NatureScot Research Report 1256 - Aerial surveys of seals in Scotland during the harbour seal moult, 2016-2019

Year of publication: 2021
Authors: Morris, C.D., Duck, C.D. and Thompson, D. (St Andrews University, Sea Mammal Research Unit)

Cite as: Morris, C.D., Duck, C.D.,and Thompson, D. 2021. Aerial surveys of seals in Scotland during the harbour seal moult, 2016-2019. NatureScot Research Report 1256.

Scotland holds around a quarter of all harbour seals (Phoca vitulina) found in Europe. Information on population size and distribution of harbour seals in Scotland is vital to inform species conservation and management, as well as to fulfil various surveillance and reporting requirements set out in legislation.

The Sea Mammal Research Unit (SMRU) has been undertaking surveys of harbour seals in Scotland for over 30 years, and currently aims to survey the entire Scottish coastline on a five-year cycle.  Surveys are carried out during the August moult period, when the numbers of animals hauled out on shore are at their highest and provide a reliable index of harbour seal abundance.  The seal count data can also be scaled-up to produce estimates of total harbour seal population.  Grey seals (Halichoerus grypus) encountered during harbour seal moult surveys are also counted to provide information on their summer distribution.

Almost the entire Scottish coastline was surveyed by helicopter between 2016 and 2019 to provide the fifth full census of harbour seals in Scotland since the mid-1990s.  This report presents these latest results in context of the long-term series of data, and provides an updated assessment of abundance and trends in harbour seals at national, regional, and local scales.

Keywords

harbour seal; Phoca vitulina; grey seal; Halichoerus grypus; population monitoring; seal distribution; regional trends; Special Area of Conservation

Background

Scotland holds around a quarter of all harbour seals (Phoca vitulina) found in Europe. Information on population size and distribution of harbour seals in Scotland is vital to inform species conservation and management, as well as to fulfil various surveillance and reporting requirements set out in legislation.

The Sea Mammal Research Unit (SMRU) has been undertaking surveys of harbour seals in Scotland for over 30 years, and currently aims to survey the entire Scottish coastline on a five-year cycle.  Surveys are carried out during the August moult period, when the numbers of animals hauled out on shore are at their highest and provide a reliable index of harbour seal abundance.  The seal count data can also be scaled-up to produce estimates of total harbour seal population.  Grey seals (Halichoerus grypus) encountered during harbour seal moult surveys are also counted to provide information on their summer distribution.

Almost the entire Scottish coastline was surveyed by helicopter between 2016 and 2019 to provide the fifth full census of harbour seals in Scotland since the mid-1990s.  This report presents these latest results in context of the long-term series of data, and provides an updated assessment of abundance and trends in harbour seals at national, regional, and local scales.

Main findings

• The latest total counts for the whole of Scotland suggest that both seal species are currently doing well on a national scale.  During the most recent August surveys of all areas, 26,846 harbour seals and 25,412 grey seals were counted in Scotland.  This is the second highest total ever recorded for harbour seals and the highest total recorded for grey seals.  Using estimated haul-out probability from telemetry data to scale the most recent counts to population size (Lonergan et al., 2013; Russell et al., 2016), produced estimates of approximately 37,300 (95% CI: 30,500-49,700) harbour seals and 106,300 (95% CI: 88,800-132,400) grey seals.
• However, the latest counts also confirm starkly contrasting regional population trends in harbour seals.  Harbour seal numbers are stable or increasing in most areas of western Scotland.  Following substantial declines in the 2000s, numbers in northern and eastern Scotland appear to be stable overall, albeit at relatively low levels compared to the 1990s.  Orkney has seen an 85% decline in harbour seal numbers since 1997.  Although the most recent harbour seal count in Orkney was slightly higher than in 2016, this does not necessarily signify the end of the decline there.
• The latest counts show that more than three-quarters (78%) of all harbour seals in Scotland are currently found in western Scotland (including the Western Isles).  This is a significant shift since the 1990s when Orkney and Shetland were proportionally the most important regions in Scotland for harbour seals.  Whereas half of all harbour seals counted during the Scotland census in 1996-1997 were recorded in Orkney and Shetland, these regions now only contribute one sixth to the Scottish total.  
• Harbour seal SACs are not always reliable indicators of wider populations.  The total number of harbour seals counted within Special Areas of Conservation (SACs) has declined continuously since surveys began.  There is no sign of harbour seal numbers recovering in those SACs that have seen the largest declines, namely Sanday SAC, Mousa SAC, Dornoch Firth and Morrich More SAC, and Firth of Tay and Eden Estuary SAC.  The most recent counts for these SACs were 90-98% lower than the maximum counts recorded in the 1990s.  In some cases, declines observed in SACs are balanced by significant increases in adjacent areas.  The reason for this is unknown.
• Ongoing studies, funded by the Scottish Government, are attempting to identify the most likely driver(s) affecting the large regional declines observed in harbour seal populations.  Among the possible causes being investigated are predation by orcas (Orcinus orca) and by grey seals, competition with grey seals, algal toxins, and diseases. 
• The August counts suggest that grey seal numbers are stable overall.  The high variability of grey seals hauled out at this time of year makes it difficult to identify clear trends.  A significant increase has occurred in East Scotland, due to grey seal numbers hauling out at the Ythan River mouth, north of Aberdeen, making it the single largest haul-out site in Scotland.

Acknowledgements

Helicopter surveys around the whole of Scotland were primarily funded by NatureScot, with additional funding from Marine Scotland.  Fixed-wing surveys in the Moray Firth and the Tay and Eden Estuaries were funded by the UK Natural Environment Research Council (National Capability Grant no. SMRU10001). 

We are very grateful to PDG Aviation Services and their pilots and ground crew, engineers, and operations staff, who were all crucial in enabling us to conduct the surveys in a safe and efficient manner.  Many thanks to Tim Whittome at Caledonian Air Surveys Ltd and Bill Giles of Giles Aviation for their help with the Moray Firth and Firth of Tay flights, as well as to Gordon Smith for piloting the survey of offshore islands.

We would also like to thank the TRAKKA team in Sweden, especially Danny Allen, for their help in getting our camera system up and running in time for the 2016 surveys, and for their efforts to further customise and improve the software ever since.

The Lismore boat survey counts were provided by Jane Dodd, NatureScot.  We are grateful to John Baxter and Morven Carruthers at NatureScot for their support in management and administration of the survey agreement.

We are also very grateful to Debbie Russell for her valuable comments on this document.

Abbreviations

Natural Environment Research Council (NERC)
Oslo-Paris Convention for the Protection of the Marine Environment of the North-East Atlantic (OSPAR)
Special Area of Conservation (SAC)
Seal Management Area subdivision (SMAsd)
Sea Mammal Research Unit (SMRU)
Site of Special Scientific Interest (SSSI)

Introduction

The Sea Mammal Research Unit’s seal count surveys play a central role in gathering knowledge on the size, distribution, and status of seal populations in the United Kingdom (UK).  The Natural Environment Research Council (NERC) is obliged to submit this information to the Scottish Government and to the Department of the Environment, Food and Rural Affairs (Defra) under the Marine (Scotland) Act 2010 and the Conservation of Seals Act 1970 respectively.  The most recent advice is available from St Andrews University Sea Mammal Research Unit.  The surveys also provide information required to satisfy surveillance and reporting obligations under the Habitats Directive (and Habitats Regulations as amended in Scotland), including in relation to the conservation status of seals within Special Areas of Conservation (SACs), as well as requirements to assess the status of the marine environment through OSPAR and under the UK Marine Strategy.

Estimates of seal abundance and population status rely on counts of animals that haul out on shore to rest, breed, or moult.  Unlike grey seals, harbour seals do not congregate at breeding colonies.  Newborn pups are able to swim from birth and follow their mothers into the water.  Therefore, harbour seal population monitoring surveys are commonly carried out during their annual moult period in August (Thompson and Rothery, 1987), when the numbers of animals hauled-out during low tide periods are generally higher and less variable than at other times of the year (Thompson and Harwood, 1990).  Counts obtained from these surveys represent an index of population size, as not all individuals are on shore at any one time.  Lonergan et al. (2013) used satellite telemetry transmitters to estimate that 72% (95% CI: 54–88%) of all harbour seals are hauled out during the standard survey window.  While land, boat, or drone surveys are suitable for monitoring seal numbers at specific haul-out sites or within relatively small areas, the most time- and cost-efficient method for covering larger areas is to carry out aerial photography surveys by plane or helicopter (Thompson and Harwood, 1990). 

The Sea Mammal Research Unit (SMRU) has been carrying out aerial surveys of harbour seals in Scotland since the late 1980s, and currently aims to cover the entire Scottish coastline on a five-year cycle, with parts of the Moray Firth and the Firth of Tay & Eden Estuary being surveyed every year.  Data collected so far have shown striking differences in population trends between regions.  Northern and eastern regions of Scotland have seen significant declines since the early 2000s, with the most dramatic changes occurring around Orkney, in Shetland, and in the Firth of Tay and Eden Estuary.  In contrast, harbour seal numbers in western regions have been either stable or increasing (Thompson et al., 2019). 

Grey seals encountered during harbour seal moult surveys are also recorded and reported, providing useful information on their summer distribution.  At this time of year, grey seal numbers at haul-outs can be more variable from day to day.  Although UK grey seal abundance estimates have historically been based on a population model that uses pup production estimates obtained from surveys of grey seal breeding colonies (Thomas et al., 2019), the August counts provide independent estimates of the grey seal population size that now feed into that model (Russell et al, 2016).

During the introduction of the Marine (Scotland) Act 2010, the Scottish coast was divided into seven Seal Management Areas (SMAs), which are used for reporting numbers of seals counted and for calculating Potential Biological Removal (PBR) values at a regional level.  The largest SMA, West Scotland, was split into three subdivisions, and North Coast & Orkney was split into two subdivisions (Figure 1).  These SMAs were divided into smaller Subunits, generally containing several tens of kilometres of coastline, to facilitate the analyses of abundance and distributional changes at a more local scale (Figure 2).

This report presents the results from the most recent series of aerial surveys carried out around the whole of Scotland, from 2016 to 2019, in the context of previous findings at a national, regional, and local level.  These data represent the fifth full Scotland census of harbour seals obtained over the last 25 years.

Methods

Survey methods

All surveys were limited to the August harbour seal moult period and followed the standard SMRU protocol.  Survey windows were restricted to periods within two hours either side of low water occurring between approximately 12:00 and 19:00, when haul-out numbers are considered to be relatively high and consistent (Thompson and Harwood, 1990; Russell et al., 2015).  The time-of-day rule needs to be relaxed occasionally to enable the surveying of haul-out sites that lie within restricted military Danger Areas, such as the outer parts of the Dornoch Firth and Morrich More SAC in the Moray Firth.

No flights were carried out during or following periods of heavy or prolonged rain, as very wet weather can affect the number of seals hauling out (Grellier et al., 1996).  Standard survey altitude was around 300m for helicopter surveys and around 200m for fixed-wing surveys, which is usually sufficiently high to avoid significant disturbance of seals and other wildlife.  High-resolution photographs were taken of all seals seen on shore.  Cameras were either connected to a GPS unit directly producing geo-tagged imagery (during helicopter surveys) or time-synced to two Garmin Foretrex 401 units that recorded detailed tracks of all flights (during fixed-wing surveys).

One of the challenges in planning intertidal surveys across large areas is making sure that all counts are carried out within the survey windows available at different locations.  Local low water times for over 160 locations around Scotland were extracted from POLTIPS (National Oceanographic Centre, Natural Environment Research Council) to create a calendar highlighting potential survey days for all areas.  Flight times recorded during previous surveys were used to estimate expected survey duration for different parts of the coast.  A provisional flight schedule was put together to minimise transect flights required before, during, and after survey sessions.  This was continually adapted based on survey progress, expected weather conditions, and aircraft availability.  Figure 3 shows the survey windows available for all SMAs in August 2016 to 2019 as well as the days on which surveys were eventually flown.

