Halichoerus Research Articles

Assessing the utility and limitations of accelerometers and machine learning approaches in classifying behaviour during lactation in a phocid seal

BackgroundClassifying behaviour with animal-borne accelerometers is quickly becoming a popular tool for remotely observing behavioural states in a variety of species. Most accelerometry work in pinnipeds has focused on classifying behaviour at sea often quantifying behavioural trade-offs associated with foraging and diving in income breeders. Very little work to date has been done to resolve behaviour during the critical period of lactation in a capital breeder. Capital breeding phocids possess finite reserves that they must allocate appropriately to maintain themselves and their new offspring during their brief nursing period. Within this short time, fine-scale behavioural trade-offs can have significant fitness consequences for mother and offspring and must be carefully managed. Here, we present a case study in extracting and classifying lactation behaviours in a wild, breeding pinniped, the grey seal (Halichoerus grypus).ResultsUsing random forest models, we were able to resolve 4 behavioural states that constitute the majority of a female grey seals’ activity budget during lactation. Resting, alert, nursing, and a form of pup interaction were extracted and classified reliably. For the first time, we quantified the potential confounding variance associated with individual differences in a wild context as well as differences due to sampling location in a largely inactive model species.ConclusionsAt this stage, the majority of a female grey seal’s activity budget was classified well using accelerometers, but some rare and context-dependent behaviours were not well captured. While we did find significant variation between individuals in behavioural mechanics, individuals did not differ significantly within themselves; inter-individual variability should be an important consideration in future efforts. These methods can be extended to other efforts to study grey seals and other pinnipeds who exhibit a capital breeding system. Using accelerometers to classify behaviour during lactation allows for fine-scale assessments of time and energy trade-offs for species with fixed stores.

Lumbering on land costs elephant seals dear

In the transition from a terrestrial lifestyle to an existence beneath the waves, elephant seals (Mirounga angustirostris) are pretty far along. With a streamlined body, blubber for insulation and the ability to carry extensive oxygen supplies for lengthy dives, elephant seals are as well equipped as many whales and dolphins. However, when the colossal mammals haul themselves onto gently shelving beaches to mate and give birth, the tables turn against them. ‘There is an energetic consequence to becoming aquatic; it becomes easier to swim but harder to walk’, says Frank Fish from West Chester University, USA; the question was, how hard? Having previously filmed and analysed the movements of relatively diminutive harbour and grey seals, which are about one-tenth the size of elephant seals, Fish and graduate student Kelsey Tennett teamed up with Dan Costa from the University of California, Santa Cruz, USA, to get up close and personal with the gigantic mammals in California's Año Nuevo State Park.‘It was in January, the time when males are trying to mate with females and the females are pupping’, says Fish, recalling how the massive seals weren't too bothered by the scientists and their cameras; they had other things on their minds. Setting up a camera about 6–12 m from a seal that was taking a brief rest after dragging itself across the sand, the team waited until the animal showed signs of moving again before filming. ‘We could tell when the animal was about to move because it would start to rise up with its head and chest’, says Fish. Having filmed the seals humping along before collapsing on the sand, Fish then dashed into shot behind the animal with a 0.5 m long stick, so that Tennett could calculate the size of the animal and measure its movements back in the lab.Analysing the seals’ cumbersome manoeuvres, Fish realised that each elephant seal initially reared its head and chest up before allowing its torso to slump forward to initiate a charge. As its chest crashed down, the animal then flexed its body like an inchworm to shift its hindflippers forward, allowing it to push down on the sand with its pelvis as the wave of movement travelled forward along its body. This then allowed it to thrust its chest, head and neck back off the sand, using its foreflippers like crutches, ready to lurch forward once again and initiate the next cycle. Sometimes the animals could only manage a few ‘strides’ covering 5–10 m before grinding to a halt, while some males maintained speeds of up to 2.5 m s−1 over 30–40 m in pursuit of a female or rival.But what did all of this mean for the giant animals’ efficiency as they thundered across the sand – were they more or less efficient than smaller seals? Fish and Tennett teamed up with physicist Anthony Nicastro, also from West Chester University, to answer the question. They calculated that the elephant seals were using approximately 40 times more energy at any instant to shuffle along at speeds of about 2 m s−1 (which equates to 0.6 times their body length), than smaller grey seals scuffling about at a similar speed – relative to their body size – of 1.3 m s−1.‘Bigger is not always better, particularly when you are highly adapted for swimming rather than terrestrial locomotion’, says Fish, adding that elephant seals are paying an energetic penalty for their aquatic lifestyle. And, having scrutinised the largest seals in the northern hemisphere, Fish is keen to visit their even more gigantic relatives in the south. ‘I want to see if they [southern elephant seals] have reached a limit in how big a seal can be’, he says.

