An automated work-flow for pinniped surveys: A new tool for monitoring population dynamics

Detecting changes in population trends depends on the accuracy of estimated mean population growth rates and thus the quality of input data. However, monitoring wildlife populations poses economic and logistic challenges especially in complex and remote habitats. Declines in wildlife populations can remain undetected for years unless effective monitoring techniques are developed, guiding appropriate management actions. We developed an automated survey workflow using unmanned aerial vehicles (drones) to quantify the number and size of individual animals, using the well-studied Scandinavian harbour seal (Phoca vitulina) as a model species. We compared ground-based counts using telescopes with manual flights, using a zoom photo/video, and pre-programmed flights producing orthomosaic photo maps. We used machine learning to identify and count both pups and older seals and we present a new method for measuring body size automatically. We evaluate the population’s reproductive success using drone data, historical counts and predictions from a Leslie matrix population model. The most accurate and time-efficient results were achieved by performing pre-programmed flights where individual seals are identified by machine learning and their body sizes are measured automatically. The accuracy of the machine learning detector was 95–97% and the classification error was 4.6 ± 2.9 for pups and 3.1 ± 2.1 for older seals during good light conditions. There was a clear distinction between the body sizes of pups and older seals during breeding time. We estimated 320 pups in the breeding season 2021 with the drone, which is well beyond the expected number, based on historical data on pup production. The new high quality data from the drone survey confirms earlier indications of a deteriorating reproductive rate in this important harbour seal colony. We show that aerial drones and machine learning are powerful tools for monitoring wildlife in inaccessible areas which can be used to assess annual recruitment and seasonal variations in body condition.

Echoes from the past: Regional variations in recovery within a harbour seal population

Terrestrial and marine wildlife populations have been severely reduced by hunting, fishing and habitat destruction, especially in the last centuries. Although management regulations have led to the recovery of some populations, the underlying processes are not always well understood. This study uses a 40-year time series of counts of harbour seals (Phoca vitulina) in the Wadden Sea to study these processes, and demonstrates the influence of historical regional differences in management regimes on the recovery of this population. While the Wadden Sea is considered one ecologically coupled zone, with a distinct harbour seal population, the area is divided into four geo-political regions i.e. the Netherlands, Lower Saxony including Hamburg, Schleswig-Holstein and Denmark. Gradually, seal hunting was banned between 1962 and 1977 in the different regions. Counts of moulting harbour seals and pup counts, obtained during aerial surveys between 1974 and 2014, show a population growth from approximately 4500 to 39,000 individuals. Population growth models were developed to assess if population growth differed between regions, taking into account two Phocine Distemper Virus (PDV) epizootics, in 1988 and 2002 which seriously affected the population. After a slow start prior to the first epizootic, the overall population grew exponentially at rates close to assumed maximum rates of increase in a harbour seal population. Recently, growth slowed down, potentially indicative of approaching carrying capacity. Regional differences in growth rates were demonstrated, with the highest recovery in Netherlands after the first PDV epizootic (i.e. 17.9%), suggesting that growth was fuelled by migration from the other regions, where growth remained at or below the intrinsic growth rate (13%). The seals' distribution changed, and although the proportion of seals counted in the German regions declined, they remained by far the most important pupping region, with approximately 70% of all pups being born there. It is hypothesised that differences in hunting regime, preceding the protection in the 1960's and 1970's, created unbalance in the distribution of breeding females throughout the Wadden Sea, which prevailed for decades. Breeding site fidelity promoted the growth in pup numbers at less affected breeding sites, while recolonisation of new breeding areas would be suppressed by the philopatry displayed by the animals born there. This study shows that for long-lived species, variable management regimes in this case hunting regulations, across a species' range can drive population dynamics for several generations.

Avoidance of wind farms by harbour seals is limited to pile driving activities

As part of global efforts to reduce dependence on carbon‐based energy sources there has been a rapid increase in the installation of renewable energy devices. The installation and operation of these devices can result in conflicts with wildlife. In the marine environment, mammals may avoid wind farms that are under construction or operating. Such avoidance may lead to more time spent travelling or displacement from key habitats. A paucity of data on at‐sea movements of marine mammals around wind farms limits our understanding of the nature of their potential impacts.

