Halichoerus Research Articles

Absence of predator control increases cod extirpation risk in a Northwest Atlantic ecosystem: inference from multispecies modelling

Atlantic cod Gadus morhua in the southern Gulf of St. Lawrence (sGSL) declined to low abundance in the early 1990s and have since failed to recover due to high natural mortality, which has been linked to predation by grey seals Halichoerus grypus. Increased grey seal harvests have been suggested to improve cod survival; however, predicting the response of cod to changes in seal abundance in the sGSL is complicated by a hypothesized triangular food web involving seals, cod, and small pelagic fishes, wherein the pelagic fishes are prey for cod and grey seals, but may also prey on young cod. Grey seals may therefore have an indirect positive effect on pre-recruit cod survival via predation on pelagic fish. Using a multispecies model of intermediate complexity fitted to various scientific and fisheries data, we found that seal predation accounted for the majority of recent cod mortality and that cod will likely be extirpated without a strong and rapid reduction in grey seal abundance. We did not find evidence that reducing grey seal abundance will impair cod recovery by causing large increases in pelagic biomass so long as pelagic fishing mortality continues at historical levels.

Gross pathology and liver mercury concentrations in harbour porpoises, harbour seals and grey seals in Denmark, Northern Europe

Here we report the first investigation of gross pathology and mercury (Hg) in liver tissue from harbour porpoises, harbour seals and grey seals from Denmark, Northern Europe. Mercury concentrations ranged between 0.2 and 248 μg/g wet weight (ww) with highest concentrations found in grey seals and subadult harbour seals from the Baltic Sea, with no relationship to body condition. Necropsy findings across all three species decreasing in the following order: pneumonia (n = 60) > respiratory parasitism (n = 56) > wounds (n = 18) > GI-parasites (stomach nematodes and/or parasitic colitis) (n = 16) > ectoparasites (skin lice) (n = 12) > hepatic parasites/lesions (n = 8) > focal alopecia (n = 5) > nephropathy (n = 4) > middle ear complex parasites (n = 3) > nasal parasites (n = 2). Heart and/or lung worms were significantly highest in subadult harbour porpoises, GI parasites and nephropathy significantly lowest in subadult harbour seals and focal alopecia significantly highest in subadult harbour seals. Most cases of pneumonia were associated with respiratory parasites (68 %), while nine cases of wounds led to signs of septicaemia. Significant positive relationships were observed between Hg and the presence of respiratory parasites in subadult harbour porpoises and between Hg and the presence of focal alopecia, nephropathy, and gastrointestinal parasites in subadult harbour seals. Levels of Hg were in the categories for low risk (16–64 μg/g ww) in 18 %, moderate risk (64–83 μg/g ww) in 3 %, high risk (83–123 μg/g ww) in 2 % and severe risk (>123 μg/g ww) in 3 % of all individuals for health effects in marine mammals. In conclusion, using marine mammals as integrative sentinel species for Danish North Sea, Inner Danish Waters and the Baltic Sea ecosystems provides monitoring of ocean health in terms of multiple stressors such as anthropogenic contaminants and infectious diseases all being important in the context of global change.

Population genomics of seal lice provides insights into the postglacial history of northern European seals.

Genetic analyses of host-specific parasites can elucidate the evolutionary histories and biological features of their hosts. Here, we used population-genomic analyses of ectoparasitic seal lice (Echinophthirius horridus) to shed light on the postglacial history of seals in the Arctic Ocean and the Baltic Sea region. One key question was the enigmatic origin of relict landlocked ringed seal populations in lakes Saimaa and Ladoga in northern Europe. We found that that lice of four postglacially diverged subspecies of the ringed seal (Pusa hispida) and Baltic gray seal (Halichoerus grypus), like their hosts, form genetically differentiated entities. Using coalescent-based demographic inference, we show that the sequence of divergences of the louse populations is consistent with the geological history of lake formation. In addition, local effective population sizes of the lice are generally proportional to the census sizes of their respective seal host populations. Genome-based reconstructions of long-term effective population sizes revealed clear differences among louse populations associated with gray versus ringed seals, with apparent links to Pleistocene and Holocene climatic variation as well as to the isolation histories of ringed seal subspecies. Interestingly, our analyses also revealed ancient gene flow between the lice of Baltic gray and ringed seals, suggesting that the distributions of Baltic seals overlapped to a greater extent in the past than is the case today. Taken together, our results demonstrate how genomic information from specialized parasites with higher mutation and substitution rates than their hosts can potentially illuminate finer scale population genetic patterns than similar data from their hosts.

