1

Smolt migration through the lower Dee and inner harbour

October 2016

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Executive Summary Declining numbers of adult salmon returning to the Dee over the last four decades and stable juvenile

stocks suggests that mortality is occurring between the smolt and adult return stage. As a first step in

investigating this window where loss occurs, an acoustic tracking study on salmon smolts was carried

out in 2016 to establish migratory behaviour and survival of smolts in the lower Dee and inner harbour.

As a first, pilot, year in a three-year work programme, 50 smolts captured in the lower catchment were

fitted with internal acoustic tags and tracked in spring 2016. These smolts were tracked as they

migrated through the lower 22 miles of the Dee and inner harbour.

26% of tagged smolts died in the river, equating to a mortality rate of 0.78% per km migrated. There

was no further mortality in the inner harbour. This in-river mortality is considered to be caused by

either predation or delayed lethal effects from the tagging, as mortality was size-related with larger

smolts having greater chance of survival.

These smolts from the lower catchment migrated through the harbour predominantly between 2 and

10 May, with all tagged smolts moving through between 1 and 23 May. Most smolts migrated quickly

in tidal and estuarine waters, possibly making use of higher river flows to reach average speeds of 1.7

km per hour.

Migration through the inner harbour was largely without disruption or hold-ups, with just one fish

straying from the main river channel into the tidal harbour.

All migration in the river and harbour was predominantly nocturnal, although this nocturnality

reduced later in the smolt run.

The findings of this pilot study have helped to define issues which will be investigated further in 2017

and 2018. However, already some useful information for river management is appearing:

1. Mortality in-river is significant and needs further investigation, but may be an area that

fisheries management can impact on.

2. A sensitive window when lower catchment smolts are migrating in the lower river and harbour

is the first two weeks of May, although this is likely to vary annually depending on river flows

and timing of spate events.

3. This pilot study has encouraged further work to be planned by Marine Scotland Science for

2017 to determine coastal migration routes of Dee smolts.

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Introduction Salmon smolts are the final product of the river environment and river management by the Board and

Trust is aligned to ensure maximum production of healthy, wild smolts. This follows NASCO’s advice

for managing salmon stocks in the river and requires a focus on all impacts in freshwater and estuarine

and coastal waters, as concluded at the international “Salmon Summit” in 2011.

Surveys carried out for many years by the Board and Trust on the Dee shows that production of

juvenile salmon to the fry and parr stage is healthy, supported by evidence of relatively stable smolt

production on the Girnock and Baddoch burns in the upper Dee1. However, the declines seen in adult

salmon returning to the Dee demonstrate high mortality of the Dee salmon stock is occurring between

smolting and adult return times.

Mortality at sea is known to be impacting Atlantic salmon stocks at an international scale. Numbers of

salmon at sea has declined from approximately 10 million fish in the early 1970s to around 3.5 million

fish in recent years (Hansen et al 2012). However, it is also clear from studies on other rivers that the

smolt migration period, particularly when smolts enter estuaries, can be a time of high mortality (Kocik

et al 2009), with predation often the main factor (Thorstad et al 2012). To try and understand when

and where mortality impacts on the Dee salmon stock, the Dee Fisheries Management Plan (2015-

2018) highlighted the aim to investigate the smolt migration phase. In particular, the plan sets out to:

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

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

3) Quantify predation impacts on smolts.

Acoustic telemetry is capable of providing the information required. Therefore, in 2016 the Board

invested in acoustic telemetry equipment to carry out a pilot study in 2016, followed by further studies

in 2017 and 2018. This report describes the 2016 study.

Methods

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

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 12 – 35 g and tag weight represented 1.9 – 5.4% of smolt body weight.

The V5 tags are smaller than the V7 tags commonly used in salmon telemetry studies, enabling this

study to tag and track smaller smolts. As a comparison, V7 tags are recommended for smolts that are

at least 135 mm in length, but only 5% of smolts caught in the Dee Board’s smolt traps were of this

size. Thus the larger tags would not have allowed us to monitor any but the largest smolts, which may

have given a biased picture of smolt migration, behaviour and survival.

1 http://www.gov.scot/Topics/marine/Salmon-Trout-Coarse/Freshwater/Monitoring/Traps/Smolts

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However, the trade-off is that smaller tags have a reduced battery size and power output compared

to larger tags: The V5 tags have a 95% battery life of 77 days and power output 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 inner harbour. The receivers were placed close

to the bed of the river/harbour 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 an 80 kg anchor weight. The rope was held upright by a sub-surface

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 enable retrieval (Fig. 2).

