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Funding: part-funded by the UK Natural Environment Research Council to SMRU (Grant no. SMRU1001). 1. Grey seals (Halichoerus grypus) were the first mammals to be protected by an Act of Parliament in the UK and are currently protected under UK, Scottish, and EU conservation legislation. Reporting requirements under each of these statutes requires accurate and timely population estimates. Monitoring is principally conducted by aerial surveys of the breeding colonies; these are used to produce estimates of annual pup production. Translating these data to estimates of adult population size requires information about demographic parameters such as fecundity and sex ratio. 2. An age‐structured population dynamics model is presented, which includes density dependence in pup survival, with separate carrying capacities in each of the four breeding regions considered (North Sea, Inner Hebrides, Outer Hebrides, and Orkney). This model is embedded within a Bayesian state–space modelling framework, allowing the population model to be linked to available data and the use of informative prior distributions on demographic parameters. A computer‐intensive fitting algorithm is presented based on particle filtering methods. 3. The model is fitted to region‐level pup production estimates from 1984 to 2010 and an independent estimate of adult population size, derived from aerial surveys of hauled‐out seals in 2008. The fitted model is used to estimate total population size from 1984 to 2010. 4. The population in the North Sea region has increased at a near‐constant rate; growth in the other three regions began to slow in the mid‐1990s and these populations appear to have reached carrying capacity. The total population size of seals aged 1 year or older in 2010 was estimated to be 116 100 (95% CI 98 400–138 600), an increase of

Aerial surveys have detected alarming declines in counts of harbour seals in several regions across Scotland. Demographic data and simple models were used to examine the recent decline in the numbers of harbour seals counted in one population within a Special Area of Conservation (SAC) on the east coast of Scotland. The models suggest that the continuation of current trends would result in the species effectively disappearing from this area within the next 20 years. While the cause of the decline is unknown, it must be reducing adult survival because the high rate of decline cannot be wholly accounted for by changes in other demographic parameters. Recovery of the population to the abundance recorded at the time the SAC was designated (2005) is likely to take at least 40 years, even if the cause of the decline is immediately identified and removed. The models suggest that partial removal of the cause can have only limited benefits to population recovery, and there are unlikely to be any long-term benefits from introducing or reintroducing additional individuals while the underlying problem persists. Therefore, if the population of harbour seals in this area is to recover it is essential that the sources of the increased mortality are identified and measures are put in place to manage these. Copyright © 2015 John Wiley & Sons, Ltd.

Detailed models have the potential to reveal important processes underlying patterns in data. However, model fitting depends on the availability of sufficient data, and the results obtained from the models depend on detailed assumptions. In a recent paper, Matthiopoulos et al. fitted Bayesian state space models to a limited dataset and attempted to explain the recent trajectory of the harbour seal population in the Moray Firth, in northern Scotland. They went on to suggest that the results could help explain recent declines in other nearby populations. This Comment describes the implications of understating the uncertainty that the model required for convergence, questions the robustness of the results, highlights the differences between the areas, and cautions against extrapolating across these populations. The distinction between models that can be fitted to a dataset and those that provide useful information about the systems that generated the data is also considered.

