Salmon farming in Scotland: quantifying the actual levels of interbreeding and gene introgression of farm escapes with wild populations

Aquaculture is fast outpacing the production of wild fisheries and there is increasing concern regarding the potential negative impacts of farm escapes on wild populations of conspecifics. Scotland has the second largest Atlantic salmon farming industry in the species’ native North Atlantic range, after Norway. In 2015, this encompassed a production of >40 million smolts and > 171,000 tonnes of salmon for market, with increased production planned for coming years. Scotland also has hundreds of rivers with wild salmon stocks that are the mainstay of a vital recreational fishing industry that is a major contributor to the nation’s economic wealth.

The project involves the exploitation of diagnostic molecular markers developed by the RLI as part of a UK Research Council aquaculture sector funded international research collaboration with partners in Norway, Scotland, Ireland and Canada to differentiate farm and wild Atlantic salmon. These will be used to assess actual levels of escaped farm salmon in rivers across Scotland, of interbreeding, and of genetic introgression. The lack of understanding of these factors precludes the effective management of the species, risking unacceptable impacts on wild stocks or holding back expansion of the farming industry, or potentially both. In Norway, genetic mixing is highly variable, from 0-47% while in Scotland only a few, ad hoc studies have been carried out on levels of direct genetic interaction and most of these are dated and provide insight into only a few rivers with general, contemporary levels being poorly documented.

Knowledge of the level of interbreeding and introgression can help guide locational development of the farming industry to minimize impacts on wild stocks and fisheries. Where it can be demonstrated to be limited or absent, this will also help to gain Marine Stewardship certification for farmed salmon products. The project will involve collaboration with local fisheries management organisations to collect contemporary samples of salmon in a representative set of Scottish rivers and to genetically screen these fish, along with archived historical samples, with the farm-wild markers. Levels of escapement, interbreeding and introgression will be quantified, mapped and the factors accounting for observed levels investigated. The implications of observed levels will be explored using an existing individual based genetic-demographic reproductive interaction model.

Supervisory Team
The student will be supervised by Dr Mark Coulson and Professor Eric Verspoor of the Rivers and Lochs Institute.

Research Facilities and Environment
The student will be based in the Rivers and Loch Institute at the University of the Highlands and Islands Inverness College on the new Inverness Campus and part of a small but growing, dynamic team of researchers focused on aquatic biodiversity conservation and management.

The RLI is recognized internationally for its expertise in genetic issues related to aquaculture-wild interactions and as well as in the development of molecular genetic markers, applied molecular population genetics, fisheries management, and fish phylogeography. It is also extending its programme of work to encompass eDNA, DNA barcoding, and metabarcoding, across the spectrum of aquatic organisms, with a focus on freshwater ecosystems.

The Institute provides a stimulating and vibrant research environment, 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 support, and in-house 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.