Figure 1. Receiver set up for in-river monitoring.

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Figure 2. Deployment of receivers and moorings in Aberdeen harbour.

Study area The smolts were captured in rotary screw traps on the Beltie and Sheeoch burns (Fig. 3). Both traps

were located on tributaries close to the main stem of the Dee (280 and 360 m, respectively). The Beltie

and Sheeoch traps were 36.8 and 25.4 km (22 and 15 miles) from the final receiver positions in the

harbour, respectively.

A total of 18 receivers were used to detect tagged fish. Six of these were in the lower river and 12

within the inner harbour (Figs 3 and 4). Because of the channel width and high background noise levels

in the harbour, the receivers were paired up to form ‘gates’, to increase the likelihood of detecting

tagged smolts (Fig. 4).

The inner harbour was monitored as far seaward as the Marine Operations Centre, so that the length

of the harbour journey over which smolts was monitored was 1.03 km (i.e. gate 1 to gate 5). There

was a further 0.75 km between gate 5 and the breakwaters (harbour exit) which was not monitored

in this pilot study, as range testing results (next section) suggested an issue with cyclical high levels of

background noise which could not be resolved in time.

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Figure 3. Map of lower River Dee, showing locations of smolt traps ( ) and acoustic receivers (●). The study area highlighted by the

dotted outline is shown in Figure 4.

Water level gauging

station at Park

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Figure 4. Map of Dee estuary and Aberdeen Harbour, with locations of acoustic receivers (●).

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Range testing To determine how effective the receivers would be in detecting tagged smolts in the noisy harbour

environment, range tests were carried out in February 2016 by experienced investigators from the

University of Glasgow. The tests involved placing receivers in the harbour and calculating the

proportion of tag transmissions they picked up when the tag was held at set distances from the

receivers. A second test was done which involved deploying the receivers at spaced intervals for one

week in the outer harbour area, along with a test tag, and then determining how many of the tag

transmissions were detected by receivers. These results were used to design the final study (Fig. 4).

Smolts 33 smolts were tagged from the Beltie burn and 17 from the Sheeoch burn, between 27 April and 6

May. The fish tagged were considered to be well-advanced in the smolting process, with a Smolt Index

of 4-5 (Table 1; Figs 5 & 6). Fish size ranged from 106 – 157 mm in length (average 124 mm) and 12 –

35 g in weight (average 20 g). The condition of these smolts (Fulton Condition Factor; a measure of an

individual fish’s health based on weight) was 0.90 – 1.29 (1.05 ± 0.07; mean ± SD). For smolts, low

condition may not represent poor health but rather the physical changes related to smolt

development. As there was no evidence of condition factor being related to tagging date (Generalised

Linear Model; P = 0.493), we assume that all fish were at an approximately similar stage of smolt

development.

46 of the tagged smolts (92%) were detected subsequently by receivers. It is assumed that the four

smolts (8%) that were never detected died as a result of delayed tagging effects. Delayed mortality

may occur for 24 – 36 hours after tagging (C. Adams, pers. comm.). The four fish that died were not

significantly different in size (average 121.8 mm length, 20.8 g weight) to the fish that successfully

made it through the inner harbour area (125.3 mm, 20.5 g weight; t-test, P > 0.4) and were tagged in

similar water temperatures (6.6 and 6.7°C respectively; P > 0.9). The four fish were tagged on different

days, released at different times of the day, and in short, there was no obvious reason why these fish

suffered mortality. It is not clear from other smolt tracking studies what mortality rates are to be

expected, as they are often not reported or confounded with natural mortalities or size-related

tagging effects. However, mortality from tagging can be negligible (Rechisky & Welch 2009).

The remainder of the analysis is based on 46 fish.

Table 1. Smolt Index criteria

Smolt Index Life Stage Criteria

1 Yolk sac fry Newly emerged with visible yolk sac

2 Fry Recently emerged with sac absorbed

Seam along mid-ventral line visible

Pigmentation undeveloped

3 Parr Seam along mid-ventral line not visible

Darkly pigmented with distinct parr marks

No silvery colouration

4 Silvery parr Parr marks visible but faded

Intermediate degree of silvering

5 Smolt Parr marks highly faded or absent

Bright silver or nearly white colouration

Black trailing edge on caudal fin

More slender body

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Figure 5. Example of a salmon with Smolt Index of 4.

Figure 6. Example of a salmon with a Smolt Index of 5.

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 had practiced tagging carried out the procedure.

