Adapting to life in an increasingly acid world: understanding tolerance to acidic waters in populations of trout (Salmo trutta), NERC GW4+ DTP, PhD in Biosciences Ref: 3320

About the award


Lead Supervisor

Dr Jamie Stevens, Dept of Biosciences, College of Life and Environmental Sciences, University of Exeter

Additional Supervisors

Dr Andrew Griffiths, Dept of Biosciences, College of Life and Environmental Sciences, University of Exeter

Dr Bruce Stockley, Westcountry Rivers Trust, Fisheries

Prof Martin Genner, University of Bristol, School of Biological Sciences

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

Main Information

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

For eligible successful applicants, the studentships comprises:

  • An index-linked stipend for 3.5 years (currently £14,777 p.a. for 2018/19);
  • Payment of university tuition fees;
  • A research budget of £11,000 for an international conference, lab, field and research expenses;
  • A training budget of £4,000 for specialist training courses and expenses.

Up to 30 fully-funded studentships will be available across the partnership.

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.

Project details

Increasingly, research is focusing on “climate change's evil twin”, i.e. ocean acidification, but many freshwater systems are also under threat from the acidifying effects of climate change and acid rain (Hasler et al. 2016). This project centres on Dartmoor National Park, a unique, protected upland habitat in southwest England, where many rivers are markedly acidic (EA data). Despite this, Dartmoor rivers host healthy populations of trout and salmon, and molecular analysis has shown trout from acid rivers to be genetically distinct (Griffiths et al. 2009). Working in collaboration with the Westcountry Rivers Trust (a large environmentally-focused charity working to restore and protect rivers in the region), this project will investigate the genetic and physiological basis of this apparent tolerance to acid waters in trout inhabiting Dartmoor rivers. This has implications for conservation, but will also provide insight into evolutionary processes of local adaptation in a species of commercial significance for both angling and aquaculture.

Project Aims and Methods

This project aims to identify the basis of tolerance to acid waters in brown trout through analysis of single nucleotide polymorphisms (SNPs) and changes in gene expression. We propose to use the complementary approaches of RADseq and RNAseq to study trout populations inhabiting acid, neutral and alkaline rivers in southern Britain. This will allow us to explore common/convergent evolutionary 'solutions' to acid tolerance.
Understanding the genetic basis of acid tolerance in trout – In the absence of a published genome, we will use RADseq analysis of fish from rivers with low pH (Dartmoor streams), neutral rivers (other rivers in Cornwall and Devon) and more alkaline waters (chalk streams, Dorset/Hampshire). We hold an extensive tissue samples from trout across these regions, and more will be collected during the project (enabling the student to conduct their own fieldwork). Critically, the sampling design allows us to eliminate the effects of differential genetic drift and catchment-specific selective pressures; this will allow us to identify SNPs that segregate definitively between the ecotypes and to identify regions of the trout genome associated with adaptions to living in a low pH environment.
Exploring changes in gene expression related to highly acidic conditions – RNAseq analysis will facilitate characterisation of changes in gene expression related to acidity, identifying genes important to physiological responses in wild trout populations.
By combining population genomic and gene expression approaches, the study will provide a better understanding of the basis of acid tolerance in salmonid fish. The project addresses long-standing questions regarding how this species thrives in an otherwise species-poor (highly acid) ecosystem. Such information will be invaluable in conservation and aquaculture in the face of global environmental change. 

CASE or Collaborative Partner 

The CASE partner, Westcountry Rivers Trust (WRT;, carries out extensive electrofishing surveys and river monitoring in a range of environment types across southwest England. WRT has extensive local knowledge and permissions from owners to access field sites; this information is absolutely critical for the collection of the sample material necessary for the success of this project. The collaboration will also provide the student with the opportunity to engage in fieldwork (electrofishing) and to participate in environmental data collection and recommendations for monitoring. The Trust will provide real insights into working with charities, local conservation, outreach/education and interactions with stakeholders.


WRT offers formal qualification in electrofishing, certified by the Institute of Fisheries Management; this will be of value to the student in terms of professional development. At Exeter the student will gain experience in cutting-edge molecular biological techniques, bioinformatic methods and landscape genetics analysis.



Fig.1 Returning Unharmed Fig.2 Electrofishing trout on Dartmoor

References / Background reading list

Griffiths, A.M., I. Koizumi, D. Bright & J.R. Stevens (2009). Evolutionary Applications, 2: 537-554.

Hasler C.T., Butman D.,Jeffrey J.D. & C.D. Suski (2016). Ecology Letters, 19: 98-108.


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.   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.

Candidate Requirements
Candidates should demonstrate a passion for the use of modern molecular methods in conservation and environmental biology – experience in population genetics would be advantageous, and training is available. Fieldwork in relatively remote areas will be required and the ability to drive would be useful.

All applicants would need to meet our English language requirements by the start of the  project


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”.

  • CV
  • 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.
  • Two References (applicants are recommended to have a third academic referee, if the two academic referees are within the same department/school).

Reference information
You will be asked to name two referees as part of the application process.  It is your responsibility to ensure that your two referees email their references to, as we will not make requests for references directly; you must arrange for them to be submitted by 7 January 2019

References should be submitted 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 midnight on 7 January 2019.  Interviews will be held between 4 and 15 February 2019.

If you have any general enquiries about the application process please email  Project-specific queries should be directed to the supervisor.


Data Sharing
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:7th January 2019
Value:£14,777 per annum for 2018-19
Duration of award:per year
Contact: PGR Enquiries