Todd, C. D., Friedland, K. D., MacLean, J. C., Whyte, B. D., Russell, I. C., Lonergan, M. E., and Morrissey, M. B. 2012. Phenological and phenotypic changes in Atlantic salmon populations in response to a changing climate. – ICES Journal of Marine Science, 69: 1686–1698. Atlantic salmon (Salmo salar) of southern European origin migrating to the Norwegian Sea currently encounter anomalously high sea-surface temperatures, and returning adults are of low mean condition factor. For the River North Esk (Scotland), time-series changes in river age-structure of emigrant smolts and returning one- and two-sea-winter (1SW and 2SW) adults are assessed. A comparison of the river age-structure of returning adults (1977–1999) with that of their respective annual emigrant smolt cohorts shows no evidence of river age-related bias in survivorship at sea. Evidence is presented of a possible transgenerational, or maternal, influence (poor somatic condition of spawners) driving reduced quality of emigrant S2 smolts in the North Esk. This effect is concurrent with an influence of freshwater climate as indicated by the North Atlantic Oscillation Index (NAOI). The maternal influence and NAOI variation in the winter immediately prior to smolt migration jointly explain approximately 29 (S2) and 17% (S3), respectively, of the variation in the mean size of smolts over the period 1975–2010. Run-timing of 1SW adult cohorts returning to Scotland shows recent delays. Variation in river flow did influence mean return date for the River Tweed, but adult condition factor, which itself shows temporal trends likely to be associated with ocean climate change, was the primary significant explanatory variable for run-timing in the rivers North Esk and Tweed. Overall, in years of poorer adult condition, 1SW salmon stay at sea longer.

Estimates of both absolute abundance and trends in abundance are among the most basic pieces of information required for planning the conservation and management of wildlife populations. They are important for understanding both the current situation of species and potential risks to them. This study presents estimates of the size of the harbour seal (Phoca vitulina) population associated with the Orkney Islands, a part of northern Scotland that used to contain one of the largest concentrations of this species in Europe. The numbers of animals counted during aerial surveys of this area have decreased substantially over the period 2001–2010. ARGOS transmitters attached to flipper tags were used to rescale the counts into estimates of abundance and to confirm the rate of decline of this population. Females hauled out for more of the survey window (0.84; bootstrap 95% CI: 0.63–0.99) than males (0.61; bootstrap 95% CI: 0.34–0.86). The animals hauled out less during weekends (0.57; bootstrap 95% CI: 0.40–0.74) than during the week (0.76; bootstrap 95% CI: 0.58–0.91). The sex-ratios of this population is unknown. Assuming it was close to 1:1, then there were around 3586 (bootstrap 95% CI: 2970–4542) harbour seals in Orkney in 2010. A female-skewed sex-ratio would reduce the population estimate, and a changing sex-ratio might mean the counts understate the real decline. The mean annual rate of decline in the Orkney population of harbour seals, over the period 2001–2010, is estimated at 13% (95% CI: 10.8–14.8). Similar data for Arisaig, on the west coast of Scotland, shows an increase of around 2% (95% CI: 1.5–2.4) and, assuming an equal sex-ratio, 923 animals (95% CI: 765–1169) in 2007. Copyright © 2012 John Wiley & Sons, Ltd.

Lonergan, M., Duck, C. D., Thompson, D., Moss, S., and McConnell, B. 2011. British grey seal (Halichoerus grypus) abundance in 2008: an assessment based on aerial counts and satellite telemetry. – ICES Journal of Marine Science, 68: 2201–2209. Recent estimates of the total size of the British grey seal population have been based on fitting age-structured models to estimates of pup production. The estimates were sensitive to whether density-dependence was considered to act on fecundity or pup survival. This study provides an alternative estimate for abundance in 2008: 91 800 animals (95% confidence interval, CI, 78 400–109 900). The estimate is consistent with the results of existing models where population density influences pup survival. It suggests that reductions in fecundity are unlikely to have been the cause of the recent slowing of the rate of growth of the population. The estimate presented is based on aerial surveys of the entire Scottish coast and the east coast of England. The surveys were carried out in August of 2007–2009 and restricted to the 2 h each side of daylight low water. Data from 107 electronic tags deployed between 1995 and 2008 were used to estimate the proportion of animals hauled out during the surveys. Overall, the animals hauled out for 31% (95% CI 15–50%) of the survey windows. No significant effects on the proportion of animals hauled out were detected from year, location, age, sex, temperature, rainfall, or the timing of low tide.