NEW APPROACH TO STRESS RESEARCH IN PHOCIDS-POTENTIAL OF DEHYDROEPIANDROSTERONE AND CORTISOL/DEHYDROEPIANDROSTERONE RATIO AS MARKERS FOR STRESS IN HARBOR SEALS ( PHOCA VITULINA) AND GRAY SEALS ( HALICHOERUS GRYPUS).

Cortisol is known to reflect the level of the stress response. However, measuring the cortisol concentration only once fails to provide sufficient information about the duration of the stress exposure. Moreover, handling is an acute stressor and increases cortisol secretion especially in wildlife species. Yet, in phocids reliable indicators are missing that reflect potential chronic effects of stress. The adrenal-derived steroid hormone dehydroepiandrosterone (DHEA) has been described as biomarker for the assessment of the stress status but has not been applied to marine mammal stress research. Therefore, DHEA, the sulfated precursor DHEAS and the cortisol/DHEA ratio were determined in serum of different seals. One group consisted of harbor ( Phoca vitulina) and gray seals ( Halichoerus grypus) that were habituated to human handling. The other two groups included healthy and free-ranging seals suffering from a disease. Blood samples were taken from 11 habituated (six males, five females), 17 wild_healthy (13 males, four females), and nine wild_diseased seals (four males, five females). No differences in serum cortisol levels could be detected between wild_healthy and wild_diseased seals. On the contrary, wild_diseased seals showed the lowest DHEA concentration compared to the other two groups. Wild_diseased seals also revealed the highest cortisol/DHEA ratio compared to the habituated_zoo (2,074.7 ± 351.4 vs. 121.5 ± 26.8, P < 0.001) and wild_healthy seals (827.9 ± 214.3, P < 0.01). DHEA and the cortisol/DHEA ratio may reflect differences in the functionality of the hypothalamic-pituitary-adrenal axis and therefore represent valuable tools for the assessment of stress-related effects in seals.

Maternal transfer of phenol derivatives in the Baltic grey seal Halichoerus grypus grypus

Studies of circulating levels in difference sex and age classes, and maternal transfer of bisphenol A, 4-tert-octylphenol and 4- nonylphenol in the Baltic grey seal were performed from 2014-2017. Blood was collected from long-term captive adult males, pregnant females and pups. Milk was collected from nursing females. The aim of this study was not only to determine the concentrations of phenol derivatives, i.e. bisphenol A (BPA), 4-tert-octylphenol (OP) and 4-nonylphenol (NP), but also to try to evaluate the transfer of these compounds to the next generation in the final stage of foetal life and in the first few weeks of life in juvenile marine mammals. The measurements were carried out using high performance liquid chromatography. The obtained data show that all phenol derivatives are present in the blood of males, females and pups (range <0.07–101 ng·cm−3) and in female milk (range <0.1–406.3 ng·cm−3). The main source of phenol derivatives in organisms is food exposure. Gender, age, or number of births were not observed to have a significant effect on changes in phenol derivative levels in seal blood within the breeding group. In the prenatal stage of life, a small amount of BPA and alkylphenols was passed on to the offspring through the placenta. In the blood of the offspring the concentration of these compounds exceeded the concentration in the mother's blood 1.5-fold. During nursing, females detoxified their systems. Level of phenol derivatives in the pups blood increased linearly with its increasing concentrations in the mother's milk. On the other hand, the seafood diet which started after the physiological fasting stage of the pup, stabilised the levels of phenol derivatives below 10 ng ∙ cm−3.