Distant offshore islands were not surveyed during the helicopter surveys, as these locations are not generally used by harbour seals.  In order to obtain comprehensive information on grey seal distribution in August, an effort was made to survey them by fixed-wing.  St Kilda and Fair Isle have not been covered properly by any of these surveys, although an attempt was made to survey Fair Isle in 2019 when transiting from Orkney to Shetland.  Conditions were not ideal, but grey seals recorded during this flight have been included in this report.  Figure 4 shows the years in which different parts of the coast were surveyed most recently. 

Helicopter thermal-imaging surveys around Scotland

Scotland’s highly intricate coastline is over 18,000km long, including over 800 islands (Baxter et al., 2011).  Seals are found in almost all Scottish coastal areas, and the only method currently available, to search the entire coast in an efficient manor, is by helicopter.  All SMRU helicopter surveys were carried out with a Eurocopter AS350/AS355 Squirrel aircraft.  The standard survey altitude was around 300m or lower and the aircraft generally remained a few hundred meters offshore where possible.  Flying speed was over 100kts when scanning straight sections of coastline, but was reduced significantly when surveying more complex shorelines or areas with high concentrations of seals.

Rocky shores make up the vast majority of Scotland’s intertidal areas, and seals are often extremely well camouflaged when lying on rocks or seaweed.  It would be impossible not to miss large numbers of hauled-out seals in this environment without using an infrared (IR) sensor.  IR cameras use heat radiation to produce a thermal image, enabling the detection of warm bodies on a cooler background (Figure 5).  Since 2016, SMRU has been using the multi-sensor camera gimbal SWE-400 by Trakka Systems, which has an integrated mapping and data recording system (Figure 6).  The gyro-stabilised gimbal contains a thermal imaging video camera, a high-definition colour video camera, a Nikon D810 photo camera fitted with a 300mm lens, and a laser range finder.  When conducting a survey both videos are recorded continuously.  High-resolution photographs are taken of all seals detected with the thermal image.  Time stamps and GPS coordinates are saved with all video and still image data.  Breadcrumbs of the flight track and polygons of the areas covered by the sensors’ field of view (FoV) are saved in a metadata file. 

Prior to 2016, a Barr and Stroud IR18 Thermal Imager was manually operated through the side door of the helicopter with the windowpane removed.  Paper maps were used to record times and locations of seal sightings.  Counts were originally made using just the thermal video recording, and the number of individuals in large groups of grey seals were estimated rather than counted in detail.  From 2006, a hand-held digital single-lens reflex (DSLR) camera was used to take oblique photographs of sightings.  This made counts of large groups more accurate and improved species identification.  An overview of changes in the methods used during helicopter surveys is given in Table 1.

Table 1. Different methods used to find, identify, count, and locate seals during helicopter surveys from 1988 to 2019.

Years	Finding seals	Identifying species	Counting animals	Locating site
1988-2005	Live video image from hand-operated thermal imager (IR-18 through open side-window)	Thermal image video (few film photographs)	Thermal image video (few film photographs)	Marked paper maps, true colour video
2006-2009	Live video image from hand-operated thermal imager (IR-18 through open side-window)	Hand-held digital photographs (8/10MP; 70-300mm lens) if available	Thermal image video & hand-held digital photographs (8/10MP; 70-300mm lens)	Marked paper maps, true colour video
2010-2015	Live video image from hand-operated thermal imager (IR-18 through open side-window)	Hand-held digital photographs (8/10MP; 70-300mm lens) if available	Thermal image video & hand-held digital photographs (8/10MP; 70-300mm lens)	GPS flight tracks, marked paper maps, true colour video
2016-2019	Live video image from thermal imager in gyro-stabilised SWE400 gimbal	Digital photographs taken with 38MP camera (300mm lens) in SWE400	Thermal image video, digital photographs recorded with SWE400	Geo-tagged imagery

Fixed-wing surveys of sandy estuaries and offshore islands

In the annually surveyed areas in the Moray Firth and in the Firth of Tay and Eden Estuary SAC, the vast majority of seals haul out on sand.  Because seals are much easier to see in this environment, and haul-out locations are well known, these areas are generally surveyed by fixed-wing aircraft using hand-held photography.  A DSLR camera fitted with a 70-300mm zoom lens is used to take images of all seals encountered.  The most commonly used aircrafts are a Cessna 172 and a Piper PA-23-250 Aztec.  Surveys are carried out at an altitude of 200m or lower.  Standard flying speeds vary between 70-100kts depending on aircraft type and wind conditions.

Seals are very well camouflaged on rocky shores and would often be impossible to detect from an aircraft without using an infrared sensor.

Data analysis

Counting and mapping

The video recordings were reviewed using the TM-100 software’s playback function, to ensure that no obvious seal groups were missed (i.e. not photographed) during the survey.  The high-resolution photographs were scrutinised in conjunction with the thermal video to obtain precise counts of harbour seals and grey seals.  All seals resting on land were counted, including partially submerged animals and potential pups of the year.  Large groups of seals were counted in Photoshop using the in-built Count Tool or by using iTag, an open source software developed for counting seals on digital photographs (Viquerat, 2015).  Counts were added to a GIS map showing the helicopter flight track and image locations (Figure 7).

Data presentation

The census totals were calculated by combining the most recent survey data available within each census period.  The most recent survey coverage for the 2016-2019 census is shown in Figure 4.  The census counts are presented in a table showing totals by SMA (subdivision).  These data were also aggregated by 10km squares in order to visualise the Scotland-wide distribution.

Line graphs that help identify potential trends in the time series of SMA counts were created by plotting all years containing significant coverage of an SMA.  If the SMA was not surveyed in its entirety in a given year, counts from the previous survey were included to represent the whole SMA.  Indeed, the lines plotted for all seven SMAs contain data points made up of counts from more than one year.  The larger a study area becomes, the more likely it is to require data collected in multiple different years to produce a total count.  The vast West Scotland SMA has never been surveyed in a single year, so all plotted data points are based on surveys carried out over two or three years.  Such amalgamation of counts over multiple years, although necessary, can potentially mask or delay detection of trends in abundance.  Care should be taken when interpreting data presented in this way.

DNA analyses have showed that harbour seals in Scotland can be split into a western genetic cluster, consisting of SMAs 1-3, and a north-eastern cluster, consisting of SMAs 4-7 (Olsen et al., 2017; Carroll et al., 2020).  This spatial split coincides with the overlying regional differences in trends observed in harbour seal counts since the early 2000s.  In order to produce useful population time-series plots for these two regions, as well as for Scotland as a whole, interpolated count values had to be generated for all years in which an SMA was not surveyed.  This enabled the summation of totals from multiple SMAs, which were then scaled using haul-out probability to create regional and Scottish harbour seal population estimates for the period 1997-2017.  For comparison, the same method was used to plot grey seal summer population size based on haul-out counts and telemetry data.  As mentioned previously, this has never been the principal method used to estimate grey seal population size in the UK, so the standard population model estimates presented in the most recent Special Committee on Seals (SCOS) report (Thomas, 2019) are also shown for comparison.

The time series of counts are more straightforward for smaller areas such as the SMA Subunits that generally contain far less than 100km of coastline.  However, even at this local scale, it is not always possible to cover the entire Subunit during each survey.  To help visualise local differences and changes over time, the Subunit counts are presented in tables with colour-filled cells, with darker shading for higher counts.

Because most Special Areas of Conservation (SACs) only cover relatively small areas, trends in the number of seals counted within an SAC are not necessarily representative of the wider population.  Therefore, 10-50km wide buffer areas were created around coastal areas lying within SACs in order to investigate how indicative SAC counts are of regional population trends.  The buffer areas were based on at-sea distances and were created using Manifold Systems GIS.

The same maps and graphs were created to present the grey seal summer counts.  Because the official UK grey seal population estimates are calculated using pup counts and a population dynamics model, and not simply by scaling haul-out counts, a pup-based population estimate was calculated for Scotland in order to compare results derived by the two methods.  The regional population estimates for regularly surveyed grey seal colonies presented by Thomas (2019) contain English colonies in the North Sea region.  This proportion was subtracted by using the relative pup production estimate totals for the Scottish and the English North Sea colonies.  The proportion of pups born at Scottish colonies that are not regularly surveyed was estimated to be around 8% of the total number of pups born at regularly surveyed colonies in recent years (SCOS, 2019).  Assuming this proportion has not changed dramatically over time, the previously calculated totals for regularly monitored colonies in 1995-2016 were then multiplied by 1.08 to produce an estimate for the whole of Scotland.

Results

Harbour seals around Scotland

The total number of harbour seals counted in Scotland was 26,846, based on data collected during the most recent surveys from August 2016-2019.  This is 9% lower than the 1996-1997 census, but 6% higher than the previous count in 2011-2015, and it is the second highest Scotland total overall (Table 2).  The August seal counts can be used as an index of total population size and are generally reported without converting them into absolute abundance estimates.  In 2013, Lonergan et al. used ARGOS telemetry data from flipper tags to estimate the mean proportion of the population hauled out during the standard survey window (i.e. available to count).  Using their results (0.72; 95% CI: 0.54-0.88) together with the latest count data produces a total population estimate for Scotland of approximately 37,300 (95% CI: 30,500-49,700) harbour seals.

The Scotland-wide distribution of harbour seals, based on the newest census data, is mapped by 10km squares in Figure 8.  The highest density areas are now found in West Scotland, the Western Isles, and Shetland rather than in Orkney, where the highest concentrations were found in the 1990s (Figure 9).  The West Scotland SMA and the North Coast & Orkney SMA both contributed 30% to the Scotland total in the 1996-1997 census, but since then the proportion of all harbour seals recorded in the former has doubled, while the proportion in the latter has dropped to 5% of the total (Figure 10).

Harbour seal counts by SMA are plotted in Figure 11.  The most recent surveys produced the highest ever numbers recorded for all three SMAs in western Scotland (SMAs 1-3).  Whereas counts in Shetland, Moray Firth, and East Scotland SMAs have remained stable over the last ten years, the decline in Orkney continued.  Although the 2019 count for Orkney, which was 85% down from the highest count made in 1997, was almost identical to the previous count in 2016, this does not necessarily mean that the decline has ended (see 3.3.4).

Population-level estimates for the two genetic clusters in western Scotland and in northern & eastern Scotland are plotted in Figure 12, where they are also summed to produce Scotland-wide population estimates.  The graph shows how the Scotland total dropped at the beginning of the 2000s, mainly driven by declines in northern and eastern areas, and reached its minimum around 2007, when the total was almost one third lower than in the late 1990s.  Shortly after that, it started increasing again at a slower rate, this time driven by increases in the western population.  The latest Scotland estimate is still around 10% lower than values calculated for the period preceding the decline.

Table 2. August counts of harbour seals in Scotland by census period.  Totals are given for each Seal Management Area (with subdivisions in italics).  Where (part of) an area was surveyed more than once within a census period, the most recent count is used.  The proportion of the population hauled out during the survey window, and available to count, is estimated to be around 72% (95% CI: 54-88%; Lonergan et al., 2013).