Ontogeny of horizontal movement patterns of rehabilitated grey seal juveniles (Halichoerus grypus) in the Baltic Sea

The ethical considerations and scepticism over the ecological benefits have fuelled debate about the rehabilitation of wildlife. Although there is evidence that many rehabilitated species are able to survive after rehabilitation, there is a paucity of research on the behaviour of rehabilitated pinnipeds, including grey seals (Halichoerus grypus). In this study, 14 rehabilitated grey seal juveniles were equipped with biotelemetry devices in order to conduct remote post-release monitoring and to investigate ontogeny of their movements in the Baltic Sea. The study revealed that their movements were similar to wild, non-rehabilitated grey seal pups when leaving their natal site: at first, they exhibited highly exploratory behaviour with largely transient movements, then switched into a resident movement pattern, while maximising foraging and minimising travelling time. Neither sex nor year of release, which varied in terms of rehabilitation time and body mass, had a significant effect on the ontogeny of these movements. Movements were significantly influenced by the time after release, suggesting that rehabilitated juveniles have gained experience and developed their movements over time in order to survive in the wild.

How low can you go? Exploring impact of drones on haul out behaviour of harbour - and grey seals

How low can you go? Exploring impact of drones on haul out behaviour of harbour - and grey seals

Establishing the limitations on using archived marine mammal samples for stable isotope analysis: an examination of differing preservation methods on tissues of harbor porpoise (Phocoena phocoena) and gray seal (Halichoerus grypus)

AbstractThe use of biological samples from museum and/or archive collections is common in stable isotope research, particularly for marine mammals. Yet, the temporal stability of isotopic values across various tissue types and the influence of different preservatives on these values are not fully understood, posing significant challenges for accurate data interpretation. Here we examine the impact of three different tissue preservation methods (DMSO, ethanol, freezing), on seven different tissues (blubber, heart, kidney, lung, liver, muscle, and skin) from both a harbor porpoise (Phocoena phocoena) and a gray seal (Halichoerus grypus) for stable isotope analysis in a 1‐year period. Our results demonstrate that storage in DMSO generates greater temporal variability in δ13C and δ15N for all tissue types, particularly in the first six months of storage. Furthermore, tissues stored in DMSO often exhibited lower δ13C and δ15N values compared to those stored frozen or in ethanol. This finding highlights a significant issue for studies utilizing tissues stored in DMSO, regardless of the storage duration. These results underscore the critical need for careful consideration of preservation methods in studies involving stored tissues, providing valuable insights for experimental design and management of tissue archives.

The Role of Play in the Social Development of Grey Seal (Halichoerus grypus) Pups with Comparative Notes on the Harbour Seal (Phoca vitulina).

Juvenile grey seals are known to be highly social, interacting with contact behaviours interpreted as gentle play. However, minimal sociality of pups with their mothers and among weaned pups has been suggested. The present study aimed to observe the natural social interactions of pups to track the early ontogeny of their sociality. Pup behaviour at a salt marsh colony on the east coast of England was video-recorded. Pups interacted with their mothers around suckling bouts and after weaning as they gathered around pools. The records were transcribed to spreadsheets in 30 s time segments to estimate the frequency and co-occurrence of different behaviours. Mother-pup interaction comprised nosing contacts and sometimes contact play, involving one laying the head and fore-flipper over the other. Initial weaned pup encounters involved tentative nosing and defensive splashing, indicating contact shyness. However, socially orientated locomotor play, supine posturing, and exaggerated raising of fore- and hind-flippers led to reduced shyness and pups following one another towards the sea. Archive data on subadult interactions and on harbour seal behaviours were re-analysed. Gentle play-like contact between mother-pup, juvenile, and adult pairs is interpreted here as a universal mode of social bonding, underscoring the social structure of both grey and harbour seals.

