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Integrating fish tracking and genetics to inform conservation management of Atlantic salmon and guide marine offshore development in Scotland

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  • Full or part time
    Dr D del Villar
    Dr E Verspoor
  • Application Deadline
    No more applications being accepted
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

The potential impacts of offshore tidal and wind farm developments on Scotland’s socio-economically valuable wild salmon resources has given rise to significant concerns related to the possible influences on their behaviour from noise or electromagnetic fields. This could potentially lead to direct impacts from collision with underwater turbines, or indirect impacts through disorienting salmon, reducing homing success or increasing predation. Thus, an accurate method for monitoring changes in salmon abundance and distribution in areas affected by offshore developments is needed. Catch statistics are notoriously problematic for monitoring population numbers as they can be affected by angling pressure which can vary spatially and temporally, with water conditions, etc. Estimates based solely on juvenile abundance are equally problematic given that juvenile numbers are regulated by density dependent processes and poorly reflect the numbers of returning spawners. The use of fish counters is also problematic largely due to the costs of their construction and operation, and the fact that they seldom work well under all water flow conditions. In contrast, the combination of fish tracking, and growth information and molecular genetic markers offer the possibility to more accurately and consistently estimate the abundance and distribution of fish and detect significant changes if they occur.

The aim of the project is to develop an integrated fish tracking-phenotypic-genetic approach to understanding Atlantic salmon biology in relation to environmental impacts on abundance. This approach will inform marine offshore development in Scotland, helping to inform the development of policies and guidelines to mitigate possible impacts on salmon stock abundance, distribution and viability. This research combines both field and experimental lab work. The project will involve formal training in fish tracking, spatial ecology, molecular genomics and population genetics and statistical analysis and involve the exploitation of existing data and generation of new data. These disciplines and different data sources will be used in combination to develop a unique approach to biological impact monitoring.

The successful applicant will have to meet the Scottish Government Baseline Personnel Security Standard.

Supervisory Team

The student will be supervised by Dr Diego del Villar and senior scientist Alan Youngson of the Environmental Research Institute, and Professor Eric Verspoor of the Rivers and Lochs Institute, University of Highlands and Islands, in collaboration with Dr Ian Davies of Marine Scotland Science, Marine Laboratory, Aberdeen.

Research Facilities and Environment

The student’s primary base will be at the Environmental Research Institute, Thurso, and secondarily at the Rivers and Loch Institute, Inverness College on the new Inverness Campus.

The Environmental Research Institute (ERI) in Thurso is uniquely placed to access some of Europe’s most distinct and unique habitats, ecosystems and environments. It is also an area of Scotland where large developments of marine renewable energy sites are planned. Based at the ERI, the student will work alongside internationally recognised researchers and a network of PhD students working on different aspects of renewable energy and the environment. The student will use state-of-the-art technologies for fish tracking (both in fresh and saltwater) and the study of the environment (CTDs, ADCPs, X-Band radar, ROV, Drones, and a research boat) to investigate the underlying mechanisms of salmon migrations. At the RLI, the student will work as part of a small growing, dynamic team of researchers focused on aquatic biodiversity conservation and management. The RLI is internationally recognized for its expertise in in the development of molecular genetic markers, applied molecular population genetics, fisheries management, and fish phylogeography. The RLI work is supported by a state-of-the-art molecular genomics facility encompassing Sanger and NexGen sequencing systems, qPCR, high throughput DNA fragment analysis instrumentation, with technical, bioinformatics, computing and statistical support. The student will receive training in manuscript writing and research presentation as well as engage in-house seminars in research skill development, and contribute to weekly alternating journal club and work presentation meetings.

There will also be opportunities to attend relevant national and international conferences.

The involvement of Marine Scotland Science will provide the student with direct contact with applied aspects of the project, understanding of regulatory requirements and processes, and contact with staff involved in advising on licensing and policy development. MSS is a key end-user of this research.

Informal project specific enquiries can be made to: [Email Address Removed]

Funding Notes

This studentship is funded by the European Social Fund and Scottish Funding Council as part of Developing Scotland’s Workforce in the Scotland 2014-2020 European Structural and Investment Fund Programme.

The studentship covers fees at the Home/EU rate only, plus a stipend at the RCUK level, for a total of 42 months (including writing-up). Funding is available for students worldwide, however non UK/EU students will be liable for the difference between home/EU and international fees.

Students must be domiciled in the Highlands and Islands transition region during the course of their study to be eligible for funding.


Bradbury, I. R., Hamilton, L. C., Dempson, B., Robertson, M. J., Bourret, V., Bernatchez, L. & Verspoor, E. (2015). Transatlantic secondary contact in Atlantic salmon, comparing microsatellites, a single nucleotide polymorphism array and restriction‐site associated DNA sequencing for the resolution of complex spatial structure. Molecular Ecology, 24(20), 5130-5144.

Malcolm, I. A., J. D. Armstrong, J. D. Godfrey, J. C. MacLean, and S. J. Middlemas. "The scope of research requirements for Atlantic salmon, sea tout and European eel in the context of offshore renewables. Pitlochry, Scotland. UK: 2013 Marine Scotland Science Report 05/13."

Malcolm, I. A., J. Godfrey, and A. F. Youngson. "Review of migratory routes and behaviour of Atlantic salmon, sea trout and European eel in Scotland’s coastal environment: implications for the development of marine renewables." Scottish Marine and Freshwater Science 1, no. 14 (2010): 1-72.

Verspoor, E., Stradmeyer, L & Nielsen, J.L. (eds). (2007) The Atlantic Salmon: Genetics, Conservation & Management. Blackwell Publishing, Oxford. 500pp.

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