Seal Management Area	1996-1997	2000-2006	2007-2009	2011-2015	2016-2019
1 Southwest Scotland	929	623	923	1,200	1,709
2 West Scotland	8,811	11,666	10,626	15,184	15,600
2a West Scotland - South	5,651	7,001	5,930	7,645	7,069
2b West Scotland - Central	2,700	3,956	4,004	6,424	7,447
2c West Scotland - North	460	709	692	1,115	1,084
3 Western Isles	2,820	1,920	1,804	2,739	3,532
4 North Coast & Orkney	8,787	4,388	2,979	1,938	1,405
4a North Coast	265	150	112	73	109
4b Orkney	8,522	4,238	2,867	1,865	1,296
5 Shetland	5,994	3,038	3,039	3,369	3,180
6 Moray Firth	1,409	1,028	776	745	1,077
7 East Scotland	764	667	283	224	343
Scotland count total	29,514	23,330	20,430	25,399	26,846

Summer distribution of grey seals in Scotland

In August, counts of harbour seals are relatively stable from day to day because they need to spend extended periods on land in order to moult efficiently (Paterson et al., 2012).  Grey seals at this time of year, on the other hand, are only hauling out to rest between foraging trips, resulting in a higher variability in haul-out counts.  In addition, because grey seals can haul out in much larger groups, containing several hundreds or even thousands of individuals, the counts made at a small number of potentially large haul-out sites can greatly affect the totals calculated for Subunits or SMAs.  For these reasons, summer counts of grey seals should be interpreted with caution.    

The total number of grey seals counted in Scotland was 25,412, based on data collected during the most recent surveys from August 2016-2019.  This is the highest total recorded to date, and is 9% higher than the previous total (Table 3).  The primary estimate of the UK grey seal population size is based largely on pup counts carried out during the autumn and in early winter (Russell et al., 2019; Thomas et al., 2019).  In the same way that harbour seal August counts are scaled to population size using flipper tag data, telemetry tags can be used to calculate an independent estimate of grey seal population size from summer counts.  Based on preliminary analyses, Russell et al. (2016) estimated the mean proportion of the grey seal population hauled out during a standard August survey window to be 23.9% (95% CI: 19.2-28.6%) which is lower than a previous estimate of 31% (95% CI: 15-50%) published by Lonergan et al. (2011).  Using the newest results, together with the latest count data, produces a total population estimate for Scotland of approximately 106,300 (95% CI: 88,800-132,400).  This is around 10% lower than the grey seal population estimate of 119,200 (95% CI: 98,400-143,000) for Scotland in 2016, derived from the UK regional population sizes presented in SCOS-BP 19/01 (SCOS, 2019).  The Scottish proportion of the North Sea region was obtained by using the ratio between pup production estimates produced for colonies in the Firth of Forth and for colonies along the English east coast.  The regional population estimates presented in the SCOS report are based on regularly monitored colonies only.  Because approximately 8% of pups are born at Scottish colonies that are not regularly surveyed by air (SCOS, 2019), the total for regularly monitored Scottish colonies, derived from the SCOS report, was multiplied by 1.08.  The time-series of Scottish grey seal population estimates using the two different methods are shown in Figure 15.  Apart from the fact that grey seal haul-out counts can be highly variable during summer, there is also substantial movement of grey seals between the summer and the breeding season (Russell et al., 2013), so that regional population sizes may change throughout the year. 

It is important to note just how much lower the mean haul-out probability is for grey seals in August compared to harbour seals.  Even though the total grey seal count for Scotland is slightly lower than the harbour seal total, converting to the population level suggests that there are almost three times as many grey seals in Scotland at this time of year.

The Scotland-wide summer distribution of grey seals, based on the newest census data, is mapped by 10km squares in Figure 14.  The highest density areas are still found in Orkney.  A visual comparison with the harbour seal distribution reveals that only a small number of 10km x 10km grid cells contain high counts of both species. 

Totals by SMA are plotted in Figure 13.  In contrast to harbour seals, the proportions of all grey seals recorded in different SMAs have not changed dramatically across the five census periods (Figure 10). 

Based on population estimates using August counts and haul-out probabilities, there were approximately 2.2 times as many grey seals as harbour seals in Scotland during the summer in 2000, when harbour seal numbers were at their highest.  Based on the most recent counts there are now approximately three times more grey seals than harbour seals (Figure 15).

Table 3. August counts of grey seals in Scotland by census period.  Totals are given for each Seal Management Area (with subdivisions in italics).  Where (part of) an area was surveyed more than once within a census period, the most recent count is used.  The proportion of the population hauled out during the survey window, and available to count, is estimated to be around 23.9% (95% CI: 19.2-28.6%; Russell et al., 2016).

Seal Management Area	1996-1997	2000-2006	2007-2009	2011-2015	2016-2019
1 Southwest Scotland	75	206	233	374	517
2 West Scotland	3,435	2,383	2,524	5,064	4,174
2a West Scotland - South	2,125	1,771	1,788	3,618	2,922
2b West Scotland - Central	931	361	559	1,056	773
2c West Scotland - North	379	251	177	390	479
3 Western Isles	4,062	3,674	3,808	4,085	5,773
4 North Coast & Orkney	9,427	10,315	8,525	8,106	8,599
4a North Coast	597	736	504	266	414
4b Orkney	8,830	9,579	8,021	7,840	8,185
5 Shetland	1,724	1,371	1,536	1,558	1,009
6 Moray Firth	551	1,272	1,113	1,917	1,657
7 East Scotland	2,328	1,898	1,238	2,296	3,683
Scotland count total	21,602	21,119	18,977	23,400	25,412

Seal Management Areas (SMAs)

The following pages present counts by Subunits within Seal Management Area (subdivisions) as shown in Figure 2.  Relevant local changes indicated by the counts in the data tables are highlighted in the text.

Southwest Scotland SMA

Harbour seal counts by Subunits within the SMA are given in Table 4.  The most recent survey in 2018 recorded the highest count of harbour seals for the SMA and was 40% higher than the previous maximum in 2015.  Since surveys began, numbers found in the far south-west of Scotland, in Dumfries and Galloway (Subunits 1-4), have remained very low.  Counts have been increasing in the Firth of Clyde, especially in northern and western areas such as in Loch Fyne and along the eastern shore of Kintyre (Figure 16).

Grey seal counts by Subunits within the SMA are given in Table 5.  The grey seal count has also been increasing, mainly due to the numbers found around the islands off the southeast end of Kintyre.  Grey seal counts have generally been around one third of the harbour seal count over the last 15 years. The difference in mean haul-out probability at this time of year suggests there are roughly the same number of animals of both species using this management area during the summer.

Table 4. August counts of harbour seals in the Seal Management Area ‘Southwest Scotland’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMA 1 - Southwest Scotland	1989	1996	2005	2007	2015	2018
1 Solway Firth to Orroland	-	0	2	0	0	1
2 Kirkcudbright, Fleet, and Wigtown Bay	-	1	12	0	0	0
3 Luce Bay	-	0	1	0	4	4
4 Outer Rhins of Galloway	-	0	0	9	0	0
5 Loch Ryan to Turnberry	8	14	54	31	79	48
6 Turnberry to Irvine	8	78	27	0	23	75
7 Ardrossan, Cumbrae Is, Loch Striven	17	52	19	14	100	112
8 Loch Long, L Goil, Gare L, River Clyde	1	12	33	16	33	57
9 Loch Fyne	136	100	14	102	205	330
10 W Bute, Loch Riddon	2	84	75	46	109	134
11 Kilbrannan Sound	24	92	76	161	237	290
12 Saddell to Southend	97	276	200	303	230	441
13 S Arran	86	195	97	147	166	201
14 E Arran	2	25	13	5	14	16
Total for SMA	-	929	623	834	1,200	1,709

 

Table 5. August counts of grey seals in the Seal Management Area ‘Southwest Scotland’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMA 1 - Southwest Scotland	1989	1996	2005	2007	2015	2018
1 Solway Firth to Orroland	-	36	23	45	0	23
2 Kirkcudbright, Fleet, and Wigtown Bay	-	0	8	6	1	11
3 Luce Bay	-	37	43	43	26	33
4 Outer Rhins of Galloway	-	0	0	2	4	19
5 Loch Ryan to Turnberry	0	2	6	18	96	38
6 Turnberry to Irvine	20	0	27	23	50	21
7 Ardrossan, Cumbrae Is, Loch Striven	7	0	13	16	24	9
8 Loch Long, L Goil, Gare L, River Clyde	8	0	0	4	6	27
9 Loch Fyne	20	0	0	6	6	4
10 W Bute, Loch Riddon	0	0	3	13	3	4
11 Kilbrannan Sound	0	0	6	11	18	16
12 Saddell to Southend	60	0	65	166	115	287
13 S Arran	0	0	12	14	21	19
14 E Arran	2	0	0	7	4	6
Total for SMA	-	75	206	374	374	517

West Scotland SMA

Harbour seal counts by Subunits within the three SMA subdivisions are given in Table 6, Table 7, and Table 8.  The large West Scotland SMA has contributed 50-60% to the total Scottish count of harbour seals since the mid-2000s (Figure 10).  The count has increased significantly from around 8,800 in 1996-1997 to 15,600 in 2017-2018 (Table 2).  Numbers found in the southern subdivision have always been high but quite variable (Figure 17) with no clear trend (range: ca. 5,650-7,650).  Whereas 64% of West Scotland harbour seals were found in the southern subdivision during the first census, this proportion has gradually decreased to 45%, as numbers in the central subdivision have grown from 2,700 (31%) to ca. 7,400 (48%).  Numbers counted in the southern region of the central subdivision have steadily increased since surveys began.  In the north-eastern region of the central subdivision counts increased rapidly between 2005 and 2014.  The greatest declines within the central subdivision were recorded in northern and western Skye between 2000 and 2007.  The highest ever numbers were observed in all three of these central regions during the most recent surveys in 2017/2018 (Figure 18).  The proportion of West Scotland harbour seals recorded in the small northern subdivision has always been around 5-7% of the SMA, and the count there has doubled from below 500 to over 1,000.  These increases were mainly observed in the southern half of this subdivision (Figure 19).

Grey seal counts by Subunits within the three SMA subdivisions are given in Table 9, Table 10, and Table 11.  Although grey seals are found throughout West Scotland, big haul-out groups are absent from large areas (Figure 14), and are generally only found on the outer islands where there are not very many harbour seals.  Even when scaling the counts using haul-out probability, there are likely to be fewer grey seals than harbour seals overall.  Harbour seals clearly outnumber grey seals in the central subdivision and in more sheltered areas within the southern subdivision. 