First report of the presence of Pseudoterranova sp. in the body cavity of salmon (Salmo salar) from the Baltic Sea

Abstract Despite salmon (Salmo salar L.) being an important fish in the Baltic Sea ecosystem and its fisheries, knowledge about the parasite fauna of this top predator is scarce. The Anisakidae nematodes (Anisakis spp., Pseudoterranova spp., Contracaecum sp.) found in Baltic Sea fish species are zoonotic parasites that are hazardous to human health. Due to the marked increase in the numbers of grey seal (Halichoerus grypus), the definitive host of Contracaecum sp. and Pseudoterranova spp., increased dispersion of these parasites has been observed in recent years. The aim of our study was to investigate salmon caught in Polish marine waters for the presence of Anisakidae nematodes. Parasitological inspection of the body cavities of 89 individual salmon was conducted in 2012 and revealed the presence of a Pseudoterranova sp. L3 larva. The presence of the parasite is reported here for the first time in the muscle tissue of salmon from the Baltic Sea. The presence of Anisakidae nematodes in commercially important fish species may have implications for human health since these parasites pose a risk of anisakidosis.

High prevalence and low intensity of Echinophthirius horridus infection in seals revealed by high effort sampling

Seal lice (Echinophthirius horridus) are bloodsucking ectoparasites of phocid seals and vectors of pathogens like the heartworm, Acanthocheilonema spirocauda. Grey and harbour seal populations are recovering in German waters and wildlife health surveillance is crucial for wildlife conservation. A new, high effort sampling protocol for seal lice was applied for grey and harbour seals along the German North- and Baltic Sea coast. Freshly dead seals were systematically sampled within a health monitoring of stranded seals over 12 months. Prevalence, intensity and distribution patterns of seal lice were analysed. 58% of harbour seals (n = 71) and 70% of grey seals (n = 10) were infected with seal lice. A majority of harbour seals displayed mild levels of infection, while three were moderately and two were severely infected. The head was the preferred predilection site, indicating that E. horridus prefers body areas with frequent access to atmospheric oxygen. Nits and different developmental stages were recorded in all age classes in grey and harbour seals in all seasons. For the first time, copulating specimens of E. horridus were recorded on a dead harbour seal, highlighting that E. horridus reproduces throughout the year on seals of all age classes in German waters.

Disappearing fish: Grey seal depredation in a Baltic net fishery

Grey seals (Halichoerus grypus) in the Baltic Sea commonly attempt to steal fish captured in net fisheries. Seal depredation reduces economic yields for small-scale net fishers in a region already highly impacted by the collapse of important fish stocks. Visible damages in looted nets consist of injured fish with bite marks, or holes in the gear, but additional losses from seals eating entire fish without leaving a trace can often remain unnoticed. In this study, we estimated the daily rates of injured and of stolen fish in a commercial gillnet fishery operating off coast of Bornholm in the Central Baltic Sea in 2021–2022. Our results show that the Atlantic cod (Gadus morhua) is generally preferred over other target species [here, European plaice (Pleuronectes platessa), European flounder (Platichthys flesus), and turbot (Scophthalmus maximus)]. Although the observed ratio of 5.65 cods disappearing for each cod retrieved with seal bite marks is similar to a study from the 2000’s, we show that average daily cod disappearance rates are linked to the duration a gear is left soaking in the same location.

Occurrence of recreational water quality monitoring general fecal indicator bacteria and fecal source identification genetic markers in gray seal scat

The number of gray seals (Halichoerus grypus) observed along the United States Northwest Atlantic region has been increasing for decades. These colonial animals often haul-out on beaches seasonally in numbers ranging from a few individuals to several thousands. While these larger aggregations are an important part of gray seal behavior, there is public concern that haul-outs could lead to large amounts of fecal waste in recreational areas, potentially resulting in beach closures. Yet, data to confirm whether these animals contribute to beach closures is lacking and minimal information is available on the occurrence of key water quality monitoring genetic markers in gray seal scat. This study evaluates the concentration of E. coli (EC23S857), enterococci (Entero1a), and fecal Bacteroidetes (GenBac3) as well as six fecal source identification genetic markers (HF183/BacR287, HumM2, CPQ_056, Rum2Bac, DG3, and GFD) measured by qPCR in 48 wild gray seal scat samples collected from two haul-out areas in Cape Cod (Massachusetts, U.S.A.). Findings indicate that FIB genetic markers are shed in gray seal scat at significantly different concentrations with the Entero1a genetic marker exhibiting the lowest average concentration (−0.73 log10 estimated mean copies per nanogram of DNA). In addition, systematic testing of scat samples demonstrated that qPCR assays targeting host-associated genetic markers indicative of human, ruminant, and canine fecal pollution sources remain highly specific in waters frequented by gray seals (>97 % specificity).

