Estuarine survival and migratory behaviour of Atlantic salmon Salmo salar smolts

Inshore and offshore marine migration pathways of Atlantic salmon post-smolts from multiple rivers in Scotland, England, Northern Ireland, and Ireland

The migratory behavior of Atlantic salmon (Salmo salar) post-smolts in coastal waters is poorly understood. In this collaborative study, 1914 smolts, from 25 rivers, in four countries were tagged with acoustic transmitters during a single seasonal migration. In total, 1105 post-smolts entered the marine study areas and 438 (39.6%) were detected on a network of 414 marine acoustic receivers and an autonomous underwater vehicle. Migration pathways (defined as the shortest distance between two detections) of up to 575 km and over 100 days at sea were described for all 25 populations. Post-smolts from different rivers, as well as individuals from the same river, used different pathways in coastal waters. Although difficult to generalize to all rivers, at least during the year of this study, no tagged post-smolts from rivers draining into the Irish Sea were detected entering the areas of sea between the Hebrides and mainland Scotland, which is associated with a high density of finfish aquaculture. An important outcome of this study is that a high proportion of post-smolts crossed through multiple legislative jurisdictions and boundaries during their migration. This study provides the basis for spatially explicit assessment of the impact risk of coastal pressures on salmon during their first migration to sea.

Comparing the migration behavior and survival of Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) smolts

Many organisms rely on migrations between habitats to maximize lifetime fitness, but these migrations can be risky due to a suite of factors. In anadromous salmonids, the smolt migration from fresh water to sea is a critical life stage, during which smolts can experience high mortality from multiple sources. This study investigated the migratory behavior and survival of Atlantic salmon (Salmo salar) and anadromous brown trout (Salmo trutta) smolts during their seaward migration using acoustic telemetry between March and May 2021. Due to the extinction of wild salmon in the River Gudenaa after the construction of the Tange hydropower plant, this study used hatchery-reared salmon originating from a nearby Danish river. A total of 75 hatchery-reared salmon smolts, 75 hatchery-reared trout smolts, and 75 wild trout smolts were tagged with acoustic transmitters and released into River Gudenaa, Denmark. The downstream movements of tagged fish were monitored using acoustic receivers deployed in the river and fjord. Hatchery-reared trout initiated migration first, followed by hatchery-reared salmon, with wild trout being the last to migrate. There was no difference in riverine progression rates among the three smolt groups, but noticeable differences emerged once in the fjord: trout (wild and hatchery) slowed down, whereas hatchery-reared salmon maintained their speed. Riverine migration was predominantly nocturnal for all smolts; however, daytime migration increased at the fjord arrays. Day-of-year significantly influenced diurnal patterns in the river and fjord, where daytime migration increased later in the year. Hatchery-reared salmon and wild trout had reasonably good overall survival from river to sea entry (≥66%), whereas hatchery-reared trout had poor survival (c.26%). The fjord was the major bottleneck for survival of hatchery-reared trout. We found no strong evidence for differences in progression rate or diurnal patterns between wild and hatchery-reared trout to explain the lower survival. This study demonstrates that salmon and trout differ in their life-history strategy already in the post-smolt phase, and that stocking is a sub-optimal strategy to aid wild populations.

The use of predator tags to explain reversal movement patterns in Atlantic salmon smolts (Salmo salar L.)

Acoustic telemetry has seen a rapid increase in utility and sophistication in recent years and is now used extensively to assess the behavior and survival rates of many aquatic animals, including the Atlantic salmon. As part of the salmon's complex life cycle, salmon smolts are thought to make a unidirectional migration from fresh water to the sea, which is initiated by changes in their physiology. However, some tag movement patterns do not conform with this and can be difficult to explain, particularly if the tagged fish has been eaten by a predator. This study combines the use of predator tags with machine learning techniques to understand the fate of migrating salmon smolts and thereby improve estimates for migration success. Over 3 years between 2020 and 2022, 217 salmon smolts (including wild and hatchery-reared ranched fish) were acoustically tagged and released into an embayment on the west coast of Ireland. Some tagged smolts were observed to return from the estuary back into a saline lagoon through which they had already migrated. To distinguish between the movement of a salmon smolt and that of a predator, predator tags were deployed in migrating smolts in 2021 and 2022. The addition of a temperature sensor in 2022 enabled the determination of predator type causing the returning movement. A significant number of predator tags were triggered, and the patterns of movement associated with these triggered tags were then used with two types of machine learning algorithms (hierarchical cluster analysis and random forest) to identify and validate the behavior of smolts tagged without extra sensors. Both models produced the same outputs, grouping smolts tagged with predator tags with smolts tagged without the additional sensors but showing similar movements. A mammalian predator was identified as the cause of most reversal movement, and hatchery-reared ranched smolts were found to be more likely predated upon by this predator than wild smolts within the lake and the estuary. However, overall migration success estimates were similar for both wild and hatchery-reared ranched fish. This study highlights the value of predator tags as an essential tool in the overall validation of detection data.

