The population structure of wild Scottish brown trout (Samo trutta L.1758) of Loch Maree, Wester Ross: spatial genetic distribution after population decline

The wild trout of Loch Maree is an understudied population that recently experienced a population decline after once having a world status for its sea trout fisheries. Tissues and specimens sampled over the last decade exist in archives and have yet to undergo population genetic analysis. This study aims firstly to determine the best approach to characterising the genetic structure of the Salmo trutta population of Wester Ross with the available archived tissues/specimens. The population structure observed will then be analysed so as to examine the effects of the Wester Ross geography and topography upon the trout population’s genetic diversity. Nine markers from the Beaufort Trout MicroPlex microsatellite panel were used to genotype 192 Salmo trutta samples sampled across 35 sites within Loch Maree and neighbouring catchments, split into four major resident regions: NW-, CW- and SE Loch Maree, and Gairloch, as well as sea trout from the Ewe and Flowerdale systems. Results suggest the population genetics of brown trout in Wester Ross are structured at regional and river scales, and suggests a genetic bottleneck caused by the population decline is still detectable. “Within-population” genetic diversity seems similar between regional populations sampled. Differences observed in population allele frequencies suggest the Gairloch and NW Loch Maree populations are the most similar regional populations analysed, with significant departures from Hardy-Weinberg equilibrium in almost all their loci, suggesting they may be under significant environmental pressure. The Wester Ross sea trout seem to be an admixture of the resident trout populations, with overlapping coastal ranges. Headwater populations have reduced genetic diversity compared downstream which may be influenced by genetic drift in isolation caused by barriers such as waterfalls and dams. A positive correlation was also observed between geo-hydrological distance and genetic divergence within regional resident trout populations, with a degree of introgression between all populations that are hydrologically connected. The analysis also suggest Loch Maree was likely colonised initially at the NW point by ancient migrant sea trout rather than a freshwater-radiation from an inland glacial refuge since the retreat of the last glacial maximum