The 1988 and 2002 phocine distemper virus epidemics in European harbour seals

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.

Heartworm and seal louse: Trends in prevalence, characterisation of impact and transmission pathways in a unique parasite assembly on seals in the North and Baltic Sea

The ectoparasitic seal louse, Echinophthirius horridus infects harbour (Phoca vitulina) and grey seals (Halichoerus grypus) in the North and Baltic Sea. The endoparasitic heartworm Acanthocheilonema spirocauda parasitizes the right heart and blood vessels of harbour seals. The complete lifecycle of the heartworm is not entirely understood although the seal louse is assumed to serve as vector for its transmission. Knowledge about the impact of both parasite species on host health are scarce. In this study, necropsy data and archived parasites of harbour and grey seals in German waters were analysed to determine long-term seal louse (SLP) and heartworm prevalence (HWP) from 2014 to 2021. Histology, microbiology and scanning electron microscopy (SEM) were applied on seal louse infected and uninfected skin to investigate associated lesions and the health impact. During the study period, HWP in harbour seals was 13%, the SLP in harbour seals was 4% and in grey seals 10%. HWP of harbour seals was significantly higher during the winter months compared to the summer. SLP in adults was significantly higher in comparison to juvenile harbour seals. SLP varied significantly between grey seals from the North and Baltic Sea. Filarial nematodes were detected in the haemocoel, pharynx, and intestine of E. horridus highlighting the seal louse as vector for heartworms. Alopecia and folliculitis were associated with the attachment posture of E. horridus and microbiological investigations isolated bacteria commonly associated with folliculitis.

Did algal toxin and Klebsiella infections cause the unexplained 2007 mass mortality event in Danish and Swedish marine mammals?

An unusual mass mortality event (MME) of harbour seals (Phoca vitulina) and harbour porpoises (Phocoena phocoena) occurred in Denmark and Sweden in June 2007. Prior to this incident, the region had experienced two MMEs in harbour seals caused by Phocine Distemper Virus (PDV) in 1988 and 2002. Although epidemiology and symptoms of the 2007 MME resembled PDV, none of the animals examined for PDV tested positive. Thus, it has been speculated that another - yet unknown - pathogen caused the June 2007 MME. To shed new light on the likely cause of death, we combine previously unpublished veterinary examinations of harbour seals with novel analyses of algal toxins and algal monitoring data. All harbour seals subject to pathological examination showed pneumonia, but were negative for PDV, influenza and coronavirus. Histological analyses revealed septicaemia in multiple animals, and six animals tested positive for Klebsiella pneumonia. Furthermore, we detected the algal Dinophysis toxin DTX-1b (1-115 ng g-1) in five seals subject to toxicology, representing the first time DTX-1b has been detected in marine vertebrates. However, no animals tested positive for both Klebsiella and toxins. Thus, while our relatively small sample size prevent firm conclusions on causative agents, we speculate that the unexplained MME may have been caused by a chance incidence of multiple pathogens acting in parallel in June 2007, including Dinophysis toxin and Klebsiella. Our study illustrates the complexity of wildlife MMEs and highlights the need for thorough sampling during and after MMEs, as well as additional research on and monitoring of DTX-1b and other algal toxins in the region.

California sea lion (Zalophus californianus) lymph-node explant reveals involvement and possible transcriptional regulation of SLAM and nectin-4 during phocine distemper virus infection

Phocine distemper virus (PDV) is a significant cause of mortality for phocid seals; however, the susceptibility of otariids to this virus is poorly understood. The authors used a lymph-node explant culture system from California sea lions (Zalophus californianus, CSL) to investigate: (1) the role of signaling lymphocyte activation molecule (SLAM) and nectin-4 in PDV infection and their cellular expression patterns, (2) if PDV induces transcriptional regulation of cell-entry receptors, and (3) the involvement of apoptosis in PDV infection. PDV replicated in the lymph-node explants with peak replication 3 days post-infection (dpi), but the replication was not sustained 4 to 5 dpi. The PDV+ cells co-localized SLAM and nectin-4. These cells expressed IBA1, indicating a histiocytic lineage. Comparison of receptor expression between infected and mock-infected lymph nodes suggested transcriptional downregulation of both receptors during the initial stage of infection and upregulation during the late stage of infection, but the values lack of statistical significance. Cleaved caspase-3+ cells were slightly increased in the infected lymph nodes compared with the mock-infected lymph node from 1 to 4 dpi, but without statistical significance, and a few apoptotic cells co-expressed PDV. The results suggest that lymph-node explants might be an important model to study PDV pathogenesis. CSLs have the potential to be infected with PDV, as they express both cell-entry receptors in histiocytes. The lack of statistical significance in the PDV replication, transcriptional regulation of viral receptors, and changes in apoptosis suggest that although CSL might be infected by PDV, they might be less susceptible than phocid species.

Stay close, but not too close: aerial image analysis reveals patterns of social distancing in seal colonies

Many species aggregate in dense colonies. Species-specific spatial patterns provide clues about how colonies are shaped by various (a)biotic factors, including predation, temperature regulation or disease transmission. Using aerial imagery, we examined these patterns in colonies on land of two sympatric seal species: the harbour seal and grey seal. Results show that the density of grey seals on land is twice as high as that of harbour seals. Furthermore, the nearest neighbour distance (NND) of harbour seals (median = 1.06 m) is significantly larger than that of grey seals (median = 0.53 m). Avoidance at small distances (i.e. social distancing) was supported by spatial simulation: when the observed seal locations were shuffled slightly, the frequency of the smallest NNDs (0-25 cm) increased, while the most frequently observed NNDs decreased. As harbour seals are more prone to infectious diseases, we hypothesize that the larger NNDs might be a behavioural response to reduce pathogen transmission. The approach presented here can potentially be used as a practical tool to differentiate between harbour and grey seals in remote sensing applications, particularly in low to medium resolution imagery (e.g. satellite imagery), where morphological characteristics alone are insufficient to differentiate between species.

