Smolt Migration Through The River Dee And Harbour

March 2019

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Executive Summary

The number of salmon returning to the river Dee has declined in recent decades. Initially, declines were

likely offset by reductions in fishing mortality and subsequently by improved survival of juveniles in the

river. However, in recent years juvenile production has also been below carrying capacity, with possible

consequences for smolt production. In an effort to maximise the number of salmon smolts that

successfully migrate through the river and estuary environment, a study has been set up to determine

sources of in-river and estuarine losses of salmon smolts in the Dee. This study uses acoustic telemetry to

investigate the migratory behaviour and survival of smolts migrating through the river and to the inner

harbour. The study has run for three years, starting in 2016.

To investigate the extent and the potential causes of in-river losses of tagged smolts in the Dee in 2018,

100 smolts were tagged in the Baddoch Burn, a long-term monitoring site operated by Marine Scotland.

Fish were implanted with a small acoustic tag that emits a signal every 30 seconds. With receivers

deployed along the river and in the harbour, individual fish were tracked along their migration. In total,

83 smolts were recorded after tagging.

In river tag losses were low – 17 out of 83 (21%) tags over ca. 73 miles of river downstream from the

release site. This is lower than the in-river loss recorded in 2017 when 40 smolts were tagged, of which

37 were subsequently recorded and 29 (70%) were lost over the same distance. In contrast to 2017, tag

losses in 2018 were higher in the harbour, where between the Boating Club and South Breakwater 23 out

of 83 (28%) tagged fish were lost over a distance of ca. 1.5 miles, compared to no losses in 2017.

There were no significant differences between the successful and unsuccessful smolts with respect to

Weight, Tag burden, Condition factor, Length or Age. This suggests that any tag losses that occurred are

unlikely a result biological factors, but rather result from external factors.

The number of detections and migration speed in the River Dee is linked to river flows, with increased

detections when river levels are high. Smolts tend to be predominantly active during the night with smolt

movements mostly occurring between 6 hours before and after midnight. The swimming speed of fish

was generally between 0 – 5 km/hr in the river but became highly variable in the harbour. Furthermore,

swimming speed was positively related to river flow (cubic metres per second) and day of the year. This

indicates that smolts swim faster when river flows are higher and also swim faster as the season

progresses. Additionally, swimming speeds are higher during the night. This led to smolts passing through

the harbour between 13th April and 15th May.

The consistent pattern of 1) strong increases in the number of smolt movements with increases in river

flows for smolts in 2017 and 2018; 2) the predominantly nocturnal activity patterns; and 3) the

relationship between swimming speed and discharge and day of the year, have clear implications for the

way the smolt migration is managed. Namely, when the river discharge is high and smolts are likely to be

actively moving, extra care needs to be taken to ensure that smolts have the best chance of migrating

undisturbed by e.g., limiting operations taking place in the river and harbour. Or when river discharge is

low and so predation risk may be greater, increasing efforts to reduce predation.

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Introduction Atlantic salmon stocks have declined across much of the North Atlantic region over the last four decades

(Limburg and Waldman, 2009). In the river Dee, reductions in adult returns were likely initially offset by

reductions in fishing mortality and subsequently by density dependent processes that improved survival

of juvenile life stages. However, in recent decades adult returns have been sufficiently low to also affect

juvenile and emigrant (smolt) production. For example, on the Girnock, a spring salmon tributary of the

Dee, maximum juvenile production has only been achieved for five of the last 20 years

(https://www2.gov.scot/Topics/marine/Salmon-Trout-Coarse/Freshwater/Monitoring/Traps/AdultReturnsPopStatus). Given

these declines, there is a need to conserve salmon stocks and to understand the causes of mortality to

assess mitigation actions. The smolt life stage is particularly important in this context because any losses

will not be compensated at later life stages (i.e. are density independent), but are potentially susceptible

to fisheries management actions, unlike mortality of adults at sea.

To improve our understanding of smolt migration in the river and where the risk of mortality is thought

to be greatest, the Dee Fisheries Management Plan (2015-2018) set out to;

1) Infer predation impacts on smolts

2) Identify timings of smolt migration and their presence in the lower river and harbour area

3) Establish near-shore habitat use of smolts and migration patterns through the estuary

Acoustic tagging and tracking has been used to investigate migration of salmon smolts in the river and

harbour from 2016-2018. Aberdeen Harbour is the busiest harbour in the UK and it was considered that

shipping traffic and harbour works could potentially interrupt smolt migration. The harbour also holds an

increased number of potential predators including: birds, estuarine fish, seals, and dolphins.

