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EASTBIO How does selection shape immunity in wild and captive populations?

School of Biological Sciences

Dr Kara Layton , Prof S Martin , Prof R Houston Wednesday, January 06, 2021 Competition Funded PhD Project (Students Worldwide)

About the Project


Dr Kara Layton (University of Aberdeen)

Professor Samuel Martin (University of Aberdeen)

Professor Ross Houston (University of Edinburgh)

Immune systems are influenced by environmental conditions and in turn pathogenic landscapes vary across geographic regions. There is a need to better understand the selective landscape of immune genes because this provides important information about adaptive genetic variation that is especially relevant in the face of a changing climate. Selection for diversity in immune genes may also vary among wild and captive populations since environmental conditions and pathogen exposure differ among them, but little work has been dedicated to investigating this. Farmed salmonids dominate the aquaculture industry in the UK (worth over £1 Billion), while their wild counterparts play a vital ecological role as keystone species in aquatic ecosystems, making this an ideal system for investigating the effects of environment and domestication on immunity. With environmental change driving salmonid declines across the globe, understanding how selection shapes the immune repertoire of this group is of critical importance.
This PhD will examine immune gene diversity in wild and captive salmonid populations to determine the effects of environment and domestication on genes involved in immune function and defence to pathogens, with a focus on Arctic Charr (Salvelinus alpinus) and Atlantic Salmon (Salmo salar). There is also the potential to examine links between life history and immune gene diversity since wild salmonids have both migratory and non-migratory ecotypes. Given the broad phylogenetic and environmental diversity across this system, there is strong potential for comparative research. The major histocompatibility complex (MHC) is an ideal candidate for this work since variation at these genes is shaped by both historical and ongoing selection. The results of the project will inform wild and farmed population management and sustainable genetic improvement in salmonid aquaculture.
The project will be supervised by Dr. Kara Layton and Prof. Samuel Martin (Scottish Fish immunology Research Centre) in the School of Biological Sciences, University of Aberdeen and by Prof. Ross Houston at the Roslin Institute, University of Edinburgh. A large collection of samples and data are already available for this work but there may be an opportunity for the student to collect additional samples through field work in the UK, Europe and Canada, expanding both the taxonomic and geographic scope of this work. The student will gain skills in molecular data generation and analysis, bioinformatics, science communication and writing, among other transferrable skills.

Application Procedure:

Please send your completed EASTBIO application form, along with academic transcripts to Alison McLeod at . Two references should be provided by the deadline using the EASTBIO reference form. Please advise your referees to return the reference form to .

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership View Website. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (limited funding is available to provide international tuition fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.

Candidates should have (or expect to achieve) a minimum of a 2:1 UK Honours degree, or the equivalent qualifications gained outside the UK, in a relevant subject.


Houston RD, Bean TP, Macqueen DJ, … Martin SAM … Robledo D. 2020. Harnessing genomics to fast-track genetic improvement in aquaculture. Nature Reviews Genetics, 21, 389 – 409.

Król E, Noguera P, Shaw S, … Martin SAM. 2020 Integration of transcriptome, gross morphology and histopathology in the gill of sea farmed Atlantic Salmon (Salmo salar): Lessons from multi-site sampling. Frontiers in Genetics, 11, 610.

Layton KKS, Snelgrove PVR, Dempson JB ... Bradbury IR. Past and future climate-linked loss in the most northerly freshwater fish. In review: Nature Climate Change.

O'Connor EA, et al. 2020. Wetter climates select for higher immune gene diversity in resident, but not migratory, songbirds. Proceedings of the Royal Society B: Biological Sciences, 287, 20192675.

Schenekar T, Weiss S. 2017. Selection and genetic drift in captive versus wild populations: an assessment of neutral and adaptive (MHC-linked) genetic variation in wild and hatchery brown trout (Salmo trutta) populations. Conservation Genetics, 18, 1011–1022.

Yáñez JM, Houston RD, Newman S. 2014. Genetics and genomics of disease resistance in salmonid species. Frontiers in Genetics, 5, 415.
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