Smolts were anaesthetised using clove oil until they were heavily sedated. They were 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 then the cut was closed using two sutures. The smolt was

then placed into a recovery unit for a minimum of two hours, until it appeared to be fully recovered

and was showing startle responses. Smolts were then released into the burn, along with other

untagged smolts captured in the trap, approximately 100 m downstream of the trap. The Standard

Operating Protocol worked to was based on guidelines from the Atlantic Salmon Federation.

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

instead of an average or ‘mean’. This simply reflects that the factor being reported on (e.g. time taken

for migration) was heavily skewed and therefore the median (the middle value) better reflected what

a ‘typical’ smolt did than the average value.

Several environmental factors were investigated to see what influence they had on smolt migration:

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1. River flow. River flows was obtained from SEPA’s gauging station at Park (Fig. 3). This records

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

2. Water temperature. Water temperature was recorded at four sites using data loggers provided

by Marine Scotland Science. Two sites were in the river (Lower Crathes and Pots & Fords) and

two sites in the harbour (Gate 1 and Gate 3). Water temperature was recorded every 10 minutes

for the duration of the study.

3. Salinity. Salinity was measured at Torry quay (Gate 1) using a MicroCAT recorder provided by

Marine Scotland Science. This records concentration of solutes in the water every 10 minutes and

was deployed through the duration of the study. The recorder was approximately 1 metre plus

tide below the surface, therefore salinity records were from the top of the water column where

it was expected that the smolts would be migrating through.

4. Photoperiod. The number of minutes of daylight each day at Aberdeen was calculated. This was

based on daylight starting 30 minutes before sunrise and continuing until 30 minutes after sunset.

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

reported on:

T-tests were used to compare differences between groups of fish - such as between surviving and non-

surviving smolts, or night-time and day-time migrators – to identify what causes differences in

behaviour or survival.

To determine what factors influence migration speed and timing of migration, stepwise regression

models were used. For these models, each factor that potentially has an effect on migration

speed/timing – e.g. smolt size, date of tagging - is added to the model, until a ‘best fit’ model is

produced. This process selects the factors that have the greatest influence on migration speed/timing.

The model uses data collected for individual fish, so that the migration speed of any smolt is related

to that its characteristics (body length, date of tagging) and environmental conditions it experienced

during its migration (photoperiod, river flow and water temperature it experienced during its

migration).

Chi square tests were used to determine if a condition occurred more frequently than would be

expected by chance alone, specifically whether smolts moved more in the daytime than at night, and

whether smolts arrived at the harbour more in high-salinity than low-salinity conditions. A positive

result would indicate that smolts had a preference to migrate more under one set of conditions than

another.

The Pearson correlation coefficient was calculated to show if smolt movements varied with river flows.

The strength of all of these statistical tests, with the exception of the Pearson correlation, are reflected

with 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 important 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 randomly.

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Findings

Fish detection Six of the 46 fish (13%) were only detected on the first receiver below the tagging site (at either Lower

Crathes or Tilbouries, depending where fish was tagged) and then disappeared. A further four fish

(9%) were detected on the first two receivers before disappearing. Two more fish (4%) were detected

on further receivers in the river but never on receivers in the harbour. Therefore, in total, 34 fish (74%)

reached the harbour but the remaining 26% were lost in the river (Fig. 7).

Due to the efficiencies of receivers in the harbour area (discussed later), it is assumed that 26% of fish

did not reach the harbour and either died in the river or decided not to migrate. The latter is

considered unlikely as all smolts were well advanced in the smolting process (Smolt Index of 4 or 5)

and all had migrated downstream since being tagged, as they were detected on receivers below the

traps.

Tag failure rate is less than 2% (for all VEMCO tags; specific failure rate for V5 tag not available) and

therefore this would not be expected to account for more than one missing fish in the study.

Figure 7. Location of smolt losses in study. Loss rate is equal to the number of fish lost in that section

of the river compared to number of smolts that arrived to the top of the river section.

The overall loss or mortality rate in the river equated to 0.78 % km-1 (per km), i.e. there was a 0.78%

chance of a smolt dying for each 1 km of river it travelled through. The rate was slightly higher for

smolts tagged on the Beltie burn (0.9% km-1) than those from the Sheeoch burn (0.55% km-1). This

mortality rate did not vary obviously within the lower river (Fig. 8).

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Figure 8. Percentage of smolts surviving after release from the fish traps until exiting gate 5.

Journey times Fish took between 2 and 25 (median 7.4) days from after being tagged in the Beltie burn to exit

through gate 5, close to the Marine Operations Centre. Fish that were tagged at the Sheeoch exited

through gate 5 between 5 and 11 (median 7.4) days after tagging (Table 2). Nearly all fish moved more

slowly from the tagging site to the first receiver, compared to the rest of their journey (Table 1, Fig.

