PhD: Ancient Viral Genomics & EpidemioCene Project

French National Research Institute for Agriculture, Food and Environment (INRAE)

Organisation/Company French National Research Institute for Agriculture, Food and Environment (INRAE) Department IHAP 1225 INRAE ENVT Research Field Medical sciences » Veterinary medicine Medical sciences » Epidemiology Researcher Profile First Stage Researcher (R1) Positions PhD Positions Application Deadline 30 Apr 2026 - 00:00 (Europe/Paris) Country France Type of Contract Temporary Job Status Full-time Offer Starting Date 1 Oct 2026 Is the job funded through the EU Research Framework Programme? Other EU programme Is the Job related to staff position within a Research Infrastructure? No

Offer Description

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

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 virusessuch 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 totrace 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– ).
• Kocher, A. et al. Ten millennia of hepatitis B virus evolution. Science 374, 182– ).
• Mühlemann, B. et al. Ancient human parvovirus B19 in Eurasia reveals its long-term association with humans. Proc. Natl. Acad. Sci. 115, 7557– ).
• Mühlemann, B. et al. Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age. Science 369, eaaw ).
• Guellil, M. et al. Ancient herpes simplex 1 genomes reveal recent viral structure in Eurasia. Sci. Adv. 8, eabo ).

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.

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 aimedat 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.

Research Field Medical sciences » EpidemiologyMedical sciences » Veterinary medicine