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

University of Exeter - Biosciences

Qualification Type: PhD
Location: Exeter
Funding for: UK Students, EU Students
Funding amount: £14,777 Per annum for 2018-19
Hours: Full Time
Placed On: 6th November 2018
Closes: 7th January 2019
Reference: 3320

Supervisory team:

Prof Jamie Stevens, University of Exeter

Dr Andrew Griffiths, University of Exeter

Bruce Stockley, Westcountry Rivers trust, Fisheries

Prof Martin Genner, University of Bristol

This project is one of a number that are in competition for funding from the NERC GW4+ Doctoral Training Partnership. 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 description: 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.

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.

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.

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