Investigating evolution in real time using genomics. Biological Sciences PhD Studentship (NERC GW4+ DTP funded) Ref: 4008
About the award
Bonnie Fraser, University of Exeter (Streatham), Biosciences
Mark Beaumont, University of Bristol, School of Biological Sciences
Alastair Wilson, University of Exeter (Penryn), Biosciences
Location: Streatham Campus, University of Exeter, Exeter, Devon
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/
For eligible successful applicants, the studentships comprises:
- An stipend for 3.5 years (currently £15,285 p.a. for 2020-21) 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.
- Up to £750 for travel and accomodation for compulsory cohort events.
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.
Trinidadian guppies, where males attract females with their colour patterns but these colours can also attract predators
Whole genome alignments between guppy and platyfish genomes
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. The project will answer three major questions:
1) How are genomes evolving over time?
2) Do independent population evolve convergently?
3) How does evolution interact with the changing ecology (i.e. population growth)?
We are looking for a student with a passion of evolutionary biology and how it relates to ecology, particularly at the genomic level. The project will use bioinformatic scripting methods (e.g. unix, python, R). Prior experience of these would certainly be an asset, but full training will be provided during the PhD so interest and willingness to learn is much more important. Field work in Trinidad is not necessary but could occur depending on how the project develops and the interest of the student.
The student will receive state-of-the-art training in genomics and bioinformatics. There will opportunities to attend workshops and conferences 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.
Background reading and references
Fraser et al. 2015 Population genomics of natural and experimental populations of guppies (Poecilia reticulata). Molecular Ecology 24:389-408.
Fraser and Whiting 2019. What can be learned by scanning the genome for molecular convergence in wild populations? Annals of the NY Academy of Science In press doi:10.1111/nyas.14177
Reznick et al. 2019. Eco-evolutionary feedbacks predict the time course of rapid life history evolution. American Naturalist In Press doi:10.1086/705380.
NERC GW4+ DTP studentships are open to UK and Irish nationals who, if successful in their applications, will receive a full studentship including payment of university tuition fees at the home fees rate.
A limited number of full studentships are also available to international students which are defined as EU (excluding Irish nationals), EEA, Swiss and all other non-UK nationals. For further details please see the NERC GW4+ website.
Those not meeting the nationality and residency requirements to be treated as a ‘home’ student may apply for a limited number of full studentships for international students. Although international students are usually charged a higher tuition fee rate than ‘home’ students, those international students offered a NERC GW4+ Doctoral Training Partnership full studentship starting in 2021 will only be charged the ‘home’ tuition fee rate (which will be covered by the studentship). International applicants need to be aware that you will have to cover the cost of your student visa, healthcare surcharge and other costs of moving to the UK to do a PhD. More information on this is available from the universities you are applying to (contact details are provided in the project description that you are interested in
The conditions for eligibility of home fees status are complex and you will need to seek advice if you have moved to or from the UK (or Republic of Ireland) within the past 3 years or have applied for settled status under the EU Settlement Scheme.
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. Applicants with a Lower Second Class degree will be considered if they also have Master’s degree. Applicants with a minimum of Upper Second Class degree and significant relevant non-academic experience are encouraged to apply.
All applicants would need to meet our English language requirements by the start of the project http://www.exeter.ac.uk/postgraduate/apply/english/.
How to apply
In the application process you will be asked to upload several documents. Please note our preferred format is PDF, each file named with your surname and the name of the document, eg. “Smith – CV.pdf”, “Smith – Cover Letter.pdf”, “Smith – Transcript.pdf”.
- Letter of application outlining your academic interests, prior research experience and reasons for wishing to undertake the project.
- Transcript(s) giving full details of subjects studied and grades/marks obtained. This should be an interim transcript if you are still studying.
- If you are not a national of a majority English-speaking country you will need to submit evidence of your current proficiency in English.
You will be asked to name 2 referees as part of the application process, however we will not expect receipt of references until after the shortlisting stage. Your referees should not be from the prospective supervisory team.
If you are shortlisted for interview, please ensure that your two academic referees email their references to the firstname.lastname@example.org, 7 days prior to the interview dates. Please note that we will not be contacting referees to request references, you must arrange for them to be submitted to us by the deadline.
References should be submitted by your referees to us directly in the form of a letter. Referees must email their references to us from their institutional email accounts. We cannot accept references from personal/private email accounts, unless it is a scanned document on institutional headed paper and signed by the referee.
All application documents must be submitted in English. Certified translated copies of academic qualifications must also be provided.
The closing date for applications is Friday 8 January 2021 2359 GMT . Interviews will be held between 8th and 19th February 2021. For more information about the NERC GW4+ DPT please visit https://nercgw4plus.ac.uk
If you have any general enquiries about the application process please email email@example.com. Project-specific queries should be directed to the lead supervisor.
During the application process, the University may need to make certain disclosures of your personal data to third parties to be able to administer your application, carry out interviews and select candidates. These are not limited to, but may include disclosures to:
- the selection panel and/or management board or equivalent of the relevant programme, which is likely to include staff from one or more other HEIs;
- administrative staff at one or more other HEIs participating in the relevant programme.
Such disclosures will always be kept to the minimum amount of personal data required for the specific purpose. Your sensitive personal data (relating to disability and race/ethnicity) will not be disclosed without your explicit consent.
|Application deadline:||8th January 2021|
|Value:||£15,285 per annum for 2020-21|
|Duration of award:||per year|
|Contact: PGR Enquiriesfirstname.lastname@example.org|