Feathered diplomacy: when birds become main factors of research design and geography on Vigur Island

Vigur Island, situated in Iceland’s Westfjords, is renowned for its diverse avian species, such as Atlantic Puffins and Black Guillemots, and its marine inhabitants including Harbour and Grey Seals. Despite its openness to tourism, the island is a subject of ongoing conservation efforts. This opinion paper argues for a more holistic approach to research on the island, highlighting the complex interplay between human activity and the island’s ecosystem. It critiques the current, often narrow, research methodologies that fail to fully account for the intricate relationships between species and their environment. The paper calls for a re-evaluation of habitat classification to incorporate the significant impact of avian populations and stresses the importance of adhering to Icelandic laws that mandate minimal disturbance to wildlife. With seasonal closures and careful management practices like eiderdown collection, Vigur Island serves as a model for balancing human interests with ecological integrity. This opinion advocates for adaptable, comprehensive research strategies that, while illustrated through the case of Vigur, should be applied universally, urging scientists to embrace broader perspectives in environmental studies globally.

Evaluating the potential impacts of grey seal predation and fishery bycatch/discards on cod productivity on the Western Scotian Shelf and in the Bay of Fundy

Abstract The recovery of many groundfish stocks in the Northwest Atlantic has been impeded by elevated mortality among older/larger individuals. The sources of groundfish mortality are generally uncertain, though predation by growing grey seal herds and unreported fishing are thought to be drivers of mortality for Atlantic cod (Gadus morhua) on the Western Scotian Shelf and Bay of Fundy (4X5Y), as well as in nearby ecosystems. We developed a statistical catch-at-age model for 4X5Y cod that accounted for grey seal predation and bycatch/discards and tested the model across a broad range of consumption and discard scenarios. We found that most cod mortality was unexplained by seal predation and fishing when cod comprised a small to moderate portion of the grey seal diet. Predation and fishing accounted for slightly more than half of recent cod mortality when cod was highly prevalent in the seal diet (45% by weight) but explained little historical mortality. Bycatch was a minor source of mortality prior to 2019 and accounted for 0.%1–8.1% of recent mortality. Increased sampling of seal diets and monitoring of emerging seal colonies is necessary for reducing uncertainties around seal predation effects in the Northwest Atlantic.

What bycatch tells us about the diet of harbor and gray seals and overlap with commercial fishermen

Northwest Atlantic harbor (Phoca vitulina vitulina) and gray (Halichoerus grypus atlantica) seal populations are recovering from early to mid-20th century exploitation, increasing their biological interactions and bycatch in Northeastern US commercial fisheries. We evaluated the seals’ diet composition and compared their prey to commercial catches to assess trophic overlap and potential competition with commercial fisherman target catches. We obtained 148 harbor and 178 gray seal stomach samples from bycatch events that occurred between 2004 and 2018. We learned from the hard part remains that the majority of seals bycaught are young-of-the-year (≤12 months old) that consume a wide breadth of prey across three trophic groups. There was a general dichotomy in extrinsic factors associated with seal diet in which 45% trophic niche separation was explained by non-overlapping harbor and gray seal phenology and pup haul-out locations that are adjacent to active fishing areas. Prey size estimated from fish otoliths and squid beaks recovered from stomach contents showed that gray seals consumed larger prey than harbor seals and prey sizes from both seals showed limited overlap with prey sizes caught by commercial gillnet fishermen. The most important prey to both seals included large (>20 cm) and small (≤20 cm) silver hake (Merluccius bilinearis), (≤40 cm) red hake (Urophycis chuss), gulf stream flounder (Citharichthys arctifrons), medium (21–40 cm) white hake (Urophycis tenuis), and (<50 cm) Atlantic cod (Gadus morhua). Important prey to harbor seals that did not overlap with gray seals were Acadian redfish (Sebastes fasciatus), Atlantic herring (Clupea harengus), longfin (Doryteuthis pealeii), and shortfin squid (Illex illecebrosus). They contrasted with prey important to gray seals that did not overlap with harbor seals: yellowtail flounder (Limanda ferruginea), sand lance (Ammodytes spp.), Urophycis spp., and fourspot flounder (Hippoglossina oblonga). Despite the potential bias associated with opportunistic bycatch sampling, this study demonstrates the importance and value of utilizing carcasses retained from bycatch events, is complimentary to newer methodologies (i.e., DNA meta-barcoding), and fills data gaps in our understanding of the role recovering harbor and gray seal populations have on Northeastern US regional food webs.