Heartworms in Halichoerus grypus: first records of Acanthocheilonema spirocauda (Onchocercidae; Filarioidea) in 2 grey seals from the North Sea

The assumed definitive host of the heartworm Acanthocheilonema spirocauda (Onchocerdidae; Filarioidea) is the harbour seal (Phoca vitulina). This filaroid nematode parasitizing in cardiac ventricles and blood vessel lumina of harbour seals (P. vitulina) has a low prevalence and seldom causes severe health impacts. The seal louse (Echinophthirius horridus) is the assumed intermediate host for transmission of A. spirocauda filariae between seals, comprising a unique parasite assembly conveyed from the terrestrial ancestors of pinnipeds. Although grey seals (Halichoerus grypus) are infected by seal lice, heartworm infection was not verified. Analysing a longterm dataset compiled over decades (1996–2021) of health monitoring seals along the German coasts comprising post mortem investigations and archived parasites, 2 cases of A. spirocauda infected male grey seals were detected. Tentative morphological identification was confirmed with molecular tools by sequencing a section of mtDNA COI and comparing nucleotide data with available heartworm sequence. This is the first record of heartworm individuals collected from the heart of grey seals at necropsy. It remains puzzling why heartworm infection occur much less frequently in grey than in harbour seals, although both species use the same habitat, share mixed haul-outs and consume similar prey species. If transmission occurs directly via seal louse vectors on haul-outs, increasing seal populations in the North- and Baltic Sea could have density dependent effects on prevalence of heartworm and seal louse infections. It remains to be shown how species-specificity of filarial nematodes as well as immune system traits of grey seals influence infection patterns of A. spirocauda.

A Review of Circumpolar Arctic Marine Mammal Health-A Call to Action in a Time of Rapid Environmental Change

The impacts of climate change on the health of marine mammals are increasingly being recognised. Given the rapid rate of environmental change in the Arctic, the potential ramifications on the health of marine mammals in this region are a particular concern. There are eleven endemic Arctic marine mammal species (AMMs) comprising three cetaceans, seven pinnipeds, and the polar bear (Ursus maritimus). All of these species are dependent on sea ice for survival, particularly those requiring ice for breeding. As air and water temperatures increase, additional species previously non-resident in Arctic waters are extending their ranges northward, leading to greater species overlaps and a concomitant increased risk of disease transmission. In this study, we review the literature documenting disease presence in Arctic marine mammals to understand the current causes of morbidity and mortality in these species and forecast future disease issues. Our review highlights potential pathogen occurrence in a changing Arctic environment, discussing surveillance methods for 35 specific pathogens, identifying risk factors associated with these diseases, as well as making recommendations for future monitoring for emerging pathogens. Several of the pathogens discussed have the potential to cause unusual mortality events in AMMs. Brucella, morbillivirus, influenza A virus, and Toxoplasma gondii are all of concern, particularly with the relative naivety of the immune systems of endemic Arctic species. There is a clear need for increased surveillance to understand baseline disease levels and address the gravity of the predicted impacts of climate change on marine mammal species.

Asymptomatic viral infection is associated with lower host reproductive output in wild mink populations

Many endemic viruses circulate in populations without hosts showing visible signs of disease, while still having the potential to alter host survival or reproduction. Aleutian Mink Disease Virus (AMDV) circulates in many American mink (Neogale vison) populations in its native and introduced ranges. In this study, we analysed how AMDV infection in female American mink affects the reproduction of a feral population. Females infected with AMDV delivered significantly smaller litters (5.8 pups) than uninfected females (6.3 pups), meaning their litter size was reduced by 8%. Larger females and yearling females had larger litters than smaller and older females. There were no significant differences in whole litter survival between infected and uninfected females; however, offspring survival until September or October within litters of infected females was 14% lower than that within those of uninfected females. This negative link between infection and reproductive output means that Aleutian disease could seriously affect the wild mink population. This study increases our understanding of the threats posed by the spread of viruses to wildlife from farm animals or humans, highlighting that viruses circulating in wildlife, even in the absence of clinical manifestation, can be important drivers of population dynamics in wildlife.

Screening for Influenza and Morbillivirus in Seals and Porpoises in the Baltic and North Sea

Historically, the seals and harbour porpoises of the Baltic Sea and North Sea have been subjected to hunting, chemical pollutants and repeated mass mortalities, leading to significant population fluctuations. Despite the conservation implications and the zoonotic potential associated with viral disease outbreaks in wildlife, limited information is available on the circulation of viral pathogens in Baltic Sea seals and harbour porpoises. Here, we investigated the presence of the influenza A virus (IAV), the phocine distemper virus (PDV) and the cetacean morbillivirus (CeMV) in tracheal swabs and lung tissue samples from 99 harbour seals, 126 grey seals, 73 ringed seals and 78 harbour porpoises collected in the Baltic Sea and North Sea between 2002–2019. Despite screening 376 marine mammals collected over nearly two decades, we only detected one case of PDV and two cases of IAV linked to the documented viral outbreaks in seals in 2002 and 2014, respectively. Although we find no evidence of PDV and IAV during intermediate years, reports of isolated cases of PDV in North Sea harbour seals and IAV (H5N8) in Baltic and North Sea grey seals suggest introductions of those pathogens within the sampling period. Thus, to aid future monitoring efforts we highlight the need for a standardized and continuous sample collection of swabs, tissue and blood samples across Baltic Sea countries.

Hidden variable models reveal the effects of infection from changes in host survival

The impacts of disease on host vital rates can be demonstrated using longitudinal studies, but these studies can be expensive and logistically challenging. We examined the utility of hidden variable models to infer the individual effects of infectious disease from population-level measurements of survival when longitudinal studies are not possible. Our approach seeks to explain temporal deviations in population-level survival after introducing a disease causative agent when disease prevalence cannot be directly measured by coupling survival and epidemiological models. We tested this approach using an experimental host system (Drosophila melanogaster) with multiple distinct pathogens to validate the ability of the hidden variable model to infer per-capita disease rates. We then applied the approach to a disease outbreak in harbor seals (Phoca vituline) that had data on observed strandings but no epidemiological data. We found that our hidden variable modeling approach could successfully detect the per-capita effects of disease from monitored survival rates in both the experimental and wild populations. Our approach may prove useful for detecting epidemics from public health data in regions where standard surveillance techniques are not available and in the study of epidemics in wildlife populations, where longitudinal studies can be especially difficult to implement.

German fishery's adaptation to historic events, Western Baltic Sea, 1890-1950

Marine social-ecological systems (SES) have been providing important cultural, social, and economic services for many centuries. They are, however, increasingly threatened by fast changing environmental, ecological, and socio-economic conditions. As historical marine research is increasingly developing into a multidisciplinary endeavour, it offers outstanding points of departure to analyse historic events and the response and adaptation of the respective SES. Such knowledge helps to inform today's fisheries management and promotes successful management of changing ecosystems. Here, we compile and analyse historical data (1890-1950) of the German Western Baltic Sea fishery SES. This period is characterised by a series of strong impacts due to political, technological, economic, and ecological changes, such as two world wars, a global economic crisis, and other economic or ecological disasters. In our opinion, potential negative effects of those events were in the past attenuated by the system's high capacity to adapt. However, most of the fishers´ historic options on how to respond and adapt have recently become no longer available. New threats (e.g. climate change) have emerged instead. We conclude that today's fisheries management needs to integrate options of adaptation by exhausting all present or future opportunities. Adaptive fisheries management should not only focus on environmental change but need to include socio-economic change as well.