In 2016, smolts were tagged in the Sheeoch and Beltie burns and the results showed that surprisingly, all

smolt losses occurred in the river and none in the harbour (Smolt migration through the lower Dee and

inner harbour, River Dee Trust 2016). This prompted an alteration in the 2017 study to investigate the in-

river losses by tagging additional smolts in the upper catchment. These fish were trapped and tagged at

the Baddoch smolt trap by MSS (https://www2.gov.scot/Topics/marine/Salmon-Trout-

Coarse/Freshwater/Monitoring/Traps). As with the 2016 study, any tag losses due to the impacts of

tagging would be expected to be high initially and then decline over time as the fish migrated downstream.

At the same time, the likelihood of predation increases as smolts migrate further downstream due to the

higher predator densities in the lower river (based on monthly piscivorous bird counts). The results from

2017 indicated that 29 out of 37 tag losses (70%) occurred in the upper-middle catchment compared to

13% in the lower catchment (Smolt migration through the River Dee and Harbour, River Dee Trust 2017).

This high loss of tags, and suspected mortality, raised further concerns over predation losses in the upper

and middle parts of the river. Therefore, in 2018 additional receivers were installed in the river to more

precisely define where losses were highest. This will provide further information on those locations along

the river where in-depth investigations into potential causes of tag losses can lead to a better protection

of smolts on their seaward migration, ultimately increasing the production of smolts for the River Dee.

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Methods

Acoustic telemetry Acoustic tags and receivers manufactured by Vemco were used for the study. The V5 tags transmit a sound

every 30 seconds (randomly generated at 15 - 45 second intervals). The sound produced by each tag is a

combination of 8 - 10 distinct pulses that give the tag a unique code, so that individual fish can be

identified. The V5 tags are 12.7 x 4.3 x 5.6 mm in size with a weight (in air) of 0.65g.

Telemetry guidelines suggest that tags should be no greater than 5 - 6.5% of the fish’s weight to avoid

adverse effects of tagging (Prentice et al 1990, Adams et al 1998, Anglea et al 2004). The smolts tagged

in this study were 16.2 – 31.2 g (average 22.4 g) and tag weight represented 2.1 – 4.0% (average 3.0%) of

smolt body weight.

V5 tags have a 95% battery life of 77 days and power output of 143 dB, presenting a maximum detection

range of approximately 300 m (albeit very dependent on background noise levels). The V5 tag is the

second smallest tag currently available, with the smallest tag considered to have an insufficient power

output to ensure tag detection against the background noise in Aberdeen Harbour.

The VR2W acoustic receivers used in this study detect the sounds from the acoustic tags on the 180 kHz

frequency. The receivers are placed underwater and make an automatic record each time a tag is

detected, recording the tag identification number, date and time, which can then be downloaded from

the receiver via Bluetooth once the receiver is retrieved from the water.

The receivers were placed underwater in the river and harbour, weighted onto the river bed with anchor

weights. In the river, receivers were attached to a metal rod and a 40-kg anchor weight, then roped off to

the bank to aid retrieval (Fig. 1). In the harbour, each receiver was attached to rope and 80 – 200 kg of

anchor weight. The rope was held vertical by a sub-trawl float so that the receiver would face upwards in

the water column. A second rope held a surface float so that the position of the receiver was known to

boat traffic. The anchor weight was roped back to the shore/quayside to ensure it was not lost in heavy

storms and to aid retrieval.

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Figure 1. Receiver set up for in-river monitoring, ready for in-water deployment.

Study area Smolts were captured in a fixed trap in the upper Dee catchment at the Baddoch burn. The Baddoch burn

trap is run by MSS. The Baddoch trap is located 122 km (approx. 76 miles) from the final receiver gate in

the harbour. The Baddoch burn is a tributary of the River Clunie, the trap is located 11 km (7 miles) from

the main stem Dee.

24 receivers were used to detect tagged fish, 16 of these were located in the main stem of the river from

Invercauld to the Boating Club (Fig. 2 and Table 1 in Appendix). Following the reliable performance of the

acoustic receivers in the harbour in 2016 and 2017, in 2018 the receivers were deployed as four sets of

gates.

