Spatial variability in farm-to-wild introgression in Scotland’s wild Atlantic salmon populations revealed using a novel spatial statistical survey design

Atlantic salmon (Salmo salar) populations are in decline across the species’ range due to multiple pressures in freshwater and marine environments. Farm-to-wild genetic introgression is a significant pressure, leading to loss of genetic adaptation, diversity, and fitness, with potentially negative consequences for life-history traits and survival. A robust understanding of the spatial extent and magnitude of genetic introgression in wild populations is required to inform sustainable management of aquaculture production and wild fish populations. This paper describes a novel approach for quantifying levels of introgression at regional and national scales across Scotland using an informative panel of single nucleotide polymorphism markers, extensive farm and wild baseline samples, and a spatial statistical survey of juvenile salmon populations (National Electrofishing Programme for Scotland, NEPS). Introgression pressures were characterized using two metrics; regional spatial extent of introgression (RSEI) (percentage of river network with hybrids present) and the magnitude of regional introgression (MRI) (mean percentage introgression in a region). RSEI provided a simple metric to link with previous studies in Scotland and elsewhere, whereas MRI allowed the magnitude of introgression to be regionally quantified for the first time. Both metrics were estimated, with standard errors, from the software that accompanies the survey design. Bootstrap hypothesis tests applied to the MRI metric were used to assess the statistical significance of regional introgression pressures. It is estimated that ca. 20% of the river network was affected by introgression at the national scale in 2021, ranging from 0% in some east coast regions to ca. 72% in west coast regions associated with high concentrations of marine aquaculture. At the national scale the mean level of introgression was estimated to be ca. 1%, ranging between 0% on the east to nearly 7% on the west. There were significant levels of introgression in 25 of the 28 regions. This study builds on recent efforts to quantify introgression pressures in support of wild fisheries management and sustainable aquaculture development. It emphasizes the importance of carefully structured juvenile sampling programmes and appropriate statistical approaches for making credible inferences as to the spatial extent and severity of introgression pressures.