9). This may be a result of ‘after-effects’ of the tagging procedure, therefore journey times to the first

receiver may not be ‘natural’ migration behaviour and are reported separately.

Table 2. Journey time of smolts tagged in the Beltie and Sheeoch burns.

Journey Distance (km)

Median time taken (days)

Range of times taken (days)

Beltie burn

Trap – Lower Crathes 8.5 4.1 0.4 – 25.2

Lower Crathes – Gate 5 28.3 2.2 0.2 – 7.0

Total journey 36.8 7.4 2.3 – 25.5

Sheeoch burn

Trap - Tilbouries 6.7 4.5 1.6 – 7.5

Tilbouries – Gate 5 18.7 3.1 2.2 - 4

Total journey 25.4 7.4 4.6 – 11.4

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Figure 9. Journey time (hours). The boxes represent the length of time that most smolts took to

migrate each portion of the journey (i.e. the ranked 25 – 75% of smolts). The horizontal line in the

box represents the median journey time. The vertical lines above and below the boxes represent the

total time ranges that the smolts took to migrate.

There was no indication that any of the areas in the lower river where receivers were positioned were

areas of residency for smolts. Whilst three of the lower-river receivers did have large numbers of tag

detections, these were from one or two smolts that spent a long time at these sites but the remainder

of the smolts moved through quickly.

Most fish moved quickly in tidal waters, for example taking only 22 minutes (median journey time) to

move from Victoria Bridge to Gate 1 (distance 400 m). However, four fish took significantly longer,

with the longest time being a fish that took nearly two days to undertake this short journey.

Migration through the harbour Smolts exited the final gate (gate 5) in the inner harbour between 1 and 23 May. The main smolt

migration through the harbour, when between 25% and 75% of the smolts moved (standard for

migration time described by Malcolm et al 2015), was 2 - 10 May.

The time spent in the inner harbour was brief: From arriving at gate 1 to leaving through gate 5 (a

distance of 1 km), median journey time was 35 minutes (migration speed of 1.7 km hr-1; km per hour),

with the quickest smolt taking just 18 minutes (3.3 km hr-1). However, there were a few fish that took

a lot longer - five fish (15%) spent over eight hours in the inner harbour, with the slowest taking 3.5

days (0.01 km hr-1).

Only a single smolt was detected in the Albert Quay/Telford jetty area of the harbour (Fig. 6), off of

the main river channel. This fish went back and forth between the turning basin and Albert Quay area

four times. In total, it spent 16 hours in the turning basin/Albert Quay area. Three other fish spent a

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Beltie: Trap to LCrathes

Sheeoch: Trap toTilbouries

Beltie: L Crathesto Waterside

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All smolts:Waterside to

Victoria Bridge

All smolts:Victoria Bridge to

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maximum of three hours swimming back and forth in the turning basin/main river channel between

gates 2 and 5 but all other fish showed a single directional migration.

Migration speeds Smolts from both traps showed low migration speeds of 0.06 – 0.2 km hr-1 (median values) in fresh

water. These speeds are calculated for the journey from either Lower Crathes – Waterside (Beltie

smolts) or Tilbouries – Waterside (Sheeoch smolts), thus excluding the journey from the trap to the

first receiver that may be influenced by recovery from tagging.

Migration speeds of smolts tended to increase as they moved further downstream to sea (Fig. 10),

and were 0.92 km hr-1 (median value) between Waterside (tidal limit) and gate 5. Smolts tagged in the

Sheeoch, for example, showed significantly greater migration speeds in tidal than fresh water (paired

t-test; P = 0.007). However, this was not seen for Beltie smolts (P = 0.52). This was because some of

the smolts from the Beltie migrated during the high flow event on 2 – 3 May and reached speeds of

over 6 km hr-1 in the river.

For the journey in tidal and harbour waters, the smolts from the Beltie and Sheeoch traps had similar

migration speeds (t-test, P = 0.53 and P = 0.17, respectively). Their overall migration speed averaged

0.8 km hr-1 from Waterside to Victoria bridge (tidal), and 1.3 km hr-1 from Victoria bridge to gate 5

(harbour).

Figure 10. Speed of migrating smolts (km per hour).

