Factors impacting sea trout (Salmo trutta) populations in changing marine environments

The brown trout (Salmo trutta L. 1758) is a widespread salmonid species that is well known for its multiple life history strategies. Some individuals remain in freshwater for the duration of their lives, and the life stages of these freshwater-resident fish have been well researched. But others implement an anadromous life history strategy where they migrate from their natal river into the marine environment before returning to their natal river to spawn. This life history strategy is beneficial to those individuals by providing them with access to additional food resources in the marine environment which ultimately leads to increased growth rates and fecundity. But with this shift in habitat comes additional risks such as increased predations and exposure to pathogens which can result in an increased level of mortality. Due to the geographic range of these anadromous fish in the marine environment, there are still several large gaps in our understanding of the movements of trout at sea, as well as the associated threats and subsequent impacts they might have on trout populations. In recent decades, it has been suggested that populations of anadromous trout (or sea trout) are experiencing a decline, however, little research has been done to quantify or explain this observed loss. This same decline was thought to have been observed in Scottish sea trout based on catch numbers, but no national trends have been reported beyond raw catch data reported by the Scottish Government on an annual basis. Using an Information Theoretic modelling approach, three measures of sea trout abundance and a variety of river, geographic and climatic variables were used to explain patterns of change in sea trout populations in Scotland. This study demonstrated overall sea trout numbers have declined 48% in the last 67 years, but that there were significant differences in the trends observed across coastal and regional spatial ranges, with some populations even showing increases in their numbers. Several river specific (river length, river gradient, geology and freshwater loch availability) and climatic variables (mean winter rainfall) were shown to act as consistent driving factors affecting population size change across this time period. One of the most consistently important drivers of sea trout populations was an interaction between river length and geographic region with longer rivers usually producing larger populations. However this relationship varied spatially and temporally and ultimately showed a significant decrease in the resilience of many sea trout populations across Scotland. The strength of the effect of some climatic variables, which vary spatially and temporally, changed with time and are predicted to continue changing given expected shifts in climate change pressures. One of the most well documented threats in the marine environment to sea trout populations is the presence of open-net pen Atlantic salmon aquaculture. This industry has been tied to numerous environmentally damaging impacts, including increased parasite levels and increased mortality in wild sea trout populations, in multiple countries in Europe and Scandinavia. The west coast of Scotland hosts one of the largest Atlantic salmon aquaculture industries that has expanded rapidly since the 1970’s. There has been little attempt to quantify the impacts of this industry on long term populations trends of sea trout on the west coast. Using an Information Theoretic modelling approach, environmental, climatic and aquaculture focused variables and three measures of abundance were used to identify drivers of change in sea trout populations on the west coast of Scotland over the last two decades. The results demonstrated that sea trout populations are reacting differently in areas with and without Atlantic salmon aquaculture but that these effects are relatively complex. Thus there is a negative effect of production biomass on sea trout populations that can be enhanced or lessened given changes in climatic variables. When sea temperatures rose above 11.0°C, sea trout populations declined with increasing net-pen biomass. During years of low winter rainfall, sea trout populations declined with increasing net-pen biomass. Given the high likelihood that these variables will change in the future due to climate change shifts, it is likely that they will impact sea trout more strongly in future years. Increased densities of Lepeophtheirus salmonis, the salmon louse, are frequently associated with areas of intensive Atlantic salmon aquaculture. At high levels, this ectoparasite can cause extensive physical damage to sea trout that can result in reduced osmoregulatory function and body condition and increased predation and mortality. To examine the range of increased lice densities on wild sea trout, sea trout populations were sampled in five sheltered coastal fjords on the Isle of Skye, Scotland at varying distances from active aquaculture sites (3 km – 48 km). While the likelihood of a sea trout having salmon lice present increased with distance from aquaculture facilities, the total lice burdens were found to be higher on individuals sampled within close proximity (within 13 km) to facility locations. The proportion of different life cycle stages of salmon lice on a sea trout was correlated with the proximity of the fish to aquaculture facilities. For example, the total lice count of a sea trout sampled near an aquaculture facility was primarily comprised of juvenile lice life stages, while sea trout sampled further away from a facility had a larger proportion of mobile adults and gravid female lice present. There is still a lack of understanding about the space use by sea trout in the marine environment in Scotland, however, it is suspected that trout populations spend part of their marine life stage in the same sheltered coastal areas that are increasingly occupied by Atlantic salmon aquaculture sites. Given the clear connection to increased salmon lice densities in the water column surrounding the aquaculture facilities in sheltered coastal areas, any overlap between habitat usage by wild sea trout and Atlantic salmon farming could have significant negative impacts on wild fish, particularly vulnerable post-smolts that have entered the marine environment for the first time. Acoustic telemetry techniques were used to gather data on the marine migration and spatial use of two different populations of sea trout post-smolts originating from two adjacent fjord systems located on the Isle of Skye, Scotland. One fjord system contained an active aquaculture facility and one did not. A total of 60 sea trout smolts were tagged and 46 of those individuals were detected on the receiver array. The study demonstrated that sea trout post-smolts maintain a strong fidelity to the coastal fjord system connected to their natal river during the first summer of their marine migration. A small percentage of the detected individuals (13 individuals, 28%) did migrate out of their natal fjord system but most (8 individuals, 17%) returned to that same fjord after a period of time foraging elsewhere. Survival and migration range were not significantly correlated to fish size. A small number of individuals (21% of detected individuals) were detected near the aquaculture facility but there was no significant difference between the amount of time spent near the facility and the amount of time spent elsewhere in the loch. The four studies presented in this thesis have combined modelling and empirical field study approaches to quantify the historical trends of sea trout populations in Scotland and identify current drivers of those trends. The results presented here can provide future insight to the predicted changes that sea trout populations will experience as their marine habitats undergo continued transformations brought on by both anthropogenic and climatic shifts