Supervisors: Dr Robbie Rae and Dr Peter Falkingham
Analysis of DNA from ancient specimens collected from archaeological digs and museums has revolutionised our evolutionary understanding of many organisms including humans, insects, plants and even bacterial pathogens (Swarts et al. 2017; Slon et al., 2018; Thomsen et al., 2009). However, temporal analysis of DNA from metazoan parasites is lacking, as many taxa (e.g. nematodes, cestodes and trematodes) are microscopic, are soft bodied and do not fossilise (Littlewood et al., 2003).
A recent discovery made at LJMU concerning the relationship between gastropods (largely terrestrial snails) and their nematode parasites could change this. These animals have been locked in a co-evolutionary arms race for over 500 MY with 108 nematode species parasitising molluscs. We have shown thatterrestrial snails such as Cepaea nemoralis (Williams and Rae, 2016), Cornu aspersum (Cowlishaw et al., 2019), Arianta arbustorum (Rae, 2018) and Lissachatina fulica (Williams and Rae, 2015) are able to encapsulate and kill nematodes using their shell. When faced with nematode infection, cells are produced by the shell that specifically target and adhere to the nematode cuticle and fuse it to the inner shell layer, often hundreds at a time within days (Rae, 2017). After encapsulation in the shell, nematodes are preserved indefinitely and are free from water, extreme temperatures and microbes that degrade DNA. We have recently managed to sequence DNA of encased nematodes from 3-year-old snail shells, and use this to identify the parasites to species level (Rae, 2017; Cowlishaw et al., 2019).
Objectives of the PhD
These exciting findings have opened up new questions ideally suited for a PhD:
- To what extent among living gastropods is this encapsulation response present? Is it only present in terrestrial snails, or is it widespread among the gastropoda?
- Can ancient DNA be recovered from encapsulated nematodes, providing phylogenetic end evolutionary information? If so, is it preserved on the order of a few years, or millenia?
- How long ago was this response to parasitism evolved? Can morphological evidence be recovered from fossil gastropods millions of years old?
To answer these questions, the PhD student will work, in the first instance, in collaboration with Liverpool and Manchester museum, examining their conchology collections which contain historical gastropod specimens from the past two centuries, and archaeological specimens from up to 5000 years ago.
After positive identification of shells with nematodes, a combined morphological and genetics approach will be applied. Shells will undergo Micro-Computed Tomography (µCT) scanning to quantify and profile where and how the nematodes are encased following preliminary work by the supervisory team (Rae and Falkingham, under review).
Next generation technologies will be used to sequence nematode DNA. PCR amplification of several known mitochondrial and nuclear genes (18SrRNA, 28SrRNA, ITS1 and COX1) commonly used for nematode species identification (Blaxter et al., 1998) will undergo ultra-deep sequencing using illumina iSeq (housed at LJMU) to discover the species present in the shells.
In addition to work on these more modern specimens, the PhD student will visit national collections of fossil gastropods to search for any morphological evidence of encapsulation in the fossil record.
The student will have the opportunity to learn a range of skills using next generation sequencing technologies, bioinformatic analysis and Micro CT scanning equipment. It is envisaged that as this research is entirely novel (we are the only laboratory in the world conducting these experiments).
Ultimately, this PhD research has the potential to begin a new branch of ancient DNA research and could be used to study spatial and temporal changes in parasite populations in the UK (and worldwide), the evolution of parasitism as well as discovery of potentially extinct species.
Please send any expressions of interest to r.rae@ljmu.ac.uk and p.l.falkingham@ljmu.ac.uk
This PhD will be put forward for funding as part of the LJMU scholarship scheme. Please view all details here: https://www.ljmu.ac.uk/research/phd-studentship-application
Process and selection criteria: Informal expressions of interest to be made via email to r.rae@ljmu.ac.uk and p.l.falkingham@ljmu.ac.uk before 8th Uly 2024. After selection of a candidate, the application will then be submitted by the lead supervisor by the 29th July
Start date: Successful students must enrol by January/February 2025
Funding: If successful, the student will receive 3 years of scholarship funding, plus £1500 per annum bench fees.
Prof. Peter L. Falkingham 