GMS Royal Society Studentship

Reconstructing the evolutionary history of pathogens using ancient DNA

About the Project 

Are you interested in using ancient DNA to understand the long-term evolution of infectious disease? This is an exciting opportunity to join the University of Oxford as a DPhil candidate, working at the intersection of ancient DNA, pathogen genomics, archaeology, and evolutionary medicine.

This four-year DPhil studentship is funded by the Royal Society for UK/home students, with fees covered at the home rate and a stipend provided at the UKRI rate. The successful candidate will join the DPhil in Genomic Medicine and Statistics programme, based at the Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford. The project will also involve close collaboration with the ancient DNA laboratory at the School of Archaeology.

Infectious diseases have been among the most powerful forces shaping human history and evolution, influencing patterns of mortality, immunity, migration, and cultural change over thousands of years. This project will focus on reconstructing the evolutionary history of zoonotic pathogens: infectious agents that can spread between animals and humans. Many of the most consequential pandemics have involved pathogens that emerged through close relationships between humans and animals, particularly following the development of farming, pastoralism, and long-term contact with domestic animals. However, we still know relatively little about how these pathogens evolved, when they became widespread, and how they moved between animal and human hosts.

Ancient DNA provides a powerful way to directly study these questions. By analysing ancient DNA preserved in archaeological remains, it is possible to detect traces of ancient pathogens and reconstruct their genomes. Most ancient pathogen research has focused on human remains, but animal bones are often more abundant in the archaeological record and domestic animals have long been important reservoirs of zoonotic disease. This project will make use of this underexplored resource by searching for ancient pathogen DNA in samples from a range of domestic and wild animal species.

The successful candidate will use a combination of wet-lab and computational approaches. The laboratory work will involve ancient DNA methods, including target enrichment strategies designed to recover low-abundance pathogen DNA from archaeological samples. The computational work will involve genomic and evolutionary analyses of ancient pathogen sequences, with the aim of understanding how zoonotic pathogens have evolved across human and animal hosts.

The successful candidate will be working in the following research areas, in addition to collaborating on other projects within the lab (including human evolution). They will also have time to develop their own research ideas.

1. Recovering pathogen DNA from archaeological remains of animals associated with humans throughout time

The project will begin by identifying and screening ancient DNA libraries from animal remains for evidence of pathogen DNA. Because pathogen DNA is often present at very low abundance, the student will help develop and apply targeted capture approaches to enrich for ancient pathogen DNA. This will involve working in specialist ancient DNA laboratory facilities and using molecular methods designed for degraded and low-coverage DNA.

2. Reconstructing the evolutionary history of ancient pathogens

Once pathogen DNA has been identified, the student will analyse sequencing data to reconstruct ancient pathogen genomes. This will involve computational approaches for taxonomic profiling, genome reconstruction, and assessment of authenticity. The student will gain experience in analysing complex ancient metagenomic data and in working with both ancient and modern pathogen reference datasets.

3. Modelling the evolution of zoonotic pathogens across hosts

The recovered pathogen genomes will be analysed alongside published ancient and modern pathogen genomes from humans and animals, using statistical and artificial intelligence (AI) approaches. This will allow the student to investigate how pathogens have changed over time, how they have moved between host species, and whether particular genetic changes are associated with host jumps or increased pathogen prevalence. The results will contribute to a broader understanding of how human-animal relationships have shaped the evolution of infectious disease.

The project will be supported by a supervisory team with complementary expertise across ancient DNA, evolutionary genomics, pathogen evolution, and archaeology. Dr Evan Irving-Pease is a Group Leader at the Nuffield Department of Medicine, whose research uses ancient DNA and statistical modelling to understand how natural selection and infectious disease have shaped genetic variation through time. Professor Greger Larson is Director of the PalaeBARN at the School of Archaeology, and is internationally recognised for his work on ancient DNA, evolutionary genomics, domestication, and the long-term history of human–animal relationships. Dr Joel Alves is an evolutionary geneticist in the School of Archaeology, and at Biopolis-CIBIO in Porto, Portugal, whose research integrates genomics, ancient DNA, archaeology, and historical evidence to investigate questions related to domestication, adaptation, and host–pathogen co-evolution.

About the Programme 

The DPhil in Genomic Medicine and Statistics is a four-year research programme that provides advanced training in the use of genomics to understand and improve human health. The programme combines experimental and analytical approaches, with training spanning genome biology, statistics, bioinformatics, genomic medicine, and related areas of biomedical research. The project will also provide specialist training in ancient DNA methods, pathogen genomics, evolutionary biology, and computational analysis. It would suit a candidate with a background in ancient DNA, pathogen genomics, molecular biology, or a related field. Prior wet-lab experience is desirable, as is experience in genomic analysis.

The student will be part of a multidisciplinary research environment spanning the Centre for Human Genetics, the Big Data Institute, and the School of Archaeology, with opportunities to interact with researchers working across genomics, population genetics, infectious disease, clinical genetics, functional biology, data science, machine learning, and archaeology. This training environment will provide an excellent foundation for the successful candidate to develop the broad set of laboratory, computational, and quantitative skills needed for this project. International travel to perform sampling and conduct research visits will also be possible.

Application deadline: Friday 17 July 2026 at midday (UK time).

To be considered for this studentship, please submit an application to the DPhil in Genomic Medicine and Statistics programme.  

Read the full DPhil in Genomic Medicine and Statistics course information on the University of Oxford admissions website.

For informal enquiries, please contact Dr Evan Irving-Pease at evan.irving-pease@bdi.ox.ac.uk