PhD position OT-28863
PhD position in ancient virus phylogenomics
31076 TOULOUSE
INRAE presentation
The French National Research Institute for Agriculture, Food, and Environment (INRAE) is a major player in research and innovation. It is a community of 12,000 people with 272 research, experimental research, and support units located in 18 regional centres throughout France. Internationally, INRAE is among the top research organisations in the agricultural and food sciences, plant and animal sciences, as well as in ecology and environmental science. It is the world’s leading research organisation specialising in agriculture, food and the environment. INRAE’s goal is to be a key player in the transitions necessary to address major global challenges. Faced with a growing world population, climate change, resource scarcity, and declining biodiversity, the Institute has a major role to play in building solutions and supporting the necessary acceleration of agricultural, food and environmental transitions.
Work environment, missions and activities
Background and aims
The frequency of infectious disease emergence has increased over the last few decades, a phenomenon attributed to modern global sociodemographic and environmental changes. However, major transformations of human mobility, lifestyles and technologies associated with large-scale repercussions on the planet's ecosystems have occurred since prehistory. Recent advances in the field of paleogenetics have opened promising perspectives to measure the impact of these dynamics on the epidemiology and evolution of pathogens in the past, by allowing the identification and genomic characterisation of various disease-causing agents from archaeological remains. The ERC-StG EpidemioCene project will leverage ancient DNA data generated from massive cohorts of ancient individuals to undertake large-scale paleoepidemiological and phylogenomic investigations. In this context, this PhD project will focus on the analysis of ancient DNA virus genomes to reconstruct past viral dynamics and evolution in relation to human migrations and socio-environmental changes throughout the Holocene.
Work environment, missions and activities
You will be welcomed at the Host-Pathogen Interaction Research Unit (IHAP; UMR1225 UT/INRAE/ENVT; Toulouse, France). IHAP is a dynamic and friendly research environment based at the National Veterinary School of Toulouse and focusing on various aspects of infectious diseases, ranging from microbiology, virology and immunology to pathogen epidemiology and evolution. The PhD project will involve close remote collaboration and regular visits and stays in Johannes Krause's Department at the Max Planck Institute for Evolutionary Anthropology (MPI-EVA; Leipzig, Germany), a world-leading institution in the field of paleogenetics. You will also collaborate with Denise Kühnert's Phylogenomics group at the Center for Artificial Intelligence in Public Health Research (RKI, Wildau, Germany).
Your mission will be to assemble and analyse large sets of ancient viral genomes using phylogenomic approaches. More specifically, you will perform the bioinformatic reconstruction of ancient viral sequences obtained from the sequencing of ancient human remains from diverse locations across the world and spanning the last ~12,000 years. You will focus on DNA viruses such as hepatitis B virus, parvovirus B19, variola virus or herpesviruses. You will employ phylogenetic analyses to reconstruct and date the evolutionary relationships of ancient and modern viral diversity. If applicable, you will employ phylogeographic and phylodynamic approaches to formally estimate past migration and epidemiological dynamics from the phylogenetic reconstruction. You will also employ gene content and selection analyses to identify evolutionary changes related to, e.g. virulence and host adaptation across time and viral lineages. Overall, this will allow you to trace geographical spread, transmission dynamics and genomic adaptations of these viruses in relation to human migrations and socio-environmental changes on large time scales. You will be in charge of interpreting and disseminating the results of your research through the publication of scientific articles and presentations at international conferences.
Supervision
Dr Arthur Kocher (IHAP; MPI-EVA) is the PI of the EpidemioCene project. He studies human and animal disease ecology and evolution using molecular approaches combined with Bayesian statistics and phylogenomics. In particular, he is an expert in ancient pathogen genomics.
Dr Claire Guinat (IHAP) is a researcher at INRAE. She studies the transmission dynamics of zoonotic and animal infectious diseases. She has a strong expertise in molecular epidemiology and viral phylodynamics.
Dr Denise Kühnert is the leader of Phylogenomics group at the Center for Artificial Intelligence in Public Health Research (RKI, Wildau, Germany). She is an expert in phylodynamic modelling and one of the developers of the popular Bayesian phylogenetic software BEAST2.
Key references
- Kocher, A., Krause, J. & Spyrou, M. A. Insights into infectious diseases through ancient pathogen genomics. Nat. Rev. Microbiol. 1–15 (2025).
- Kocher, A. et al. Ten millennia of hepatitis B virus evolution. Science 374, 182–188 (2021).
- Mühlemann, B. et al. Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans. Proc. Natl. Acad. Sci. 115, 7557–7562 (2018).
- Mühlemann, B. et al. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age. Science 369, eaaw8977 (2020).
- Guellil, M. et al. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. Sci. Adv. 8, eabo4435 (2022).
Training and skills
Candidates should have completed, or be close to completing, a Master's degree in evolutionary biology, epidemiology or a related topic. Some experience in bioinformatics and a specific interest in molecular epidemiology and viral evolution are expected. Experience in computational phylogenetics would be advantageous. The position is aimed at students excited to study the (pre)history and evolution of pathogens using ancient DNA data, but specific experience in this regard is not required. Wetlab experience is also not required, but a good understanding of the basic principles of molecular biology would be appreciated. Candidates should have proficient English skills and a strong motivation for teamworking in an international context. French language skills are not required.
INRAE's life quality
By joining our teams, you benefit from (depending on the type of contract and its duration):
- up to 30 days of annual leave + 15 days "Reduction of Working Time" (for a full time);
- parenting support: CESU childcare, leisure services;
- skills development systems: training, career advise;
- social support: advice and listening, social assistance and loans;
- holiday and leisure services: holiday vouchers, accommodation at preferential rates;
- sports and cultural activities;
- collective catering.
How to apply
How to apply
Please send a single PDF document containing a cover letter (2 pages max.), a CV, a proof of your last degree, and up to two reference letters with contact information of the referees.
By email : arthur.kocher@eva-mpg.de
Deadline to apply: April 30 2026
All persons employed by or hosted at INRAE, a public research establishment, are subject to the Civil Service Code, particularly with regard to the obligation of neutrality and respect for the principle of secularism. In carrying out their functions, whether or not they are in contact with the public, they must not express their religious, philosophical or political convictions through their behaviour or by what they wear. > Find out more: fonction publique.gouv.fr website (in French)