Investigating the behaviour of Atlantic salmon (Salmo salar L.) post-smolts during their early marine migration through the Clyde Marine Region

It is thought that survival during migration is particularly poor for Atlantic salmon post-smolts immediately after entry into sea and particularly in the estuarine environment. Nonetheless, there is currently a lack of information on Atlantic salmon post-smolt movement behaviour in estuaries in the UK. This study used acoustic tagging to estimate loss rates and compare the behaviour of Atlantic salmon post-smolts migrating from two distinctly different rivers draining into the Clyde Estuary, the River Endrick (n = 145) and the Gryffe (n = 102). Contrary to most literature, post-smolts undertook rapid migrations through the estuary, potentially decreasing their exposure to predators/anthropogenic stressors and reducing their estimated loss rates (river: 1%-3% km^-1 ; estuary: 0.20%-0.60% km^-1 ). The low loss rates in the estuary occurred despite post-smolts engaging in passive reversal movements with the tide upon entering the estuary, possibly allowing them more time to adapt to the increased salinity. Atlantic salmon post-smolts from both the rivers used similar migration pathways exiting into the coastal marine zone during ebbing tide. This study provides novel information on the timing and migratory routes of Atlantic salmon post-smolts in the Clyde Estuary that can ultimately be used to inform management decisions on how to assess and reduce the potential impacts of current natural and anthropogenic stressors. Temporal repeatability of this study over multiple years is required to determine if there is variation in the factors driving the migratory patterns and loss rates of smolts in this system.

Application of machine learning and acoustic predation tags to classify migration fate of Atlantic salmon smolts

Mortality and predation of tagged fishes present a serious challenge to interpreting results of acoustic telemetry studies. There is a need for standardized methods to identify predated individuals and reduce the impacts of "predation bias" on results and conclusions. Here, we use emerging approaches in machine learning and acoustic tag technology to classify out-migrating Atlantic salmon (Salmo salar) smolts into different fate categories. We compared three methods of fate classification: predation tag pH sensors and detection data, unsupervised k-means clustering, and supervised random forest combined with tag pH sensor data. Random forest models increased predation estimates by 9-32% compared to relying solely on pH sensor data, while clustering reduced estimates by 3.5-30%. The greatest changes in fate class estimates were seen in years with large class imbalance (one or more fate classes underrepresented compared to the others) or low model accuracy. Both supervised and unsupervised approaches were able to classify smolt fate; however, in-sample model accuracy improved when using tag sensor data to train models, emphasizing the value of incorporating such sensors when studying small fish. Sensor data may not be sufficient to identify predation in isolation due to Type I and Type II error in predation sensor triggering. Combining sensor data with machine learning approaches should be standard practice to more accurately classify fate of tagged fish.

Migration and survival of Atlantic salmon Salmo salar smolts in a large natural lake

An investigation with acoustic telemetry of the passage of Salmo salar smolts through a large natural lake found heavy mortality occurred at the river-to-lake confluences (mean 31.2% km^-1 ), but was lower in the main body of the lake (mean 2.4% km^-1 ). Predation was a significant pressure on emigrating smolts as tagged pike Esox lucius aggregated at river-to-lake confluences during the peak of the smolt run. Tagged smolts mainly emmigrated into the lake in the late evening after dusk, possibly as a predator-avoidance behaviour.