Survey of selected pathogens in free-ranging pinnipeds in Uruguay

Marine mammals, regarded as sentinels of aquatic ecosystem health, are exposed to different pathogens and parasites under natural conditions. We surveyed live South American fur seals Arctocephalus australis and South American sea lions Otaria flavescens in Uruguay for Leptospira spp., canine distemper virus (CDV), Mycobacterium spp., Toxoplasma gondii, and Neospora caninum. Samples were collected from 2007 to 2013. The seroprevalence of Leptospira spp. was 37.6% positive, 50.9% negative, and 11.5% suspect for A. australis (n = 61) while for O. flavescens (n = 12) it was 67% positive, 25% negative, and 8% suspect. CDV RNA was not detected in any of the analyzed samples. Most animals tested seropositive to tuberculosis antigens by WiZo ELISA (A. australis: 29/30; O. flavescens: 20/20); reactivity varied with a novel ELISA test (antigens MPB70, MPB83, ESAT6 and MPB59). Seroprevalence against N. caninum and T. gondii was 6.7 and 13.3% positive for O. flavescens and 0 and 2.2% positive for A. australis respectively. To evaluate possible sources of infection for pinnipeds, wild rats Rattus rattus and semi-feral cats Felis catus were also tested for Leptospira spp. and T. gondii respectively. Water samples tested for Leptospira revealed saprofitic L. bioflexa. Pathogenic Leptospira were detected in the kidneys of 2 rats, and cats tested positive for T. gondii (100%). These results represent a substantial contribution to the study of the health status of wild pinnipeds in Uruguay.

Sequence diversity and differences at the highly duplicated MHC-I gene reflect viral susceptibility in sympatric pinniped species

Differences in disease susceptibility among species can result from rapid host-pathogen coevolution and differences in host species ecology that affect the strength and direction of natural selection. Among two sympatric pinniped species that differ in sociality and putative disease exposure, we investigate observed differences in susceptibility through an analysis of a highly variable, duplicated gene family involved in the vertebrate immune response. Using high-throughput amplicon sequencing, we characterize diversity at the two exons that encode the peptide binding region of the major histocompatibility complex class I (MHC-I) gene in harbor (N = 60) and gray (N = 90) seal populations from the Northwest Atlantic. Across species, we identified 106 full-length exon 2 and 103 exon 3 sequence variants and a minimum of 11 duplicated MHC-I loci. The sequence variants clustered in 15 supertypes defined by the physiochemical properties of the peptide binding region, including a putatively novel Northwest Atlantic MHC-I diversity sublineage. Trans-species polymorphisms, dN/dS ratios, and evidence of gene conversion among supertypes are consistent with balancing selection acting on this gene. High functional redundancy suggests particularly strong selection among gray seals at the novel Northwest Atlantic MHC-I diversity sublineage. At exon 2, harbor seals had a significantly greater number of variants per individual than gray seals, but fewer supertypes. Supertype richness and private supertypes are hypothesized to contribute to observed differences in disease resistance between species, as consistently, across the North Atlantic and many disease outbreaks, gray seals appear to be more resistant to respiratory viruses than harbor seals.

Origin and expansion of the world's most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina)

The harbour seal (Phoca vitulina) is the most widely distributed pinniped, occupying a wide variety of habitats and climatic zones across the Northern Hemisphere. Intriguingly, the harbour seal is also one of the most philopatric seals, raising questions as to how it colonised virtually the whole of the Northern Hemisphere. To shed light on the origin, remarkable range expansion, population structure and genetic diversity of this species, we used genotyping-by-sequencing to analyse ~13,500 biallelic SNPs from 286 individuals sampled from 22 localities across the species' range. Our results point to a Northeast Pacific origin, colonisation of the North Atlantic via the Canadian Arctic, and subsequent stepping-stone range expansions across the North Atlantic from North America to Europe, accompanied by a successive loss of genetic diversity. Our analyses further revealed a deep divergence between modern North Pacific and North Atlantic harbour seals, with finer-scale genetic structure at regional and local scales consistent with strong philopatry. The study provides new insights into the harbour seal's remarkable ability to colonise and adapt to a wide range of habitats. Furthermore, it has implications for current harbour seal subspecies delineations and highlights the need for international and national red lists and management plans to ensure the protection of genetically and demographically isolated populations.

Blast injury on harbour porpoises (Phocoena phocoena) from the Baltic Sea after explosions of deposits of World War II ammunition

Harbour porpoises are under pressure from increasing human activities. This includes the detonation of ammunition that was dumped in large amounts into the sea during and after World War II. In this context, forty-two British ground mines from World War II were cleared by means of blasting in the period from 28 to 31 August 2019 by a NATO unit in the German Exclusive Economic Zone within the marine protected area of Fehmarn Belt in the Baltic Sea, Germany. Between September and November 2019, 24 harbour porpoises were found dead in the period after those clearing events along the coastline of the federal state of Schleswig-Holstein and were investigated for direct and indirect effects of blast injury. Health evaluations were conducted including examinations of the brain, the air-filled (lungs and gastrointestinal tract) and acoustic organs (melon, acoustic fat in the lower jaw, ears and their surrounding tissues). The bone structure of the tympano-periotic complexes was examined using high-resolution peripheral quantitative computed tomography (HR-pQCT). In 8/24 harbour porpoises, microfractures of the malleus, dislocation of middle ear bones, bleeding, and haemorrhages in the melon, lower jaw and peribullar acoustic fat were detected, suggesting blast injury. In addition, one bycaught animal and another porpoise with signs of blunt force trauma also showed evidence of blast injury. The cause of death of the other 14 animals varied and remained unclear in two individuals. Due to the vulnerability and the conservation status of harbour porpoise populations in the Baltic Sea, noise mitigation measures must be improved to prevent any risk of injury. The data presented here highlight the importance of systematic investigations into the acute and chronic effects of blast and acoustic trauma in harbour porpoises, improving the understanding of underwater noise effects and herewith develop effective measures to protect the population level.

Pathological Findings in Eurasian Otters (Lutra lutra) Found Dead between 2015-2020 in Schleswig-Holstein, Germany

In times of massive biodiversity loss and ongoing environmental crises, it is extremely important to ensure long-term conservation efforts of threatened species like Eurasian otters (Lutra lutra). To gain insights into the status of Northern Germany's otter population, 92 otters found dead in Schleswig-Holstein between 2015-2020 were collected and underwent detailed dissection with the aim to establish a monitoring program for this population. Examinations followed a protocol especially designed for otters, including various biological data assessments and extended sampling. The finding sites showed a clear concentration in the Continental region. Seasonal concentration differed among the years, yet peaks were seen from fall to winter. Overall, more males than females were found, although this differed among the years. The majority of otters that could be aged were between 1-3 years. Placental scars and pregnancy were recorded in only few females. Nutritional status was good in most cases. Infectious diseases found included Vagococcus lutrae, Toxoplasma gondii, and Emmonsia spp. A major cause of death was roadkill. Known sample bias in studies focusing on roadkill was considered in the finding interpretation. Continuation of the population health investigations is mandatory to analyze potential trends and to establish an actual monitoring program for Eurasian otters in Schleswig-Holstein.

