic and population genomic analyses will aim to understand the evolutionary forces that shaped the genomes and their capacity to respond to the epizootic.
2. Impact of the epizootic on population genetic health. Measure changes in genetic diversity and genetic load by comparing genomic data before (work package 1) and during/after the epizootic. To do this, new genomes from ~20 individuals (10 deceased from H5N1 and 10 exposed but healthy) will be compared to the historical cohort. This step will aim to identify new signatures of genetic selection and model population resilience through population genomics.
3. Inter-species differences in vulnerability/sensitivity to H5N1 - Molecular evolution. Analyze molecular evolution at a broad taxonomic scale of candidate genes identified in work package 2 and in the literature as likely to contribute to intra- and inter-species variations in virus vulnerability/resistance to H5N1. Particular emphasis will be placed on genes involved in innate antiviral response.
4. Functional validation in collaboration with Institut Pasteur Paris. For the most relevant candidate genes, evaluate and compare antiviral activity of mammalian/avian and human orthologs through cell engineering and molecular virology approaches. This step will allow testing the potential for virus pre-adaptation to humans in mammalian species.
Since samples have already been collected during previous field campaigns, the project does not include fieldwork missions. Most of the whole genome data has already been generated and validated, the majority of the thesis work will be based on their bioinformatic, computational, and evolutionary genomic analyses.

Your Work Environment

The phD student will be hosted at the MIVEGEC Research Unit in Montpellier, within the EVCO Team, under the supervision of Michael C. Fontaine. MIVEGEC is specialized in the study of infectious diseases and the ecological, evolutionary, and genetic processes between hosts, pathogens, and vectors. MIVEGEC brings together 123 senior researchers, lecturers, engineers, and technicians from the IRD, CNRS, University of Montpellier and INRAE, working in Montpellier and around the world. The thesis will be conducted in collaboration between the following laboratories: MIVEGEC (MC Fontaine, S Jacquet), RBIV - Institut Pasteur Paris (N Naffakh), CEBC (T Bonnet, C Guinet, C Barbaud), and CEFE (C Lebohec, T Boulinuer). It will benefit from the support of a bioinformatician, the iTrop bioinformatics platform of the IRD, and local and national computing and data storage infrastructure (IFB, iTrop, MIVEGEC, and CNRS). The thesis will include a stay within N. Naffakh's team at the Virology Unit of Institut Pasteur Paris, for conducting functional analyses (work package 4).

Constraints and risks

The recruited phD candidate will have solid background in population genetics and evolutionary genomics, and will be proficient in a (bio-)informatics programming language (e.g., R, Python, bash), and be familiar with high-throughput computing clusters. The candidate will have direct experience in analyzing sequencing data, particularly in handling large sets of next-generation genomic data. The candidate will be able to communicate in English, as part of the host laboratory is non-francophone. The phD candidate should have strong communication skills, autonomy, ability to work in a team, capacity to synthesize ongoing work, and be committed to applying appropriate procedures ensuring the reproducibility of bioinformatic analyses, particularly through implementation of transparent and reproducible procedures. Prior experience in molecular biology and laboratory work (DNA extraction, library construction) would be an advantage, but is not essential.

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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