Table 6. August counts of harbour seals in the Seal Management Area subdivision ‘West Scotland - South’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMAsd 2a - West Scotland - South	1996	2000	2007	2009	2014	2015	2019
1 SW Kintyre	62	51	56	17	-	46	48
2 Gigha & West Loch Tarbert	491	162	199	215	-	359	369
3 Snd of Jura, L Sween, L Caolisport	514	691	492	527	-	843	732
4 SE Jura	44	343	308	268	-	699	514
5 SE Islay	593	877	808	666	-	1,154	757
6 Laggan Bay	2	88	79	104	-	91	102
7 W Islay	0	119	88	0	-	45	70
8 N Islay	6	3	13	6	-	19	3
9 Colonsay & Oronsay	83	177	61	87	-	65	91
10 W Jura	35	138	137	213	-	93	109
11 NW Jura to Seil	306	313	262	275	284	263	314
12 Seil to SW Loch Linnhe	455	537	326	530	351	-	503
13 Loch Etive	26	31	27	-	41	-	89
14 Inner Loch Linnhe, Loch Creran	420	381	256	316	374	-	401
15 NE Loch Linnhe, L Eil, L Leven	101	78	11	-	62	-	75
16 Loch Buie	46	40	25	53	79	-	53
17 SW Ross of Mull	186	140	171	223	125	-	143
18 Loch Scridain	224	481	207	414	398	-	228
19 Loch na Keal, Ulva, Loch Tuath	446	621	408	571	486	-	581
20 Treshnish Isles	41	31	14	-	0	-	10
21 NW Mull, SW Ardnamurchan	46	89	67	78	84	-	115
22 Sound of Mull	114	274	219	273	242	-	226
23 Loch Sunart	125	281	121	-	243	-	323
24 NE Coll	464	485	279	-	614	-	508
25 E Tiree, SW Coll	649	772	553	-	759	-	523
26 W Tiree	172	87	89	-	94	-	166
27 Skerryvore	-	-	-	-	12	-	-
28 Dubh Artach	-	-	-	-	4	-	-
Total for SMAsd	5,651	7,290	5,276	-	-	7,645	7,053

Table 7. August counts of harbour seals in the Seal Management Area subdivision ‘West Scotland - Central’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMAsd 2b - West Scotland - Central	1996	2000	2005	2007	2014	2017	2018
1 Hyskeir, Canna, W Rum	19	-	219	-	381	-	293
2 E Rum, N Eigg	2	-	3	-	24	-	49
3 S Eigg, Muck, NW Ardnamurchan	101	94	246	235	199	-	322
4 Loch Moidart, Arisaig	219	715	771	819	1,264	-	1,258
5 Sound of Sleat	185	146	162	154	232	244	477
6 L Eishort, L Slapin, L Scavaig, Soay	356	530	438	379	535	616	-
7 L Eynort	17	0	0	0	0	0	-
8 L Bracadale	95	64	112	85	182	290	-
9 L Dunvegan	446	628	385	440	347	555	-
10 L Snizort	373	483	423	322	493	680	-
11 Fladda Chuain island group	22	65	58	37	21	15	-
12 N Snd of Raasay, N Inner Sound	137	320	230	412	868	807	-
13 S Snd of Raasay and Lochs	4	29	53	2	26	126	-
14 S Inner Sound	519	603	570	602	1,113	1,036	-
15 L Alsh, L Duich, Kyle Rhea	39	36	72	63	118	205	-
16 L Carron	156	150	194	227	428	410	-
17 L Torridon	3	36	20	53	188	288	-
18  L Gairloch	7	-	0	1	5	20	-
Total for SMAsd	2,700	3,927	3,956	4,053	6,424	-	7,447

 

Table 8. August counts of harbour seals in the Seal Management Area subdivision ‘West Scotland - North’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMAsd 2c - West Scotland - North	1991	1997	2005	2008	2014	2017
1 Loch Ewe	7	1	28	33	20	67
2 Gruinard Bay, L Brooms, Summer Is	84	125	372	337	666	459
3 Enard bay	6	13	30	38	56	140
4 Eddrachillis Bay	207	252	257	277	355	378
5 Loch Laxford, Loch Inchard	33	69	22	7	18	40
Total for SMAsd	337	460	709	692	1,115	1,084

Table 9. August counts of grey seals in the Seal Management Area subdivision ‘West Scotland - South’ 2019 by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMAsd 2a - West Scotland - South	1996	2000	2007	2009	2014	2015	2019
1 SW Kintyre	3	3	0	4	-	70	14
2 Gigha & West Loch Tarbert	3	9	13	2	-	22	25
3 Snd of Jura, L Sween, L Caolisport	0	20	8	10	-	30	21
4 SE Jura	0	21	43	10	-	36	40
5 SE Islay	1	5	37	0	-	21	22
6 Laggan Bay	4	18	3	44	-	29	25
7 W Islay	143	33	59	257	-	230	100
8 N Islay	293	343	445	351	-	489	362
9 Colonsay & Oronsay	265	399	416	455	-	1,099	787
10 W Jura	25	9	23	33	-	41	42
11 NW Jura to Seil	2	4	9	10	14	26	19
12 Seil to SW Loch Linnhe	0	27	3	5	21	-	6
13 Loch Etive	0	0	0	-	0	-	8
14 Inner Loch Linnhe, Loch Creran	0	1	1	6	8	-	8
15 NE Loch Linnhe, L Eil, L Leven	0	0	0	-	0	-	3
16 Loch Buie	0	4	5	2	9	-	3
17 SW Ross of Mull	32	43	52	41	66	-	208
18 Loch Scridain	6	23	13	17	6	-	20
19 Loch na Keal, Ulva, Loch Tuath	23	7	13	17	13	-	21
20 Treshnish Isles	170	65	73	-	85	-	209
21 NW Mull, SW Ardnamurchan	1	11	17	23	17	-	16
22 Sound of Mull	1	0	0	0	5	-	3
23 Loch Sunart	0	5	0	-	3	-	3
24 NE Coll	53	146	22	-	117	-	65
25 E Tiree, SW Coll	240	158	83	-	466	-	234
26 W Tiree	860	420	323	-	653	-	602
27 Skerryvore	-	-	-	-	29	-	-
28 Dubh Artach	-	-	-	-	27	-	-
Total for SMAsd	2,125	1,774	1,661	-	-	3,618	2,866

Table 10. August counts of grey seals in the Seal Management Area subdivision ‘West Scotland - Central’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMAsd 2b - West Scotland - Central	1996	2000	2005	2007	2014	2017	2018
1 Hyskeir, Canna, W Rum	479	-	126	-	563	-	221
2 E Rum, N Eigg	50	-	9	-	6	-	9
3 S Eigg, Muck, NW Ardnamurchan	22	22	39	39	94	-	37
4 Loch Moidart, Arisaig	0	4	9	4	8	-	10
5 Sound of Sleat	2	19	7	1	4	5	2
6 L Eishort, L Slapin, L Scavaig, Soay	5	7	6	10	26	9	-
7 L Eynort	0	9	9	6	13	17	-
8 L Bracadale	76	61	16	39	26	40	-
9 L Dunvegan	9	7	8	32	7	21	-
10 L Snizort	75	104	17	31	61	40	-
11 Fladda Chuain island group	213	135	74	64	98	271	-
12 N Snd of Raasay, N Inner Sound	0	9	11	13	70	39	-
13 S Snd of Raasay and Lochs	0	0	0	0	5	2	-
14 S Inner Sound	0	3	6	12	18	18	-
15 L Alsh, L Duich, Kyle Rhea	0	1	19	4	24	9	-
16 L Carron	0	1	0	0	1	1	-
17 L Torridon	0	0	5	0	28	17	-
18 L Gairloch	0	0	0	3	4	10	-
Total for SMAsd	931	911	361	393	1,056	-	773

Table 11. August counts of grey seals in the Seal Management Area subdivision ‘West Scotland - North’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMAsd 2c - West Scotland - North	1991	1997	2005	2008	2014	2017
1 Loch Ewe	0	15	1	3	22	10
2 Gruinard Bay, L Brooms, Summer Is	21	24	87	68	164	116
3 Enard bay	9	51	7	7	9	85
4 Eddrachillis Bay	3	153	116	54	166	210
5 Loch Laxford, Loch Inchard	157	136	40	45	29	58
Total for SMAsd	190	379	251	177	390	479

Western Isles SMA

Harbour seal counts by Subunits within the SMA are given in Table 12.  The five surveys carried out between 1996 and 2008 suggested that harbour seal numbers in the Western Isles were declining (from 2,820 to 1,804).  However, the 2011 count was very similar to the 1996 count, and the most recent survey in 2017 produced the highest count on record by 25% (3,532).  There have been significant changes in harbour seal distribution.  While numbers along the west side of the Western Isles have remained fairly low but stable throughout, the Sounds of Barra and Harris contained over half of all harbour seal sightings in 1992 but now contribute only 8%.  In contrast, there has been a steep rise in the number of harbour seals found in the sea lochs and bays along the eastern coast of the Western Isles (Figure 20).

Grey seal counts by Subunits within the SMA are given in Table 13.  Grey seal numbers have been very variable over the years, but the highest count was also recorded during the most recent survey in 2017 (5,773).  Large groups of grey seals are found on the Monach Isles.  On average, these islands have contributed around 50% to the total grey seal count in the Western Isles.  During the 2011 survey, there were relatively few grey seals hauled out on the Monach Isles, but hundreds of animals were visible in the shallow water close to shore.  The very warm weather on the day of the survey may have kept many grey seals from leaving the water.  The 2008 count was used for the Monach Isles until they were surveyed again in 2014.

Table 12. August counts of harbour seals in the Seal Management Area subdivision ‘Western Isles’ by Subunits.  Subunit boundaries are shown in Figure 2.  The difference in fill-opacity reflects the size of a count relative to all Subunit counts in the table.  A grey font is used to indicate counts that contain data from a previous year.  Harbour seals are unlikely to haul out at the offshore islands in subunits 23-25.

Subunits within SMA 3 - Western Isles	1992	1996	2000	2003	2006	2008	2011	2017
1 Butt of Lewis	0	3	0	0	0	0	0	0
2 Broad Bay	47	105	131	175	121	113	96	236
3 Outer Eye Pen., Stornoway Harbr	0	1	4	0	1	0	10	31
4 Loch Liurbost, Loch Èireasort	19	34	58	32	26	9	18	177
5 Loch Sealg, Shiant Islands	0	1	2	1	0	0	1	78
6 L Bhrolluim, L Claidh, L Seaforth	97	258	174	96	146	138	171	390
7 Scalpay, East Loch Tarbert	22	103	43	69	96	71	142	184
8 SE Harris	1	28	13	29	3	61	86	235
9 Sound of Harris	341	471	323	242	229	103	136	49
10 Loch Maddy, Loch Euphort	78	218	290	180	-	260	268	160
11 SE N'Uist, E Benbecula, NE S'Uist	277	301	299	246	312	285	502	644
12 Loch Eynort, Loch Boisdale	208	182	352	278	255	178	578	683
13 Sound of Barra	908	694	371	288	243	165	208	238
14 SW Barra to Berneray	60	1	0	34	28	43	92	78
15 W South Uist	15	43	98	120	78	130	146	123
16 Monach Isles, W N'Uist, Haskeir	2	0	0	8	7	10	1	4
17 N N'Uist, Pabbay, Shillay	131	211	143	185	141	170	216	53
18 Taransay, West Loch Tarbert	17	25	44	7	1	28	33	86
19 Gairsay, Scarp, Braigh Mor	0	0	0	0	0	0	0	2
20 Islibhig to Valtos	0	0	0	0	0	0	0	0
21 Loch Roag	103	141	68	77	53	40	35	81
22 NW Lewis	0	0	0	0	0	0	0	0
23 North Rona & Sula Sgeir	-	-	-	-	0	-	-	0
24 Flannan Isles	-	-	-	-	0	-	-	0
25 St Kilda	-	-	-	-	-	-	-	-
Total for SMA	2,326	2,820	2,413	2,067	1,920	1,804	2,739	3,532

Table 13. August counts of grey seals in the Seal Management Area ‘Western Isles’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.  Subunits 23 and 24 were first surveyed in 2005.  St Kilda has never been surveyed.