Longitudinal analysis of pinnipeds in the northwest Atlantic provides insights on endemic circulation of phocine distemper virus

Phocine distemper virus (PDV) is a morbillivirus that circulates within pinnipeds in the North Atlantic. PDV has caused two known unusual mortality events (UMEs) in western Europe (1988, 2002), and two UMEs in the northwest Atlantic (2006, 2018). Infrequent cross-species transmission and waning immunity are believed to contribute to periodic outbreaks with high mortality in western Europe. The viral ecology of PDV in the northwest Atlantic is less well defined and outbreaks have exhibited lower mortality than those in western Europe. This study sought to understand the molecular and ecological processes underlying PDV infection in eastern North America. We provide phylogenetic evidence that PDV was introduced into northwest Atlantic pinnipeds by a single lineage and is now endemic in local populations. Serological and viral screening of pinniped surveillance samples from 2006 onward suggest there is continued circulation of PDV outside of UMEs among multiple species with and without clinical signs. We report six full genome sequences and nine partial sequences derived from harbour and grey seals in the northwest Atlantic from 2011 through 2018, including a possible regional variant. Work presented here provides a framework towards greater understanding of how recovering populations and shifting species may impact disease transmission.

Emergence and radiation of distemper viruses in terrestrial and marine mammals

Canine distemper virus (CDV) and phocine distemper virus (PDV) are major pathogens to terrestrial and marine mammals. Yet little is known about the timing and geographical origin of distemper viruses and to what extent it was influenced by environmental change and human activities. To address this, we (i) performed the first comprehensive time-calibrated phylogenetic analysis of the two distemper viruses, (ii) mapped distemper antibody and virus detection data from marine mammals collected between 1972 and 2018, and (iii) compiled historical reports on distemper dating back to the eighteenth century. We find that CDV and PDV diverged in the early seventeenth century. Modern CDV strains last shared a common ancestor in the nineteenth century with a marked radiation during the 1930s-1950s. Modern PDV strains are of more recent origin, diverging in the 1970s-1980s. Based on the compiled information on distemper distribution, the diverse host range of CDV and basal phylogenetic placement of terrestrial morbilliviruses, we hypothesize a terrestrial CDV-like ancestor giving rise to PDV in the North Atlantic. Moreover, given the estimated timing of distemper origin and radiation, we hypothesize a prominent role of environmental change such as the Little Ice Age, and human activities like globalization and war in distemper virus evolution.

Measuring reproducibility of virus metagenomics analyses using bootstrap samples from FASTQ-files

MOTIVATION

High-throughput sequencing data can be affected by different technical errors, e.g. from probe preparation or false base calling. As a consequence, reproducibility of experiments can be weakened. In virus metagenomics, technical errors can result in falsely identified viruses in samples from infected hosts. We present a new resampling approach based on bootstrap sampling of sequencing reads from FASTQ-files in order to generate artificial replicates of sequencing runs which can help to judge the robustness of an analysis. In addition, we evaluate a mixture model on the distribution of read counts per virus to identify potentially false positive findings.

RESULTS

The evaluation of our approach on an artificially generated dataset with known viral sequence content shows in general a high reproducibility of uncovering viruses in sequencing data, i.e. the correlation between original and mean bootstrap read count was highly correlated. However, the bootstrap read counts can also indicate reduced or increased evidence for the presence of a virus in the biological sample. We also found that the mixture-model fits well to the read counts, and furthermore, it provides a higher accuracy on the original or on the bootstrap read counts than on the difference between both. The usefulness of our methods is further demonstrated on two freely available real-world datasets from harbor seals.

AVAILABILITY AND IMPLEMENTATION

We provide a Phyton tool, called RESEQ, available from https://github.com/babaksaremi/RESEQ that allows efficient generation of bootstrap reads from an original FASTQ-file.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Tooth Microwear Texture in the Eastern Atlantic Harbour Seals (Phoca vitulina vitulina) of the German Wadden Sea and Its Implications for Long Term Dietary and Ecosystem Changes

Marine mammals are increasingly threatened in their habitat by various anthropogenic impacts. This is particularly evident in prey abundance. Understanding the dietary strategies of marine mammal populations can help predict implications for their future health status and is essential for their conservation. In this study we provide a striking example of a new dietary proxy in pinnipeds to document marine mammal diets using a dental record. In this novel approach, we used a combination of 49 parameters to establish a dental microwear texture (DMTA) as a dietary proxy of feeding behaviour in harbour seals. This method is an established approach to assess diets in terrestrial mammals, but has not yet been applied to pinnipeds. Our aim was to establish a protocol, opening DMTA to pinnipeds by investigating inter- and intra-individual variations. We analysed the 244 upper teeth of 78 Atlantic harbour seals (Phoca vitulina vitulina). The specimens were collected in 1988 along the North Sea coast (Wadden Sea, Germany) and are curated by the Zoological Institute of Kiel University, Germany. An increasing surface texture roughness from frontal to distal teeth was found and related to different prey processing biomechanics. Ten and five year old individuals were similar in their texture roughness, whereas males and females were similar to each other with the exception of their frontal dentition. Fall and summer specimens also featured no difference in texture roughness. We established the second to fourth postcanine teeth as reference tooth positions, as those were unaffected by age, sex, season, or intra-individual variation. In summary, applying indirect dietary proxies, such as DMTA, will allow reconstructing dietary traits of pinnipeds using existing skeletal collection material. Combining DMTA with time series analyses is a very promising approach to track health status in pinniped populations over the last decades. This approach opens new research avenues and could help detect dietary shifts in marine environments in the past and the future.

Drivers and constraints on offshore foraging in harbour seals

Central place foragers are expected to offset travel costs between a central place and foraging areas by targeting productive feeding zones. Harbour seals (Phoca vitulina) make multi-day foraging trips away from coastal haul-out sites presumably to target rich food resources, but periodic track points from telemetry tags may be insufficient to infer reliably where, and how often, foraging takes place. To study foraging behaviour during offshore trips, and assess what factors limit trip duration, we equipped harbour seals in the German Wadden Sea with high-resolution multi-sensor bio-logging tags, recording 12 offshore trips from 8 seals. Using acceleration transients as a proxy for prey capture attempts, we found that foraging rates during travel to and from offshore sites were comparable to offshore rates. Offshore foraging trips may, therefore, reflect avoidance of intra-specific competition rather than presence of offshore foraging hotspots. Time spent resting increased by approx. 37 min/day during trips suggesting that a resting deficit rather than patch depletion may influence trip length. Foraging rates were only weakly correlated with surface movement patterns highlighting the value of integrating multi-sensor data from on-animal bio-logging tags (GPS, depth, accelerometers and magnetometers) to infer behaviour and habitat use.