In 1988 and 2002 dramatic and well-documented phocine distemper epizootics occurred in Europe. While their progression and impact were remarkably similar and consistent over much of Europe, mortality in the UK varied greatly between and within the 2 epizootics. We use antibody lev- els in blood samples to show that 51% (Bayesian 95% CI: 41 to 61%) of the individuals alive in 5 UK harbour seal populations at the end of the 1988 epizootic had been exposed to the virus, and that the equivalent figure after the 2002 outbreak was 22% (95% CI: 16 to 30%). Antibody prevalence was significantly higher in females than males after the 2002 epizootic. Combining these estimates with information on reductions in the numbers of animals observed hauled out during surveys of the Wash, Moray Firth, and Orkney populations and a simple epidemiological model, suggests that the differences between the 2 epizootics were primarily due to a 27% (95% CI: 8 to 43%) fall in R0, the basic reproductive rate of the virus. The large geographic variation in population effects observed within the UK during each epizootic appears to have been mainly due to differences in case mortal- ity, with R0 being remarkably similar in all the populations investigated.

1.Compliance with conservation legislation requires knowledge on the behaviour, abundance and distribution of protected species. Seal life history is characterized by a combination of marine foraging and a requirement to haul out on a solid substrate for reproduction and moulting. Thus understanding the use of haul out sites, where seals are counted, as well as their at-sea movements is crucial for designing effective monitoring and management plans. 2.This study used satellite transmitters deployed on 24 harbour seals in western Scotland to examine movements and haul-out patterns. 3.The proportion of time harbour seals spent hauled out (daily means of between 11 and 27%) varied spatially, temporally and according to sex. The mean haul-out duration was 5 h, with a maximum of over 24 h. 4.Patterns of movement were observed at two geographical scales; while some seals travelled over 100 km, 50% of trips were within 25 km of a haul-out site. These patterns are important for the identification of a marine component to designated protected areas for the species. 5.On average seals returned to the haul-out sites they last used during 40% of trips, indicating a degree of site fidelity, though there was wide variation between different haul-out sites (range 0% to >75%). 6.Low fidelity haul-out sites could form a network of land-based protected areas, while high fidelity sites might form appropriate management units. Copyright © 2008 John Wiley & Sons, Ltd.

Ocean climate impacts on survivorship and growth of Atlantic salmon are complex, but still poorly understood. Stock abundances have declined over the past three decades and 1992–2006 has seen widespread sea surface temperature (SST) warming of the NE Atlantic, including the foraging areas exploited by salmon of southern European origin. Salmon cease feeding on return migration, and here we express the final growth condition of year-classes of one-sea winter adults at, or just before, freshwater re-entry as the predicted weight at standard length. Two independent 14-year time series for a single river stock and for mixed, multiple stocks revealed almost identical temporal patterns in growth condition variation, and an overall trend decrease of 11–14% over the past decade. Growth condition has fallen as SST anomaly has risen, and for each yearclass the midwinter (January) SST anomalies they experienced at sea correlated negatively with their final condition on migratory return during the subsequent summer months. Stored lipids are crucial for survival and for the prespawning provisioning of eggs in freshwater, and we show that under-weight individuals have disproportionately low reserves. The poorest condition fish (� 30% under-weight) returned with lipid stores reduced by � 80%. This study concurs with previous analyses of other North Atlantic top consumers (e.g. somatic condition of tuna, reproductive failure of seabirds) showing evidence of major, recent climate-driven changes in the eastern North Atlantic pelagic ecosystem, and the likely importance of bottom-up control processes. Because salmon abundances presently remain at historical lows, fecundity of recent year-classes will have been increasingly compromised. Measures of year-class growth condition should therefore be incorporated in the analysis and setting of numerical spawning escapements for threatened stocks, and conservation limits should be revised upwards conservatively during periods of excessive ocean climate warming.