Variations in antimicrobial resistance genes present in the rectal faeces of seals in Scottish and Liverpool Bay coastal waters

Antibiotic resistance genes originating from human activity are considered important environmental pollutants. Wildlife species can act as sentinels for coastal environmental contamination and in this study we used qPCR array technology to investigate the variety and abundance of antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and integrons circulating within seal populations both near to and far from large human populations located around the Scottish and northwest English coast. Rectal swabs were taken from 50 live grey seals and nine live harbour seals. Nucleic acids were stabilised upon collection, enabling extraction of sufficient quality and quantity DNA for downstream analysis. 78 ARG targets, including genes of clinical significance, four MGE targets and three integron targets were used to monitor genes within 22 sample pools. 30 ARGs were detected, as well as the integrons intl1 and intl2 and tnpA transposase. Four β-lactam, nine tetracycline, two phenicol, one trimethoprim, three aminoglycoside and ten multidrug resistance genes were detected as well as mcr-1 which confers resistance to colistin, an important drug of last resort. No sulphonamide, vancomycin, macrolide, lincosamide or streptogramin B (MLSB) resistance genes were detected. Resistance genes were detected in all sites but the highest number of ARGs (n = 29) was detected in samples derived from grey seals on the Isle of May, Scotland during the breeding season, and these genes also had the highest average abundance in relation to the 16S rRNA gene. This pilot study demonstrates the effectiveness of a culture-independent workflow for global analysis of ARGs within the microbiota of live, free-ranging, wild animals from habitats close to and remote from human habitation, and highlights seals as a valuable indicator species for monitoring the presence, abundance and land-sea transference of resistance genes within and between ecosystems.

120-years of ecological monitoring data shows that the risk of overhunting is increased by environmental degradation for an isolated marine mammal population: The Baltic grey seal.

The Baltic Sea is home to a genetically isolated and morphologically distinct grey seal population. This population has been the subject of 120-years of careful documentation, from detailed records of bounty statistics to annual monitoring of health and abundance. It has also been exposed to a range of well-documented stressors, including hunting, pollution and climate change. To investigate the vulnerability of marine mammal populations to multiple stressors, data series relating to the Baltic grey seal population size, hunt and health were compiled, vital demographic rates were estimated, and a detailed population model was constructed. The Baltic grey seal population fell from approximately 90,000 to as few as 3000 individuals during the 1900s as the result of hunting and pollution. Subsequently, the population has recovered to approximately 55,000 individuals. Fertility levels for mature females have increased from 9% in the 1970s to 86% at present. The recovery of the population has led to demands for increased hunting, resulting in a sudden increase in annual quotas from a few hundred to 3550 in 2020. Simultaneously, environmental changes, such as warmer winters and reduced prey availability due to overfishing, are likely impacting fecundity and health. Future population development is projected for a range of hunting and environmental stress scenarios, illustrating how hunting, in combination with environmental degradation, can lead to population collapse. The current combined hunting quotas of all Baltic Nations caused a 10% population decline within three generations in 100% of simulations. To enable continued recovery of the population, combined annual quotas of less than 1900 are needed, although this quota should be re-evaluated annually as monitoring of population size and seal health continues. Sustainable management of long-lived slowly growing species requires an understanding of the drivers of population growth and the repercussions of management decisions over many decades. The case of the Baltic grey seal illustrates how long-term ecological time series are pivotal in establishing historical baselines in population abundance and demography to inform sustainable management.

