Investigating evolution in real time using genomics. PhD in Biosciences (NERC GW4 + DTP)

Lead Supervisor
Dr Bonnie Fraser, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors
Professor Mark Beaumont, School of Biological Sciences, University of Bristol
Professor Alastair Wilson, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter

Location: University of Exeter, Streatham Campus, Exeter, EX4 4QJ

This project is one of a number that are in competition for funding from the NERC GW4+ Doctoral Training Partnership (GW4+ DTP). The GW4+ DTP consists of the GW4 Alliance of research-intensive universities: the University of Bath, University of Bristol, Cardiff University and the University of Exeter plus five unique and prestigious Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology & Hydrology, the Natural History Museum and Plymouth Marine Laboratory. The partnership aims to provide a broad training in the Earth, Environmental and Life sciences, designed to train tomorrow’s leaders in scientific research, business, technology and policy-making. For further details about the programme please see http://nercgw4plus.ac.uk/

For eligible successful applicants, the studentships comprises:

- An stipend for 3.5 years (currently £15,009 p.a. for 2019/20) in line with UK Research and Innovation rates
- Payment of university tuition fees;
- A research budget of £11,000 for an international conference, lab, field and research expenses;
- A training budget of £3,250 for specialist training courses and expenses.
- Travel and accommodation is covered for all compulsory DTP cohort events.
- No course fees for courses run by the DTP

We are currently advertising projects for a total of 10 studentships at the University of Exeter


Project Background

How populations adapt to new and changing environments is becoming more and more important for understanding our rapidly changing world. While, we know that these rapid changes are often heritable we don’t know much about the genetics underlying these changes. We are now at stage where whole genomes can be examined for many organisms, and therefore we can target rapidly evolving populations to examine the genetic basis of rapid adaptation.

This proposal will take advantage of a unique evolution experiment in the wild. Here, guppies (small tropical fish) were transplanted from a high predation locality upstream above waterfall barriers where they are free from predation in four independent streams. Phenotypic data shows that the populations quickly adapted to their new environments by becoming larger and more colourful; traits that evolve in naturally colonized low predation localities. We have shown that after just 5 years, these populations are diverging from their source at isolated parts of the genome, indicating adaptive genetic changes.

Project Aims and Methods

The proposal aims to study evolution in action by taking advantage of a unique experimental fish system. The successful student will investigate how newly introduced populations adapted to their new environments by looking at whole genome sequences (WGS) from across multiple time points.

This project will use WGS of the four newly introduced populations at different sampling time points (5 years, and 10 years after introduction), their source population, and naturally colonized low predation populations. Our lab has extensive expertise in working with whole genome datasets including developing genome assembly resources. This project also will have the unique opportunity to compare genomics data to population demography and phenotypic data collected monthly in Trinidad as part of a large mark recapture program.

The project will answer three major questions:

- How are genomes evolving over time?
- Do independent population evolve convergently?
- How does evolution interact with the changing ecology (i.e. population growth)?