Physiological preparedness and performance of Atlantic salmon Salmo salar smolts in relation to behavioural salinity preferences and thresholds

This study investigated the relationships between behavioural responses of Atlantic salmon Salmo salar smolts to saltwater (SW) exposure and physiological characteristics of smolts in laboratory experiments. It concurrently described the behaviour of acoustically tagged smolts with respect to SW and tidal cycles during estuary migration. Salmo salar smolts increased their use of SW relative to fresh water (FW) from April to June in laboratory experiments. Mean preference for SW never exceeded 50% of time in any group. Preference for SW increased throughout the course of smolt development. Maximum continuous time spent in SW was positively related to gill Na(+), K(+)-ATPase (NKA) activity and osmoregulatory performance in full-strength SW (measured as change in gill NKA activity and plasma osmolality). Smolts decreased depth upon reaching areas of the Penobscot Estuary where SW was present, and all fish became more surface oriented during passage from head of tide to the ocean. Acoustically tagged, migrating smolts with low gill NKA activity moved faster in FW reaches of the estuary than those with higher gill NKA activity. There was no difference in movement rate through SW reaches of the estuary based on gill NKA activity. Migrating fish moved with tidal flow during the passage of the lower estuary based on the observed patterns in both vertical and horizontal movements. The results indicate that smolts select low-salinity water during estuary migration and use tidal currents to minimize energetic investment in seaward migration. Seasonal changes in osmoregulatory ability highlight the importance of the timing of stocking and estuary arrival.

Condition-dependent migratory behaviour of endangered Atlantic salmon smolts moving through an inland sea

The Bras d'Or Lake watershed of Cape Breton Island, Nova Scotia, Canada is a unique inland sea ecosystem, UNESCO Biosphere Reserve and home to a group of regionally distinct Atlantic salmon (Salmo salar) populations. Recent population decreases in this region have raised concern about their long-term persistence. We used acoustic telemetry to track the migrations of juvenile salmon (smolts) from the Middle River into the Bras d'Or Lake and, subsequently, into the Atlantic Ocean. Roughly half of the tagged smolts transited the Bras d'Or Lakes to the Atlantic Ocean, using a migration route that took them through the Gulf of St Lawrence's northern exit at the Strait of Belle Isle (∼650 km from the home river) towards feeding areas in the Labrador Sea and Greenland. However, a significant fraction spent >70 days in the Lakes, suggesting that this population has an alternative resident form, in which smolts limit their migrations within the Bras d'Or. Smolts in good relative condition (as determined from length-to-mass relationships) tended to be residents, whereas fish in poorer condition were ocean migrants. We also found a covarying effect of river temperature that helped to predict residence vs. ocean migration. We discuss these results relative to their bioenergetic implications and provide suggestions for future studies aimed at the conservation of declining salmon populations in Canada.

Residency and movement patterns of Arctic charr Salvelinus alpinus relative to major estuaries

Estuarine residency and marine movements of 43 anadromous Arctic charr Salvelinus alpinus (mean ± s.d. fork length = 523 ± 97 mm) were examined using acoustic tracking in inner Frobisher Bay (IFB; 63° N; 68° W), Canada, from July to September 2008 and 2009. A mean ± s.d. migration duration of 63 ± 7 days occurred from late June to early September. Detected S. alpinus were either continuously (maximum 34 days) or intermittently present in estuarine zones, on average residing approximately one third of time tracked and returning once every 9 days. Significantly higher estuarine residency during the final 15 migration days suggested that a transition phase may occur prior to freshwater re-entry. Low travel rates during flood tide suggested individuals staged before accessing intertidal and estuarine zones. Although the two main estuaries were c. 22 km apart, 19% of tagged individuals used both. Individuals remained relatively close to freshwater overwintering systems, although late-migration inter-estuarine movements may have indicated natal homing. Approximately half of the individuals exhibited extra-estuarine travel, mostly during mid-migration, but remained within 3 km of shore ranging < 30 km straight line distance (SLD) of either estuary. It was concluded that IFB S. alpinus (1) spent a significant portion of their migration within or adjacent to the estuaries and (2) had a restricted marine distribution within 30 km SLD of the river mouths.