Reports

A summary of the work conducted every year under the Harbour Seal Decline Project is compiled in the form of annual reports. Below are the executive summaries and links to the full report for Years 1 to 4 of the project.

Arso Civil, M., Smout, S., Onoufriou, J., Thompson, D., Brownlow, A., Davison, N., Duck, C., Morris, C., Cummings, C., Pomeroy, P., McConnell, B. and Hall, A.J. 2016. Harbour Seal Decline – vital rates and drivers. Report to Scottish Government HSD2.

A pdf copy of the Year 1 report on the Harbour Seal Decline Project can be downloaded from here

Executive summary:

Numbers of harbour seals (Phoca vitulina) have dramatically declined in several regions of the north and east of Scotland, while numbers have remained stable or have increased in regions on the west coast. For any management and mitigation plans to address this situation, the relative contribution of various factors in the decline of harbour seals in Scotland needs to be identified, understood and assessed. Potential drivers of the decline include changes in prey quality and/or availability, increasing grey seal population size which may be influencing harbour seal populations through direct predation or competition for prey resources, and the occurrence and exposure of seals to toxins from harmful algae.
Previous work by Matthiopoulos et al. (2014) and Caillat and Smout (2015) developed and fitted an age-structured population model to data from the well-studied subpopulation of harbour seals in Loch Fleet (Moray Firth), to evaluate the contributions of different potential proximate causes to the observed decline. After reviewing the existing software, this model has been re-coded directly into R, a framework that will allow for future development and maintenance, and has been designed to be adapted to different model structures and future data sets. Preliminary results are consistent with those obtained from the original OpenBUGS modelling. Future work will have as its key objective the identification of the important drivers of population change in harbour seals, from those being studied as listed above. Temporal and spatial variation in these drivers will be incorporated into the population model.
Harbour seal haulout sites located in different regions of Scotland were visited in the spring and the summer of 2015 to collect information on their suitability for long-term monitoring of harbour seal populations, including their suitability for live captures, scat sampling, aerial and ground survey counts during pupping and moulting and photo-identification. This will allow empirical data to be collected and vital rates (fecundity and survival) to be estimated, for inclusion in the population model.
A haulout site located in West Burray (Orkney) has been selected to represent a region of decline, and a haulout site by Peninver (East Kintyre) has been selected to represent a region of stability or increase. In addition, photo-identification data will also be collected in Dunvegan Loch (Isle of Skye). The regional scope of local populations at each study site (Orkney, Kintyre and Isle of Skye) has been defined to direct future collation of any relevant environmental and biological data. Existing aerial survey counts of harbour and grey seals at each of the defined areas have been collated for use in the age-structured population model.
As part of the live captures programme, female harbour seals will be fitted in 2016 with low-cost electronic location tags, developed to allow a larger number of captured seals to be tagged and designed to regularly relay GPS locations from terrestrial locations. Data from these tags and from ten SMRU GPS/GSM phone tags will inform and direct the extent of the photo-identification re-sighting effort at haulout sites in 2016.
Domoic acid (DA) concentrations have been measured in urine and faecal samples collected from harbour seals in 2015, as a continuation of the work carried out by Jensen et al. (2015). DA is still being found in harbour seals around the Scottish coast and whilst concentrations vary between the different matrices (blood, faeces and urine) and samples, due to variation in exposure and time from uptake to excretion, some individuals appear to be consuming relatively high levels of toxin. Data from the monitoring of biotoxins in shellfish by the Centre for Fisheries and Aquaculture Science (Cefas) and Harmful Algal Blooms (HABs) by the Scottish Association for Marine Science (SAMS) were available for all of 2015 and January 2016. These datasets provide some indication of the occurrence of HABs and toxin-producing blooms in the regions of interest.
To further improve understanding of potential drivers of population change, initial contacts have been made to investigate the availability of prey samples relevant to seals foraging from the study sites, as well as the availability of prey abundance data from long-term fish surveys in the different regions of interest.
An update is provided on the current state of knowledge of the causes of spiral lacerations in seals based on necropsy results of stranded individuals since November 2014. Occurrences around Scotland are summarised along with objective assessments of the cause of the wound patterns, based on a weighted scoring system.