Bernal, M., Ibaibarriaga, L., Lago de Lanzós, A., Lonergan, M. E., Hernández, C., Franco, C., Rasines, I., Valdés, L., and Borchers, D. L. 2008. Using multinomial models to analyse data from Iberian sardine egg incubation experiments: a comparison with traditional techniques. – ICES Journal of Marine Science, 65: 51–59. Multinomial rather than traditional models were applied to improve data analysis of incubation experiments for Iberian sardine (Sardina pilchardus) eggs. Incubation experiments were carried out in 2002 in the Gulf of Cádiz, southwestern Spain, and data were taken from the literature for the Cantabrian Sea area. Rigorous review of the traditional models revealed shortcomings in the statistical framework for modelling the developmental progression of egg stages as well as a lack of transparency of the inherent assumptions. Multinomial model results show that egg stage duration varies for all stages, with stages 3 and 4 having the shortest duration. Comparison of the results between multinomial and traditional models shows that multinomial models provide improved insight into developmental mechanisms than that can be achieved using traditional models.

This study presents an analysis of changes in the regional abundance of harbour seals Phoca vitulina based on repeated aerial surveys of haulouts, and demonstrates the use of sparse data to deliver advice about population status and management. Generalized linear models with negative binomial errors were used to represent these overdispersed data. The shape parameter of the negative binomial distribution was directly estimated from the data where this was possible. Information from time-series of counts where there were few gaps in the data was used to improve the estimation of this parameter in areas where fewer surveys had been carried out. The results show that the number of harbour seals in eastern England has not increased since the end of the 2002 phocine distemper epidemic. There is also evidence of a general decline in most of the large harbour seal colonies around Britain. The populations in the Inner Hebrides were an exception, with numbers appearing to be stable or increasing. Between 2001 and 2006, the population in Orkney and Shetland declined by 40% (95% confidence interval: 30–50%), indicating harbour seals in these areas experienced substantially increased mortality or very low recruitment over this period. The widespread declines, ranging from Shetland to The Wash, suggest that the causes may have been present over a large part of the North Sea.

Planktonic cyprid larvae of the intertidal barnacle, Semibalanus balanoides (L.) and the infralittoral/sublittoral Balanus crenatus Brug., are readily captured in small, chambered, passive traps deployed on rocky shores. Several structural developments of a previous trap design improved urea (killing solution) retention and capture of cyprids of both species. The design adopted for assessment of the larval supply/settlement relationship of the focal species, S . balanoides , included additional internal baffles and the replacement of the cylindrical trap opening with a coned aperture. Three sizes of cone aperture area were compared, with the intermediate size (1 cm 2 ) being optimal for measuring larval supply over the full range of wave action on local shores. Most daily catches included larvae that were recognizable as having been dead before they were trapped, and had recently passed through the guts of grazing limpets ( Patella vulgata L.). One site showed that ∼32% of trapped S . balanoides were so-called ‘faecal’ cyprids. An inability to distinguish these in trap samples would lead to a significant over-estimation of larval supply. Preliminary data indicated that S . balanoides larval supply to the intertidal is enhanced by onshore winds (or perhaps increased wave turbulence), whereas B . crenatus supply was positively correlated with offshore winds (or decreased turbulence). A clear ‘supply/settlement’ relationship for S . balanoides at six sites along ∼40 km of coastline was derived from 1 cm 2 coned trap catches and daily counts of settlement on ceramic tiles. There were no instances of disproportionately high settlement in relation to larval supply, but at five sites there were days when settlement apparently failed. The identification and explanation of settlement success and failure is fundamental to understanding the importance of larval supply in structuring marine benthic populations and communities.