Subunits within SMA 3 - Western Isles	1992	1996	2000	2003	2006	2008	2011	2017
1 Butt of Lewis	107	106	211	72	68	23	58	59
2 Broad Bay	4	40	45	122	48	97	17	316
3 Outer Eye Pen., Stornoway Harbr	2	9	31	0	3	1	4	9
4 Loch Liurbost, Loch Eireasort	3	0	7	3	0	4	1	21
5 Loch Sealg, Shiant Islands	19	99	121	0	150	193	114	250
6 L Bhrolluim, L Claidh, L Seaforth	5	7	16	13	16	29	7	31
7 Scalpay, East Loch Tarbert	0	0	0	0	0	1	2	6
8 SE Harris	0	12	22	8	1	7	4	6
9 Sound of Harris	183	157	474	212	211	179	285	299
10 Loch Maddy, Loch Euphort	0	3	8	3	-	0	1	0
11 SE N'Uist, E Benbecula, NE S'Uist	1	0	11	14	7	12	42	61
12 Loch Eynort, Loch Boisdale	8	19	29	6	5	10	45	52
13 Sound of Barra	223	289	634	417	214	281	420	382
14 SW Barra to Berneray	124	781	316	295	227	280	670	681
15 W South Uist	43	212	196	103	82	159	201	118
16 Monach Isles, W N'Uist, Haskeir	1,808	2,059	2,622	1,372	2,043	1,529	1,613	2,895
17 N N'Uist, Pabbay, Shillay	113	58	106	199	30	145	107	41
18 Taransay, West Loch Tarbert	34	45	92	95	11	99	67	65
19 Gairsay, Scarp, Braigh Mor	90	117	133	117	40	296	60	56
20 Islibhig to Valtos	7	13	3	5	0	15	3	11
21 Loch Roag	52	36	99	8	114	45	20	119
22 NW Lewis	0	0	3	0	0	2	2	0
23 North Rona & Sula Sgeir	-	-	-	-	179	-	-	209
24 Flannan Isles	-	-	-	-	222	-	-	86
25 St Kilda	-	-	-	-	-	-	-	-
Total for SMA	2,826	4,062	5,179	3,064	3,674	3,808	4,144	5,773

Monach Isles count in 2008 also used in 2011.
Subunits 23 and 24 surveyed in 2005 and 2014.

North Coast & Orkney SMA

Harbour seal counts by Subunits within the two SMA subdivisions are given in Table 14 and Table 15.  This management area has seen the most dramatic decline in harbour seal numbers.  Although counts in the North Coast subdivision have always been relatively low, the highest counts were recorded in the 1990s.  In Orkney, the latest harbour seal count in 2019 was 1,296, 85% lower than the highest count in 1997 (8,522), but very similar to the previous count in 2016 (1,240).  In the 1990s, Orkney was the region with the highest harbour seal concentration in the UK.  Since 2001, the counts indicate an average rate of decline of around 10% per year (Lonergan et al., 2007; Thompson et al, 2019).  Even though the latest count in 2019 was slightly higher than the previous count for the first time since the decline started, this does not mean that harbour seal numbers in Orkney are not still declining at the same rate.  The higher count could simply be due to the variability in the proportion of animals hauled out at any one time.  Although numbers have dropped across all of Orkney, there appear to be some local differences (Figure 21).  Since 2001, numbers found in the outer islands to the northeast (Westray, Sanday, Stronsay) have shown the greatest decline, closely followed by southern areas including Scapa Flow.  The total count for the area north of Mainland Orkney (excluding the outer north-eastern areas) did not start declining until after 2006, and numbers have dropped at a slightly slower rate.  Whether this apparent deviation is due to actual differences in how these areas are being affected by the factors driving the decline, or whether it is due to the redistribution of remaining animals around the whole of Orkney, is unclear.  The pre-decline counts by Subunit do show, however, that large shifts in harbour seals from one subunit to another probably aren’t uncommon (e.g. the drop in Subunit 6 from 746 to 169 between 1993-1997, when the overall Orkney count increased, or the increase in Subunit 1 from 570 to 1,043 between 1997-2001, when the overall Orkney count dropped).

Grey seal counts by Subunits within the two SMA subdivisions are given in Table 16 and Table 17.  Several large haul-out groups (containing hundreds of animals) are found in the northeast and the south of Orkney.  The numbers counted at these haul-outs can be very variable and obviously have a major effect on the total grey seal count for Orkney.  For example, the counts made in Subunit 8 (containing Stroma, Swona, Pentland Skerries) ranged from 501 to 3,862.  In 2001, fewer than 3,000 grey seals were counted in Orkney overall.  While the actual surveys were carried out in dry weather, a number of days were lost due to prolonged bouts of heavy rain that extended through much of August.  This persistent rain is likely to have influenced whether or not grey seals hauled out in their ‘usual’ numbers.  Although Orkney was the main UK hot spot for harbour seals before numbers started declining in the 2000s, it is worth noting that Orkney has been even more of a hot spot for grey seals, both in terms of absolute numbers as well as in terms of the proportion of the total population.  Even when the harbour seal count peaked in 1997, more grey seals were counted, meaning there were likely to be around three times more animals when scaling to population size.  Although grey seal pup production was highest in the Outer Hebrides during the 1980s and the early 1990s, a rapid increase in Orkney during the 1990s meant that Orkney has been the most productive breeding region for grey seals since the mid-1990s (Russell et al., 2019).

Table 14. August counts of harbour seals in the Seal Management Area subdivision ‘North Coast’ by Subunits.  Subunit boundaries are shown in Figure 2. 

Subunits within SMAsd 4a - North Coast	1991	1997	2005	2008	2013	2016
1 Cape Wrath to Faraid Head	16	0	0	3	0	0
2 Faraid Head to Strathan	147	32	39	0	0	4
3 Strathan to Strathy Pt	48	92	34	26	14	24
4 Strathy Point to Thurso	0	0	0	0	2	0
5 Thurso to Duncansby Head	0	141	101	83	57	81
6 Sule Skerry & Sule Stack	-	-	0	0	0	0
Total for SMAsd	211	265	174	112	73	109

Table 15. August counts of harbour seals in the Seal Management Area subdivision ‘Orkney’ by Subunits.  Subunit boundaries are shown in Figure 2.

Subunits within SMAsd 4b - Orkney	1993	1997	2001	2006	2007	2008	2010	2013	2016	2019
1 N Westray & Papa Westray	519	570	1,043	219	229	200	181	99	72	71
2 N Sanday & N'Ronaldsay	1,735	1,829	1,369	702	602	521	297	228	208	189
3 S Sanday, Stronsay, E Eday	1,138	1,283	1,055	489	413	342	294	156	63	91
4 NW Eday, S Westray	264	264	297	278	167	144	127	127	87	60
5 N Mainland, Rousay, N Shap.	580	1,261	1,021	800	612	572	715	330	171	280
6 Finstown to Mull Head	746	169	203	392	310	304	254	217	188	207
7 Mull Head to Grim Ness	433	596	338	8	20	55	32	30	20	34
8 S S'Ron. & islands to S	122	57	91	46	24	14	25	6	0	1
9 SW Hoy	43	59	13	2	24	4	8	0	1	0
10 Scapa Fl. (Houton to Switha)	1,884	1,511	1,692	882	649	478	513	390	291	249
11 N Hoy & SW Mainland	401	892	627	398	291	225	221	234	107	84
12 W Mainland	8	31	3	22	33	8	20	48	32	30
Total for SMAsd	7,873	8,522	7,752	4,238	3,374	2,867	2,687	1,865	1,240	1,296

Table 16. August counts of grey seals in the Seal Management Area subdivision ‘North Coast’ by Subunits.  Subunit boundaries are shown in Figure 2. 

Subunits within SMAsd 4a - North Coast	1991	1997	2005	2008	2013	2016
1 Cape Wrath to Faraid Head	60	203	41	45	68	21
2 Faraid Head to Strathan	26	365	309	190	31	169
3 Strathan to Strathy Pt	2	29	3	43	10	4
4 Strathy Point to Thurso	0	0	0	1	0	0
5 Thurso to Duncansby Head	1	0	2	65	86	149
6 Sule Skerry & Sule Stack	-	-	160	-	-	71
Total for SMAsd	89	597	515	504	355	414

Table 17. August counts of grey seals in the Seal Management Area subdivision ‘Orkney’ by Subunits.  Subunit boundaries are shown in Figure 2.  The grey seal counts from the 2001 survey were exceptionally low.  Very wet weather conditions in the period preceding the survey may have kept a large number of grey seals from returning to haul-out sites to rest.

Subunits within SMAsd 4b - Orkney	1993	1997	2001	2006	2007	2008	2010	2013	2016	2019
1 N Westray & Papa Westray	153	551	178	287	756	895	557	364	501	321
2 N Sanday & N'Ronaldsay	1,368	1,495	480	1,335	1,508	678	264	808	1,303	1,513
3 S Sanday, Stronsay, E Eday	1,621	3,669	822	1,914	1,672	2,368	2,407	2,513	2,048	2,471
4 NW Eday, S Westray	350	389	689	669	613	670	460	632	401	308
5 N Mainland, Rousay, N Shap.	229	790	246	715	604	769	435	506	346	581
6 Finstown to Mull Head	122	66	21	175	108	112	92	311	66	200
7 Mull Head to Grim Ness	177	757	86	443	162	354	535	657	571	538
8 S S'Ron. & islands to S	2,481	501	183	3,372	1,187	1,602	3,862	1,182	2,830	1,154
9 SW Hoy	165	31	0	30	111	298	200	2	276	163
10 Scapa Fl. (Houton to Switha)	35	268	17	351	249	196	175	540	691	748
11 N Hoy & SW Mainland	115	292	163	288	125	79	94	318	258	187
12 W Mainland	5	21	28	0	20	0	2	7	9	1
Total for SMAsd	6,821	8,830	2,913	9,579	7,115	8,021	9,083	7,840	9,300	8,185

Shetland SMA

Harbour seal counts by Subunits within the SMA are given in Table 18.  Shetland is the region that has seen the second largest drop in harbour seal numbers after Orkney. Although the decline seems to have started at around the same time, after reaching 50% in 2006 the total count has not dropped any further.  There are even some areas of Shetland where numbers have not declined at all, i.e. along the western side of Mainland Shetland (Figure 22).  In contrast, numbers in Subunit 6, containing the harbour seal SAC Mousa, have continued to drop (Table 18).  The 2019 count for that Subunit was 183, 85% down from the highest count in 1993 (1,262).

Grey seal counts by Subunits within the SMA are given in Table 19.  In the two most recent August censuses, Shetland has been the SMA with the second lowest grey seal count after Southwest Scotland.  As with most other areas, counts within Subunits can be very variable.

Table 18. August counts of harbour seals in the Seal Management Area ‘Shetland’ 2019 by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMA 5 - Shetland	1991	1993	1997	2001	2006	2009	2015	2019
1 N Unst	7	11	11	15	1	1	7	4
2 E&S Unst, E Yell, Fetlar	611	791	500	177	55	98	96	106
3 SE Yell, NE Mainland	337	266	336	248	165	147	262	293
4 Out Skerries, Whalsay, Dury Voe	784	850	571	564	144	280	197	216
5 South Nesting Bay to Bressay	253	377	373	193	189	183	316	285
6 SE Mainland (Lerwick to Exnaboe)	723	1,262	1,176	1,016	698	618	307	183
7 SW Mainland (Exnaboe to St Ninian's)	262	335	265	211	106	88	121	99
8 St Ninian's to The Deeps	209	323	352	255	343	255	447	395
9 Gruting Voe, Vaila Sound	50	70	72	73	62	50	70	81
10 Dale to Busta Voe, Papa Stour & Ve Sk.	293	568	527	765	345	486	463	429
11 N St Magnus Bay, Esha Ness	154	243	208	244	155	121	268	294
12 Ronas Voe, W North Roe	60	6	26	31	15	14	16	17
13 Fethaland, Yell Sound, Sullom Voe	827	869	1,357	987	659	589	733	692
14 N Yell, W Unst	227	253	217	104	65	73	48	60
15 Foula	0	3	-	-	36	-	18	26
16 Fair Isle	-	-	-	-	-	-	-	0
Total for SMA	4,797	6,227	5,994	4,886	3,038	3,039	3,369	3,180

Table 19. August counts of grey seals in the Seal Management Area ‘Shetland’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.  Fair Isle was first surveyed in 2019.