Arso Civil, M., Smout, S.C., Thompson, D., Brownlow, A., Davison, N., Doeschate, M., Duck, C., Morris, C., Cummings,, McConnell, B. and Hall, A.J. 2017. Harbour Seal Decline – vital rates and drivers. Report to Scottish Government HSD2.

A pdf copy of the Year 2 report on the Harbour Seal Decline Project can be downloaded from here

Executive summary:

Numbers of harbour seals (Phoca vitulina) have dramatically declined in several regions of the north and east of Scotland, while numbers have remained stable or have increased in regions on the west coast. For any management and mitigation plans to address this situation, the relative contribution of various factors in the decline of harbour seals in Scotland needs to be identified, understood and assessed. Potential drivers of the decline include changes in prey quality and/or availability, increasing grey seal population size which may be influencing harbour seal populations through direct predation or competition for prey resources, and the occurrence and exposure of seals to toxins from harmful algae.
Previous work by Matthiopoulos et al. (2014) and Caillat and Smout (2015) developed and fitted an age-structured population model to data from the well-studied subpopulation of harbour seals in Loch Fleet (Moray Firth), to evaluate the contributions of different potential proximate causes to the observed decline. Work has continued to build on the original Moray Firth study, re-coding a simplified version of the population model in JAGS language. A decision support tool (DST) has also been developed to include a biologically realistic simulation model and a model-fitting step that attempts to recover the parameters used in the simulation. A simple population model was successfully fitted to historical data for Scapa Flow (Orkney), with the Markov chain Monte Carlo (MCMC) converging and estimating reasonable-seeming parameter values. The DST was used to explore fitting limited data sets. The simulation/fitting approach showed that the fitting software was able to estimate parameters from the data even when the data set was ‘thinned’ (data not available for every year) and when no pup count data were available.
Live capture-release studies were conducted in Orkney in April and May 2016 under the SMRU Animal (Scientific Procedures) Act, 1986, (Home Office Licence No. 192CBD9F). Adult and juvenile harbour seals were captured, individual covariate data were collected from each seal and telemetry tags (GSM/GPS and LO tags) were deployed on adult seals, primarily on females, to direct the photo-identification effort prior to and during the pupping season. Pregnancy status was determined from progesterone concentrations in the plasma and in blubber, and from 17 beta-oestradiol concentration in plasma. Results show the blubber concentrations of progesterone may be a much more reliable indicator of pregnancy than levels in plasma. The proportion of the live-captured adult females that were pregnant was 61.5% (95% CI 35% – 88%), which is lower than would have been expected. However, given the small sample size further investigations must be carried out before any conclusions can be drawn. Domoic acid concentrations in the urine and faecal samples collected from the live capture-release animals were determined. Two animals had levels below the limit of detection, but the majority (88%) were above this level, indicating some low level exposure. Additionally, a further six scats collected at the capture haulout sites during May and June were also analysed. Of these, three were positive for DA but the remainder were below the limit of detection or samples were too small for analysis. Two fishing trips to collect prey samples were undertaken in the waters off Scapa Flow on the west coast of Orkney mainland. A total of 85 fish guts were sampled: 35 cod samples, 12 haddock, 36 ling and two torsk. All fish viscera were analysed for domoic acid content, using the same method as for the seal samples. All samples were positive for domoic acid at or above the limit of detection, although, in general, concentrations in all fish sampled were at low levels.
Moult aerial helicopter surveys were conducted in August 2016 in Orkney as part of the annual surveys conducted by SMRU. Breeding aerial surveys were also conducted in 2016 in Scapa Flow (Orkney), Kintyre and Isle of Arran, and Loch Dunvegan, using a fix-wing aircraft and digital photography. The difficulty of locating seals at haulouts from the aircraft and the impossibility of identifying age classes in the digital photographs led to the decision of excluding such data from the population model.
A summary of all seal carcasses reported to SMASS within and nearby the study sites between June 2016 and March 2017 is provided, with details on species, age class and proximate cause of death when available.