Loop-mediated isothermal amplification (LAMP) as a confirmatory and rapid DNA detection method for grey seal (Halichoerus grypus) predation on harbour porpoises (Phocoena phocoena)

An increasing number of harbour porpoises along the coastlines of northern Europe are victims of attacks by preying grey seals. To confirm grey seal attacks at a molecular level, a fast loop-mediated isothermal amplification (LAMP) method was developed, based on the amplification of the cytochrome b target gene. With this method, saliva residues within bite marks, presumably originating from grey seal attacks, can be detected on-site, using a swab-based method in combination with a portable real-time fluorometer (Genie® II). The developed LAMP assay included an internal amplification control and was validated for the sensitivity, specificity, limit of detection and a spiking experiment was performed with saliva samples from two grey seals. Finally, three stranded harbour porpoises, with injury patterns presumably originating from grey seal attacks, were analysed. Grey seal DNA was successfully determined in a bite mark of one harbour porpoise with the LAMP method. For direct on-site molecular biological investigations without the opportunity to perform more time-consuming and equipment intensive PCR investigations, the developed rapid LAMP assay offers the possibility to confirm that injuries, probably caused by a grey seal, indeed resulted from a grey seal attack.

Fine-scale hydrodynamic metrics underlying predator occupancy patterns in tidal stream environments

Whilst the development of the tidal stream industry will help meet marine renewable energy (MRE) targets, the potential impacts on mobile marine predators using these highly dynamic environments need consideration. Environmental impact assessments (EIAs) required for potential MRE sites generally involve site-specific animal density estimates obtained from lengthy and costly surveys. Recent studies indicate that whilst large-scale tidal forcing is predictable, local hydrodynamics are variable and often result in spatio-temporal patchiness of marine predators. Therefore, understanding how fine-scale hydrodynamics influence animal distribution patterns could inform the placing of devices to reduce collision and displacement risks. Quantifying distributions requires animal at-sea locations and the concurrent collection of high-resolution hydrodynamic measurements. As the latter are routinely collected during tidal resource characterization at potential MRE sites, there is an untapped opportunity to efficiently collect information on the former to improve EIAs. Here we describe a survey approach that uses vessel-mounted ADCP (Acoustic Doppler current profiler) transects in combination with marine mammal surveys to collect high-resolution and concurrent hydrodynamic data in relation to pinniped (harbour seals Phoca vitulina, grey seals Halichoerus grypus) at-sea occupancy patterns within an energetic tidal channel (peak current magnitudes >4.5 ms−1). We identified novel ADCP-derived fine-scale hydrodynamic metrics that could have ecological relevance for seals using these habitats. We show that our local acoustic backscattering strength metric (an indicator for macro-turbulence) had the highest influence on seal encounters. During peak flows, pinnipeds avoided the mid-channel characterized by extreme backscatter. At-sea occupancy further corresponded with the increased shear and eddies that are strong relative to the mean flows found at the edges of the channel. Our approach, providing oceanographic context to animal habitat use through combined survey methodologies, enhances environmental management of potential MRE sites. The cost-effective collection of such data and the application of our metrics could streamline the EIA process in the early stages of the consenting process.

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds.

Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.