The final eight receivers were located within the inner harbour (Fig. 2, Table 1 in Appendix). Due to the

width of the harbour and the high level of background noise, the receivers located within the harbour

were paired up into ‘gates’ to increase the likelihood of detecting the tags. These gates proved successful

in 2016 and 2017 so the same method was used again. The harbour was monitored as far seaward as the

Old South Breakwater, so that the length of the harbour over which smolts were monitored was ~1.5 km

(i.e. Gate 1 to Gate 4, Fig. 2).

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Figure 2: Map of the River Dee catchment showing the locations of receivers present in 2017 (green) and

receivers added in 2018 (orange). Lower map shows a zoomed-in view of Aberdeen Harbour and the pairs

of receivers forming “gates”.

Smolts 100 smolts were tagged at the Baddoch Burn by MSS personnel. Fish were chosen to spread tagging over

the duration of the run and to cover the range of smolt sizes >120 mm. Up to 20 smolts were tagged per

day and this was completed as quickly as possible between 6 and 20 April 2018 (Table 2 in Appendix).

Smolts were 2 – 4 years old. Tagged fish were in the length range of 120 - 152 mm (130 ± 7.4, mean ± SD).

The body weight of smolts ranged from 16.2 - 31.2 g (22.4 ± 3.4, mean ± SD). All tagged fish showed the

physical attributes of smolt development (Fig. 3). The condition of these smolts (Fulton Condition Factor;

a measure of an individual fish’s health based on length and weight) was 0.87 - 1.19 (1.0 ± 0.06; mean ±

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SD). For smolts, a low condition factor does not necessarily represent poor health but potentially the

physical change related to smolt development.

Figure 3: Atlantic salmon smolt showing silver colouration with loss of parr markings, streamlined body

and black edges to fins.

Tagging Smolts were tagged close to the river to reduce handling and transport. The surgical procedure was carried

out on a table using sterile equipment that was re-sterilised between each fish. Only staff that had been

trained and demonstrated post-training competence carried out the procedure.

Smolts were anaesthetised using MS-222 until they were heavily sedated. Each smolt was measured,

weighed and photographed prior to the tag being inserted. The tag was inserted into the body cavity via

a cut made into the belly of the fish and the cut was closed using one suture. Next, smolts were placed

into a recovery unit for 5 hours on average (3 – 9 hours), until it appeared to be fully recovered and was

showing startle responses. After the recovery period, smolts were released into the burn, along with other

untagged smolts captured in the trap, approximately 100 m downstream from the smolt trap. The

Standard Operating Procedure for tagging was based on guidelines from the Atlantic Salmon Federation.

Based on scale sampling, in 2018 there were three two-year-old, 62 three-year-old, and 33 four-year-old

smolts. Additionally, there were two smolts for which no scales were taken and thus no age estimate was

available. This represents a positively biased sample of smolt sizes and ages from the catchment.

Data and analysis Much of the subsequent information on the tagged smolts is summarised using the ‘median’ value or the

‘mean’ value. The ‘median’ is used to describe the amount of time between migration events (for

example, migration from one receiver station to the next) or fish measurements like length or weight. This

simply reflects that the data is often skewed (i.e., many similar values and a few outliers) and therefore

the median (the middle value) better reflected a ‘typical’ smolt than the ‘mean’ value.

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Various statistical analyses were undertaken to interpret the data and the type of test used is always

reported. T-tests and Mann-Whitney U tests were used to compare differences between two groups of

fish - such as between successful and failed smolt migrations – to identify what causes differences in

behaviour or losses. The strength of statistical tests is reflected in the P-value. P-values weigh up the

strength of the evidence from the data: A P-value will be between 0 and 1 and the most crucial point is

the 0.05 level - a P-value less than 0.05 indicates that the test has found strong evidence of a real effect

or relationship in the data, with only a 5% chance that this could have occurred by chance.

The efficiency of receivers was determined as the percentage of unique tag IDs that were detected at a

given receiver with respect to detections of unique tag IDs on all receivers downstream. Hence, detection

efficiency could not be calculated for Gate 4, beyond which there are no more receivers. For example, if

receiver ‘A’ detected 20 unique tag IDs, but downstream receivers picked up the same 20 unique tag IDs

but an additional tag ID as well, receiver ‘A’ was assigned an efficiency of (20/21)*100=95%. To determine

travel times between two receivers ‘A’ and ‘B’, the time difference was calculated between last detection

at receiver ‘A’ and the first detection at receiver ‘B’. This information was also used to determine the

migration speeds, where time (in hours) between two receivers was divided by the distance (in

kilometres). Overall downstream migration time was determined by calculating the number of hours after

release from the tagging site up to the first detection at a receiver. Any summary statistics on migration

timing and speed are displayed in boxplots which report median values.

