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Germline SDHA mutations are reported in a minority of pheochromocytoma/paraganglioma (PPGL) cases but are associated with an increased risk of malignancy, leading some to advocate cascade genetic testing and surveillance screening of "at-risk" first-degree relatives. However, such approaches rely on accurate estimates of variant pathogenicity and disease penetrance, which may have been subject to ascertainment and reporting biases, although the recent provision of large population-based DNA sequence data sets may provide a potentially unbiased resource to aid variant interpretation. Thus, the aim of the current study was to evaluate the pathogenicity and penetrance of SDHA variants reported in literature-based PPGL cases by comparing their frequency to those occurring in the Genome Aggregation Database (GnomAD) data set, which provides high-quality DNA sequence data on 138,632 individuals. In total, 39 different missense or loss-of-function (LOF) SDHA variants were identified in 95 PPGL index cases. Notably, many of the PPGL-associated SDHA alleles were observed at an unexpectedly high frequency in the GnomAD cohort, with ~1% and ~0.1% of the background population harboring a rare missense or LOF variant, respectively. Although the pathogenicity of several SDHA alleles was supported by significant enrichment in PPGL cases relative to GnomAD controls, calculations of disease penetrance based on allele frequencies in the respective cohorts resulted in much lower estimates than previously reported, ranging from 0.1% to 4.9%. Thus, although this study provides support for the etiological role of SDHA in PPGL formation, it suggests that most variant carriers will not manifest PPGLs and are unlikely to benefit from periodic surveillance screening.

COPD exacerbations are associated with worsening symptoms including cough, shortness of breath, sputum production and worsening airflow obstruction. Increased number of exacerbations is associated with morbidity and mortality [1]. Footnotes This manuscript has recently been accepted for publication in the European Respiratory Journal . It is published here in its accepted form prior to copyediting and typesetting by our production team. After these production processes are complete and the authors have approved the resulting proofs, the article will move to the latest issue of the ERJ online. Please open or download the PDF to view this article. Conflict of interest: Dr. Keir has nothing to disclose. Conflict of interest: Dr. Dicker has nothing to disclose. Conflict of interest: Dr. Lonergan has nothing to disclose. Conflict of interest: Dr. Crichton has nothing to disclose. Conflict of interest: Dr. Miller reports other from GSK, outside the submitted work. Conflict of interest: Dr. Tal-Singer reports other from GSK, outside the submitted work. Conflict of interest: Dr. Chalmers reports grants from Glaxosmithkline, during the conduct of the study; grants and personal fees from Glaxosmithkline, grants and personal fees from Boehringer-Ingelheim, grants from Astrazeneca, grants and personal fees from Pfizer, grants and personal fees from Bayer Healthcare, grants and personal fees from Grifols, personal fees from Napp, personal fees from Aradigm corporation, grants and personal fees from Insmed, outside the submitted work.

Background The sputum microbiome has a potential role in disease phenotyping and risk stratification in chronic obstructive pulmonary disease (COPD), but few large longitudinal cohort studies exist. Objective Our aim was to investigate the COPD sputum microbiome and its association with inflammatory phenotypes and mortality. Methods 16S ribosomal RNA gene sequencing was performed on sputum from 253 clinically stable COPD patients (4-year median follow-up). Samples were classified as Proteobacteria or Firmicutes (phylum level) and Haemophilus or Streptococcus (genus level) dominant. Alpha diversity was measured by using Shannon-Wiener diversity and Berger-Parker dominance indices. Survival was modeled by using Cox proportional hazards regression. A subset of 78 patients had label-free liquid chromatography with tandem mass spectrometry performed, with partial least square discriminant analysis integrating clinical, microbiome, and proteomics data. Results Proteobacteria dominance and lower diversity was associated with more severe COPD according to the Global Initiative for Chronic Obstructive Lung Disease classification system (P = .0015), more frequent exacerbations (P = .0042), blood eosinophil level less than or equal to 100 cells/μL (P Conclusion The sputum microbiome is associated with clinical and inflammatory phenotypes in COPD. Reduced microbiome diversity, associated with Proteobacteria (predominantly Haemophilus) dominance, is associated with neutrophil-associated protein profiles and an increased risk of mortality.