Arso Civil, M., Smout, S.C., Duck, C., Morris, C., Cummings, C., Langley, I., Law, A., Morton, C., Brownlow, A., Davison, N., Doeschate, M., Lacaze, J-P., McConnell, B., and Hall, A.J. 2018. Harbour Seal Decline – vital rates and drivers. Report to Scottish Government HSD2. Sea Mammal Research Unit, University of St Andrews, pp. 63.

A pdf copy of the Year 3 report on the Harbour Seal Decline Project can be downloaded from here

Numbers of harbour seals (Phoca vitulina) have dramatically declined in several regions of the north and east of Scotland, while numbers have remained stable or have increased in regions on the west coast. For any management and mitigation plans to address this situation, the relative contribution of various factors in the decline of harbour seals in Scotland needs to be identified, understood and assessed. Potential drivers of the decline include changes in prey quality and/or availability, increasing grey seal population size which may be influencing harbour seal populations through direct predation or competition for prey resources, and the occurrence and exposure of seals to toxins from harmful algae (domoic acid and saxitoxins).

Population model: Work continued to develop an integrated harbour seal population model. The model-fitting process was built upon, using a decision-support simulation tool to fit an age-structured population model to harbour seal count data, investigating the effect of ‘reducing’ the data by only including moult counts (excluding pup counts) and thinning the number of available data points. A visualisation tool was developed to support discussions about the relative impacts of effects that might be important during the different phases of harbour seal life-history. Based on simulated data, a number of scenarios were explored in which additional mortality, fecundity, and adult and pup survival were allowed to vary within plausible limits. The resulting effect on the predicted (simulated) population growth was visualised by means of a surface plot.

Photo-identification mark-recapture to estimate fecundity and survival: Photo-identification data were collected at selected harbour seal haulout sites in Orkney, Kintyre and Loch Dunvegan (Isle of Skye) during the pupping season in 2016 and 2017, primarily during the months of June and July. All photographs were graded for quality and individual seals identified from the unique patterns in their pelage. Photo-identification data collected in 2017 is currently being processed. For 2016, a summary of all catalogued seals by area with details on approximate age class and reproductive history has been made. Loch Dunvegan produced the highest number of catalogued seals. One of the monitored haulout sites in Kintyre was male-dominated, while mum-pup pairs were found in other sites.

Live capture-release studies: Live capture-release studies were conducted in Isle of Skye in March and Orkney in April and May 2017 in accordance with the SMRU Animal (Scientific Procedures) Act, 1986, (Home Office Licence No. 192CBD9F). Adult and juvenile harbour seals were captured, individual covariate data were collected from each seal, and telemetry tags (GSM/GPS and LO tags) were deployed primarily on adult females. Pregnancy status was determined from progesterone concentrations in the plasma and in blubber. The proportion of the live-captured adult females that were pregnant was 100% (95% CI 95% – 100%) in Isle of Skye and 67% (95% CI 39% – 95%) in Orkney, but the proportions were not statistically significantly different. Given the small sample size, further investigations must be carried out before any conclusions can be drawn. Domoic acid concentrations in the urine and faecal samples collected from the live capture-release animals were determined. Domoic acid concentrations were lognormally distributed, with some individuals having very high levels but in most animals concentrations were low. There was no difference in the median concentrations by region, with the Skye animals also being exposed to domoic acid.

Prey samples: Two fishing trips to collect prey samples were undertaken in July and November 2017 in the waters of Scapa Flow. Additionally, opportunistic fish samples were collected in North Ronaldsay. All fish viscera were analysed for domoic acid content, using the same method as for the seal samples. All samples were above the limit of detection, with the bullrout, and mackerel caught in the summer showing the highest concentrations. Fish guts sampled in Orkney in July 2017 and in Sinclair Bay (Caithness) in June 2017 were analysed for PSP toxins, but none of the samples contained any detectable level of saxitoxin.

