title: The behaviour of Atlantic salmon (Salmo salar) on first migration to sea
Creators: name: Lilly, Jessie Marie
Publisher: name: University of Glasgow
Year: 2023

description: The Atlantic salmon, Salmo salar Linnaeus 1758, is a charismatic species due to its cultural and economic importance across the North Atlantic. In addition, Atlantic salmon is one of the most well researched finfish species. However, there are still considerable knowledge gaps concerning their life history, particularly for salmon smolts migrating from rivers in the British Isles. To date management and research efforts have been largely focussed on improving and understanding salmonid migration through fresh water habitats. Despite these management efforts, Atlantic salmon populations continue to decline. This has led researchers to speculate that the decline may be related to factors encountered at sea, particularly within the early marine environment. This thesis has filled in knowledge gaps concerning the migratory behaviour of Atlantic salmon smolts migrating from rivers draining into the West Coast of Scotland and Ireland using acoustic telemetry. Despite the fresh water environment being the main focus of Atlantic salmon research, very little is known about how Atlantic salmon navigate through fresh water standing bodies of water. This is concerning, as previous studies have suggested that smolts experience high rates of mortality in these regions and display non-directional movements. Through combining acoustic telemetry data with a correlated random walk model, I sought to determine what factors may increase the likelihood of smolts completing a successful migration through Scotland's largest lake. This study demonstrated that consistent with previous literature smolts experienced high overall loss (43%), slow migrations, and non-directional movements. Furthermore, there were no behavioural or morphological factors that differentiated a successful versus unsuccessful migrant, with most individuals travelling upwards of 50 km within the lake. In addition, migratory pathways of smolts closely resembled random walk models, suggesting that successful migration of smolts through lakes is due to chance. However, once smolts came near the lake outlet they tended to make a direct exit. Within the main body of most lakes, surface currents are largely driven by the wind. However, near the lake outlet currents are often directed towards the lake outflow. Future studies are required to determine whether currents are the main environmental cue used by smolts to navigate through fresh water standing bodies of water. Once Atlantic salmon smolts transit through their fresh water environment, many populations must first navigate through estuaries prior to reaching the early marine environment. Estuaries are thought to be a region of high mortality for Atlantic salmon post-smolts as they are exposed to a variety of novel natural and anthropogenic stressors such as predators and aquaculture sites. Scotland is one of the worlds largest producers of farmed salmon, with most aquaculture sites being present along the north-western coast within sea lochs and estuaries. However, despite the rapid expansion of aquaculture sites in the UK, there is limited knowledge concerning the behaviour of wild Atlantic salmon in estuaries and whether they could experience spatial overlap with these sites. The Clyde estuary located in west central Scotland is a region that currently contains 16 operational aquaculture sites with plans to develop more in the future. Using acoustic telemetry coupled with a mark-recapture model, this study predicted the migratory pathways and estimated loss rates of Atlantic salmon post­smolts from two distinctly different river systems (Endrick Water &amp; River Gryffe). In comparison to most literature assessing smolt post-survival through estuaries, loss rates were low &lt;1 %km -1. This is despite 37% of post-smolts making~ 2 reversal movements near the riverine outlet upon entering the estuary, which is thought to be related to a need to adapt to the increase in salinity. In addition, post-smolts were found to make rapid migrations through this region and appeared to exit the estuary with the outgoing tide. Due to their rapid migrations through this region, and high rates of survival, it does not appear that aquaculture sites in the main body of the Clyde estuary have a significant effect on Atlantic salmon post­smolts from the Endrick Water and River Gryffe. This information is currently being used by the Scottish Environment Protection Agency (SEPA) to develop models assessing the impact of sea lice on wild Atlantic salmon. Research directed surface trawls conducted along the continental shelf of Scotland have indicated that once post-smolts leave rivers located along the western coast of UK and Ireland they migrate north towards the slope current, using this current to reach their feeding grounds in the Norwegian Sea. However, to date very little is known about the migratory pathways taken and environmental cues used by post-smolts to reach the slope current. Particle tracking studies conducted along the western coast of Scotland have indicated that for post-smolts to reach the slope current during the period when they are captured by trawling studies, they would have to deviate from local current patterns early on in their migration. This thesis was the first to ground truth particle tracking studies in the Irish Sea region through collecting acoustic telemetry data from 582 Atlantic salmon post-smolts from 13 rivers in England (n = 1) and Scotland (n = 12) detected on a large acoustic telemetry array deployed at the Irish Sea exit (n = 108 receivers). Furthermore, using circular statistics detection data was combined with two hydrodynamic models (current/temperature data) to determine potential drivers of early marine migration. Post-smolts from all river systems were found to undergo relatively rapid migrations through the Irish Sea(&gt; 10 km.day-1) and loss rates were low. However, when loss rates were multiplied by the total distance travelled there was still substantial overall loss for post-smolts migrating from English and Scottish rivers. Post-smolts exit from the Irish Sea appeared to be initiated by water temperature with most post-smolts exiting when temperatures ranged from 9 - 11 °C. These temperatures are similar to those reported when post-smolts are captured in the slope current. In addition, most post-smolts exited this region when currents were directed westwards towards the slope current located off the continental shelf. Thus, results from this study suggest that temperature and current direction may serve as environmental cues used by post-smolts during their early marine migration to determine when and where to migrate. Similar to their migration through the Irish Sea, prior to this thesis there was limited information concerning the migratory pathways post-smolts may use to migrate along the west coast of Scotland towards the Norwegian Sea. Further research was needed, as the highest density of anthropogenic stressors ( e.g. aquaculture sites, renewable energy developments) in Scotland are located to the east of the Outer Hebrides. Through collaborating with a colleague at the Atlantic Salmon Trust and combining data from seven acoustic telemetry projects taking place in England, Scotland, and Ireland during 2021, we were able to document the migration pathways of post-smolts through this region. This study incorporated data from 23 rivers (n = 1806 post-smolts), 398 acoustic receivers and one submersible glider. In total 34.7% of tagged post-smolts (n = 416) that left their natal river (n = 1200) were detected in the coastal marine environment. Furthermore, consistent with the results from my previous chapter, most post-smolts travelling from rivers south of the Outer Hebrides were found migrate in a north­westerly direction towards the slope current located off the continental shelf of Scotland. However, post-smolts migrating from rivers to the east of the Outer Hebrides travelled directly through the Minch. The four chapters presented in this thesis have utilized acoustic telemetry data to model the behaviour and survival of Atlantic salmon smolts from multiple populations in lakes, estuaries, and the early marine environment. The results obtained from this thesis will be used by researchers and managers to help develop future studies aimed at identifying and mitigating the effects of potential stressors unique to each Atlantic salmon population mentioned in this project.