Repeatability and reproductive consequences of boldness in female gray seals

Wild animals show consistent individual variation in behavior across time and/or contexts, now referred to as animal personality. While this variability may have important ecological and evolutionary implications, how and why variation in animal personality is maintained in a natural population remains unclear. In this study, we assessed the influence of environmental and biological sources of variation on behavioral responses measured along the shy-bold continuum in a long-lived, iteroparous marine mammal, the gray seal (Halichoerus grypus). Between 2008 and 2016, 469 females from the Sable Island, Nova Scotia breeding colony of gray seals were given a boldness score in response to a human approach, designed to stimulate maternal defense of offspring. Using generalized linear mixed-effects models (GLMM) in a Bayesian framework, we show that boldness is highly repeatable between and within years. There were age differences in boldness, with younger females being less bold than older, more experienced females providing some support for the life history trade-off hypothesis. We further used GLMMs to assess sources of variation on offspring weaning mass. We found that young females that were bolder produced heavier pups than shyer counterparts, and that pups produced by bolder females were on average ~ 2 kg heavier than pups of shy females. These results provide further evidence that personality influences life history strategies, and illustrates the evolutionary potential of animal personality in response to selection. Consistent individual differences in behavior influence various aspects of ecology including species interactions, species distributions, and life history strategies. However, how and why this individual variation is maintained in a natural population remains uncertain. In this study, we assessed the influence of boldness, specifically maternal defense of offspring, on a component of reproductive success in a long-lived marine mammal. We showed highly repeatable behavioral differences, and found that boldness varied with age, with younger individuals being less bold than older individuals. Younger individuals that were bolder produced heavier offspring than shyer counterparts. Our study contributes to an under-represented group of animals, wild marine mammals, in the personality literature, and further prompts the investigation into the proximate and ultimate factors influencing personality in an ecologically important marine predator.

Исследование обоняния серых и гренландских тюленей с помощью метода оперантного обучения

Исследование обоняния серых и гренландских тюленей с помощью метода оперантного обучения

Detecting spiny dogfish in grey seal diets

Grey seal (Halichoerus grypus) populations declined dramatically in U.S. waters during the nineteenth and twentieth centuries, but have rebounded in recent decades as a result of legal protection. In the Gulf of Maine, increasing grey seal populations have the potential to impact commercially important groundfish species such as cod and haddock, but the potential also exists for more complex ecological interactions to occur given the recent increase of spiny dogfish (Squalus acanthias), another potential groundfish predator. Specifically, seal predation on dogfish could free groundfish species from additional predation pressure. Little quantitative data exists on intraguild predation rates by grey seals on spiny dogfish, in part because of the limitations of current methods of food habits analysis for grey seals. We report the development, validation, and field testing of a non-invasive genetic method for the detection of spiny dogfish in grey seal diets using DNA collected from seal feces. Our method amplified spiny dogfish DNA from 10 of 10 positive control scats from a captive seal with a known diet, and amplified spiny dogfish DNA from 0 of 10 negative control scats. We field tested the method on 20 scats from wild seals and detected spiny dogfish in two of the samples. All positive amplifications were sequenced to verify the species identify, and all were spiny dogfish. Our method has the potential to provide valuable information about changing predator prey dynamics in the Gulf of Maine and elsewhere.

BRUCELLA PINNIPEDIALIS IN GREY SEALS ( HALICHOERUS GRYPUS) AND HARBOR SEALS ( PHOCA VITULINA) IN THE NETHERLANDS.

Brucellosis is a zoonotic disease with terrestrial or marine wildlife animals as potential reservoirs for the disease in livestock and human populations. The primary aim of this study was to assess the presence of Brucella pinnipedialis in marine mammals living along the Dutch coast and to observe a possible correlation between the presence of B. pinnipedialis and accompanying pathology found in infected animals. The overall prevalence of Brucella spp. antibodies in sera from healthy wild grey seals ( Halichoerus grypus; n=11) and harbor seals ( Phoca vitulina; n=40), collected between 2007 and 2013 ranged from 25% to 43%. Additionally, tissue samples of harbor seals collected along the Dutch shores between 2009 and 2012, were tested for the presence of Brucella spp. In total, 77% (30/39) seals were found to be positive for Brucella by IS 711 real-time PCR in one or more tissue samples, including pulmonary nematodes. Viable Brucella was cultured from 40% (12/30) real-time PCR-positive seals, and was isolated from liver, lung, pulmonary lymph node, pulmonary nematode, or spleen, but not from any PCR-negative seals. Tissue samples from lung and pulmonary lymph nodes were the main source of viable Brucella bacteria. All isolates were typed as B. pinnipedialis by multiple-locus variable number of tandem repeats analysis-16 clustering and matrix-assisted laser desorption ionization-time of flight mass spectrometry, and of sequence type ST25 by multilocus sequence typing analysis. No correlation was observed between Brucella infection and pathology. This report displays the isolation and identification of B. pinnipedialis in marine mammals in the Dutch part of the Atlantic Ocean.