Here, we present the results of a telemetry study on harbour seals Phoca vitulina in The Wash, south‐east England, an area where wind farms are being constructed using impact pile driving. We investigated whether seals avoid wind farms during operation, construction in its entirety, or during piling activity. The study was carried out using historical telemetry data collected prior to any wind farm development and telemetry data collected in 2012 during the construction of one wind farm and the operation of another.

Within an operational wind farm, there was a close‐to‐significant increase in seal usage compared to prior to wind farm development. However, the wind farm was at the edge of a large area of increased usage, so the presence of the wind farm was unlikely to be the cause.

There was no significant displacement during construction as a whole. However, during piling, seal usage (abundance) was significantly reduced up to 25 km from the piling activity; within 25 km of the centre of the wind farm, there was a 19 to 83% (95% confidence intervals) decrease in usage compared to during breaks in piling, equating to a mean estimated displacement of 440 individuals. This amounts to significant displacement starting from predicted received levels of between 166 and 178 dB re 1 μPa_(p‐p). Displacement was limited to piling activity; within 2 h of cessation of pile driving, seals were distributed as per the non‐piling scenario.

Synthesis and applications. Our spatial and temporal quantification of avoidance of wind farms by harbour seals is critical to reduce uncertainty and increase robustness in environmental impact assessments of future developments. Specifically, the results will allow policymakers to produce industry guidance on the likelihood of displacement of seals in response to pile driving; the relationship between sound levels and avoidance rates; and the duration of any avoidance, thus allowing far more accurate environmental assessments to be carried out during the consenting process. Further, our results can be used to inform mitigation strategies in terms of both the sound levels likely to cause displacement and what temporal patterns of piling would minimize the magnitude of the energetic impacts of displacement.

Our spatial and temporal quantification of avoidance of wind farms by harbour seals is critical to reduce uncertainty and increase robustness in environmental impact assessments of future developments. Specifically, the results will allow policymakers to produce industry guidance on the likelihood of displacement of seals in response to pile driving; the relationship between sound levels and avoidance rates; and the duration of any avoidance, thus allowing far more accurate environmental assessments to be carried out during the consenting process. Further, our results can be used to inform mitigation strategies in terms of both the sound levels likely to cause displacement and what temporal patterns of piling would minimize the magnitude of the energetic impacts of displacement.

Phocine distemper virus: current knowledge and future directions

Phocine distemper virus (PDV) was first recognized in 1988 following a massive epidemic in harbor and grey seals in north-western Europe. Since then, the epidemiology of infection in North Atlantic and Arctic pinnipeds has been investigated. In the western North Atlantic endemic infection in harp and grey seals predates the European epidemic, with relatively small, localized mortality events occurring primarily in harbor seals. By contrast, PDV seems not to have become established in European harbor seals following the 1988 epidemic and a second event of similar magnitude and extent occurred in 2002. PDV is a distinct species within the Morbillivirus genus with minor sequence variation between outbreaks over time. There is now mounting evidence of PDV-like viruses in the North Pacific/Western Arctic with serological and molecular evidence of infection in pinnipeds and sea otters. However, despite the absence of associated mortality in the region, there is concern that the virus may infect the large Pacific harbor seal and northern elephant seal populations or the endangered Hawaiian monk seals. Here, we review the current state of knowledge on PDV with particular focus on developments in diagnostics, pathogenesis, immune response, vaccine development, phylogenetics and modeling over the past 20 years.

Modelling beyond data is uninformative: a comment on "State-space modelling reveals proximate causes of harbour seal population declines" by Matthiopoulos et al

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.

Length of intervals between epidemics: evaluating the influence of maternal transfer of immunity

