NERC GW4+ DTP PhD Studentship: Evolutionary and ecological factors shaping genome composition of a social microbe

This project is one of a number that are in competition for funding from the NERC Great Western Four+ Doctoral Training Partnership (GW4+ DTP). The GW4+ DTP consists of the Great Western Four alliance of the University of Bath, University of Bristol, Cardiff University and the University Exeter plus six Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology and Hydrology, the Met Office, the Natural History Museum and Plymouth Marine Laboratory. The partnership aims to provide a broad training in earth and environmental sciences, designed to train tomorrow’s leaders in earth and environmental science. For further details about the programme, please see https://nercgw4plus.ac.uk/ .

Supervisory team -

Main Supervisor: Prof. Jason Wolf, Department of Biology and Biochemistry, University of Bath
Co-Supervisor: Dr. Alex Hayward, Department of Biosciences, University of Exeter
Co-Supervisor: Prof. Sam Sheppard, Department of Biology and Biochemistry, University of Bath

Project background -

The social amoeba Dictyostelium discoideum (‘Dicty’) lives as single celled individuals in the soil, where they consume bacteria and undergo vegetative growth. However, when food becomes scarce they aggregate to form a multicellular slug that migrates and forms a fruiting body composed of a dead stalk that holds aloft a sorus of viable spores. This process of aggregation and developmental differentiation represents a social stage where cells cooperate to form a functioning fruiting body and compete for space in the sporehead. Consequently, Dicty have been used as an ecological model to study predation and as an evolutionary model to study sociality. We have pursued these areas of research by sequencing large numbers of Dicty strains collected from natural populations. This prior work forms the foundation for this project, which will utilize and build on our existing datasets to analyse a series of questions about the evolutionary and ecological processes that have shaped the composition of the Dicty genome.

Project aims and methods -

The project aims are hierarchical and flexible, proving many opportunities for student led avenues of inquiry. The goal is to first characterise patterns of gene gain and loss across lineages sampled from natural populations. For this we will utilise existing sequence, but we will complement our existing data with acquisition of new sequence data as needed. We will then relate these profiles to ecological factors across populations and to patterns of sequence evolution within and among closely related species. This aspect is especially flexible and can allow students to pursue their own directions across a range of factors. Finally, we will apply a number of fine-scale tools that can dissect the independent evolutionary histories of different genes and genome regions to understand the mosaic nature of evolutionary and ecological processes shaping the genome.

Candidate -

This project will apply modern and cutting-edge approaches from the field population genetics and bioinformatics. Therefore, some familiarity with computer programming, bioinformatics, and statistics (e.g., R) will be beneficial, but not essential.

Training -

The student will be trained in aspects of computer programming (e.g., Matlab, Python) and statistical programming (using R). They will also receive training in statistical theory, bioinformatics, analysis of sequence evolution, and evolutionary mathematical modelling. In addition to these project specific components of training, the student will benefit from the career development, research and transferrable skills training provided by the NERC GW4+ DTP.

Anticipated start date: 30 September 2019

Candidates should apply using University of Bath’s online application form https://www.bath.ac.uk/study/pg/applications.pl#bio-sci

You may apply for more than one project if you wish but you should submit a separate personal statement relevant to each one.

Further information on the Department of Biology & Biochemistry may be found here http://www.bath.ac.uk/departments/department-of-biology-biochemistry/