Accumulation of PBDEs in stranded harp (Pagophilus groenlandicus) and hooded seals (Cystophora cristata) from the Northeastern United States

Polybrominated diphenyl ethers (PBDEs) are highly lipophilic components of brominated flame retardants that are environmentally persistent and bioaccumulate. PBDEs are taken up from the gastrointestinal tract and accumulate mainly in fat depots and liver tissues. Seal species inhabiting Arctic and sub-Arctic regions can have upwards of 30% of their body mass composed of blubber. When those blubber stores are mobilized for energy, stored toxicants are also released into circulation. Most studies reporting accumulation of PBDEs in seals have focused on harbor and grey seals with few examining harp and hooded seals. In this study, PBDEs concentrations were analyzed in seal blubber from 21 stranded harp and 9 stranded hooded seals sampled along the northeast coast of the U.S. (1999–2010). A PBDE congener profile was determined for each individual. The results show that both species of seals are accumulating PBDEs with BDE-47 being the dominant congener. Mean ƩPBDE concentrations in harp seals were 70.55 ± 33.59 ng/g ww and for hooded seals 94.28 ± 42.65 ng/g ww. The results of this study are consistent with previous studies reporting a decrease in bioaccumulation with an increase in bromination. For both species, BDE-47 represented the highest percentage of the ƩPBDEs, composing over 50% of the ƩPBDEs in harp seals. When compared to stranding condition code, animals found alive had overall higher PBDE concentrations than those found in a state of moderate decomposition. This difference could be due to decreased blubber levels in the decomposed animals or potential degradation of the compounds in the blubber. Almost all seals used in this study were yearlings which is the most likely age class to strand. Yearling seals are at a crucial stage of development, especially of their immune system, which can be impacted by high levels of contaminants like PBDEs and increase the susceptibility to disease.

A novel quantitative real-time PCR diagnostic assay for seal heartworm (Acanthocheilonema spirocauda) provides evidence for possible infection in the grey seal (Halichoerus grypus).

The distinct evolutionary pressures faced by Pinnipeds have likely resulted in strong coevolutionary ties to their parasites (Leidenberger et al., 2007). This study focuses on the phocid seal filarial heartworm species Acanthocheilonema spirocauda. A. spirocauda is known to infect a variety of phocid seals, but does not appear to be restricted to a single host species (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). However, to date, seal heartworm has never been reported in grey seals (Halichoerus grypus) (Measures et al., 1997; Leidenberger et al., 2007; Lehnert et al., 2015). The proposed vector for seal heartworm is Echinophthirius horridus, the seal louse. Seal lice are known to parasitize a wide array of phocid seal species, including the grey seal. With the advent of climate change, disease burden is expected to increase across terrestrial and marine mammals (Harvell et al., 2002). Accordingly, increased prevalence of seal heartworm has recently been reported in harbor seals (Phoca vitulina) (Lehnert et al., 2015). Thus, the need for improved, rapid, and cost-effective diagnostics is urgent. Here we present the first A. spirocauda-specific rapid diagnostic test (a quantitative real-time PCR assay), based on a highly repetitive genomic DNA repeat identified using whole genome sequencing and subsequent bioinformatic analysis. The presence of an insect vector provides the opportunity to develop a multifunctional diagnostic tool that can be used not only to detect the parasite directly from blood or tissue specimens, but also as a molecular xenomonitoring (XM) tool that can be used to assess the epidemiological profile of the parasite by screening the arthropod vector. Using this assay, we provide evidence for the first reported case of seal heartworm in a grey seal.