Migration speed of the smolts in the river (from first receiver to gate 1) was most influenced by river

flows (mean discharge during each fish’s migration period) whilst start date of migration (date of

arrival at first receiver) also influenced migration speed to a smaller extent: River flow explained 30%

of all variation in fish migration speeds (stepwise regression modelling; P=0.001), whilst start date

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River Tidal river Harbour

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explained a further 23% of the variation in fish migration speeds (P =0.001). Water temperature (mean

temperature during migration period), photoperiod (mean day length during migration period), date

of tagging and individual fish length did not influence a smolt’s migration speed (P> 0.19).

What influenced survival of smolts to the harbour? The 34 smolts that successfully reached the harbour were significantly greater in length (125.3 ± 8.6

SD mm) than the smolts that died in the river (119.4 ± 6.5 mm; t-test, P = 0.04), although the difference

in weight was marginally non-significant (20.5 g ± 4.2 and 18.2 g ± 3.4 respectively; P = 0.09). There

was no other difference detected between these two groups of fish: Condition factor was similar for

the surviving smolts (1.03 ± 0.06) and the smolts that were lost in the river (1.06 ± 0.09; t-test; P =

0.26); There was no difference in water temperatures during the tagging times of survivors and non-

survivors (P = 0.84), all fish were well-advanced in their physical smolting appearance (all tagged fish

had a smolt index of 4 or 5), all survivors and non-survivors were tagged over the full range of dates

and at both sites - 21 (64%) smolts from the Beltie and 13 (76%) from the Sheeoch reached the

harbour.

Although smolt migration speed was slower following tagging, this did not relate to whether the fish

subsequently survived, as the journey times between the Beltie trap and the first receiver was not

significantly different between fish that survived (median 4.1, range 0.4 – 25.2 days) and the fish that

died in the river (median 5.5, range 0.5 – 25.2 days; t-test, P = 0.72). There also appeared to be no

difference in journey time from the Sheeoch trap to the first receiver, for fish that survived (median

4.5 days) and those that died (median 3.9 days), although this latter group only included two fish.

Factors influencing migration

Diurnal patterns All migration was predominantly nocturnal (night is defined as between 30 minutes after sunset to 30

minutes before sunrise), particularly at the start of the migration journey: 92% of smolts arrived at

Lower Crathes and Tilbouries during darkness. Lower down the river (Waterside – Harbour), an

average of 70% of smolt movements occurred at night. Statistically, migration occurred more during

the night than would be expected if migration timing was random (Lower Crathes/Tilbouries: Chi

square; P < 0.0001; Waterside – Harbour: P < 0.0001), showing that smolts are selecting to migrate at

night.

More smolts also travelled through the inner harbour at night: 21 smolts (72%) moved from gate 1 to

gate 5 entirely at night; Six fish (17%) moved entirely during daytime; and movement of the final three

fish (10%) covered both day and night (i.e. early morning or late evening). The five fish that spent a

long time in the harbour area (> 8 hours) were excluded from this comparison as they were

presumably not actively migrating for this full period and hence their movement times are uncertain.

Whether the smolts migrated during daylight or at night was influenced by the stage of the smolt run

- smolts that migrated during the night were in the harbour significantly earlier (median date 9 May)

than smolts that migrated during the daytime (median date 13 May; t-test, P = 0.009). Smolts

migrating during early morning/late evening migrated through the harbour on (median date) 12 May.

River flows There were no particularly high flow events during the period when tagged smolts were migrating (27

April – 23 May). Average daily flow at Park during this period was 56 m3 per second (m3 s-1). The highest

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flow event recorded was 166 m3 s-1 on 2 May. There was also a small rise on 10/11 May (64 - 66 m3 s-

1) and 22/23 May (64 – 74 m3 s-1).

Smolt migration occurred during nearly all days of the study, however, the number of smolt

movements in a day increased with river flows (Pearsons correlation coefficient = 0.71; based on scale

of 0 (no relationship) to 1 (perfect positive relationship); Fig. 11). The peak time for smolts reaching

the harbour was 2 - 3 May (Fig. 12), coinciding with the peak flow event.

The most important factor that influenced the date that a smolt arrived at the harbour (gate 1) was

river flow (mean discharge during migration period; stepwise linear regression; P < 0.001), which

explained 60% of the variation in arrival date. However, river flows did not influence when a smolt

initiated its migration in the main stem (date of arrival at first receiver; P > 0.08).

Figure 11. Smolt movements (initial detections at each receiver; bars) compared to river flows (line).

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ADAA Bon Accord Victoria Bridge

Gate 1 Mean discharge at Park

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Figure 12. Arrival date at the harbour (gate 1), compared to river flows (line).

