Population genomics of evolution in action in the Trinidadian guppy

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 of Exeter plus five Research Organisation partners: British Antarctic Survey, British Geological Survey, Centre for Ecology and Hydrology, 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 http://nercgw4plus.ac.uk/

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

Supervisory team:
Dr Bonnie Fraser, Department of Biosciences, College of Life and Environmental Sciences, University of Exeter.
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.

Project details:
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 but that the majority of the genome remains similar. This indicates that transplanting fish didn’t result in a large bottleneck and that these divergent regions could be underlying adaptive changes, especially where the same regions are seen across many populations.

Project Aims and Methods
The proposal aims to study evolution in action by taken advantage of a unique experimental fish system. The successful student will investigate how these 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. We have access 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:

1-How are alleles selected for overtime?

2-Do independent populations evolve along the same trajectory?

3-How does evolution interact with changes in population growth and mortality?

Training
The student will receive state-of-the-art training in genomics and bioinformatics. There will opportunities to attend workshops either in the UK or Europe where the student will be taught by leaders in the field of genomics. There will also be opportunities to travel to Trinidad to examine the experimental evolution populations.