To determine the controls on migration speed in different sections of the river, a simple generalized

additive model (GAM) was fitted. A GAM allows for linear and non-linear responses. For these models,

each variable that potentially affects migration speed– e.g. smolt weight, river discharge- is added or

removed from the model until a ‘best fit’ model is produced. This process selects the variables that have

the greatest influence on migration speed. The model uses data collected for individual fish, so that the

migration speed of any smolt between two receiver stations is related to its characteristics. A factor for

river section and Tag ID was included to ensure statistical assumptions are not violated. Tagging date was

included; weight; condition factor gives information on the smolting stage of fish (Fulton Condition Factor:

a measure of an individual fish’s health based on fork length and weight and an indicator for smolting

stage); age; and whether or not an individual fish was detected at Gate 4 (successful/failed). A number of

environmental conditions were included that describe the conditions a fish experienced during its

migration: day of the year (DoY); average river flow (m3s-1); night/day. River flow data were obtained from

SEPA’s gauging station at Mar Lodge, Polhollick, Woodend, and Park

(http://apps.sepa.org.uk/waterlevels/). Given that the four hydrographs were highly similar during the

migration window (Fig. 1 in Appendix), it was decided to use only the discharges at Park (see Fig. 2 for

location). This records discharge (cubic metres per second, m3sec-1 or ‘cumecs’) every 15 minutes, which

was aggregated to a mean daily discharge. Although not all parts of the river network will respond

synchronously to e.g., snow melt or westerly or easterly frontal systems, the average was calculated over

the time taken for migration between two receiver stations (i.e., a river section) for each smolt. Day or

night time migration was based on sunset and sunrise times, respectively.

Findings

Smolt characteristics An analysis was done to investigate whether there were differences in smolt characteristics or possible

treatment effects between smolts that were and were not detected at the final gate (Figure 2 in

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Appendix). These characteristics were: age (years), fork length (mm), weight (grams), condition factor,

recovery time after surgery (minutes), tag burden (percentage of body weight), and release date.

Following Holme’s procedure to correct for performing multiple statistical tests on the same data set

(Holm 1979), no significant differences were found for any of the smolt related characteristics (age:

Wilcoxon rank sum test adjusted p-value = 1.0; fork length: two sample t-test adjusted p-value = 1.0;

weight: two sample t-test adjusted p-value = 1; condition factor: two sample t-test adjusted p-value =

0.49; recovery time: Wilcoxon rank sum test adjusted p-value = 1.0; tag burden: two sample t-test

adjusted p-value = 1.0; and release time: Wilcoxon rank sum test adjusted p-value = 0.6). Hence, none of

these characteristics affected whether a smolt was successful in reaching the harbour or not.

Fish detection In total 83 (83%) of the 100 smolts tagged at the Baddoch were subsequently detected by any receiver.

The fate of the 17 smolts that were not detected is unknown and these fish could have either died

following surgery (delayed tagging mortality can occur up to 36 hours after surgery, C. Adams pers. comm.,

or from an infection after that), not migrated, or tags could have been shed. These fish were excluded

from further analysis.

The Lower Blackhall and Kineskie receiver had the lowest efficiency (29.6%); the receivers at Culter and

Dess had efficiencies of 73.5% and 74.7%, respectively; the remaining 17 receivers had efficiencies > 80%;

detection efficiency was 100% from the Boating Club onwards.

Fish showed more activity (i.e., receivers detected more tags) during increased river flows (discharges),

with peak detections generally occurring during periods of high discharges and as river levels were

dropping off (Figure 4).

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Figure 4: Average daily discharge (river flow, in m3s-1) at the Park gauging station (blue line, left vertical

axis) and the number of first arrivals of individual fish at receiver stations (coloured bars, right vertical

axis). Note that fish swim faster when discharges are higher and fish can pass multiple receiver stations in

a single day, consequently the total count of arrivals can quickly exceed the total number fish.

Fish tend to be actively migrating during the night with both new arrivals and departures at receiver

stations being lowest around mid-day and highest either side of midnight (Fig. 5). This is indicated by the

shape of density plots. In the upper river there are two distinct “peaks” in the curve just after and before

midnight. However, as fish move further down the River Dee, the number of daytime migrations increases,

as indicated by the flattening shape of the density curves (Fig. 5). A very similar pattern was seen for

departure times.

