Quantifying the Rate and Fate of Bacterial Gene Content Evolution - Medicine, PhD (BBSRC SWBio DTP Funded)

The South West Biosciences Doctoral Training Partnership (SWBio DTP) is a BBSRC-funded PhD training programme in the biosciences, delivered by a consortium comprising the Universities of Bristol (lead), Bath, Cardiff, Exeter, and Rothamsted Research. Together, these institutions present a distinctive cadre of bioscience research staff and students with established international, national and regional networks and widely recognised research excellence. The partnership has a strong track record in advancing knowledge through high quality research and teaching in partnership with industry and government.

This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP). Up to 4 fully-funded studentships are being offered to start in September 2018 at the University of Exeter.

Supervisory Team:

Main supervisor: Dr Michiel Vos
Co-supervisor: Prof Edward Feil
Co-supervisor: Ben Temperton
Collaborator: Prof Adam Eyre-Walker

Location: University of Exeter, Truro, Cornwall

Project description:

Bacteria are the most abundant and diverse life forms on earth, vital to the functioning of all ecosystems and to human health and wellbeing. Bacteria rely on a highly diverse array of mechanisms to create genomic changes which, combined with usually enormous population sizes, can result in rapid evolutionary change. Most bacterial species have ‘fluid’ genomes, where a stable core genome is complemented by an accessory set of genes that can be rapidly taken up through lateral transfer and lost through deletion

(1). Such Gene Content Changes (GCC) have been estimated to occur at rates similar to nucleotide substitution in the core genome and are likely to have more significant effects on fitness

(2). Despite its importance to bacterial evolution, the rate of gene content turnover and the selective effects of GCC are not well-understood. Some researchers argue that most changes have only small effects on fitness

(3), whereas others argue that most variation in accessory genes is adaptive

(4). As the tempo and mode of bacterial evolution is fundamental to a wide range of fields, from molecular epidemiology to biotechnology, this controversy needs to be resolved.

This project takes a comparative genomics approach to

1) explicitly measure the rate of GCC in a range of different bacteria and

2) develop novel tests of selection to quantify the selective effects of gene content change.

Entry requirements:

Applicants should have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology. Applicants with a Lower Second Class degree will be considered if they also have Masters degree or have significant relevant non-academic experience.

In addition, due to the strong mathematical component of the taught course in the first year and the quantitative emphasis in our projects, a minimum of a grade B in A-level Maths or an equivalent qualification or experience is required.

If English is not your first language you will need to have achieved at least 6.5 in IELTS and no less than 6.5 in any section by the start of the project. Alternative tests may be acceptable, please see http://www.bristol.ac.uk/study/language-requirements/profile-c/.

Students from EU countries who do not meet the residency requirements may still be eligible for a fees-only award but no stipend. Applicants who are classed as International for tuition fee purposes are not eligible for funding. Further information about eligibility can be found in the following document: http://www.bbsrc.ac.uk/documents/studentship-eligibility-pdf/