Introduction: COPD is a heterogenous disease which makes identifying patients more likely to respond to a particular treatment or at higher risk of poor clinical outcomes challenging. Methods: Microbiome characterization by 16S bacterial rRNA gene sequencing was performed on sputum samples obtained from 297 COPD patients studied during stable disease with a median follow up of 4 years. Samples were classified at the phyla level as proteobacteria or firmicutes dominant whilst at the genera level samples were classed as Haemophilus or Streptococcus dominant. If no phyla or genera was represented at greater than 40% these were classed as “balanced microbiomes”. The results were compared to clinical characteristics to determine the utility of stable disease microbiome in predicting outcomes. Results: Proteobacteria dysbiosis and loss of microbiota diversity (Shannon-Wiener Diversity Index) was associated with more severe COPD by GOLD stage (P=0.0007), more frequent prior exacerbations (P=0.0057), low blood eosinophil counts ( Proteobacteria dysbiosis was associated with an increased risk of mortality (HR 2.39 95% CI 1.23-4.66, p=0.01) compared to those with a balanced or firmicutes dominated microbiome. Uniquely among Firmicutes, patients with a Streptococcus dominated microbiome had an increased mortality risk (HR 2.58 95% CI 1.03-6.46, p= 0.043) when compared to those with balanced microbiomes. Conclusions: Reduced microbiome diversity, driven by Proteobacteria (predominantly Haemophilus) or Streptococcus dysbiosis is associated with increased mortality and may indicate COPD endotypes at increased risk of negative outcomes. Funder: GSK

We are grateful to Professor Morice for his reminder of the limits of observational data, and the need for caution in its interpretation [1]. And we accept that it is unlikely to ever be proved conclusively that the dramatic restrictions imposed as countries locked down caused the dramatic changes in epidemic trajectories, even though the epidemiological changes seemed to follow the behavioural changes. However, there is also a large logical leap from observing the Swedish data to inferring that social distancing “measures can only have had a minor effect”., There are limitations to inferring causality from observational data, but lockdowns have almost certainly saved lives worldwide

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.

A method of dating the marine growth circuli on Atlantic salmon (Salmo salar L.) scales is presented. Data were available for 54 salmon, intercepted as smolts at the completion of their downstream migration in the River North Esk, Scotland. Smolts were tagged, released, and recaptured as return adults after either one (1SW) or two (2SW) winters at sea. Dating of circuli was achieved by fitting a simple quadratic model to the circuli pertaining to fixed points on the scale. For 1SW fish, the latter were the dates of river emigration and completion of marine migration, and the midpoint circulus (equal to the winter solstice) of the winter annulus. For 2SW salmon, these were the date of emigration and the two winter annulus midpoints. A key assumption is that winter annulus formation arises from constraints of light availability on foraging, and hence, reduced growth rate. Comparative analyses indicate the method to be robust and effectively transferable to salmon of known capture date — but of unknown smolt emigration date — by assuming a fixed date of emigration; in such cases, circuli could still be allocated with confidence to a calendar month.

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.

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.

Sandeels are known to be negatively affected by climate change in a number of ways. This study investigated whether these changes are affecting the harbour porpoise (Phocoena phocoena), a species which consumes sandeels. Porpoise diet was examined in spring (March-May), a critical time of year for survival when sandeels are important prey, from 1993 to 2001 to provide baseline information on the proportion of sandeels consumed. When data from spring 2002 and 2003 were compared to these baseline data, the diet was found to be substantially different, with a significant and substantially smaller proportion of sandeels being consumed in March and May. There were also differences in the number of porpoises starving between the two time periods (33% in spring 2002 and 2003 died of starvation, but only 5% in the baseline period). This suggests that a lower proportion of sandeels in the diet of porpoises in spring increases the likelihood of starvation. Therefore, we suggest that the negative effects of climate change on sandeel availability may have serious negative effects on harbour porpoise populations in the North Sea by increasing the likelihood of starvation in spring.