Comparative Anatomy of the Larynx in Pinnipeds (Seal, Sea lion, Walrus)

Pinnipeds (e.g., seal, sea lion, walrus) are marine mammals that spend time both in and out of the water. All are able to vocalize in air using the pneumatically driven vocal fold vibrations, a mechanism common to terrestrial mammals. This is no surprise, as their ancestors were once terrestrial mammals. Pinnipeds, however, are also able to vocalize underwater. It is not known how they generate or transmit these sounds. This study explores pinniped laryngeal anatomy in: harbor seal (Phoca vitulina), gray seal (Halichoerus grypus), elephant seal (Mirounga angustirostris), California sea lion (Zalophus californianus), and walrus (Odobenus rosmarus). Comparisons were made with the laryngeal anatomy of several closely related terrestrial species including: dog (Canis familiaris) and black bear (Ursus americanus), and several semiaquatic species including: polar bear (Ursus maritimus), sea otter (Enhydra lutris), river otter (Lontra canadensis), beaver (Castor canadensis), muskrat (Ondatra zibethicus), and hippo (Hippopotamus amphibius). Comparisons were also made to fully aquatic mammals that can vocalize underwater including: manatee (Trichechus manatus), baleen whales (Caperea marginata, Balaena glacialis, Megaptera novaeangliae, Balaenoptera musculus, B. physalus, B. borealis, B. acutorostrata), and over 20 species of toothed whales (including sperm whales, beaked whales, dolphins, and porpoises). Results indicate that the harbor and gray seals have an unremarkable larynx that appears grossly similar to that of most other mammals. Elephant seal, sea lion, and walrus larynges, however, were unusual in having arytenoid cartilages that are extremely large and rounded on their rostral surface. The arytenoids form a valve across approximately half of the laryngeal lumen. Interestingly, this feature also occurs in sea otters. The corniculate and cuneiform cartilages are difficult to detect in the elephant seal, sea lion, and walrus. The epiglottic cartilage is very short in the sea lion and walrus, similar to the manatee, but robust in the elephant seal. The vestibular fold of the elephant seal is very prominent, and appears connected to the arytenoid cartilage. Harbor seal, gray seal, and walrus vocal folds are oriented perpendicular to airflow, as in other terrestrial mammals. Elephant seal and sea lion vocal folds are rotated, compared with other terrestrial mammals, with the ventral attachment located more rostrally. Their vocal folds are thus positioned near the ventral aspect of the larynx. This orientation is similar to those of the hippo, baleen whales, and toothed whales. None of the pinnipeds have vocal folds resembling the smooth sloped vocal folds of the manatee, or the thickened vocal folds of the polar bear. The unusual arytenoid size and vocal fold orientation in some pinnipeds may indicate evolutionary convergence with other underwater laryngeal vocalizers (e.g., hippo, baleen whales). It is unclear whether laryngeal morphologies of elephant seal, sea lion, and walrus are functional adaptations representing autapomorphies (uniquely derived features) of these species. Further work should be directed towards understanding whether laryngeal specializations may relate to variations in underwater sounds or in‐air vocalizations. More pinniped species need to be studied, particularly deep diving seals that are very vocal (e.g., Weddell seal) or fur seals (having external morphology and behaviors very similar to sea lions).This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