Subunits within SMA 5 - Shetland	1991	1993	1997	2001	2006	2009	2015	2019
1 N Unst	25	62	75	17	1	5	16	0
2 E&S Unst, E Yell, Fetlar	102	17	38	10	19	106	144	52
3 SE Yell, NE Mainland	0	2	63	1	14	42	95	69
4 Out Skerries, Whalsay, Dury Voe	10	0	436	247	129	143	425	344
5 South Nesting Bay to Bressay	1	0	86	5	157	165	126	49
6 SE Mainland (Lerwick to Exnaboe)	2	29	60	24	134	85	69	57
7 SW Mainland (Exnaboe to St Ninian's)	45	605	639	705	70	383	84	67
8 St Ninian's to The Deeps	20	27	22	4	4	68	106	25
9 Gruting Voe, Vaila Sound	0	1	0	0	6	13	16	11
10 Dale to Busta Voe,Papa Stour & Ve Sk.	29	349	84	185	451	225	223	96
11 N St Magnus Bay, Esha Ness	44	37	43	20	91	17	62	34
12 Ronas Voe, W North Roe	30	71	35	28	35	0	9	9
13 Fethaland, Yell Sound, Sullom Voe	12	31	70	18	64	92	126	80
14 N Yell, W Unst	20	21	35	14	18	14	8	11
15 Foula	37	38	-	-	178	-	49	24
16 Fair Isle	-	-	-	-	-	-	-	81
Total for SMA	377	1,290	1,724	1,316	1,371	1,536	1,558	1,009

Moray Firth SMA

Harbour seal counts by Subunits within the SMA are given in Table 20.  Most harbour seals in the Moray Firth are found within the area surveyed every year between Helmsdale and Findhorn.  More detailed subarea counts from these surveys are given in Table 22.  Numbers in the Moray Firth as a whole have not been following a clear trend.  However, counts in some areas have declined dramatically: in the Dornoch Firth from 662 in 1992 to 62 in 2019; in the Beauly Firth from 220 in 1992 to 24 in 2019 (Figure 23).  Numbers within Loch Fleet are now significantly higher compared to the 1990s and 2000s, but the largest increase has occurred at Culbin.  The first small groups of seals there were recorded in the mid-2000s.  In 2019, 588 harbour seals were counted at Culbin (Figure 24).

Grey seal counts by Subunits within the SMA are given in Table 21.  Subarea counts for the annually surveyed area between Helmsdale and Findhorn are given in Table 23.  Since surveys began, the Dornoch Firth has generally been the main haul-out area for grey seals in the Moray Firth.  However, small numbers of grey seals began using the Culbin Sands lagoon at the same time as harbour seals, and counts have increased over the last 15 years, so that more grey seals are now regularly counted in the Culbin & Findhorn area compared with the Dornoch Firth.

Table 20. August counts of harbour seals in the Seal Management Area ‘Moray Firth’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMA 6 - Moray Firth	1994	1997	2005	2008	2011	2013	2016	2019
1 Duncansby Head to Wick	1	0	1	1	-	-	-	5
2 Wick to Lybster	0	0	0	0	0	-	-	0
3 Lybster to Helmsdale	1	1	0	0	0	-	-	0
4 Helmsdale to Loch Fleet	108	220	184	155	200	205	185	126
5 Dornoch Firth	542	593	191	145	208	143	85	62
6 Fearn Peninsula	0	0	0	0	0	0	0	0
7 Cromarty Firth	95	95	106	90	101	63	72	84
8 Beauly Firth to Fort George	203	219	127	150	57	30	30	24
9 Ardersier to Findhorn	279	280	303	237	358	417	520	729
10 Burghead Bay to River Spey	0	0	0	0	0	0	0	0
11 River Spey to Macduff	0	1	3	0	22	33	45	45
12 Macduff to Fraserburgh	0	0	0	0	7	6	2	2
Total for SMA	1,229	1,409	915	778	954	898	940	1,077

Table 21. August counts of grey seals in the Seal Management Area ‘Moray Firth’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMA 6 - Moray Firth	1994	1997	2005	2008	2011	2013	2016	2019
1 Duncansby Head to Wick	8	0	18	7	-	-	-	19
2 Wick to Lybster	25	0	31	2	4	-	-	31
3 Lybster to Helmsdale	0	0	10	0	4	-	-	0
4 Helmsdale to Loch Fleet	0	3	101	450	163	99	59	208
5 Dornoch Firth	903	456	431	523	679	604	387	401
6 Fearn Peninsula	0	0	0	0	0	0	0	0
7 Cromarty Firth	0	0	0	0	2	3	1	0
8 Beauly Firth to Fort George	2	3	0	0	3	5	2	1
9 Ardersier to Findhorn	36	24	66	217	253	327	745	954
10 Burghead Bay to River Spey	30	21	76	8	12	0	38	38
11 River Spey to Macduff	0	11	51	30	6	86	1	1
12 Macduff to Fraserburgh	0	33	78	23	0	172	4	4
Total for SMA	1,004	551	862	1,260	1,133	1,311	1,252	1,657

Table 22. August counts of harbour seals in the annually surveyed western Moray Firth between Helmsdale and Findhorn.  Mean values are given for areas surveyed more than once in a single season.  fw: fixed-wing survey; ti: thermal imager helicopter survey.

Area	1992	1994	1997	2000	2002	2003	2004	2005	2006	2007	2008
	fw	fw	ti	fw	fw&ti	fw	2fw	2fw&1ti	fw&ti	fw&ti	fw&ti
Helmsdale to Brora	-	-	193	-	188	-	-	113	150	54	73
Loch Fleet	-	-	27	33	59	56	64	71	80	83	82
Dornoch Firth	662	542	593	405	220	290	231	191	257	144	145
Cromarty Firth	41	95	95	38	42	113	88	106	106	102	90
Beauly Firth	220	203	219	204	66	151	178	127	176	146	150
Ardersier	-	221	234	191	110	205	202	210	197	154	145
Culbin & Findhorn	-	58	46	111	144	167	49	93	58	79	92
Total	-	-	1,407	-	829	-	-	911	1,024	762	777

Area	2009	2010	2011	2012	2013	2014	2015	2016	2017	2018	2019
	fw	fw	ti	fw	fw	fw	fw	ti	fw	fw	fw
Helmsdale to Brora	19	101	87	102	70	1	21	40	22	30	17
Loch Fleet	65	114	113	133	135	156	144	145	138	152	109
Dornoch Firth	166	219	208	157	143	111	120	85	39	117	62
Cromarty Firth	90	140	101	144	63	100	22	72	20	43	84
Beauly Firth	85	140	57	60	30	37	34	30	5	30	24
Ardersier	277	368	195	183	199	28	34	36	81	98	116
Culbin & Findhorn	73	123	163	254	218	260	330	484	526	444	613
Total	775	1,205	924	1,033	858	693	705	892	831	914	1,025

Table 23. August counts of grey seals in the annually surveyed western Moray Firth between Helmsdale and Findhorn.  Mean values are given for areas surveyed more than once in a single season.  fw: fixed-wing survey; ti: thermal imager helicopter survey.

Area	1992	1994	1997	2000	2002	2003	2004	2005	2006	2007	2008
	fw	fw	ti	fw	fw&ti	fw	2fw	2fw&1ti	fw&ti	fw&ti	fw&ti
Helmsdale to Brora	-	-	3	-	6	-	-	101	102	52	449
Loch Fleet	-	-	0	0	0	0	0	0	1	3	1
Dornoch Firth	233	903	456	121	321	79	473	431	748	516	523
Cromarty Firth	9	0	0	0	0	0	0	0	1	0	0
Beauly Firth	8	2	3	8	0	0	0	0	3	4	0
Ardersier	-	36	24	85	0	3	44	55	142	74	142
Culbin & Findhorn	-	0	0	0	0	10	0	11	11	28	75
Total	-	-	486	-	327	-	-	598	1,008	677	1,190

Area	2009	2010	2011	2012	2013	2014	2015	2016	2017	2018	2019
	fw	fw	ti	fw	fw	fw	fw	ti	fw	fw	fw
Helmsdale to Brora	72	635	156	316	81	27	161	28	201	147	191
Loch Fleet	0	7	7	20	18	7	10	31	22	15	17
Dornoch Firth	819	717	679	74	604	127	716	387	273	321	401
Cromarty Firth	0	1	2	1	3	1	0	1	0	0	0
Beauly Firth	0	2	3	1	5	2	0	2	0	1	1
Ardersier	94	331	74	24	109	2	14	28	87	83	98
Culbin & Findhorn	58	58	179	121	218	93	743	717	548	144	856
Total	1,043	1,751	1,100	557	1,038	259	1,644	1,194	1,131	711	1,564

East Scotland SMA

Harbour seal counts by Subunits within the SMA are given in Table 24.  Subarea counts for the annually surveyed Firth of Tay and Eden Estuary SAC are given in Table 26.  In 1997, when the East Scotland SMA was surveyed in its entirety for the first time, over 80% of harbour seals were counted within the SAC.  The average SAC count since 2013 (43) is over 94% lower than the highest count made in 1992 (773).  This massive drop in numbers has obviously resulted in fewer harbour seals counted in East Scotland overall, but areas outside the SAC have not seen similar declines (Figure 26).  The total for the areas outside the SAC, from the most recent surveys in 2016 and 2018, is the second highest after 2005 (302 and 325 respectively).

Grey seal counts by Subunits within the SMA are given in Table 25.  Subarea counts for the annually surveyed Firth of Tay and Eden Estuary SAC are given in Table 27.  Grey seal numbers in East Scotland have always been higher than harbour seal numbers, both within and outside of the harbour seal SAC.  Whereas the largest aggregations were traditionally found on the sandbanks off Tentsmuir, over 2,000 grey seals can now be found at the Ythan River mouth, a haul-out site that has grown extraordinarily fast since 2010.

Table 24. August counts of harbour seals in the Seal Management Area ‘East Scotland’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMA 7 - East Scotland	1997	2005	2007	2013	2015	2016	2018
1 Fraserburgh to Ythan estuary	0	14	22	2	-	8	-
2 Aberdeen to Doolie Ness	15	22	0	0	-	17	-
3 Montrose to Carnoustie	0	9	2	16	-	28	-
4 Tay and Eden estuaries	633	335	275	50	60	51	40
5 Fife Ness, Isle of May	0	0	0	0	-	0	-
6 Inner Firth of Forth	0	17	10	23	-	-	45
7 Outer Firth of Forth	116	249	138	123	-	-	204
8 Bass Rock to Pease Bay	0	14	0	-	0	-	0
9 Pease Bay to border	0	0	0	-	0	-	0
10  Bell Rock	-	-	-	-	-	-	-
Total for SMA	764	660	447	214	-	-	342

Table 25. August counts of grey seals in the Seal Management Area ‘East Scotland’ by Subunits.  Subunit boundaries are shown in Figure 2.  Italic font is used to indicate counts that contain data from a previous year.

Subunits within SMA 7 - East Scotland	1997	2005	2007	2013	2015	2016	2018
1 Fraserburgh to Ythan estuary	130	400	388	987	-	2,197	-
2 Aberdeen to Doolie Ness	15	11	12	2	-	64	-
3 Montrose to Carnoustie	0	0	0	2	-	4	-
4 Tay and Eden estuaries	1,891	843	1,519	482	836	936	765
5 Fife Ness, Isle of May	65	21	158	87	-	85	-
6 Inner Firth of Forth	0	8	1	11	-	-	19
7 Outer Firth of Forth	224	78	182	364	-	-	471
8 Bass Rock to Pease Bay	2	1	47	-	0	-	76
9 Pease Bay to border	1	0	0	-	26	-	81
10 Bell Rock	-	-	-	-	-	-	-
Total for SMA	2,328	1,362	2,307	1,982	-	-	3,762

Table 26. August counts of harbour seals in the annually surveyed Firth of Tay and Eden Estuary SAC.  Mean values are given for areas surveyed more than once in a single season.  fw: fixed-wing survey; ti: thermal imager helicopter survey.

