Ancient Zoo: Parasite diversity and zoonotic events in ancient Britain

Background

Emerging infectious diseases (diseases that have newly appeared in a population¹; EIDs) are one of the greatest threats to human health and global stability ^2–4. However, for almost all EIDs, nothing is known of their prevalence in the past. This historic information is essential for assessing trajectories of population abundance, and in turn determine whether a disease is genuinely newly emerging, and any long-term changes in prevalence⁵. An understanding of the presence/absence of parasites in the past would enable contextualisation of present-day parasite diversity, providing a springboard for future studies to confirm or update EID priorities and classifications.

 Aims

1. Improve our methods for detecting infection, and our understanding of wildlife pathology, by investigating the correlation between morphological and molecular measures of infection in faunal remains.
2. Identify first occurrence and changes in parasite diversity across British wildlife through historic and prehistoric times, and investigate correlations with landscape management, animal husbandry, proximity to settlement, and wildlife biodiversity and abundance.
3. Reconstruct the ancestry and evolutionary history of our present-day wildlife diseases, and the extent to which they have undergone molecular evolution and adaptation over time, with respect to changes in climate, and land use.

This project will be a collaboration between School of Biosciences (BIOSI), School of History, Archaeology and Religion (SHARE), Aberystwyth University, and the Natural History Museum, London. 

Methods

 Wildlife archives (bone pathology and macroparasites) at Aberystwyth University (School of Veterinary Science) will be used as references to identify pathological specimens in zooarchaeological and museum assemblages. Bioinformatic methods (e.g. ⁶) will be used to molecularly identify the presence of parasites in publicly available whole genome sequencing data, and newly generated shotgun sequencing data, and from the reference and ancient faunal remains. Overlap will be assessed between the reference and ancient datasets, and the morphological and molecular approaches will be compared to assess Type I and Type II error. We will use contextual information and 14C dating to identify the first occurrence of any parasite DNA identified. The project will focus on large- and medium-bodied mammals from archaeological archives and museum collections (including Cardiff Archaeology and the NHM, London), dating from the Holocene (c. 11.7 KYA) until the present-day. Ancient molecular lab work will be carried out at the newly formed Cardiff University ancient DNA (CUAD) laboratory.

Student experience

This project will be based at the vibrant and welcoming, “Organisms and Environment” division of the Cardiff University, School of Biosciences, with opportunities for sampling visits to Museum Wales and The Natural History Museum, London. This is a truly interdisciplinary project, with supervisory experience spanning wildlife disease (Dr. Sarah Perkins, BIOSI), evolutionary genetics and ancient DNA (Dr. David Stanton, BIOSI and Dr. Selina Brace, Natural History Museum, London), molecular helminthology (Dr Iain Chalmers) and zooarchaeology (Dr. Richard Madgwick, SHARE). The student will gain experience in ancient DNA molecular lab work, bioinformatic analysis, and zooarchaeological methodologies (such as species/element identification and faunal pathology). The project is sufficiently broad and novel that the student will have opportunity to develop their own preferences for research direction, for example:

●       Focussing on specific parasites, e.g. bovine Tb: When did it first appear in Britain? Was this emergence associated with domestic animals or wild? When and where did zoonosis events occur?

●       How well do morphological proxies of infection correlate with molecular proxies, and how does this affect their utility as a screening method?

●       How does diversity correlate with prevalence of zoonoses throughout history, i.e. testing the “dilution effect” hypothesis⁷

●       Changes in susceptibility loci in wildlife for prion diseases, such as chronic wasting disease in red deer as a proxy for cryptic zoonotic diseases⁸

Supervisory Team - Dr David Stanton (Cardiff - BIOSI), Dr Richard Madgwick (Cardiff - SHARE), Dr Sarah Perkins (Cardiff - BIOSI), Dr Iain Chalmers (Aberystwyth) and Dr Selina Brace (National History Museum, London)

We welcome applicants with a Master’s or relevant research experience. An understanding of molecular genetics and bioinformatics would be advantageous. To discuss the project further please contact [Email Address Removed]

A very high standard of applications is typically received, the successful applicant is likely to have a very good first degree (a First or Upper Second class BSc Honours or equivalent) and/or be distinguished by having relevant research experience.

How to apply:

We welcome applicants with a Master’s or relevant research experience. An understanding of molecular genetics and bioinformatics would be advantageous.

You can apply online - consideration is automatic on applying for a PhD with an October 2023 start date.

Please use our online application service at: https://www.cardiff.ac.uk/study/postgraduate/research/programmes/programme/biosciences-phd-mphil-md

and specify in the funding section that you wish to be considered for UKRI OneZoo funding.

Please specify that you are applying for this particular project and name the supervisor.

Information on the application process can be found here

If not successful in being shortlisted for this particular studentship you could be considered for other studentships within the OneZoo program, please see the full list here: https://peter-kille.github.io/OneZoo/projects_2023.html’

Application deadline: 1^st May 2023 with interviews (either in person or online) being held on or around end of May and decisions being made by June 2023 for a 1^st Oct 2023 start.

You must also by 1 May 2023 send the following to [Email Address Removed] (title of the email must include the name of the host institution to which you are applying, and the surname of the principal supervisor) e.g. "Cardiff_Cable"

• Completed  CDT application Form - available to download here
• Completed Equal Opportunities Form - available to download here
• 2 page CV
• Copy of passport photo page