Uniting museum collections and genomics to trace emerging pathogens across the Anthropocene

specimens stored in glass jars in alcoholic spirit

This project will investigate how chytrid fungi lineages have developed and spread across Africa and out-of-Asia.

The studentship starts in October 2020 and is funded by NERC. 

Apply for this course

Applicants should apply directly to the lead supervisor, Prof Matthew Fisher, with a CV and cover letter.

Application deadline: 6 January 2020

Project background

A decade of NERC-funded research on global amphibian declines has enabled us to identify Asia as the global centre of diversity for chytrid fungi that have driven panzootics of disease in amphibians.

These disease outbreaks have led to the most aggressive losses in biodiversity caused by infections ever documented. Yet, we still lack a nuanced understanding of exactly where these infections originated, when they emerged, and how they managed to establish in naïve ecosystems worldwide.

Uniting field and museum collections using genomics technologies holds huge promise to shed light on these important questions.


1. The student will reconstruct spatio-temporal transmission pathways from population genomic data. An accurate reconstruction of genetic diversity is the baseline for inferring evolutionary patterns, including demographic and adaptive histories from genomic data.

The student will refine current coarse-scale global analyses by broadening the use of our non-lethal toe-clip isolation protocol to sample the breadth of amphibian-associated chytrids with a focus on the center of Batrachochytrium diversity in Asia and Africa, where at least two invasions by chytrids have occurred that have resulted in species extinction.

The NHM amphibian collection contains more than 80,000 specimens collected as early as the 18th century. Chytrid infected specimens and ancient-DNA technologies that we have used to recent good effect will be used to recover and sequence historic pathogen nucleic acids from Asian and African amphibians; NHM collections of these amphibians are known to harbour chytrid.

These datasets will then be integrated in a phylodynamic framework to track the invasion and spread of chytrids across Africa and out-of-Asia.

2. The student will then focus on regions where chytrid lineages are re-contacting in Africa, and are known to form recombinant genotypes. By using field-work and experimentation in models, they will identify whether recombination is resulting in the development of novel pathogen diversity, perhaps leading to novel phenotypes of relevance such as virulence or adaptation to endemic host species.

By capitalising on, and extending, a Southern African dataset the landscape-level movement of specific lineages will be traced in time and space.


1. Developing an understanding of links between fungal phylogeography and globalisation in human networks of trade

2. Development and use of novel cutting-edge techniques in archival DNA sequencing and bioinformatics

3. Development of spatially and temporally-explicit assessments of pathogen fitness, with the aim of detecting epidemiologically-relevant phenotypes and subsequent impact on host populations and species

4. Understanding of the importance of ecological-niche breadth on infectious disease transmission


To be eligible for a full award a student must have:

  • British Citizenship or; 
  • Settled status in the UK, meaning they have no restrictions on how long they can stay,
  • Been ‘ordinarily resident’ in the UK for 3 years prior to the start of the studentship - (For non-EU citizens, this must NOT have been in full time education.)
    This means they must have been normally residing in the UK (apart from temporary or occasional absences). This does not apply to UK nationals. 

For more information, download this PDF.

How to apply

Applicants should apply directly to the lead supervisor, Prof Matthew Fisher, with a CV and cover letter.

The deadline for applications is 6 January 2020.

Any questions?

If you have any questions about the project please contact

Main supervisor: Prof Matthew Fisher


Imperial College London

Main supervisor: Prof Matthew Fisher

The Natural History Museum

Co-supervisor: Dr Jeff Streicher

North West University, South Africa

Co-supervisor: Dr Che Weldon

Science and Solutions for a Changing Planet (SSCP) doctoral training partnership

This is a joint project between The Science and Solutions for a Changing Planet (SSCP) Doctoral Training Partnership at Imperial College London and The Natural History Museum.

Funded by