PhD position for Unlocking the Genomic History of Pathogens Through Pathology Archives

Details

Pathogen genomics provides a powerful framework for studying evolutionary processes through time. Yet for many pathogens that have profoundly influenced human and animal health, genomic data remain largely confined to contemporary isolates, limiting our ability to understand how present-day populations emerged and responded to past selective pressures. Medical collections, public health archives, and museum specimens preserve an underexplored record of historical infections spanning periods before the widespread introduction of antibiotics, vaccines, and modern disease control measures. These archives provide a unique opportunity to investigate pathogen evolution across changing selective environments and to address evolutionary questions that cannot be resolved using modern genomes alone.

This PhD project will apply ancient DNA approaches to recover pathogen genomes from clinical and veterinary specimens spanning the past two centuries. By generating genomic data from archived slides, biopsies, and other historical specimens, the project will establish temporal genomic datasets that bridge critical transitions in the history of infectious disease control. These data will enable direct comparisons of pathogen populations before and after major medical interventions, allowing the reconstruction of transmission and demographic histories, estimation of long-term evolutionary rates, and identification of the selective pressures associated with adaptation, virulence, and antimicrobial resistance.

The studentship also offers substantial opportunities for public engagement through collaborations with partner museums and heritage collections, highlighting the continuing relevance of historical archives to contemporary genomics and public health.

Objectives

The successful candidate will contribute to the following aims:

1. Recover and sequence historical pathogen genomes. Apply state-of-the-art ancient DNA extraction and sequencing methods to degraded archival specimens, with strategic sampling across pre- and post-antibiotic and vaccine eras.
2. Reconstruct evolutionary histories. Integrate recovered genomes into phylogenetic frameworks to quantify transmission dynamics, lineage turnover, and pathogen adaptation over decades to centuries.
3. Investigate long-term evolutionary change. Analyse genomic data to identify shifts in evolutionary rates, resistance mechanisms, and virulence-associated variation across major transitions in medical treatment and public health practice.

Training environment and skillset

The project combines laboratory-based ancient DNA work with computational analyses including comparative genomics, phylogenetics, population genetics, and molecular evolution. The student will join a friendly, collaborative, and multidisciplinary research environment in UCL Genetics Institute with access to dedicated ancient DNA facilities, museum collections, and an extensive engagement network.

Applicants with expertise or strong interests in any of the following areas are encouraged to apply:

• Ancient DNA
• Microbial genomics
• Phylogenomics
• Population genetics
• Molecular evolution
• Bioinformatics

Evaluation

Interested candidates should contact Lucy van Dorp (lucy.dorp.12@ucl.ac.uk). To apply please submit a single PDF containing:

1. Curriculum vitae
2. A short supporting statement (<500 words) describing your research interests and relevant experience
3. Contact details for two academic referees

There is no strict application deadline, we will review applications from 27th July 2026 and continue to do so until the post is filled.

Funding Notes

The 3-year PhD studentship is supported by the Evolution Education Trust. Eligibility is restricted to applicants who qualify for UK home fee status (including UK citizens and those with settled or pre-settled status). In addition to the stipend and tuition support, substantial funding is available for laboratory reagents, genome sequencing, training opportunities, and attendance at national and international conferences.