Water temperatures and day length Water temperatures increased through the study period. Water temperatures in the river ranged from

6.0 – 12.7°C, whereas the harbour ranged from 6.6 – 11°C. The harbour waters were warmer than the

river at the end of April, however this reversed in early May and harbour water temperatures dropped

below river temperatures, averaging 1.3°C below river temperatures for the remainder of the study.

The main smolt run through the harbour (when 25 – 75% of tagged smolts arrived) occurred between

2 and 10 May, corresponding to water temperatures in the harbour of 8.3 – 10.9°C.

Temperature and day length both appeared to have the greatest influence on date of onset of

migration in the main stem (date of arrival at first receiver; stepwise regression; P<0.0001); Similarly,

water temperature was related to the date that smolts arrived at the harbour (P<0.0001), being the

second most important factor after river flow. However, as both water temperature and day length

are very closely linearly related to day of the year it was hard to separate out the independent effects

that these two factors had on the smolt migration. These results relating to water temperature and

day length are therefore likely to be biased.

Tidal patterns and salinity There was no clear influence of tidal cycle on smolt migration through the harbour. Smolt arrival at

the harbour (gate 1) occurred throughout the tidal cycle, although slightly more smolts arrived

preceding low tide (Fig. 13). The five smolts that took longer to migrate through the harbour also did

not appear to be influenced by tidal patterns, arriving at gate 1 between 4 and 11 hours after high

tide.

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Gate 1 Mean discharge at Park

18

Figure 13. Number of smolts arriving at the harbour (gate 1). Black vertical line represents low tide.

Salinity The harbour area is predominantly salt water, however salinity varied from nearly freshwater (0.054

ppt) to almost pure sea water (33.84 ppt; measured at gate 1). Smolt arrival at the harbour was

significantly related to salinity, with more smolts arriving at conditions of high salinity (> 22 ppt) and

avoiding low-salinity conditions (< 22 ppt) than would be expected if their arrival was unrelated to

salinity (Chi square; P = 0.02).

Receiver detection performance The survival rates for tracked smolts are only accurate if the receivers do not miss tagged smolts. The

18 receivers generally performed well and recorded over 30,000 fish detections. As there was a total

of 18 receivers, there was a high likelihood that a smolt that was just missed on one receiver would

be detected on one of the other receivers further down. We can calculate maximum receiver

efficiency, based on the number of smolts that are known to have been missed (i.e. smolts that were

subsequently detected on receivers further downstream) relative to the total number of smolts that

could have been detected.

Based on this, receivers had 88 – 100% maximum detection efficiency. Receivers in the river had an

average maximum detection rate of 95.6% and those in the harbour had an average maximum

detection rate of 96.2%.

Ten receivers in the harbour formed five gates, i.e. a pair of receivers with one positioned on each side

of the channel. There was no evidence that any gates missed smolts, as of the 34 smolts detected in

the lower river, all 34 smolts were detected at each of the gates, with between 30 and 34 of the smolts

detected on individual receivers comprising the gates.

As the harbour is a noisy environment and we had most concern about detection of fish in this area,

sentinel tags were deployed throughout the study to determine receiver efficiency. Sentinel tags are

acoustic tags similar to those that smolts were tagged with, but they have an attachment so that they

0

1

2

3

4

5

6

0-1

hr

1-2

hr

2-3

hr

3-4

hr

4-5

hr

5-6

hr

6-7

hr

7-8

hr

8-9

hr

9-1

0 h

r

10

-11

hr

11

-12

hr

Nu

mb

er o

f sm

olt

s

Hours before high tide

19

can be tied off to moorings. They are placed in the river/harbour and transmit throughout the study

period. Calculating the proportion of their transmissions that are detected by receivers allows the

efficiency of the receiver to be determined, and hence what chance there is that they will miss a

tagged fish. Sentinel tags were placed at Victoria Bridge and gates 1 - 4. The sentinel tags transmitted

every 10 minutes (random between 8 min 20 sec and 11 min 40 sec). Over the course of deployment

(7 April to 20 June; 75 days) these tags would have transmitted 10,800 times. The number of times

that any receiver detected these transmissions was used to calculate efficiency of that receiver, for

the set distance between that receiver and the tag. For a gate to be effective requires both receivers

to consistently detect tags to a distance of half the width of the gate. Alternatively, one receiver could

have greater detection efficiency than the other, provided that between them the full width of the

gate was covered.

The sentinel tags showed that the gates would generally have good ability to detect tagged fish (Table

3). The only gate not to have 100% detection efficiency was gate 3, the widest gate. However, gate 3

did detect all 34 smolts.