Summary 1 Harbour seals Phoca vitulina in eastern England were heavily exploited in the 1960s and 1970s, and affected by phocine distemper virus (PDV) epidemics in 1988 and 2002. Information on their historical and current status is required for their management. To maximize the effectiveness of limited population survey effort we need to both estimate and minimize error. 2 Presented here are data from annual aerial surveys of the population. Sporadic, synoptic surveys in The Wash, England, were used with more frequent counts of subpopulations in the Moray Firth, Scotland, to determine optimum timing of surveys. 3 We developed models that explicitly account for variability in both observation and population growth processes to show that the proportion of animals observed is much more variable than the annual growth rates. The latter can therefore be treated as constant within each period, and estimated along with the epidemic mortalities during the study and the precision of the survey results. 4 The Wash population increased at around 3·1% per annum (pa) [95% confidence interval (CI) 2·1–4·1] between 1973 and 1988. It fell by approximately 52% (95% CI 44–59) as a result of the 1988 PDV epidemic, and subsequently increased at 5·7% pa (95% CI 4·8–6·7). These growth rates were below those reported for European mainland populations, but showed no indication of density-dependent effects. 5 The recurrence of PDV in 2002 caused approximately 22% mortality (95% CI 9–33), significantly less than the 1988 epidemic and less than half that in European mainland populations in 2002. 6 Synthesis and applications. Combining sparse, systematic survey data with sporadic counts produced robust estimates of growth rates and epidemic mortality. The results indicate the value of even limited and sporadic survey effort for monitoring populations. The study has highlighted significant differences in both population dynamics and the severity of disease events between English and European harbour seal populations.

Phocine distemper virus (PDV) may have killed a small number of grey seals Hali- choerus grypus in European waters in 2002, as it was thought to have done in 1988. PDV is known to affect harbour seal population and distribution patterns, but grey seal pup production trends did not correlate consistently with PDV outbreaks. Numbers of known mothers missing from study colonies do not increase in PDV years and pre-weaning pup mortality is similar to that in other years. Pup growth rates are similar in PDV and non-PDV years. Therefore, no direct evidence links PDV out- breaks to changes in grey seal reproductive parameters at the population, colony, or individual level. Investigation of exposure of grey seals to PDV used CDV virus-neutralisation tests on sera collected from breeding seals pre-1988, 1988, 2001 and 2002. No positive sera (≥titre 1:64) were detected prior to 1988. In 1988, 2001 and 2002 the prevalence was 96, 59 and 83%, respectively. In 2001, prevalence in 'old' mothers (of breeding age by 1988, ≥13 yr old) was 63% compared to 0% in 'young' mothers (born after 1989

In 2002 phocine distemper virus (PDV) reappeared in the European harbour seal (Phoca vitulina) population. This outbreak seems to have followed a similar pattern to the 1988 one which killed almost 60% of individuals in most localities. Harding et al. (2002) suggested that there is a relatively high (18%) risk that recurrent outbreaks of PDV could reduce the European harbour seal population by 90%. We show that incorporating the effects of observation error during population surveys and of the long-term immunity of survivors of morbillivirus outbreaks indicate a much lower level of risk (

The management of anthropogenic impacts on marine mammal populations involves the setting of targets that are built on assumptions and choices. Scientific methods can be used to investigate the implications of management actions, but the choice of overall objectives and priorities lies outside science. A recent paper ( Potential biological removal and other currently used management rules for marine mammal populations : A comparison in Marine Policy ), summarised the characteristics of the main approaches currently used to set conservation management targets for marine mammal populations in order to provide a basis for discussion of the targets they contain. Cooke et al. ( Management rules for marine mammal populations : A response to Lonergan in Marine Policy ) responded, giving some important additional information about these management rules. However most of that paper's criticisms were incorrect or misplaced. Specifically, it erroneously treated an example of how PBR could be reworked, to make its abundance explicit, as a proposal to ignore uncertainty in managing populations. This paper addresses Cooke's main criticisms, and suggests that explicit justifications should be an important part of the process of setting targets for the management of marine mammal populations.

Evans et al. [1] correctly state that complex models can represent more possibilities than simple models. However, that flexibility is of limited interest unless there is some connection between the outputs of the models and reality. Although complex models are able to match patterns closely, their use or testing depends on parameterisation and comparison with data. The question that Evan et al. pose – ‘do simple models lead to generality in ecology?’ – is secondary to that of which models provide useful answers to which questions on the basis of available, or collectable, data.

