Immunogenetic status of salmonid populations in Scotland

The genetic integrity of wild salmon in Scotland is being challenged by interaction with escaped farmed fish. Gene introgression from farmed to wild fish can result in genetic pollution of maladaptive alleles, the dilution and disruption of natural adaptive gene complexes, and in declining populations the erosion of standing genetic diversity which compromises the relationship between genetic variation and resilience to immune insult. Moreover, the spill over of pathogens and parasites from aquaculture can exert strong selective pressures on wild individuals that drive selective sweeps within populations, or expose wild fish to novel immunogenetic challenge.

There is a recognised need to characterise immunogenomic diversity in wild Atlantic salmon around Scotland, and examine how this is influenced by interaction with aquaculture mediated by both gene introgression and novel selection pressures. This project will detail immune gene diversity in natural populations using multiple approaches including targeted sequencing of key genes such as the MHC, and RADseq to identify genomic regions associated with immunological adaptation to or elevated levels of population genetic divergence consistent with the effects of directional selection.

The project will exploit two unique sample sets that allow for assessment of both spatial and temporal variation in immunogenetic diversity in salmon populations. First, samples collected as part of the National Electrofishing Programme for Scotland (NEPS) that covers over 400 sites and 11,000 samples across Scotland. Second, historic material (scales and tissue samples) held at Marine Scotland Science Freshwater Fisheries Lab.

The studentship will be structured around key questions that include: How much spatial and temporal immunogenetic variation exists among populations of wild salmon in Scotland? Do the levels of diversity and patterns of structure at adaptive immunogenetic markers mirror those observed for non-functional, neutral markers? How much genetic introgression has there been through escapes of farmed genetic variants associated with pathogen resistance? Can signatures of adaptation to pathogens associated with farming be detected in wild populations? Are these signatures more acute in areas associated with aquaculture? Does any historical variation in the frequency of gene variants associated with introgression or adaptation correspond with farming activity?

It is an exceptional training opportunity for a student to exploit leading edge molecular genetic approaches in an applied context that interfaces with both industry and conservation. You will be become part of a vibrant, supportive and international research team, and receive in-depth training in modern molecular and sequencing techniques, bioinformatics and statistical modelling.

The student will also benefit from wider interactions with other projects funded by the Scottish Universities Partnership for Environmental Research (SUPER) Doctoral Training Partnership (NERC) and collaboration with the Marine Scotland Science freshwater fisheries laboratory.