Effects of external tags on maternal postpartum, offspring body mass and breeding frequency in gray seals Halichoerus grypus

AbstractFew studies have examined the impacts of externally fitted data‐loggers and telemetry tags on pinnipeds. We tested for instrument effects on body mass of lactating female gray seals and their offspring and probability of pupping in the next breeding season. Known‐age adult females (n = 216) were fitted with instruments in winter, spring, and fall from 1992 to 2018 at Sable Island, Nova Scotia. Of those tagged in spring and fall, 61 of 135 returning females and 59 of their offspring were weighed within 5 days postpartum and 79 pups were weighed at weaning. Instrumented females were assigned to treatments based on tag frontal area sums, tag mass, deployment duration, and acoustic tag presence compared to control females without instruments using linear mixed‐effects models. None of the treatment effects were included in the preferred models predicting birth mass of offspring or probability of breeding in the following year. The small negative effect (−3% to −7%) on postpartum maternal mass and pup weaning mass (−4.7%) for females instrumented in fall may be an artifact as longer spring deployments showed no effect. Overall, we found that the instruments deployed had no detectable negative effects on the maternal and offspring variables measured.

Faster inference from state space models via GPU computing

Inexpensive Graphics Processing Units (GPUs) offer the potential to greatly speed up computation by employing their massively parallel architecture to perform arithmetic operations more efficiently. Population dynamics models are important tools in ecology and conservation. Modern Bayesian approaches allow biologically realistic models to be constructed and fitted to multiple data sources in an integrated modelling framework based on a class of statistical models called state space models. However, model fitting is often slow, requiring hours to weeks of computation. We demonstrate the benefits of GPU computing using a model for the population dynamics of British grey seals, fitted with a particle Markov chain Monte Carlo algorithm. Speed-ups of two orders of magnitude were obtained for estimations of the log-likelihood, compared to a traditional ‘CPU-only’ implementation, allowing for an accurate method of inference to be used where this was previously too computationally expensive to be viable. GPU computing has enormous potential, but one barrier to further adoption is a steep learning curve, due to GPUs' unique hardware architecture. We provide a detailed description of hardware and software setup, and our case study provides a template for other similar applications. We also provide a detailed tutorial-style description of GPU hardware architectures, and examples of important GPU-specific programming practices.

Impact of fishery observer protocol on estimated bycatch rates of marine mammals

Abstract Managing fishing operations’ threat to marine mammal populations hinges on accurate bycatch estimates, often derived from fishery observer or monitoring programmes. Much global marine mammal bycatch occurs in gillnets, and observer protocols that do not include watching the haulback of gillnets may miss animals that drop out of the net. We investigated whether trips using a fish-focused observer protocol (no requirement to watch the haulback) in US northwestern Atlantic gillnet fisheries from 1994 to 2019 had different observed bycatch rates from trips under a mammal-focused observer protocol (watching the haulbacks) for grey seals (Halichoerus grypus atlantica), harbour seals (Phoca vitulina vitulina), and harbour porpoise (Phocoena phocoena phocoena). We found that observer protocol was likely to affect observed drop-out and bycatch rates. Under the fish-focused protocol, the ratio of animals removed from the net to those that fell from the net was generally higher than under the mammal-focused protocol, suggesting fish-focused observers missed bycatch that fell. Bycatch rates of animals removed from the net by fishers differed significantly between observer protocols for seals, but not for harbour porpoise, perhaps because of differences in entanglement and manner of decomposition. We estimate bycatch was underreported by 3–25% because of unobserved drop-outs on fish-focused observer protocols.

Static Acoustic Monitoring of Harbour (Phoca vitulina) and Grey Seals (Halichoerus grypus) in the Malin Sea: A Revolutionary Approach in Pinniped Conservation

Harbour and grey seals rely on acoustic signals to mate, socialise and defend their territory. Previous studies have focused on their behaviour, movements and communication from the coast, leaving a knowledge gap in the offshore environments, and therefore being unable to determine the proper use they give to those areas and the risks they face around them. Acoustic data collected with a SoundTrap were analysed to assess the detectability of both species in the Malin Sea. Vocalisations were classified based on aural and visual features, as well as using non-parametric classification trees. Differences in the vocalisation rate of grey seals per diel, season and tidal state were also assessed through Generalised Linear Mixed Models, obtaining significant results, and finding similarities in the vocalisations of grey seals with the Scottish and Irish populations. A small sample of adult and pup harbour seals was detected, and differences in call type and number of detections per type were found across the seasons. These results show the importance of the area for both species, and lay the foundations for future studies, which will help to implement proper conservation measures such as Marine Protected Areas.