Although no sentinel tag was deployed at gate 5, the tag on the south bank at gate 4 was detected by

the receiver on the north bank at gate 5 over 60% of the time. This suggests that sound detection in

this area of the harbour is reasonable and as the distance between the two receivers in gate 5 is less

than 109 m, it is expected that this gate would provide full coverage of the harbour width.

Table 3. Detection efficiencies of gates in the harbour.

Gate number

Receiver locations Detection efficiency Gate width (m)

Gate fully covered

1 Petrofac & Torry Quay South-side receiver had 84% detection efficiency of tag on north side.

99 Yes

2 Point Law & sewage outfall

South-side receiver had 65% detection efficiency for tag on north side. North side receiver tested in range testing (Feb 2016) – detection efficiencies >90% at distances up to 169 m

80 Yes

3 Pilot jetty & Old capstan South-side receiver had 16% detection efficiency for tag on north side

163 No

4 North wall & South beach North-side receiver had 62% detection efficiency for tag on south side.

142 Yes

5 Abercrombie jetty & Skate’s nose

North-side receiver had 64% detection efficiency for the receiver on the south bank at gate 4 (135 m).

109 Yes

20

Conclusions

Survival 26% of tagged smolts died in the river, but no mortality occurred in the inner harbour. This equates

to a mortality rate of 0.78% km-1 of river migration. Whilst surprisingly high in our expectations, it is

actually at the lower end of the scale for a range of published studies, which find in-river mortality of

0.3 – 7% km-1 (median 2.3%; Thorstad et al 2012). Similarly, the 0% mortality rate in the inner harbour

is well below published estuarine mortality rates of 0.6 – 36% km-1 (median 6%; Thorstad et al 2012).

However, the mortality rates found in this study are almost identical to that found on the River

Deveron (Lothian, unpublished), where in-river mortality rates were 0.77% km-1 and bay mortality was

0% km-1 in 2016.

Survival was significantly related to smolt size, with the larger smolts having higher survival. The size

difference was relatively small, with survivors being just 6 mm longer, on average, than non-survivors.

Body size was not related to migration speed or timing of migration, so it is unlikely that smaller fish

died because of indirect impacts (natural or as a result of tagging) on migratory behaviour. We

consider that higher survival of larger smolts may be related to either size-selective predation or

delayed lethal tagging effects affecting smaller smolts:

In terms of size-related tagging mortality, we used tags of appropriate size for the smolts, and indeed

other studies have used relatively bigger tags and found no effect (Newton et al 2016). However,

whilst we kept smolts for at least two hours following tagging, and used widely-practiced tagging

techniques, it is possible for a delayed mortality to occur, for example from infected wounds.

Predation is thought to be the largest cause of smolt mortality (reviewed by Thorstad et al. 2012),

although it varies substantially between rivers. Higher survival of large smolts may result from

improved escaping from size-selective predators (Holtby et al 1990, Jonsson & Jonsson 2011). For

example, auklet seabirds have been shown to selectively target smaller juvenile Pacific salmon in

poorer condition than larger juveniles (Tucker et al 2015). Predators in the lower Dee include birds

(particularly goosanders and cormorants), fish (particularly sea trout kelts) and seals.

Natural mortality may also occur in the river from physical trauma, such as collisions with dams

(Thorstad et al 2012). However, given the lack of obstructions in the lower Dee and the lack of spates

in spring 2016, this is suspected to be a minor factor. Therefore, in terms of the most likely cause of

mortality, which is considered to be predation or tagging, it is not possible to determine between

which of these is responsible for the size-related survival here, but will be the focus of further study

next year (described later on). It should be recognised that in this pilot year only the inner harbour

was monitored and it is possible that further mortality (particularly from predators) may occur in the

outer harbour.

Migration time The tagged smolts from the lower Dee catchment reached the harbour between 2 and 10 May.

Assuming that these tagged smolts represent the general run timing for smolts from the lower

catchment, this provides a ‘window of sensitivity’ (Malcolm et al 2015) for activities that have the

potential to harm smolts. The Dee’s timing is slightly later than average migration times across other

Scottish rivers, which is between 28 April and 7 May (when 25 to 75% of the cumulative smolt run

reaches the coast; Malcolm et al 2015), although there is variation, such that on the earliest river 25%

of smolts reach the coast by 13 April and the latest time when 75% of smolts reach the coast is 25

May. Generally, the Dee’s timings fits with other studies whereby most of the run occurs in 1-2 weeks

but the full migration period may be 3-7 weeks (Thorstad et al. 2012).