Area	1990	1991	1992	1994	1997	2000	2002	2003	2004	2005	2006	2007
	1fw	1fw	1fw	1fw	1ti	1fw	1fw	1fw	1fw	2fw,1ti	1fw	1fw,1ti
Upper Tay	27	73	148	89	113	115	51	83	134	91	91	63
Broughty Ferry	77	83	97	64	35	52	0	90	55	51	31	27
Buddon Ness	13	86	72	53	0	113	109	142	66	25	96	64
Tentsmuir	319	428	456	289	262	153	167	53	126	63	34	31
Eden Estuary	31	0	0	80	223	267	341	93	78	105	90	90
SAC total	467	670	773	575	633	700	668	461	459	335	342	275

Area	2008	2009	2010	2011	2012	2013	2014	2015	2016	2017	2018	2019
	2fw	1fw	1fw	1fw	1fw	1ti	1fw	1fw	1ti	1fw	1fw	1fw
Upper Tay	49	45	41	16	40	36	21	51	41	28	32	36
Broughty Ferry	13	28	15	18	16	3	0	2	4	0	4	2
Buddon Ness	27	8	23	11	8	10	1	3	0	0	2	0
Tentsmuir	50	8	9	0	5	0	0	0	1	0	0	0
Eden Estuary	83	22	36	32	19	1	7	4	5	1	2	3
SAC total	222	111	124	77	88	50	29	60	51	29	40	41

Table 27. August counts of grey seals in the annually surveyed Firth of Tay and Eden Estuary SAC.  Mean values are given for areas surveyed more than once in a single season.  fw: fixed-wing survey; ti: thermal imager helicopter survey.

Area	1990	1991	1992	1994	1997	2000	2002	2003	2005	2006	2007	2008
	1fw	1fw	1fw	1fw	1ti	1fw	1fw	1fw	2fw,1ti	1fw	1fw,1ti	2fw
Upper Tay	0	0	18	20	61	64	78	50	42	22	27	26
Broughty Ferry	0	3	0	9	0	0	0	16	0	8	1	8
Buddon Ness	0	0	1	104	0	101	0	33	11	25	85	7
Tentsmuir	912	1,546	1,191	1,335	1,820	2,088	1,490	1,560	763	1,267	1,375	483
Eden Estuary	0	0	16	0	10	0	25	4	27	57	31	33
SAC total	912	1,549	1,226	1,468	1,891	2,253	1,593	1,663	843	1,379	1,519	557

Area	2009	2010	2011	2012	2013	2014	2015	2016	2017	2018	2019
	1fw	1fw	1fw	1fw	1ti	1fw	1fw	1ti	1fw	1fw	1fw
Upper Tay	55	98	16	39	127	62	115	132	78	52	43
Broughty Ferry	0	0	2	3	0	2	0	0	0	0	0
Buddon Ness	0	12	22	13	18	0	2	0	0	0	0
Tentsmuir	395	1,406	1,265	1,111	323	531	687	738	596	667	561
Eden Estuary	0	39	17	36	14	39	32	66	76	46	82
SAC total	450	1,555	1,322	1,202	482	634	836	936	750	765	686

Special Areas of Conservation (SACs) for harbour seals

All SAC harbour seal counts are shown in Table 28 and plotted in Figure 27.  Thompson et al. (2019) carried out a trend analyses for harbour seal SACs using data collected from 1990 to 2017.  The new counts made in 2018 and 2019 are in line with the results from those analyses.  No clear trend was found in four of the SACs (3 in West Scotland, 1 in Shetland).  All other SACs have seen significant declines without subsequent recovery.

When the EU Habitats Directive was adopted in 1992, the total harbour seal count in all areas currently (in the process of being) designated as harbour seal SACs was over 6,000 (Table 28).  This total was just over 2,000 in the most recent census (all SACs were last surveyed between 2017 and 2019).  During the first full Scotland census in 1996-1997, over 20% of all harbour seals were counted within the current SACs.  During the most recent census in 2016-2019, this proportion dropped to around 8%.

Trends observed for counts made within the boundaries of an SAC are not necessarily representative of the harbour seal numbers recorded within a wider area.  Therefore, graphs provided in the following subsections present the SAC counts in the context of buffer areas, representing 10-50km at-sea distances from the SAC low water line, as well as in relation to the relevant Seal Management Area (subdivision).  The buffer areas are shown on a map in Figure 28.

Table 28. August counts of harbour seals in Special Areas of Conservation (SACs).

Year	South-East Islay Skerries	Eileanan agus Sgeiran Lios mor	Ascrib, Isay and Dunvegan	Sound of Barra	Sanday	Mousa	Yell Sound Coast	Dornoch Firth and Morrich More	Firth of Tay and Eden Estuary	Most recent totals of all SACs combined	% of Scottish total
1990	493	476	393	-	-	-	-	-	467	-	-
1991	-	405	278	-	-	388	210	-	670	-	-
1992	-	337	272	878	-	-	-	662	773	-	-
1993	-	596	618	-	1,498	455	245	-	-	6,218	-
1994	-	-	-	-	-	-	-	542	575	-	-
1995	-	-	-	-	-	-	-	-	-	-	-
1996	552	603	656	576	-	-	-	-	-	-	-
1997	-	-	-	-	1,458	402	501	593	633	5,974	20.2%
1998	-	-	-	-	-	-	-	-	-	-	-
1999	-	-	-	-	-	-	-	-	-	-	-
2000	812	453	968	276	-	-	-	405	700	-	-
2001	-	-	-	-	1,148	235	351	-	-	5,348	-
2002	-	-	-	249	-	-	-	220	668	-	-
2003	-	-	-	201	-	-	-	290	461	-	-
2004	-	-	664	-	-	-	-	231	459	-	-
2005	-	-	678	-	-	-	-	191	335	-	-
2006	-	-	-	179	478	83	212	257	342	3,494	14.9%
2007	741	325	719	-	425	-	-	144	275	-	-
2008	-	-	-	92	260	-	-	145	222	-	-
2009	666	498	-	-	308	93	168	166	111	2,821	13.8%
2010	-	-	-	-	107	-	-	219	124	-	-
2011	-	-	-	116	-	-	-	208	77	-	-
2012	-	-	-	-	180	-	-	157	88	-	-
2013	-	-	-	-	92	-	-	143	50	-	-
2014	-	380	434	-	-	-	-	111	29	-	-
2015	1,087	-	-	-	-	23	205	120	60	2,517	9.9%
2016	-	-	-	-	72	-	-	85	51	-	-
2017	-	-	712	132	-	-	-	39	29	-	-
2018	706	238	-	-	-	-	-	117	40	-	-
2019	-	-	-	-	77	7	209	62	41	2,184	8.1%

South-East Islay Skerries SAC

Harbour seals appear to be doing well in the South-East Islay Skerries SAC, even though the most recent 2018 count was 35% lower than the previous count in 2015 (Table 28).  Remarkably, the SAC consistently contributed 34% to the 50km-buffer count in all four censuses between 1996 and 2015, before this proportion dropped to 27% in 2018 (Figure 29).  The overall contribution to the West Scotland – South SMA subdivision also remained stable between 10-14% throughout, suggesting that the SAC is a good indicator of overall harbour seal numbers found in this SMA subdivision.  This may be due to the fact that there are no major haul-out sites within 10km swimming distance of the SAC, making it less likely for large groups of seals to switch from sites that lie inside the SAC to sites that are outside, and vice versa.

Eileanan agus Sgeiran Lios mor SAC

Harbour seal numbers within the Eileanan agus Sgeiran Lios mor SAC have remained fairly stable.  The counts produced by the aerial surveys may look like they represent a slow decline, but a relatively high count recorded during a NatureScot boat survey in 2016 suggests that this is due to natural variation (Figure 27).  This can be expected, given that there are a number of other significant haul-out sites within 2-8km of the SAC.  Indeed, the highest count for the wider area up to 50km from the SAC was recorded during the most recent survey in 2018 (Figure 30).  There is potential for significant variations in the SAC count, due to the close proximity of other haul-out sites.  The proportion of the 50km-buffer count (and of the SMA subdivision total) recorded within the SAC has declined over time.  This suggests that the SAC is not a good indicator of seal numbers found over a wider area.

Ascrib, Isay and Dunvegan SAC

The harbour seal count in the Ascrib, Isay and Dunvegan SAC was close to 700 in four of the five censuses.  The lower count in 2014 was compensated for by other haul-out sites in Loch Snizort that lie within 10km of the SAC (Figure 31).  There are hardly any significant haul-out sites around 10-30km from the SAC.  Just beyond that lie some of the high density areas along the eastern coast of the Western Isles, and within 50km are the harbour seal hotspots to the east of Skye on North Rona and Raasay.  The fairly consistent counts recorded within the SAC are not representative of the large increase observed in the West Scotland – Central SMA subdivision as a whole, where the count increased from 2,700 in 1996 to over 7,400 in 2017.

Sound of Barra SAC

In 1992, 38% of all harbour seals counted in the Western Isles were recorded inside the boundaries of the Sound of Barra SAC (Table 12 and Table 28).  Over the next 16 years numbers decreased and, since 2008, the SAC has contributed 5% or less to the SMA total (Figure 32).  The SAC count is even less representative of the 50km-buffer count that has increased significantly over the last ten years.

Sanday SAC

In the 1990s, approximately 1,500 harbour seals were counted within the Sanday SAC, contributing 5% to the Scotland total during the first full census in 1996-1997.  Since then, the SAC count has declined by 95%, even more dramatically than the Orkney total count, to which it now contributes only around 5% (Figure 33). This means that the Sanday SAC is one of the local areas hit hardest by the harbour seal decline observed in northern and eastern areas of Scotland.

Mousa SAC

Between 1997 and 2006, the harbour seal count for Shetland decreased by 50%, and subsequently remained stable.  The count for the 50km-buffer area around the Mousa SAC followed a similar pattern up until 2009, and contributed around 40% to the Shetland count during this time.  Over the last 10 years, numbers within the SAC and up to around 20km from the SAC have continued to decline, a trend that has not been observed in other parts of Shetland (Figure 34). 

Yell Sound Coast SAC

The Yell Sound SAC is just over 50km swimming distance to the north of the Mousa SAC, so large parts of the two 50km-buffer areas overlap.  However, the Yell Sound SAC count has closely followed the trends observed over the wider area and in Shetland as a whole.  During all five census counts, this SAC contributed 10-13% to the 50km-buffer area count and 6-8% to the Shetland total (Figure 35).  This consistency is slightly surprising, given that there are several significant haul-out sites within 5km of the SAC, so that one might expect the numbers within the SAC to fluctuate quite considerably.

Dornoch Firth and Morrich More SAC

The harbour seal count for the Dornoch Firth and Morrich More SAC has declined continuously since the 1990s.  This is neither representative of the wider area defined by the 50km-buffer area or of the Moray Firth SMA (Figure 36).  Especially the establishment of Culbin Sands, just over 30km from the SAC, as the main harbour seal haul-out area in the Moray Firth, has compensated for the decrease of numbers found in the SAC.  The proportion that the SAC contributes to the SMA total has decreased from 42% in 1997 to 6% in 2019.  During a study carried out in 2014 and 2015, 23 harbour seals tagged at Ardersier produced telemetry data for at least one month.  All of these animals used the haul-out sites at Culbin and Findhorn, but none of them hauled out in the Dornoch Firth (Onoufriou et al., 2016).  During the same project, four harbour seals tagged in the Dornoch Firth produced telemetry data for at least one month.  Two of these animals alternated between the SAC and Ardersier approximately once every 18 days.