Smolts were present in Aberdeen Harbour (Gate 1 – Gate 4) between 13 April and 15 May 2018. This was

different from 2016 and 2017 (Fig. 6), but the dates agree with modelled timings of smolt presence in

coastal areas from Malcolm et al., (2015). Overall, the main period of presence of tagged smolts appears

to be between the middle of April and the end of May (Fig. 6). Figure 6 shows a density plot of smolt

presences in the harbour for the three years of smolt tracking to date. The timing of presence in the

Aberdeen Harbour is variable between years but limited to a relatively narrow time window of about a

month in all three years. This is likely influenced by the differences in river flows between the three years

as well as tagging dates. The latter is also dependent on flow conditions, because tagged fish are caught

in the traps when they are moving downstream.

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Figure 5: Density plots for new arrivals at receiver stations along the River Dee. The timing of arrivals are

centred around midnight and the plot covers a full day (-12 hours before midnight to 12 hours after

midnight). The height of the curves is scaled to the highest density of points (grey dots) across all receiver

stations and so is a relative value. Colours relate to the different receiver stations. Note that the receiver

at Invercauld (“1_Invercauld_301975”) is not here as for this station no departure time from a previous

station is available (it is the first station).

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Figure 6: Density plots of smolts present in Aberdeen Harbour in years 2016 (red), 2017 (yellow), and

2018 (blue). A higher presence of smolts is indicated by peaks.

Swimming Speed The median swimming speed of fish was between 0 – 5 km/hr for most sections of the river (Fig. 7). The

highest median speed was between Park and Drum at a median swimming speed of 5.4 km/hr and the

lowest speed was between Lower Woodend and Lower Blackhall & Kinneskie with a speed of 0.2 km/hr.

However, this latter value is uncertain, likely caused by issues with the receiver during the recording

period. Uncertainty in swimming speeds increases dramatically in the harbour (Fig. 7).

Figure 7: Median downstream swimming speed for different sections of river (see Fig. 2). Purple dots

indicate the median (middle) value, the bars indicate the 95% confidence interval.

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The best fitting model for swimming speed (based on the lowest Bayesian Information Criterion value)

showed that the factors that most influenced swimming speed were average discharge experienced

during migration between two receiver stations (m3s-1), day of the year, a factor for day/night time

migration, and a factor for the different river section between each set of receiver stations. Fish related

characteristics like body weight, condition factor, age, a factor for tagging date, and a factor for whether

a fish was detected at Gate 4 or was lost, were all excluded from the best model. This suggests that these

variables had little influence on swimming speed. The fact that the model explains ca. 31% of the variation

in the swimming speeds indicates that there are other variables that influence swimming speed that are

not currently considered. These could be related to e.g., land-use, lunar phase, upstream catchment area,

river width, channel characteristics, social/behavioural cues from other smolts, and other fish species.

Swimming speed is positively related to average discharge (m3/s-1) and the day of the year (DoY). The

relationship with average discharge (Average_Q in Fig. 8) is positive and shows a peak between 100-120

m3s-1 after which the swimming speed decreases. This decrease could be 1) a result of smolts seeking

refuge from very high discharges, 2) a tendency for smolts to start moving actively after the peak discharge

and during the decline in discharge (i.e., with falling river levels), or a combination of these two factors.

Swimming speed increases linearly with DoY for the tagged smolts (Fig. 8). This suggests that as the season

progresses, smolts move faster which can reflect their ‘eagerness’ to get out to sea. Furthermore,

swimming speed is higher at night (Fig. 8). Swimming speed is significantly lower between Invercauld to

Abergeldie than other river sections (see Fig. 3 in Appendix), except between Lower Woodend and Lower

Blackhall & Kinneskie.

Figure 8: Relationship between swimming speed of fish (displayed as Log10(speed) in km/hr) and Average

discharge (m3s-1) in left graph and day of the year (DoY) on the right. The effect of day or night time

migration is shown by the red and purple lines, respectively.

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Loss rates Loss of tags was limited in the river with 80% of tagged smolts that were recorded at the first receiver

station at Invercauld (14 km downstream from tagging site) also recorded at the Boating Club in Aberdeen

(118 km downstream from tagging site) (Fig. 9).

Figure 9: Proportion of detected smolts along their journey from the Baddoch tagging site (black line),

plotted with the average cormorant density in April-May 2018 (left graph), and goosander density over

the same period (right graph).