Time series of abundance estimates are commonly used for analyses of population trends and possible shifts in growth rate. We investigate if trends in age composition can be used as an alternative to abundance estimates for detection of decelerated population growth. Both methods were tested under two forms of density dependence and different levels of environmental variation in simulated time series of growth in Baltic gray seals. Under logistic growth, decelerating growth could be statistically confirmed after 16 years based on population counts and 14 years based on age composition. When density dependence sets in first at larger population sizes, the age composition method performed dramatically better than population counts, and a decline could be detected after 4 years (versus 10 years). Consequently, age composition analysis provides a complementary method to detect density dependence, particularly in populations where density dependence sets in late.

1. For British grey seals, as with many pinniped species, population monitoring is implemented by aerial surveys of pups at breeding colonies. Scaling pup counts up to population estimates requires assumptions about population structure; this is straightforward when populations are growing exponentially, but not when growth slows, since it is unclear whether density dependence affects pup survival or fecundity. 2. We present an approximate Bayesian method for fitting pup trajectories, estimating adult population size and investigating alternative biological models. The method is equivalent to fitting a density dependent Leslie matrix model, within a Bayesian framework, but with the forms of the density dependent effects as outputs rather than assumptions. 3. This approach requires fewer assumptions than the state space models currently used, and produces similar estimates. The simplifications made the models easier to fit, reducing their computational intensity and allowing regional differences in demographic parameters to be considered. 4. The approach is not restricted to situations where only a single component of the population is observable, but, particularly in those cases, provides a practical method for extracting information from limited datasets. 5. We discuss the potential and limitations of the method and suggest that this approach provides a useful tool for at least the preliminary analysis of similar datasets. Publisher PDF

Managers of many ungulate populations seek to maximize the number and quality of mature males that can be harvested each year rather than the total harvest. Since competition between the sexes in dimorphic ungulates is commonly asymmetric and increasing population density depresses the growth and survival of males more than females, different culling policies may need to be applied to the two sexes to realize this objective. In this paper, we use observed density-dependent changes in reproduction and survival in an unculled red deer (Cervus elaphus) population in the North Block of the Isle of Rum to model the responses of males and females to different levels of culling or predation

The authors acknowledge the support of the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) in the completion of this study (grant reference HR09011). In assessing impacts of a changing environment on the structure and functioning of marine ecosystems, the challenge remains to distinguish the effects of noise and of temporal and spatial autocorrelation from environmental drivers of biotic change. One analytical approach is to de-trend the data and use the resulting residuals; an alternative method involves use of the raw anomalies and a reduction of the degrees of freedom (df) to make the hypothesis testing more conservative. Here, we assess the comparability of 3 gridded sea surface temperature (SST) datasets—ERSST V3b, HadISST, and OISST V2—to in situ measurements. The 1° gridded HadISST and OISST V2 showed the highest similarity, while the weaker correlations with ERSST V3b probably are attributable to its coarser 2° grid. We investigated the performance of 2 commonly applied statistical methods to resolving autocorrelation, and proceeded to correlation analyses between the SST datasets and 2 contemporaneous 15 yr time-series of the somatic growth condition of annual cohorts of Atlantic salmon Salmo salar, which migrate to the Norwegian Sea. For these latter analyses, reducing df could not fully resolve the problem of high positive autocorrelation. The 3 oceanographic datasets do not provide the same correlative outcomes and levels of significance with the salmon time-series. When analysing time-series that pre-date the availability of satellite data, the choice of dataset is restricted to either ERSST V3b or HadISST; but for recent studies (1982 onwards) OISST V2 also is available, and it will be important to assess the relative merits of the 3 SST data sources when interpreting contrasting correlative outcomes. Publisher PDF