This work was conducted as part of a PhD, which was funded by the Natural Environment Research Council (NERC), UK and by SMRU Marine, St Andrews, UK. BACKGROUND: The neuropeptide oxytocin is increasing the focus of many studies investigating human and animal social behaviours and diseases. However, interpretation and comparison of results is made difficult by a lack of consistent methodological approaches towards analysing this hormone. NEW METHOD: This study determined the sample collection and analysis protocols that cause the least amounts of protocol dependant variation in plasma oxytocin concentrations detected by ELISA. The effect of vacutainer type, sample extraction prior to analysis and capture and restraint protocol were investigated while validating an assay protocol for two novel species, grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina). RESULTS: Where samples are extracted prior to analysis, vacutainer type (EDTA mean: 8.25±0.56pg/ml, heparin mean: 8.25±0.62pg/ml, p=0.82), time taken to obtain a sample and restraint protocol did not affect the concentration of oxytocin detected. However, concentrations of oxytocin detected in raw plasma samples were significantly higher than those in extracted samples, and varied significantly with vacutainer type (EDTA mean: 534.4±43.7pg/ml, heparin mean: 300.9±19.6pg/ml, p

This research was funded by the Scottish Government (www.scotland.gov.uk), Scottish Natural Heritage (www.snh.gov.uk) and the Natural Environment Research Council (www.nerc.ac.uk). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The harbour seal population in Orkney, off the north coast of Scotland, has reduced by 65% between 2001 and 2010. The cause(s) of this decline are unknown but must affect the demographic parameters of the population. Here, satellite telemetry data were used to test the hypothesis that increased pup mortality could be a primary driver of the decline in Orkney. Pup mortality and tag failure parameters were estimated from the duration of operation of atellite tags deployed on harbour seal pups from the Orkney population (n = 4) and from another population on the west coast of Scotland (n = 24) where abundance was stable. Survival probabilities from both populations were best represented by a common gamma distribution and were not different from one another, suggesting that increased pup mortality is unlikely to be the primary agent in the Orkney population decline. The estimated probability of surviving to 6 months was 0.390 (95% CI 0.297 – 0.648) and tag failure was represented by a Gaussian distribution, with estimated mean 270 (95% CI = 198 – 288) and s.d. 21 (95% CI = 1 – 66) days. These results suggest that adult survival is the most likely proximate cause of the decline. They also demonstrate a novel technique for attaining age-specific mortality rates from telemetry data. Publisher PDF

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

This paper uses simple mathematical models to examine the long-term dynamic consequences of the 1988 epizootic of phocine distemper virus (PDV) infection in Northern European common seal populations. In a preliminary analysis of single outbreaks of infection deterministic compartmental models are used to estimate feasible ranges for the transmission rate of the infection and the level of disease-induced mortality. These results also indicate that the level of transmission in 1988 was probably sufficient to eradicate the infection throughout the Northern European common seal populations by the end of the first outbreak. An analysis of longer-term infection dynamics, which takes account of the density-dependent recovery of seal population levels, corroborates this finding. It also indicates that a reintroduction of the virus would be unlikely to cause an outbreak on the scale of the 1988 epizootic until the seal population had recovered for at least 10 years. The general ecological implications of these results are discussed.

This paper describes how multinomial models can be used to study developmental rates of biological processes and how these are affected by different factors such as temperature or parental effects. First, the most common multinomial models for ordinal categorical data (namely, proportional odds, continuation-ratio, and extended continuation-ratio models) are described within the particular framework of developmental rates for discrete and ordered stage classified biological processes. Then, the extraction from the fitted models of a series of biologically meaningful parameters is proposed. In particular, maximum probable age and several alternative definitions for stage duration are presented and pros and cons of each of them are discussed. As an example, the methodology is applied to analyze the temperature dependent development of anchovy (Engraulis encrasicolus) eggs in the Bay of Biscay.

The UK holds approximately 40% of the European harbour seal population, with the majority found around the coasts of Scotland. Harbour seal populations in the UK have been monitored through a series of repeated aerial surveys of animals hauled out during the annual moult in early August. This moult count is used as a consistent index of population size. Survey methods and frequencies vary. The Scottish and English east coast populations mainly haul out in tidal estuariesand are surveyed annually, using fixed wing aircraft and digital photography. Populations in north and west Scotland often haul out on rocky shores and are surveyed less frequently, using helicopters fitted with thermal imagers. Overall, the most recent minimum estimate of the UK harbour seal population is 24,250 seals of which 19,800 are in Scotland, 3,200 in England and 1,250 in Northern Ireland. The results show that the number of harbour seals in eastern Englandwas increasing before the 1988 and 2002 phocine distemper (PDV) epizootic but has not increased since the end of the 2002 epizootic. There is also evidence of a general decline in most of the large harbour seal colonies around Scotland. The populations along the north and northwest mainland coast were an exception, with numbers appearing to be stable. Between 2001 and 2008, the population in Orkney declined by 67% and Shetland declined by 40%, indicating harbourseals 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 and waters off western Scotland.

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