This equates to a loss rate of 0.20% per kilometre of river travelled, along 103 km of river. This contrasted

starkly with tag losses in the harbour where from the Boating Club down to Gate 4 a further 28% of tags

were lost (Fig. 9). This means the loss rate over the final 2.3 km was 12.17% per km, which is 2 orders of

magnitude greater than in the river. There was no obvious relationship between the densities of

cormorants and goosanders and the proportion of tags left.

Discussion

Loss rates Of the 83 tagged smolts that were tracked, 43 (52%) were detected at Gate 4 and are thought to have

successfully migrated out the river. Of the remaining 40 tagged smolts, 17 (20%) were lost in the river and

23 (28%) were lost in the harbour.

Loss rates of Baddoch smolts in 2018 contrasted in the upper river with those in 2017. The highest loss

rate in 2017 occurred between Craigendinnie and Crathes (Fig. 2), with a loss rate of 1.6% km-1, whereas

in 2018 loss rate in the same section was much lower at 0.27% km-1. The overall loss rate in 2018 of 0.2%

km-1 is in correspondence with other river systems (e.g., 0.7% km-1 in River Deveron (Lothian 2016), 0.3-

7.0% km-1 for rivers in Canada, Norway, Denmark, and the UK (Thorstad et al., 2012). The loss rate in the

harbour of 12.2% km-1 is still within the range reported for estuary migration but should be seen in the

context of the Dee estuary, which is small compared to for example the Forth estuary and is completely

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enclosed by Aberdeen Harbour. The largest number of tags lost on a single day was 12, with all final

detections being on 18th April. This coincided with high river levels and a high number of movements (Fig.

4). All 12 losses occurred between the Boating Club and Gate 4 (Fig. 2).

The date and time a tag is lost reflects the last known location of a smolt and not the exact location, time

and date that a tag is lost. A potential scenario could be that the high losses that occurred in the Aberdeen

Harbour are a result of a compounded issue of high river levels stimulating large numbers of smolts to

migrate out to sea and delays and confusion of fish upon entry into the harbour, in addition this increased

number of smolts could have attracted predators (e.g., seals, dolphins, piscivorous birds). Harbour

maintenance dredging took place in Aberdeen Harbour from 19th April – 15th May (K. Harris, pers. comm.):

intermittent dredging took place between 19th April and 8th May, and between 13th and 15th May, which

coincides with the presence of tagged smolts (Fig. 6). This could potentially have increased vulnerability

of smolts. However, it is not currently possible to assess the effect of diel timings of harbour operations

on tag loss rates. As Figure 6 clearly indicates, the majority of smolt movements occur during the hours

after sunset or before sunrise although increased daytime migration occurs in the lower river. Out of the

23 tags that were lost in the harbour, 11 were last detected during daylight hours.

Predation was thought to have had a serious impact on smolts in 2017 with a high rate of tag losses co-

occurring with high goosander densities. The 2018 tracking study aimed to get a higher resolution of loss

rates in the middle part of the river. However, despite the likely presence of similar numbers of

goosanders (based on monthly goosander counts), they had no apparent effect on tag loss rates (Fig. 9).

A potential explanation for this difference is that discharges were higher in 2018 and swimming speeds

were higher in the river which means they could have been less susceptible to high levels of predation, or

there were additional pressures on smolts that resulted in high tag loss rates in 2017 that were not present

in 2018.

Notwithstanding differences in river levels between 2017 and 2018, the current understanding of

goosander presence is limited to monthly counts only and at a relatively coarse spatial coverage. Hence,

in 2019 the DDSFB and RDT will undertake an in-depth study of predation pressures during the migration

period. This project ties in with a national effort by Marine Scotland Science to better understand

predation pressures by goosanders on Atlantic salmon.

Fish detection Tagged smolts that were recorded at the last pair of receivers in Aberdeen Harbour are assumed to be

surviving smolts that made their way out to sea. Conversely, tags that were lost during the in-river

migration are assumed to be failed migrations and likely fish mortalities. This is assumption is thought to

be reasonable, because 1) tags are surgically inserted making it unlikely for tags to be “shed” without

harm to individual fish; 2) tag battery failure is unlikely given that battery life was longer than the observed

migration window for tagged fish; 3) tag detection throughout the river was high, making it unlikely that

any single tag would be missed throughout the entire river and harbour.