Life cycle bioenergetics of the gray seal (Halichoerus grypus) in the Baltic Sea: Population response to environmental stress

Wildlife population dynamics are shaped by multiple natural and anthropogenic factors, including predation, competition, stressful life history events, and external environmental stressors such as diseases and pollution. Marine mammals such as gray seals rely on extensive blubber layers for insulation and energy storage, making this tissue critical for survival and reproduction. This lipid rich blubber layer also accumulates hazardous fat soluble pollutants, such as polychlorinated biphenyls (PCBs), that can directly impact adipose function or be mobilized during periods of negative energy balance or transferred to offspring to exert further impacts on target tissues or vulnerable life stages. To predict how marine mammals will respond to ecological and anthropogenic stressors, it is necessary to use process-based modelling approaches that integrate environmental inputs, full species life history, and stressor impacts with individual dynamics of energy intake, storage, and utilization. The purpose of this study was to develop a full lifecycle dynamic energy budget and individual based model (DEB-IBM) that captured Baltic gray seal physiology and life history, and showcase potential applications of the model to predict population responses to select stressors known to threaten gray seals and other marine mammals around the world. We explore variations of three ecologically important stressors using phenomenological simulations: food limitation, endocrine disrupting chemicals that reduce fertility, and infectious disease. Using our calibrated DEB-IBM for Baltic gray seals, we found that continuous incremental food limitation can be more detrimental to population size than short random events of starvation, and further, that the effect of endocrine disruptors on population growth and structure is delayed due to bioaccumulation, and that communicable diseases significantly decrease population growth even when spillover events are relatively less frequent. One important finding is the delayed effect on population growth rate from some stressors, several years after the exposure period, resulting from a decline in somatic growth, increased age at maturation and decreased fecundity. Such delayed responses are ignored in current models of population viability and can be important in the correct assessment of population extinction risks. The model presented here provides a test bed on which effects of new hazardous substances and different scenarios of future environmental change affecting food availability and/or seal energetic demands can be investigated. Thus, the framework provides a tool for better understanding how diverse environmental stressors affect marine mammal populations and can be used to guide scientifically based management.

Male grey seal commits fatal sexual interaction with adult female harbour seals in the German Wadden Sea

Males of several seal species are known to show aggressive copulating behaviour, which can lead to injuries to or suffocation of females. In the North Sea, grey seal predation on harbour seals including sexual harassment is documented and represents violent interspecific interaction. In this case series, we report pathological and molecular/genetic findings of 11 adult female harbour seals which were found dead in Schleswig–Holstein, Germany, within 41 days. Several organs of all animals showed haemorrhages and high loads of bacteria, indicating their septic spread. All females were pregnant or had recently been pregnant. Abortion was confirmed in three cases. Lacerations were seen in the uterus and vagina in six cases, in which histology of three individuals revealed severe suppurative inflammation with intralesional spermatozoa. Molecular analysis of vaginal swabs and paraffin-embedded samples of the vagina identified grey seal DNA, suggesting violent interspecific sexual interaction with fatal outcome due to septicaemia. This is the first report of female harbour seals dying after coercive copulation by a male grey seal in the Wadden Sea.

Unchartered waters: Climate change likely to intensify infectious disease outbreaks causing mass mortality events in marine mammals

Infectious disease emergence has increased significantly over the last 30 years, with mass mortality events (MMEs) associated with epizootics becoming increasingly common. Factors influencing these events have been widely studied in terrestrial systems, but remain relatively unexplored in marine mammals. Infectious disease-induced MMEs (ID MMEs) have not been reported ubiquitously among marine mammal species, indicating that intrinsic (host) and/or extrinsic (environmental) ecological factors may influence this heterogeneity. We assess the occurrence of ID MMEs (1955-2018) across extant marine mammals (n = 129) in relation to key life-history characteristics (sociality, trophic level, habitat breadth) and environmental variables (season, sea surface temperature [SST] anomalies, El Niño occurrence). Our results show that ID MMEs have been reported in 14% of marine mammal species (95% CI 9%-21%), with 72% (n = 36; 95% CI 56%-84%) of these events caused predominantly by viruses, primarily morbillivirus and influenza A. Bacterial pathogens caused 25% (95% CI 14%-41%) of MMEs, with only one being the result of a protozoan pathogen. Overall, virus-induced MMEs involved a greater number of fatalities per event compared to other pathogens. No association was detected between the occurrence of ID MMEs and host characteristics, such as sociality or trophic level, but ID MMEs did occur more frequently in semiaquatic species (pinnipeds) compared to obligate ocean dwellers (cetaceans; χ²  = 9.6, p = .002). In contrast, extrinsic factors significantly influenced ID MMEs, with seasonality linked to frequency (χ²  = 19.85, p = .0002) and severity of these events, and global yearly SST anomalies positively correlated with their temporal occurrence (Z = 3.43, p = 2.7e-04). No significant association was identified between El Niño and ID MME occurrence (Z = 0.28, p = .81). With climate change forecasted to increase SSTs and the frequency of extreme seasonal weather events, epizootics causing MMEs are likely to intensify with significant consequences for marine mammal survival.

Evolutionary history of a Scottish harbour seal population

Efforts to conserve marine mammals are often constrained by uncertainty over their population history. Here, we examine the evolutionary history of a harbour seal (Phoca vitulina) population in the Moray Firth, northeast Scotland using genetic tools and microsatellite markers to explore population change. Previous fine-scale analysis of UK harbour seal populations revealed three clusters in the UK, with a northeastern cluster that included our Moray Firth study population. Our analysis revealed that the Moray Firth cluster is an independent genetic group, with similar levels of genetic diversity across each of the localities sampled. These samples were used to assess historic abundance and demographic events in the Moray Firth population. Estimates of current genetic diversity and effective population size were low, but the results indicated that this population has remained at broadly similar levels following the population bottleneck that occurred after post-glacial recolonization of the area.