MomentuHMM: R package for generalized hidden Markov models of animal movement

Abstract Discrete‐time hidden Markov models (HMMs) have become an immensely popular tool for inferring latent animal behaviours from telemetry data. While movement HMMs typically rely solely on location data (e.g. step length and turning angle), auxiliary biotelemetry and environmental data are powerful and readily‐available resources for incorporating much more ecological and behavioural realism. However, complex movement or observation process models often necessitate custom and computationally demanding HMM model‐fitting techniques that are impractical for most practitioners, and there is a paucity of generalized user‐friendly software available for implementing multivariate HMMs of animal movement. Here, we introduce an open‐source R package, momentuHMM, that addresses many of the deficiencies in existing HMM software. Features include: (1) data pre‐processing and visualization; (2) user‐specified probability distributions for an unlimited number of data streams and latent behaviour states; (3) biased and correlated random walk movement models, including dynamic “activity centres” associated with attractive or repulsive forces; (4) user‐specified design matrices and constraints for covariate modelling of parameters using formulas familiar to most R users; (5) multiple imputation methods that account for measurement error and temporally irregular or missing data; (6) seamless integration of spatio‐temporal covariate raster data; (7) cosinor and spline models for cyclical and other complicated patterns; (8) model checking and selection; and (9) simulation. After providing an overview of the main features of the package, we demonstrate some of the capabilities of momentuHMM using real‐world examples. These include models for cyclical movement patterns of African elephants, foraging trips of northern fur seals, loggerhead turtle movements relative to ocean surface currents, and grey seal movements among three activity centres. momentuHMM considerably extends the capabilities of existing HMM software while accounting for common challenges associated with telemetry data. It therefore facilitates more realistic hypothesis‐driven animal movement analyses that have hitherto been largely inaccessible to non‐statisticians. While motivated by telemetry data, the package can be used for analysing any type of data that is amenable to HMMs. Practitioners interested in additional features are encouraged to contact the authors.

Assessing the disturbance potential of small unoccupied aircraft systems (UAS) on gray seals (Halichoerus grypus) at breeding colonies in Nova Scotia, Canada.

The use of small unoccupied aircraft systems (UAS) for ecological studies and wildlife population assessments is increasing. These methods can provide significant benefits in terms of costs and reductions in human risk, but little is known if UAS-based approaches cause disturbance of animals during operations. To address this knowledge gap, we conducted a series of UAS flights at gray seal breeding colonies on Hay and Saddle Islands in Nova Scotia, Canada. Using a small fixed-wing UAS, we assessed both immediate and short-term effects of surveys using sequential image analysis and between-flight seal counts in ten, 50 m2 random quadrats at each colony. Counts of adult gray seals and young-of-the-year animals between first and second flights revealed no changes in abundance in quadrats (matched pair t-test p > 0.69) and slopes approaching 1 for linear regression comparisons (r2 > 0.80). Sequential image analysis revealed no changes in orientation or posture of imaged animals. We also assessed the acoustic properties of the small UAS in relation to low ambient noise conditions using sound equivalent level (Leq) measurements with a calibrated U-MIK 1 and a 1/3 octave band soundscape approach. The results of Leq measurements indicate that small fixed-wing UAS are quiet, with most energy above 160 Hz, and that levels across 1/3 octave bands do not greatly exceed ambient acoustic measurements in a quiet field during operations at standard survey altitudes. As such, this platform is unlikely to acoustically disturb gray seals at breeding colonies during population surveys. The results of the present study indicate that the effects of small fixed-wing UAS on gray seals at breeding colonies are negligible, and that fixed-wing UAS-based approaches should be considered amongst best practices for assessing gray seal colonies.

Seal carrion is a predictable resource for coastal ecosystems

The timing, magnitude, and spatial distribution of resource inputs can have large effects on dependent organisms. Few studies have examined the predictability of such resources and no standard ecological measure of predictability exists. We examined the potential predictability of carrion resources provided by one of the UK's largest grey seal (Halichoerus grypus) colonies, on the Isle of May, Scotland. We used aerial (11 years) and ground surveys (3 years) to quantify the variability in time, space, quantity (kg), and quality (MJ) of seal carrion during the seal pupping season. We then compared the potential predictability of seal carrion to other periodic changes in food availability in nature. An average of 6893 kg of carrion ∙yr−1 corresponding to 110.5 × 103 MJ yr−1 was released for potential scavengers as placentae and dead animals. A fifth of the total biomass from dead seals was consumed by the end of the pupping season, mostly by avian scavengers. The spatial distribution of carcasses was similar across years, and 28% of the area containing >10 carcasses ha−1 was shared among all years. Relative standard errors (RSE) in space, time, quantity, and quality of carrion were all below 34%. This is similar to other allochthonous-dependent ecosystems, such as those affected by migratory salmon, and indicates high predictability of seal carrion as a resource. Our study illustrates how to quantify predictability in carrion, which is of general relevance to ecosystems that are dependent on this resource. We also highlight the importance of carrion to marine coastal ecosystems, where it sustains avian scavengers thus affecting ecosystem structure and function.