Although some in-river receivers operated at lower efficiencies and miss detections can’t be ruled out

completely, high detection efficiencies in the lower river (i.e., 100% from Boating Club onwards) give

confidence in the assessment of tag losses. This means that it is unlikely that we have underestimated the

number of tagged fish coming through the harbour. The detection efficiency seems overall somewhat

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lower compared to 2016/2017 for some of the receivers. This is not considered to be an issue because of

the high efficiency of the receivers in the lower river that provide confidence that any smolt swimming

through the lower river and harbour was recorded. The only effect of lower efficiency that is noticeable

in the results, is a minor increase in the uncertainty around swimming speeds for individual sections (see

Fig. 7). The strong response in the number of movements in relation to river discharge that was seen in

2018 (Fig. 4), was also seen in the 2016 and 2017 tracking studies, giving further evidence that smolt

migration in the River Dee is strongly linked to river discharge.

Swim speeds Swimming speed was generally higher in 2018 than in 2017 for Baddoch smolts. The average speed in the

river was 3.14 km hr-1 compared to 0.22 km hr-1. This could result from a difference in discharges during

the early period of migration where river flows were higher in 2018 compared to 2017. Again, migration

speeds in the tidal river were slightly higher in 2018, with an average of 1.6 km hr-1 compared to 0.8 km

hr-1. This is also likely influenced by the exceptional low flows in 2017. Finally, in the harbour migration

speeds were similar with speeds of ~1.8 km hr-1 and ~2.3 km hr-1 in 2017 and 2018, respectively. It is

noticeable that the difference between the two years diminishes further downstream, which may reflect

an increasing tidal influence which could decouple the link between river discharge and swimming speed

to a degree. Despite this, in both years the average discharge remains the primary factor that determines

swimming speed (see section Swimming Speed). The positive relationship between discharge and swim

speed is perhaps not surprising as the velocity of the water increases with discharge, however, velocity

was not included in the model. Consequently, it is currently not possible to determine whether swimming

speeds are higher than river velocity (i.e., active swimming) or whether they are the similar (i.e., passive

swimming), or even lower (i.e., swimming against the current, which could happen to avoid for example

risk of harm in high velocity areas).

Conclusions and outlook This is the third year of the smolt tracking programme on the River Dee to investigate where in the

riverine, estuarine, and coastal environments the risk smolt mortality is highest. Because of the absence

of compensatory survival when salmon reach the smolt stage (Gurney et al. 2010; Bacon et al. 2015;

Jepsen et al., 2018), a total tag loss of 48%, with 28% of tags lost in the harbour represents a potential

significant reduction in adult returns. Smolt presence in Aberdeen Harbour is different between years,

which probably results from differences in time of tagging and discharges between the years, but covers

the period between mid-April and the end of May.

The consistent pattern of 1) strong increases in the number of smolt movements with increases in

discharge for Baddoch smolts in 2017 and 2018; 2) the predominantly nocturnal activity patterns; and 3)

the relationship between swimming speed and discharge and day of the year, have clear implications for

the way the smolt migration and human activities in the river are managed. Namely, when the river

discharge is high and smolts are likely to be actively moving, extra care needs to be taken to ensure that

smolts have the best chance of migrating undisturbed by e.g., limiting operations taking place in the river

and harbour during the critical migration window. Or when river discharge is low and therefore predation

risk is greater, fish losses need to be minimised through e.g., increased efforts to reduce predation.

16

In 2019, further smolt tracking will be carried out with the support of Marine Scotland Science. Up to 70

smolts will be tagged in the upper catchment as pre-smolts, the remainder will be tagged as smolts. This

will allow the pre-smolts to migrate naturally with no subsequent effects of trapping and handling at the

delicate smolt stage, as well as time to recover from tagging before an assessment of losses on

downstream migration. Moreover, the downstream tag losses from the two types of tagging can be

determined. Additionally, a goosander exclusion trial will be run. This involves high frequency monitoring

of goosander numbers and the exclusion of goosanders from certain sections of the river. This is being

undertaken to determine if and to what degree in-river smolt survival is linked to goosander predation

pressure. Smolt migration behaviour and predation will be monitored within and outwith areas of

intensive goosander control, with receivers at the boundaries between the different zones.

Acknowledgements This work has been possible due to support from various people and groups:

Marine Scotland Science; Aya Thorne, Stephen McLaren and Denise Stirling undertook the smolt tagging

on the Baddoch Burn. Iain Malcolm, Ross Glover and John Armstrong commented on the study design, in

particular the time of tagging, size of fish and choice of tags. Rob Main assisted with the deployment and

retrieval of receivers. Iain Malcolm provided valuable feedback on draft versions of this report.