Perturbation drives changing metapopulation dynamics in a top marine predator

Metapopulation theory assumes a balance between local decays/extinctions and local growth/new colonisations. Here we investigate whether recent population declines across part of the UK harbour seal range represent normal metapopulation dynamics or are indicative of perturbations potentially threatening the metapopulation viability, using 20 years of population trends, location tracking data (n = 380), and UK-wide, multi-generational population genetic data (n = 269). First, we use microsatellite data to show that two genetic groups previously identified are distinct metapopulations: northern and southern. Then, we characterize the northern metapopulation dynamics in two different periods, before and after the start of regional declines (pre-/peri-perturbation). We identify source-sink dynamics across the northern metapopulation, with two putative source populations apparently supporting three likely sink populations, and a recent metapopulation-wide disruption of migration coincident with the perturbation. The northern metapopulation appears to be in decay, highlighting that changes in local populations can lead to radical alterations in the overall metapopulation's persistence and dynamics.

Health effects from contaminant exposure in Baltic Sea birds and marine mammals: A review

Here we review contaminant exposure and related health effects in six selected Baltic key species. Sentinel species included are common eider, white-tailed eagle, harbour porpoise, harbour seal, ringed seal and grey seal. The review represents the first attempt of summarizing available information and baseline data for these biomonitoring key species exposed to industrial hazardous substances focusing on anthropogenic persistent organic pollutants (POPs). There was only limited information available for white-tailed eagles and common eider while extensive information exist on POP exposure and health effects in the four marine mammal species. Here we report organ-tissue endpoints (pathologies) and multiple biomarkers used to evaluate health and exposure of key species to POPs, respectively, over the past several decades during which episodes of significant population declines have been reported. Our review shows that POP exposure affects the reproductive system and survival through immune suppression and endocrine disruption, which have led to population-level effects on seals and white-tailed eagles in the Baltic. It is notable that many legacy contaminants, which have been banned for decades, still appear to affect Baltic wildlife. With respect to common eiders, changes in food composition, quality and contaminant exposure seem to have population effects which need to be investigated further, especially during the incubation period where the birds fast. Since new industrial contaminants continuously leak into the environment, we recommend continued monitoring of them in sentinel species in the Baltic, identifying possible effects linked to climate change, and modelling of population level effects of contaminants and climate change.

Decline and diversity in Swedish seas: Environmental narratives in marine history, science and policy

Before the mid-twentieth century, there was no comprehensive narrative about empirical conditions in Swedish seas. Around 1970, this view changed profoundly. In line with growing research and the emergence of 'the environment' as a defining concept, conditions in Swedish seas were framed as a 'narrative of decline'. Marine scientists have since recorded more diverse developments than are described by an overall declensionist narrative. Data show trends of interrupted decline, variability and even recovery, taking place at least partly in response to effective policy and legislation. We suggest that beyond the specialised fields of marine sciences and marine environmental history, the overarching narrative of decline has persisted, paying little attention to local and regional particularities as well as cultural and political dimensions of the marine environment. This overly uniform narrative risks obscuring historical reality and, hence, fails to adequately inform policy and the public about developments and outcomes of interventions in Swedish seas.

A review of pathogens in selected Baltic Sea indicator species

Here we review the state-of-the-art of pathogens in select marine and terrestrial key species of the Baltic Sea, i.e. ringed seal (Pusa hispida), harbour seal (Phoca vitulina), grey seal (Halichoerus grypus), harbour porpoise (Phocoena phocoena), common eider (Somateria mollissima), pink-footed goose (Anser brachyrhynchus) and white-tailed eagle (Haliaeetus albicilla). This review is the first to merge and present available information and baseline data for the FP7 BONUS BaltHealth project: Baltic Sea multilevel health impacts on key species of anthropogenic hazardous substances. Understanding the spread, prevalence and effects of wildlife pathogens is important for the understanding of animal and ecosystem health, ecosystem function and services, as well as human exposure to zoonotic diseases. This review summarises the occurrence of parasites, viruses and bacteria over the past six decades, including severe outbreaks of Phocine Distemper Virus (PDV), the seroprevalence of Influenza A and the recent increase in seal parasites. We show that Baltic high trophic key species are exposed to multiple bacterial, viral and parasitic diseases. Parasites, such as C. semerme and P. truncatum present in the colon and liver Baltic grey seals, respectively, and anisakid nematodes require particular monitoring due to their effects on animal health. In addition, distribution of existing viral and bacterial pathogens, along with the emergence and spread of new pathogens, need to be monitored in order to assess the health status of key Baltic species. Relevant bacteria are Streptococcus spp., Brucella spp., Erysipelothrix rhusiopathiae, Mycoplasma spp. and Leptospira interrogans; relevant viruses are influenza virus, distemper virus, pox virus and herpes virus. This is of special importance as some of the occurring pathogens are zoonotic and thus also pose a potential risk for human health. Marine mammal handlers, as well as civilians that by chance encounter marine mammals, need to be aware of this risk. It is therefore important to continue the monitoring of diseases affecting key Baltic species in order to assess their relationship to population dynamics and their potential threat to humans. These infectious agents are valuable indicators of host ecology and can act as bioindicators of distribution, migration, diet and behaviour of marine mammals and birds, as well as of climate change and changes in food web dynamics. In addition, infectious diseases are linked to pollutant exposure, overexploitation, immune suppression and subsequent inflammatory disease. Ultimately, these diseases affect the health of the entire ecosystem and, consequently, ecosystem function and services. As global warming is continuously increasing, the impact of global change on infectious disease patterns is important to monitor in Baltic key species in the future.

Intestinal displacements in older harbour and grey seals

Intestinal displacements including volvulus, torsion and invagination have been reported in various terrestrial and marine mammals. We conducted pathological investigations on 157 seals that had either stranded on the coasts of the North or Baltic Sea between 1996 and 2015 (115 harbour seals, >19 mo old; 21 grey seals, >13 mo old) or died while in human care (18 harbour seals, >19 mo old; 3 grey seals, >13 mo old). Intestinal displacements were found in 23% of the examined free-living harbour seals, in 5% of the stranded grey seals and in 17% of the harbour seals in human care. Intestinal volvulus, found in 24 cases, was characterized by twisting of the intestine along the mesenteric axis (180-540°) resulting in vascular obstruction and haemorrhagic infarction. In harbour seals, the sex ratio of individuals suffering from volvulus tended to be biased towards females during April to June, suggesting an elevated risk for pregnant females around birth time. Invagination was detected in 11 cases, 5 of which suffered from additional volvulus. Pathological findings associated with intestinal volvulus and invagination were sero-haemorrhagic effusions in the abdominal cavity. Enteritis, parasitic infection with gastric nematodes and intestinal acanthocephalans and bacterial infection with predominantly Clostridium perfringens and Escherichia coli were observed in most of the affected animals. In total, 30 investigated harbour and grey seals suffered from intestinal displacements. Pregnant females seemed to be more vulnerable around birth time. Causes of intestinal displacements remain undetermined, but are likely multifactorial.