Bio accumulation of radioactive caesium in marine mammals in the Baltic Sea – Reconstruction of a historical time series

Radionuclides from the Chernobyl accident in 1986 still circulate in the Baltic marine ecosystem and activity levels in water, sediments and fish species such as herring and perch are monitored annually. However, the activity levels of radionuclides in marine mammals have only been sporadically reported. Tissue samples from a museum collection were analysed in two species of seals, and the trends over time in activity level of radioactive caesium (Cs-137) after the Chernobyl accident were reconstructed. We also performed a literature review summarizing activity levels in marine mammals world-wide. We found activity concentrations of Cs-137 in Baltic ringed seals and grey seals to be elevated also in the most recent samples, and during the entire study period measurements ranged between 19 and 248 Bq/kg wet weight. A declining trend in time over the last 30 years follow the general trend of decline in activity levels in other Baltic biota. Accumulation was found to be species specific in the two seal species studied, with 9 times higher activity concentration in grey seals compared to herring, and 3.5 times higher in ringed seals compared to herring. We discuss potential paths and rates of bioaccumulation of radioactive caesium in the Baltic Sea including species specific prey choice of the two seal species and estimate life time exposure. The study contributes one important piece of information to predictive models in risk assessments for nuclear accidents.

Investigating microplastic trophic transfer in marine top predators

Microplastics are highly bioavailable to marine organisms, either through direct ingestion, or indirectly by trophic transfer from contaminated prey. The latter has been observed for low-trophic level organisms in laboratory conditions, yet empirical evidence in high trophic-level taxa is lacking. In natura studies face difficulties when dealing with contamination and differentiating between directly and indirectly ingested microplastics. The ethical constraints of subjecting large organisms, such as marine mammals, to laboratory investigations hinder the resolution of these limitations. Here, these issues were resolved by analysing sub-samples of scat from captive grey seals (Halichoerus grypus) and whole digestive tracts of the wild-caught Atlantic mackerel (Scomber scombrus) they are fed upon. An enzymatic digestion protocol was employed to remove excess organic material and facilitate visual detection of synthetic particles without damaging them. Polymer type was confirmed using Fourier-Transform Infrared (FTIR) spectroscopy. Extensive contamination control measures were implemented throughout. Approximately half of scat subsamples (48%; n = 15) and a third of fish (32%; n = 10) contained 1–4 microplastics. Particles were mainly black, clear, red and blue in colour. Mean lengths were 1.5 mm and 2 mm in scats and fish respectively. Ethylene propylene was the most frequently detected polymer type in both. Our findings suggest trophic transfer represents an indirect, yet potentially major, pathway of microplastic ingestion for any species whose feeding ecology involves the consumption of whole prey, including humans.

Evaluating the use of stable isotope analysis to infer the feeding ecology of a growing US gray seal (Halichoerus grypus) population.

Gray seals (Halichoerus grypus) have been rapidly recolonizing the Northeast US coast, eliciting concern from the fishing industry. However, the ecological effect of this recovery is still unknown and as such, research is needed to better understand how the diet composition of gray seals in US waters will contribute to the ecological impact. While previous research on seal diets has focused on the analysis of hard prey remains, stable isotope analysis presents an alternative method that can be used to describe marine mammal diets when direct observation is impossible. To address this issue, we used stable isotope analysis of gray seal pup vibrissae and lanugo from Monomoy Island, Cape Cod, MA during the 2015/2016 winter breeding season to estimate adult female diet composition during pregnancy. Stable isotope mixing models (SIMM) suggested adult female gray seals were consuming greater amounts of cephalopod prey and less sand lance than previously indicated from analysis of hard prey remains. However, using SIMMs to estimate the diet composition of gray seals remains difficult due to the large number of isotopically similar prey species and uncertainty in tissue-specific, stable isotope trophic enrichment factors. Even so, by combining prey sources into ecologically informative groups and integrating prior information into SIMMs it is possible to obtain additional insights into the diet of this generalist predator.