Aberdeen Harbour Board provided vessel, crew and maintenance staff to deploy and retrieve receivers in

the harbour and assist with moorings for the receivers.

SEPA provided river flow data from their gauging stations at Mar Lodge, Polhollick, Woodend, and Park.

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swimming performance and predator avoidance of juvenile Chinook Salmon. North American Journal of

Fisheries Management 24, 162–170.

Bacon, P.J., Malcolm, I.A., Fryer, R.J., Glover, R.S., Millar, C.P. & Youngson, A.F. (2015) Can Conservation

Stocking Enhance Juvenile Emigrant Production in Wild Atlantic Salmon? Transactions of the American

Fisheries Society, 144, 642-654.

Gurney, W.S.C., Bacon, P.J., McKenzie, E., McGinnity, P., Mclean, J., Smith, G. & Youngson, A. (2010) Form

and uncertainty in stock-recruitment relations: observations and implications for Atlantic salmon (Salmo

salar) management. Canadian Journal of Fisheries and Aquatic Sciences, 67, 1040-1055.

Hansen LP, Hutchinson P, Reddin DG & Windsor ML (2012). Salmon at Sea: Scientific Advances and their

Implications for Management: an introduction. ICES Journal of Marine Science, 69, 1533–1537.

Holm, S. (1979) A Simple Sequentially Rejective Multiple Test Procedure. Scandinavian Journal of

Statistics, 6, 65-70.

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Jepsen N, Flávio H, Koed A. 2018. The impact of Cormorant predation on Atlantic salmon and Sea trout

smolt survival. Fisheries Management and Ecology 0 (0) 1-4.

Kocik JF, Hawkes JP, Sheehan TF, Music PA & Beland KF (2009). Assessing estuarine and coastal migration

and survival of wild Atlantic salmon smolts from the Narraguagus river, Maine using ultrasonic telemetry.

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Malcolm, I.A., Millar, C.P. & Millidine, K.J. (2015) Spatio-temporal variability in Scottish smolt emigration

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18

Appendix Table 1: Distance from the Baddoch release site to a receiver station in kilometres. Receiver numbers

correspond to numbers in Fig. 2. Receiver codes are used in Figures throughout this report.

Distance from Baddoch (km) Receiver number Receiver code

14.83 1 1_Invercauld_301975

28.9 2 2_Abergeldie_301990

42.66 3 3_Monaltire_301980

58.94 4 4_Craigendinnie_301976

64.97 5 5_Aboyne_Water_301988

70.23 6 6_Dess_301984

74.69 7 7_Borrowston_301978

80.48 8 8_Lower_Woodend_301983

85.59 9 9_L.Blackhall_&_Kineskie_301973

90.7 10 10_Crathes_301981

96.98 11 11_Park_302176

101.91 12 12_M.Drum_301982

106.22 13 13_Culter_302174

110.79 14 14_Ardoe_302177

114.21 15 15_Waterside_302175

117.4 16 16_Boating_Club_302178

118.2 17 & 18 Gate_1

118.8 19 & 20 Gate_2

119.2 21 & 22 Gate_3

119.7 23 & 24 Gate_4

Table 2: Tagging dates and number of smolts tagged on the day.

Tagging date Number of smolts tagged

06/04/2018 2 09/04/2018 20 13/04/2018 19 16/04/2018 20 18/04/2018 20 19/04/2018 15 20/04/2018 4

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Figure 1: Hydrographs for four gauging stations on the River Dee. Mar Lodge is furthest upstream,

followed by Polhollick, Woodend and Park. Data provided by SEPA.

Figure 2: Boxplots showing characteristics of smolts that successfully migrated to the sea (blue) and those

that failed to make it to the outer harbour (orange). None of the characteristics are significantly different

between the two groups. The median (middle) and the 25th (bottom) and 75th (top) percentiles are shown

in the coloured boxes. Whiskers indicate the range within 1.5 times the distance between the median and

the 25th or 75th percentile (the normal range of the data), extreme points that fall outwith this distance

are indicated with dots. Blue boxes are successful migrants, orange boxes are failed migrations (i.e., tag

losses).

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Figure 3: Left: relationship between swimming speed of fish (displayed as Log10(speed) in km/hr) and

Average discharge (m3s-1) in left graph; right: day of the year (DoY). The effect of different river sections

is shown by the individual coloured lines.