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Adapting to life in an increasingly acid world: understanding tolerance to acidic waters in populations of trout (Salmo trutta)

  • Full or part time
  • Application Deadline
    Monday, January 07, 2019
  • Competition Funded PhD Project (European/UK Students Only)
    Competition Funded PhD Project (European/UK Students Only)

Project Description

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

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

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.

Funding Notes

“NERC GW4+ funded studentship available for September 2019 entry. For eligible students, the studentship will provide funding of fees and a stipend which is currently £14,777 per annum for 2018-19.


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.”


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.

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