Firth of Tay and Eden Estuary SAC

An even greater decline in harbour seal numbers has been recorded in the second harbour seal SAC along the eastern coast of Scotland, the Firth of Tay and Eden Estuary SAC.  Small groups of animals that still use the SAC to haul out are mainly found in the Firth of Tay upstream of the road bridge (Table 26).  This is the most isolated harbour seal SAC in Scotland in terms of connectivity to other haul-out areas.  Whereas there are a few more haul-out sites in the Firth of Forth, 40-90km from the SAC, the nearest large aggregation of harbour seals is at Findhorn and Culbin in the Moray Firth, over 260km away.  Of the 48 harbour seals tagged with telemetry devices inside the SAC (in the Eden estuary or at Abertay) between 2001 and 2012, only three animals visited the Firth of Forth, two of which hauled out in the Forth (SMRU, unpublished data).  Four harbour seals tagged in the Firth of Forth (near Kirkcaldy) in 2013 remained in the Forth for as long as the tags stayed attached.  Sites in East Scotland, which are not inside the SAC, have not seen the same declines as the SAC.  Although numbers of harbour seals were never very high at these sites, counts have remained stable or increased slightly.  During the first census in 1996-1997, the SAC count represented 83% of the SMA total.  Since then, this has decreased to 12% (Figure 37). 

Sites of Special Scientific Interest (SSSIs) for harbour seals

Of the five harbour seal SSSIs in Scotland, only two are not covered by existing harbour seal SACs.  These are the Eynhallow site in Orkney and the North Fetlar site in Shetland.  All SSSI counts are shown in Table 29.  Since the late 1990s, harbour seal numbers have declined very significantly in all five SSSIs.  Whereas these sites combined contained 10% of all harbour seals counted in Scotland during the first census in 1996-1997, this proportion dropped to below 1% in 2016-2019.

Table 29. August counts of harbour seals in Sites of Special Scientific Interest (SSSIs).  

Year	East Sanday Coast	Eynhallow	Mousa	North Fetlar	Tayport - Tentsmuir Coast	Total within all SSSIs	% of Scottish total
1990	-	-	-	-	319	-	-
1991	-	-	388	236	428	-	-
1992	-	-	-	-	456	-	-
1993	1,504	106	455	428	-	2,949	-
1994	-	-	-	-	289	-	-
1995	-	-	-	-	-	-	-
1996	-	-	-	-	-	-	-
1997	1,481	632	402	182	262	2,959	10.0%
1998	-	-	-	-	-	-	-
1999	-	-	-	-	-	-	-
2000	-	-	-	-	153	-	-
2001	1,152	620	235	71	-	2,231	-
2002	-	-	-	-	167	-	-
2003	-	-	-	-	53	-	-
2004	-	-	-	-	126	-	-
2005	-	-	-	-	63	-	-
2006	479	228	83	12	34	836	3.6%
2007	435	206	-	-	31	-	-
2008	260	216	-	-	50	-	-
2009	315	238	93	53	8	707	3.5%
2010	115	243	-	-	9	-	-
2011	-	-	-	-	0	-	-
2012	193	115	-	-	5	-	-
2013	99	104	-	-	0	-	-
2014	-	-	-	-	0	-	-
2015	-	-	23	9	0	235	0.9%
2016	74	2	-	-	1	-	-
2017	-	-	-	-	0	-	-
2018	-	-	-	-	0	-	-
2019	78	76	7	44	0	205	0.8%

East Sanday Coast SSSI

The intertidal coverage of the East Sanday Coast SSSI is almost identical to that of the Sanday SAC (see 3.4.5).

Eynhallow SSSI

The largest single haul-out of harbour seals in Scotland used to be found on Eynhallow in Orkney during the 1980s and early 1990s, when groups containing several hundred individuals were recorded.  The most recent count for the Eynhallow SSSI in 2019 (76) was 88% lower than the highest count recorded in 1997 (632).

Mousa SSSI

The intertidal coverage of the Mousa SSSI is identical to that of the Mousa SAC (see 3.4.6).

North Fetlar SSSI

The most recent harbour seal count for the North Fetlar SSSI in 2019 (44) was 90% lower than the highest count recorded in 1993 (428).  The five counts made since 2000 have ranged from 9 to 71.

Tayport – Tentsmuir Coast SSSI

The intertidal coverage of the Tentsmuir Coast SSSI is identical to the Tentsmuir subarea used for presenting the Firth of Tay and Eden Estuary SAC counts (Table 26).  The largest groups of harbour seals ever counted in the East Scotland SMA were recorded within the Tentsmuir Coast SSSI in the 1990s (456 in 1992).  Over the last seven years, only one harbour seal was recorded here by the annual surveys (in 2016).

Discussion

Harbour seals

During their recent examination of the status of harbour seals in the UK, Thompson et al. (2019) used count data collected up until August 2017 to analyse harbour seal abundance trends within Scottish Seal Management Areas (SMAs) and Special Areas of Conservation (SACs).  Additional data, from surveys conducted in 2018 and 2019 and described here, confirm findings by Thompson et al. that the current Scottish harbour seal population is similar to estimates from the late 1990s, but there have been significant declines in some subpopulations and increases in others.

Counts of seals on shore represent a proportion of the total population, as not all animals are ever hauled out at the same time.  There is not a lot of data available to calculate this proportion during the harbour seal moult season when abundance surveys are conducted.  It is not possible to use data from the majority of telemetry tags deployed on animals as the most common tags are glued to the fur and fall off when animals begin to moult.  The only study conducted in the UK to estimate the proportion of harbour seals available to count during the aerial surveys was presented by Lonergan et al. (2013).  Flipper tag data from 10 seals tagged in West Scotland and 15 seals tagged in Orkney were used to estimate a proportion of 0.72 (95% CI: 0.54–0.88).  This is within the range of estimates (0.65-0.81) produced by studies carried out in Alaska and in California using VHF radio tags (Harvey and Goley, 2011; Simpkins et al., 2003).

Cunningham et al. (2010) calculated a coefficient of variation of 15% for aerial harbour seal counts during the moult season.  However, this study used repeat surveys of disconnected subareas around or near the Isle of Skye, and thus the result may not be indicative of the true proportion, as animals may have hauled out at neighbouring sites that were not surveyed.  Apart from day-to-day variation, various other factors can produce regional or local counts that under- or over-represent true population size.  Whereas some haul-out sites are completely covered by water during the high tide period, other sites are accessible to seals throughout the tidal cycle, potentially reducing the proportion of seals hauled out during surveys.  If local foraging conditions are better during low tide periods, this could further reduce the proportion of animals hauled out at this time.  However, the vast majority of haul-out sites are likely to be used mainly during low tides, so this is not considered to be an issue for population monitoring.  Regional counts are more likely to be lower than expected if a significant proportion of the population hauls out in caves, where they are missed by the aerial surveys.  Caves are more commonly used by grey seals than by harbour seals, but it is very difficult to quantify.  It is assumed that these numbers are negligible when looking at overall abundance.  Both high water haul-outs and caves slightly reduce the proportion of the population that can be counted during the standard surveys.

Changes in the age structure or in the sex ratio over time can affect whether or not a consistent subset of the population is being counted from year to year.  All individual seals hauled out during the August surveys are included in the count, independent of which age class they belong to.  Because the harbour seal moult season closely follows the harbour seal pupping season, some of the animals counted will be recently born pups.  These weaned pups can look very similar to yearlings making it impossible to distinguish them when counting from aerial photographs (Thompson and Rothery, 1987).  Harbour seal pups often disperse after leaving their mothers and probably do not haul out as much as older animals that need to moult in August.  Therefore, it is assumed that the number of pups counted during the moult surveys is negligible (Thompson and Harwood, 1990).  It is not known whether the proportion of pups found on haul-out sites decreases throughout August.  In addition, one would expect to find a higher proportion of pups counted in regions where populations are increasing, i.e. where fecundity is higher and/or pre-weaning pup mortality is lower.  An increase in the relative number of pups could lead to a small overestimate of the rate of increase calculated for a population based on the count data.

It is possible that the timing of the moult season can change over several years, or that the timing may vary regionally, resulting in different proportions available to count.  This could make it even harder to identify long-term trends or to precisely estimate total population size.  However, there are no data to suggest that this is the case in Scotland.

Whereas Carroll et al. (2020) showed that harbour seals in the western genetic cluster belonged to a single local population, they recognised three genetically distinct local populations within the north-eastern cluster.  The Moray Firth animals belong to the same population as harbour seals in North Coast & Orkney, and this population was identified as a source region for the two separate populations in Shetland and in East Scotland.  Possible causes for the declines observed in northern and eastern Scotland are discussed in Thompson et al. (2019).  They include: predation by orcas (Orcinus orca) and by grey seals, competition with grey seals, algal toxins, and diseases.  Ongoing studies, funded by the Scottish Government, are attempting to identify the most likely driver(s) affecting harbour seal populations.  Population models indicate that a decrease in adult survival is required to explain a decline of the magnitude observed in Orkney, as changes in fecundity and pup survival alone are not enough (Arso Civil et al., 2019).

Harbour seal SACs generally do not appear to be reliable indicators of wider populations.  This is especially evident for the Sound of Barra SAC, where harbour seal numbers have declined dramatically since the 1990s.  In contrast, surrounding areas have seen a significant increase in numbers.  To varying degrees, all SACs now represent a smaller proportion of the wider population than in the past.  This consistency seems rather odd, and it is not known why this is the case.  Because these protected areas were selected based on high counts, it may be that these areas were closer to a maximum capacity at the time and numbers were always more likely to decline at higher rates compared to areas with lower densities.  It makes sense that a small area with a high density of animals is more likely to see a decline in numbers than further increases.

Grey seals

The summer counts suggest that the grey seal population has increased over the last 20 years without any regional declines as observed for harbour seals.  This is consistent with grey seal pup production estimates.  Pup production in Scotland grew at an almost exponential rate through the 1980s up until the mid-1990s, when production in the Inner and Outer Hebrides, started levelling off (Russell et al., 2019).  Production in the other main breeding region, Orkney, followed the same trend around five years later.  Although pup production estimates for Scottish breeding regions have been significantly higher from 2012 onwards, it is currently unclear to what extent this may be a result of upgrading the camera system used to photograph the breeding colonies (SCOS, 2018).  It is clear, however, that grey seal pup production is increasing rapidly in the North Sea, especially at some newer colonies on the east coast of England that were of little importance to overall UK numbers in the 1990s (Russell et al., 2019).  Over the last 20 years, the summer haul-out counts of grey seals in eastern England have been growing at a similar rate (approximately 16% p.a.) as the pup production at these thriving colonies (SCOS, 2019).  Whereas the large number of harbour seals found in the southern North Sea belong to a genetically different metapopulation compared to animals in Scotland (Olsen et al., 2017), this is not the case for grey seals.  Grey seals can travel great distances during foraging trips or between foraging and breeding regions (McConnell et al., 1999; Russell et al., 2013), so that large changes in one region are more likely to affect numbers in another.

Conclusion

The increases in the whole of Scotland total counts of grey seals and harbour seals over recent years suggest that both seal species are currently doing well on a national level.  However, there is a major difference between the two species in that there are starkly contrasting regional population trends for harbour seals.  Eastern and northern areas, that have seen large declines in the numbers of harbour seals counted since ca. 2000, have shown no sign of recovery.  Although it is not possible to calculate trends over short time periods using the approximately 5-yearly snapshots available for most areas, and sudden changes may not be identified very quickly, the duration of the long-term monitoring project allows us to identify overriding population trends.  The time series of harbour seals counted within Special Areas of Conservation (SACs) compared with numbers found within 50km of an SAC show that it is not possible to use the existing SACs as indicator sites for the wider population.  Seals are highly mobile, and comprehensive surveys are necessary in order to understand whether harbour seal populations are likely to be stable, increasing, or declining.

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