outbreaks. Other evolutionary processes that lead to rapid spreading of bacterial ancestral lineages include rapid selection and extreme host-to host transmission bottlenecks. Understanding these processes is essential for studying bacterial evolution, the emergence of antibiotic resistance, and the spread of infectious diseases. However, most statistical population models used to analyse bacterial genomic diversity were originally developed for the other kingdoms of life and often assume that ancestral lineages are more stable and do not spread rapidly. Consequently, recent studies show that such population models do not explain all bacterial datasets well.
Alternative statistical models for describing rapidly spreading ancestral lineages exist, but have yet to be thoroughly employed in bacterial genomics The main aim of this project is to test and apply these models to real-world genomic datasets and investigate how different evolutionary processes play out in real bacterial populations. To this end, you will analyse in-house and publicly available genomic datasets to: i) identify rapidly evolving ancestral lineages; ii) characterize the genetic signatures associated with rapid evolutionary processes; and iii) develop a novel, simulation-based framework to distinguish between alternative evolutionary scenarios/models.
This project will contribute new tools for understanding bacterial evolution and predicting the spread of clinically important lineages.
Techniques that will be undertaken during the project
- Bioinformatics to handle genomic data sets and extract genetic diversity measures
- Understanding population genomics theoretical models for genetic diversity, linking these to biological, ecological and epidemiological features of
- genomics data sets of bacteria.
- Applied statistical method adjustment and development to compare models of genetic diversity with genomic data
- Machine learning techniques, e.g. Approximate Bayesian Computation, and simulation of genomic data
Enquiries
Project Enquiries to ff95@leicester.ac.uk
Programme enquiries to mibtp-admin@leicester.ac.uk
To apply please refer to
https://le.ac.uk/study/research-degrees/funded-opportunities/bbsrc-mibtp
Funding Notes
All MIBTP students will be provided with a 4 year studentship. This includes: Tuition fees at the UK fee rate*, a tax free stipend which for 2026/7 is £21,805 per year (2027/8 stipend to be confirmed), a travel allowance over years 1-3, a travel/conference budget, a generous consumables budget, use of a laptop for the duration of the programme. The University of Leicester will provide full overseas fee waivers for the duration of their study to all international students accepted at Leicester. The funder, UKRI, allows us to appoint up to 30% overseas students.