The length of intervals between epidemic outbreaks of infectious diseases is critical in epidemiology. In several species of marine mammals and birds, it is pivotal to also consider the life history of the species of concern, as the contact rate between individuals can have a seasonal flux, for example, due to aggregations during the breeding season. Recently, particular interest has been given to the role of the dynamics of immunity in determining the intervals between epidemics in wild animal populations. One potentially powerful, but often neglected, process in this context is the maternal transfer of immunity. Here, we explore theoretically how the transfer of maternal antibodies can delay the recurrence of epidemics using Phocine Distemper in harbor seals as an example of a system in which epidemic outbreaks are followed by pathogen extinction. We show that the presence of temporarily protected newborns can significantly increase the predicted interval between epidemics, and this effect is strongly dependent on the degree of synchrony in the breeding season. Furthermore, we found that stochasticity in the onset of epidemics in combination with maternally acquired immunity increases the predicted intervals between epidemics even more. These effects arise because newborns with maternal antibodies temporarily boost population level immunity above the threshold of herd immunity, particularly when breeding is synchronous. Overall, our results show that maternal antibodies can have a profound influence on the dynamics of wildlife epidemics, notably in gregarious species such as many marine mammals and seabirds.

The world's northernmost harbour seal population-how many are there?

This study presents the first abundance estimate for the world's northernmost harbour seal (Phoca vitulina) population, which resides in Svalbard, Norway, based on three digital stereoscopic photographic surveys conducted in 2009 and 2010. The counts from these high resolution 3D images were combined with a novel method for estimating correction factors for animals that were in the water at the time of the surveys, in which extensive behavioural data from radio-tagged harbour seals were used together with age distribution data to estimate the proportion of seals of various age and sex classes hauled out at the times of the surveys. To detect possible seasonal shifts in age distribution between surveys, lengths of hauled out seals were measured from the stereoscopic images. No body-length differences were detected between the surveys; but, this may be due to a high degree of sexual dimorphism exhibited in this population. Applying the modelled correction factors, a total of 1888 (95% CI: 1660-3023), 1742 (1381-3549) and 1812 (1656-4418) harbour seals were estimated for the surveys flown on 01 August 2009, 01 August 2010 and 19 August 2010, respectively. The similarity between the three survey estimates (despite significant differences in the number of animals actually counted on the photos from each survey effort) suggests that the variation in numbers of hauled out seals is reasonably accurately adjusted for by the haul-out probability model. The low population size, the limited spatial distribution of the population and its reduced genetic diversity make this population vulnerable to chance events, such as disease epidemics.

Linking climate trends to population dynamics in the Baltic ringed seal: impacts of historical and future winter temperatures

A global trend of a warming climate may seriously affect species dependent on sea ice. We investigated the impact of climate on the Baltic ringed seals (Phoca hispida botnica), using historical and future climatological time series. Availability of suitable breeding ice is known to affect pup survival. We used detailed information on how winter temperatures affect the extent of breeding ice and a climatological model (RCA3) to project the expected effects on the Baltic ringed seal population. The population comprises of three sub-populations, and our simulations suggest that all of them will experience severely hampered growth rates during the coming 90 years. The projected 30, 730 seals at the end of the twenty-first century constitutes only 16 % of the historical population size, and thus reduced ice cover alone will severely limit their growth rate. This adds burden to a species already haunted by other anthropogenic impacts.

Detecting density dependence in recovering seal populations

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.

Shifting trends: detecting environmentally mediated regulation in long-lived marine vertebrates using time-series data

Assessing the status and trends in animal populations is essential for effective species conservation and management practices. However, unless time-series abundance data demonstrate rapid and reliable fluctuations, objective appraisal of directionality of trends is problematic. We adopted a multiple-working hypotheses approach based on information-theoretic and Bayesian multi-model inference to examine the population trends and form of intrinsic regulation demonstrated by a long-lived species, the southern elephant seal. We also determined the evidence for density dependence in 11 other well-studied marine mammal species. (1) We tested the type of population regulation for elephant seals from Marion Island (1986-2004) and from 11 other marine mammal species, and (2) we described the trends and behavior of the 19-year population time series at Marion Island to identify changes in population trends. We contrasted five plausible trend models using information-theoretic and Bayesian-inference estimates of model parsimony. Our analyses identified two distinct phases of population growth for this population with the inflexion occurring in 1998. Thus, the population decreased between 1986 and 1997 (-3.7% per annum) and increased between 1997 and 2004 (1.9% per annum). An index of environmental stochasticity, the Southern Oscillation Index, explained some of the variance in r and N. We determined analytically that there was good evidence for density dependence in the Marion Island population and that density dependence was widespread among marine mammal species (67% of species showed evidence for population regulation). This approach demonstrates the potential functionality of a relatively simple technique that can be applied to short time series to identify the type of regulation, and the uncertainty associated with the phenomenon, operating in populations of large mammals.