Pathological findings in North Sea and Baltic grey seal and harbour seal intestines associated with acanthocephalan infections

Grey seals Halichoerus grypus and harbour seals Phoca vitulina are common seal species in the North and Baltic seas and final hosts of Corynosoma acanthocephalans. C. strumosum and C. magdaleni infect the small intestines of both seal species. In contrast to harbour seals, Baltic grey seals in the past have regularly displayed severe C. semerme infections in the caecum and colon, with associated tunica muscularis hypertrophy, inflammation and ulcerations as part of the Baltic seal disease complex (BSDC). Pathogenesis and correlation of acanthocephalan infections with these lesions are still unknown. This study describes the intestinal pathology and parasitic distribution in each seal species. Grey seal (n = 83) and harbour seal (n = 1156) intestines of all age groups and sexes, collected in Poland, Germany and Estonia from 1998 to 2017, were investigated. Most harbour seals came from the North Sea, whereas grey seals were predominantly derived from the Baltic Sea. Both species featured mild to moderate small intestinal infections. Grey seals showed colonic infections not found in harbour seals and featured a chronic erosive to ulcerative, eosinophilic or lympho-plasmacytic colitis with tunica muscularis hypertrophy, indicating still prevailing clinical signs of the BSDC. Harbour seals displayed granulomatous, eosinophilic, lympho-plasmacytic or catarrhal enteritis. The prevalence of acanthocephalan infections in harbour seals increased from 2012 onwards. Furthermore, significant associations between acanthocephalan infection and the presence of intestinal inflammation were found for both seal species. This study suggests that the level of acanthocephalan infection and associated lesions are suitable seal population health indicators, with the colon being a specific target organ for Baltic grey seal health monitoring.

Detection and Preliminary Characterization of Phocine Distemper Virus in a Stranded Harp Seal (Pagophilus groenlandicus) from the Gulf of St. Lawrence, Canada

A lethargic juvenile male harp seal (Pagophilus groenlandicus) in poor nutritional condition was found on the beach on the north shore of Prince Edward Island, Canada, in June 2017. Microscopic examination revealed a severe nonsuppurative encephalitis positive for morbillivirus antigen on immunohistochemistry. Virus isolation attempts were negative. However, phocine distemper virus (PDV) was detected in brain tissue RNA extracts by a seminested reverse transcription PCR that targeted the paramyxovirus RNA-dependent RNA polymerase (pol) gene. Comparison of the resulting partial PDV pol nucleotide sequence revealed it was nearly identical to PDV strains isolated from eastern Atlantic harbor seals (Phoca vitulina vitulina) during a 1988 epizootic in the Wadden and Irish seas, and a western Atlantic harbor seal (Phoca vitulina concolor) that stranded in Maine, US, in 2006. Our study confirmed that closely related PDV strains are circulating in multiple seal species along the coastlines of North America and Europe.

Pathological findings and survey for pathogens associated with reproductive failure in perinatal Steller sea lions Eumetopias jubatus

Steller sea lions (SSLs) Eumetopias jubatus experienced a population decline in the 1960s, leading to the listing of the western stock as endangered and the eastern stock as threatened under the US Endangered Species Act. A decrease of births in the western stock beginning in the late 1960s indicates that reproductive failure may have contributed to the decline. We evaluated the role pathogens play in spontaneous abortions, premature births and neonatal deaths in SSLs. Archived tissues from carcasses (n = 19) collected in Alaska from 2002 to 2015 were tested by PCR for Coxiella burnetii, Brucella spp., Chlamydia and morbilliviruses. Animals examined included 47% premature pups, 32% aborted fetuses, 11% neonates and 11% intrauterine fetuses. Gross necropsy and histology findings were summarized in the context of the PCR findings. Tissues were negative for Chlamydia and C. burnetii. Brucella spp. were detected in the lung tissues of 3 animals, including 1 positive for the ST27 strain, the first detection of Brucella spp. DNA in SSLs. Phocine distemper virus was detected in 3 animals in 2 skin lesions and 1 placenta by hemi-nested diagnostic qRT-PCR. Both skin and the placental lesions had vesiculoulcerative changes, and 1 skin lesion contained inclusion bodies in syncytia and upon histologic examination, suggesting that the lesions may be associated with an infection reminiscent of phocine distemper virus, the first in SSLs. We highlight the continuing need for disease surveillance programs to improve our understanding of the prevalence and potential population impacts of these infectious disease agents for pinnipeds in Alaskan waters.

Viral emergence in marine mammals in the North Pacific may be linked to Arctic sea ice reduction

Climate change-driven alterations in Arctic environments can influence habitat availability, species distributions and interactions, and the breeding, foraging, and health of marine mammals. Phocine distemper virus (PDV), which has caused extensive mortality in Atlantic seals, was confirmed in sea otters in the North Pacific Ocean in 2004, raising the question of whether reductions in sea ice could increase contact between Arctic and sub-Arctic marine mammals and lead to viral transmission across the Arctic Ocean. Using data on PDV exposure and infection and animal movement in sympatric seal, sea lion, and sea otter species sampled in the North Pacific Ocean from 2001-2016, we investigated the timing of PDV introduction, risk factors associated with PDV emergence, and patterns of transmission following introduction. We identified widespread exposure to and infection with PDV across the North Pacific Ocean beginning in 2003 with a second peak of PDV exposure and infection in 2009; viral transmission across sympatric marine mammal species; and association of PDV exposure and infection with reductions in Arctic sea ice extent. Peaks of PDV exposure and infection following 2003 may reflect additional viral introductions among the diverse marine mammals in the North Pacific Ocean linked to change in Arctic sea ice extent.

Genomics of host-pathogen interactions: challenges and opportunities across ecological and spatiotemporal scales

Evolutionary genomics has recently entered a new era in the study of host-pathogen interactions. A variety of novel genomic techniques has transformed the identification, detection and classification of both hosts and pathogens, allowing a greater resolution that helps decipher their underlying dynamics and provides novel insights into their environmental context. Nevertheless, many challenges to a general understanding of host-pathogen interactions remain, in particular in the synthesis and integration of concepts and findings across a variety of systems and different spatiotemporal and ecological scales. In this perspective we aim to highlight some of the commonalities and complexities across diverse studies of host-pathogen interactions, with a focus on ecological, spatiotemporal variation, and the choice of genomic methods used. We performed a quantitative review of recent literature to investigate links, patterns and potential tradeoffs between the complexity of genomic, ecological and spatiotemporal scales undertaken in individual host-pathogen studies. We found that the majority of studies used whole genome resolution to address their research objectives across a broad range of ecological scales, especially when focusing on the pathogen side of the interaction. Nevertheless, genomic studies conducted in a complex spatiotemporal context are currently rare in the literature. Because processes of host-pathogen interactions can be understood at multiple scales, from molecular-, cellular-, and physiological-scales to the levels of populations and ecosystems, we conclude that a major obstacle for synthesis across diverse host-pathogen systems is that data are collected on widely diverging scales with different degrees of resolution. This disparity not only hampers effective infrastructural organization of the data but also data granularity and accessibility. Comprehensive metadata deposited in association with genomic data in easily accessible databases will allow greater inference across systems in the future, especially when combined with open data standards and practices. The standardization and comparability of such data will facilitate early detection of emerging infectious diseases as well as studies of the impact of anthropogenic stressors, such as climate change, on disease dynamics in humans and wildlife.