Counts of harbour seals during the moult

Aerial surveys of harbour seals numbers hauled out during the moult were conducted in the study sites of Kintyre, Scapa Flow (Orkney) and Loch Dunvegan (Isle of Skye) in August 2015, 2016 and 2017, respectively, as part of the annual surveys conducted by SMRU (funded by Scottish Natural Heritage (SNH) and Natural Environment Research Council (NERC)). Results on the number of harbour and grey seals counted within the defined study areas are presented.

Stranded seals: A summary of all seal carcasses reported to Scottish Marine Animal Stranding Scheme (SMASS) within and nearby the study sites between March 2017 and February 2018 is provided, with details on species, age class and proximate cause of death when available.

Arso Civil, M., Langley, I., Law, A., Hague, E., Jacobson, E., Thomas, L., Smout, S.C., Hewitt, R., Duck, C., Morris, C., Brownlow, A., Davison, N., Doeschate, M., McConnell, B., and Hall, A.J.2019. Harbour Seal Decline – vital rates and drivers.Report to Scottish Government HSD2. Sea Mammal Research Unit, University of St Andrews, pp. 46

A pdf copy of the Year 4 report on the Harbour Seal Decline Project can be downloaded from here.

This report is dedicated to the memory of naturalist Andy Law, who meticulously collected all the photo-ID data from the Isle of Skye. He will be sorely missed.

Numbers of harbour seals (Phoca vitulina) have dramatically declined in several regions of the north and east of Scotland, while numbers have remained stable or increased in regions on the west coast. For any management and mitigation plans to address this situation, the relative contribution of various factors in the decline of harbour seals in Scotland need to be identified, understood and assessed. Potential drivers of the decline include changes in prey quality and/or availability, increasing grey seal population size which may be influencing harbour seal populations through direct predation or competition for prey resources, and the occurrence and exposure of seals to toxins from harmful algae (domoic acid and saxitoxins).

Integrated population model

In Year 4, efforts towards developing an integrated harbour seal population model included review and expert elicitation of plausible ranges for harbour seal vital rates, simulation of population trends with different sets of vital rates, and analysis of population sensitivity to changes in individual vital rates. Through the expert elicitation process, participants decided on consensus distributions that reflected the availability and uncertainty of published estimates of vital rates for harbour seals. The simulation exercise demonstrated that the population is sensitive to changes in adult survival, and that a decrease in adult survival is required to explain a decline of the magnitude observed at sites like Scapa Flow, Orkney. The next step will be to incorporate photographic mark-recapture data and environmental covariates into the integrated population model framework.

Photo-identification mark-recapture to estimate fecundity and survival

Photo-identification data were collected at selected harbour seal haulout sites in Orkney, Kintyre and Loch Dunvegan (Isle of Skye) during the pupping seasons of 2016, 2017 and 2018, primarily during the months of June and July. To build individual sighting and reproductive histories, which will be then used to estimate fecundity and survival rates, all photographs are first graded for photographic quality, and then individual seals are identified from the unique patterns on their pelage. Photo-identification data collected in 2018 are currently being processed. For 2016 and 2017, a summary of all catalogued seals by area with details of estimated age class and reproductive history is provided. The total number of seals identified in each area and year ranged between 155 and 550 seals, with Isle of Skye having the largest numbers, both for adults and pups. There was a consistency in the proportion of females seen with a pup and/or pregnant between years in each area. However, these proportions should not be interpreted as fecundity rates. The re-sighting rates of adult females that had pupped in 2016 were high in all three areas (range 77.8 % to 88.5%), and 59.0% to 61.1% of these females were seen again with a new pup in 2017.