Age- and sex-specific mortality patterns in an emerging wildlife epidemic: the phocine distemper in European harbour seals

Analyses of the dynamics of diseases in wild populations typically assume all individuals to be identical. However, profound effects on the long-term impact on the host population can be expected if the disease has age and sex dependent dynamics. The Phocine Distemper Virus (PDV) caused two mass mortalities in European harbour seals in 1988 and in 2002. We show the mortality patterns were highly age specific on both occasions, where young of the year and adult (>4 yrs) animals suffered extremely high mortality, and sub-adult seals (1-3 yrs) of both sexes experienced low mortality. Consequently, genetic differences cannot have played a main role explaining why some seals survived and some did not in the study region, since parents had higher mortality levels than their progeny. Furthermore, there was a conspicuous absence of animals older than 14 years among the victims in 2002, which strongly indicates that the survivors from the previous disease outbreak in 1988 had acquired and maintained immunity to PDV. These specific mortality patterns imply that contact rates and susceptibility to the disease are strongly age and sex dependent variables, underlining the need for structured epidemic models for wildlife diseases. Detailed data can thus provide crucial information about a number of vital parameters such as functional herd immunity. One of many future challenges in understanding the epidemiology of the PDV and other wildlife diseases is to reveal how immune system responses differ among animals in different stages during their life cycle. The influence of such underlying mechanisms may also explain the limited evidence for abrupt disease thresholds in wild populations.

Climate and demography of the planktivorous Cassin's auklet Ptychoramphus aleuticus off northern California: implications for population change

1. We performed demographic analyses on Cassin's auklet Ptychoramphus aleuticus, a zooplanktivorous seabird inhabiting the variable California Current System, to understand how temporal environmental variability influences population dynamics. 2. We used capture-recapture data from 1986 to 2002 to rank models of interannual variation in survival, breeding propensity, breeding success, and recruitment. 3. All demographic parameters exhibited temporal variability. Interannual variation in survival was best modelled as a nonlinear function of the winter Southern Oscillation Index (SOI). Breeding propensity was best modelled as a threshold function of local sea surface temperature. Breeding success and recruitment were best modelled with year-dependent annual variation. 4. Changes in the SOI force El Niño/La Niña events, which in turn alter prey availability to seabirds in this system. Demographic responses varied during El Niños/La Niñas. Survival diminished substantially during the 1997-98 El Niño event, while breeding propensity was affected during both the 1992 and 1998 El Niños. Breeding success was reduced during the 1992, 1993, and 1998 El Niños, but was unusually high in 2002. Recruitment was higher at the beginning and end of this time-series. 5. While demographic responses varied interannually, parameter values covaried in a positive fashion, a situation conducive to rapid population change. During the 11 years study period, the Farallon auklet breeding population declined at 6.05 +/- 0.80% (SE) per year, a cumulative decline of 49.7%. This study demonstrates how climate variability has influenced key demographic processes for this diminished marine bird population.

Acquired Immunity and Stochasticity in Epidemic Intervals Impede the Evolution of Host Disease Resistance

Disease can generate intense selection pressure on host populations, but here we show that acquired immunity in a population subject to repeated disease outbreaks can impede the evolution of genetic disease resistance by maintaining susceptible genotypes in the population. Interference between the life-history schedule of a species and periodicity of the disease has unintuitive effects on selection intensity, and stochasticity in outbreak period further reduces the rate of spread of disease-resistance alleles. A general age-structured population genetic model was developed and parameterized using empirical data for phocine distemper virus (PDV) epizootics in harbor seals. Scenarios with acquired immunity had lower levels of epizootic mortality compared with scenarios without acquired immunity for the first PDV outbreaks, but this pattern was reversed after about five disease cycles. Without acquired immunity, evolution of disease resistance was more rapid, and long-term population size variation is efficiently dampened. Acquired immunity has the potential to significantly influence rapid evolutionary dynamics of a host population in response to age-structured disease selection and to alter predicted selection intensities compared with epidemiological models that do not consider such feedback. This may have important implications for evolutionary population dynamics in a range of human, agricultural, and wildlife disease settings.