21

Migration speed Dee smolts migrated through the lower river at rates of 0.06 – 0.2 km hr-1, through tidal waters at 0.92

km hr-1 and through the inner harbour at 1.7 km hr-1. As sustained swimming speed of smolts is

approximately 2.2 body lengths sec-1 (Scruton et al 1998) - equivalent to 0.9 km hr-1 - it is clear that

smolts migrating through the harbour must utilise tidal movements or river flows to increase their

speed. Whilst this study found no influence of tidal cycle on smolt arrival at the harbour, there was a

strong effect of river flows, which perhaps indicates smolts can benefit from high river flows to carry

them through the inner harbour. As there were no particularly high flow events in spring 2016, it

would be expected that migration speeds could be much higher in other years.

Triggers for smolt migration This study found that the key factor influencing when smolts actively migrate is river flows, with more

migration occurring during high flow conditions. McCormick et al (1998) also reports that river flow

and temperature are the main environmental triggers to initiate migration, whereas day length

determines the range of dates that migration can occur. Other studies have identified river and ocean

temperatures, day length and the lunar cycle as all having an influence on smolt migration (Thorstad

et al 2012).

This study also found clear evidence of nocturnal migration being preferred, although this preference

weakened through the course of the smolt run. This has been seen in other studies (Ibbotson et al

2006, Veselor et al 1998), where smolt migration is predominantly nocturnal up until water

temperatures of 12°C is reached, following which more diurnal migration occurs.

The influence of water temperatures was difficult to interpret, because water temperature generally

increased throughout the study period, as expected. A review (Hvidsten et al 2009) showed that

smolts entered the sea at different times on different rivers, but all entered the sea when sea

temperatures reached 8°C. Dee smolts also fit with this finding, as the likely start of the smolt

migration (when the first 25% of the tagged smolts had reached the harbour) occurred when water

temperatures in the harbour was 8.3°C. Water temperatures below 8°C is related to higher mortality

of smolts and smolt runs appear to be timed to coincide with conditions for favourable survival

(Friedland et al 2000).

Other studies have found an influence of tidal cycle on smolt migration, for example in England smolts

migrate on a falling tide (Moore et al 1992, 1995). We did not find any evidence of tidal cycle

influencing movement times in the harbour, however, it is possible that this effect may be population-

specific depending on the estuary (Kocik et al 2009). It does appear that no period of acclimation is

necessary for smolts upon reaching salt water (Moore et al 1995) and this was evident in our study,

with smolts migrating quickly through the tidal reaches and harbour without waiting for tidal cycles.

2017 programme of work Following this pilot study in 2016, further tracking of 100 tagged smolts will be carried out in 2017.

The focus for the 2017 work will be:

1. To tag a further 60 smolts from the Beltie and Sheeoch burns to confirm findings of the pilot study.

2. To tag 40 smolts from the upper catchment to assess whether these smolts have a different

migration time and thus a different period of sensitivity. MSS have offered support to tag 40 smolts

from the fish trap in the Baddoch burn, which is a tributary of the Clunie.

3. To further investigate in-river survival, using more in-river receivers to look at stage-specific

mortalities.

22

4. To determine whether in-river mortality is caused by size-dependent tagging effects. A separate

acoustic tracking study on Dee smolts being carried out by MSS, using larger smolts and larger tags,

will enable a comparison of tagging effects between the two studies.

As set out in the Dee Fisheries Management Plan, the aim of the tracking programme of work is to

extend into the marine environment to identify coastal routes of smolts exiting the river. We are

currently supporting Marine Scotland Science’s work planned for 2017 to investigate Dee smolt

migration patterns off the Aberdeenshire coast. This would provide an understanding of migration

routes earlier than was anticipated in the Management Plan.

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

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

in the harbour and assist with moorings for the receivers.

We benefitted from advice from people with expertise in salmon acoustic telemetry to design this

study. In particular Jon Carr (Atlantic Salmon Federation, Canada) trained staff in tagging procedures

and offered advice on study design, Dr Matt Newton and Professor Colin Adams (University of

Glasgow) undertook range testing and provided advice on study design and equipment, and Stephanie

Smedbol (Vemco, Canada) provided further study design and data analysis guidance. Jon and

Stephanie were able to participate in our acoustic telemetry conference and workshop in February

2016 thanks to financial support from the Atlantic Salmon Trust.

Marine Scotland Science Oceanography provided MicroCATs and data loggers to record salinity and

water temperature and data support.

Chain links were kindly donated by John Lawrie (Aberdeen) Ltd.

SEPA provided river flow data from their gauging station at Park.

23

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