Live capture-release studies

Pregnancy rates: Further analysis of the proportion of live captured females that were pregnant in each region was carried out. A proportion of the sampled females (n=23) were subsequently observed during the photo-ID fieldwork in Orkney and the Moray Firth. This provided a training dataset of animals observed pregnant or with a pup. Combining these observations with the pregnancy hormone, progesterone, concentrations in the blood and blubber for these animals resulted in a probability estimate of the proportion of pregnant females in each region. There was no difference in the percentage of animals that, according to their hormone levels, had a >60% probability of pupping among the different regions, despite a lower percentage in Orkney compared to elsewhere (Moray Firth 83%, Pentland Firth 88%, Skye 83%, Orkney 69%). This was largely due to the small sample sizes and the degree of regional variability. However, comparing these results with the regional fecundity estimates may indicate if reproduction is indeed lower in the regions of decline.

Nutritional stress indicators: Serum and plasma samples were analysed for selected clinical chemistry parameters to determine nutritional condition. A principal component analysis (PCA) was used to investigate whether there were any differences between the samples collected from the animals on Isle of Skye compared to Orkney. The variability in the data was much greater for Orkney than for Isle of Skye but the values were all within what would be considered clinically normal for this species. Thus, from these data there was no evidence that the captured seals are experiencing nutritional stress or were malnourished.

Toxins in prey and live captured seals

Toxins from harmful algal blooms continue to be found in the urine of harbour seals. Low levels of domoic acid were measured in live captured animals. However, these levels probably underestimate the peak levels that individuals would have been potentially exposed to during feeding bouts, due to the short half-life of domoic acid and the time elapsed between feeding and sampling. Work is currently underway to estimate peak exposure.

The role of toxins in harbour seal health may also be inferred by measuring their levels in prey items. Samples of fish prey of various species found in the diet of harbour seals in two of the study areas, Scapa Flow in Orkney and Loch Dunvegan on Isle of Skye, were obtained. Concentrations of domoic acid were low in all species although all fish were sampled outside a toxic bloom event period. To better understand how the toxin levels in prey relate to the domoic acid levels found in urine and faeces, estimated domoic acid ingestion rates were compared to toxic thresholds. Results showed that up to 6% of adults and 31% of juveniles could be consuming levels high enough to affect kidney and reproductive function. However, all were below any lethal thresholds. If possible, further samples will be collected during bloom events in these regions.

During the fish-sampling fieldwork at sea, opportunity was taken to evaluate different methods to characterise prey presence at a selection of the putative seal feeding areas, inferred from telemetry movement data. The methods included sonar logs and baited camera traps. In addition, the species of fish caught at each sampling location also served as a (biased) proxy of species presence. This evaluation is on-going.

Counts of harbour seals during the moult

Aerial surveys of harbour seal numbers hauled out during the moult were conducted in the study sites of Kintyre, Scapa Flow (Orkney) and Loch Dunvegan (Isle of Skye) in August 2015, 2016 and 2017, respectively, as part of the annual surveys conducted by SMRU (funded by Scottish Natural Heritage (SNH) and Natural Environment Research Council (NERC)). Results on the number of harbour (and grey) seals counted within the defined study areas are presented and the population trends have not changed (stable in Kintyre and Skye, declining in Orkney). The Kintyre area was also surveyed in 2018; photographs taken and resulting counts are currently being processed.

Stranded seals

A summary of all seal carcasses reported to Scottish Marine Animal Stranding Scheme (SMASS) within and nearby the study sites between March 2018 and March 2019 is provided, with details on species, age class and proximate cause of death when available. A total of 162 seal carcasses were reported in this period, mostly reported in Orkney (n=133). These included 123 grey seals, 19 harbour seals, and 20 seals for which species could not be determined. Post-mortem examination could only be conducted for one carcass, as the others were not in good condition or could not be recovered. Proximal cause of death was determined for 26 seals from observations, 25 of which were possible cases of grey seal attack, including three harbour seals, 21 grey seals (mostly weaned pups) and 1 seal of unknown species.