Insights Into Dolphins' Immunology: Immuno-Phenotypic Study on Mediterranean and Atlantic Stranded Cetaceans

Immunology of marine mammals is a relatively understudied field and its monitoring plays an important role in the individual and group management of these animals, along with an increasing value as an environmental health indicator. This study was aimed at implementing the knowledge on the immune response in cetaceans stranded along the Italian coastline to provide a baseline useful for assessing the immune status of bottlenose (Tursiops truncatus) and striped (Stenella coeruleoalba) dolphins. In particular, since the Mediterranean Sea is considered a heavily polluted basin, a comparison with animals living in open waters such as the Atlantic Ocean was made. Formalin-fixed, paraffin-embedded spleen, thymus, and lymph node tissues from 16 animals stranded along Italian and 11 cetaceans from the Canary Island shores were sampled within 48 h from death. Information regarding stranding sites, gender, and age as well as virologic, microbiological, and parasitological investigations, and the cause and/or the death mechanism were also collected in order to carry out statistical analyses. Selected tissues were routinely stained with hematoxylin-eosin (H&E) and with immunohistochemical techniques (IHC). For IHC analysis, anti-human CD5 monoclonal mouse antibody to identify T lymphocytes, CD20 monoclonal mouse antibody for the identification of mature B lymphocytes and HLA-DR antigen (alpha-chain) monoclonal mouse antibody for the identification of the major histocompatibility complex type II were previously validated for both species by Western-blotting technique. T-test method applied to quantitative evaluation of IHC positive cells showed a significant relationship between the number of (expression) of CD20 stained lymphocytes and normal and hypoplastic lymph nodes, respectively. No other significant correlations were noticed. Analyses for organochlorines (OC) compounds were performed in animals (n°5) having frozen blubber tissue available. A simple linear regression was calculated to predict if the amount of OCs could influence the number of inflammatory cell subpopulations and a moderate negative correlation was found between the presence of high quantity of contaminants and the number of T lymphocytes. Future analysis should be aimed to understand the effect of the major immunomodulatory pathogens on sub-populations of B and T cells.

Phylogenomic insights to the origin and spread of phocine distemper virus in European harbour seals in 1988 and 2002

The 1988 and 2002 phocine distemper virus (PDV) outbreaks in European harbour seals Phoca vitulina are among the largest mass mortality events recorded in marine mammals. Despite its large impact on harbour seal population numbers, and 3 decades of studies, many questions regarding the spread and temporal origin of PDV remain unanswered. Here, we sequenced and analysed 7123 bp of the PDV genome, including the coding and non-coding regions of the entire P, M, F and H genes in tissues from 44 harbour seals to shed new light on the origin and spread of PDV in 1988 and 2002. The phylogenetic analyses trace the origin of the PDV strain causing the 1988 outbreak to between May 1987 and April 1988, while the origin of the strain causing the 2002 outbreak can be traced back to between June 2001 and May 2002. The analyses further point to several independent introductions of PDV in 1988, possibly linked to a southward mass immigration of harp seals in the winter and spring of 1987-1988. The vector for the 2002 outbreak is unknown, but the epidemiological analyses suggest the subsequent spread of PDV from the epicentre in the Kattegat, Denmark, to haul-out sites in the North Sea through several independent introductions.

Evaluating exposure of northern fur seals, Callorhinus ursinus, to microplastic pollution through fecal analysis

Environmental microplastics are widely documented in marine life and bioaccumulation may present risks to marine predators. Investigations of microplastics in marine mammals are increasing, though none have examined animals routinely consumed by humans. Here, we investigate microplastic exposure in the northern fur seal (Callorhinus ursinus), a species consumed by humans, using fecal material. We examined 44 feces (scat) at sites encompassing the seals' eastern Pacific range. Multiple contamination control measures were implemented, including field and laboratory controls. Fragments were the most common microplastic recovered, in 55% (24/44) of scat and no controls (range 1 to 86 fragments/scat, mean 16.6, sd 19.1). Microplastic fibers were recovered from 41% of scats (18/44), though some controls contained fibers confounding fiber results. Fecal analysis documented northern fur seal exposure to microplastics throughout their eastern Pacific range.

Dental anomalies and lesions in Eastern Atlantic harbor seals, Phoca vitulina vitulina (Carnivora, Phocidae), from the German North Sea

Skulls of 1,901 Eastern Atlantic harbor seals (Phoca vitulina vitulina) were systematically studied for externally visible dental anomalies and lesions. The sample comprised 927 males and 974 female individuals, with age at death ranging between 1 week and 25 years. Most of the skulls originated from animals collected in 1988, when the population suffered from a mass mortality event caused by the phocine distemper virus (PDV). Mean age (± SD) of females (6.7 ± 6.4 years) was higher (p = 0.002) than that of males (5.9 ± 5.2 years). In 264 individuals, one or more teeth were missing either congenitally (n = 26 animals, 1.4%) or due to intravital loss (n = 238 animals, 12.5%). One male exhibited congenital absence of all teeth (anodontia). As this animal had been reported to be almost hairless, the condition was tentatively diagnosed as a case of hypohidrotic ectodermal dysplasia. Males were more frequently (p = 0.002) affected by intravital tooth loss (15.0%) than females (10.2%). Supernumerary teeth were found in 3.4% of the skulls, with females (4.7%) showing hyperodontia more frequently (p < 0.001) than males (1.9%). Fifty-nine individuals (3.1%; 28 males, 31 females, p = 0.84) exhibited abnormal tooth morphology. Tooth fractures were noted in 40 seals (2.1%), with males being more frequently affected than females (p = 0.017). Periapical lesions were diagnosed in 143 skulls, with a tendency (p = 0.05) for males (8.7%) to be more frequently affected than females (6.4%). Enamel hypoplasia was not observed in the study sample. Analyzing the occurrence of dental anomalies and lesions in wild mammals can substantially contribute to an assessment of population health and thereby broaden the basis for effective species conservation and informed management decisions.

Avian cholera outbreaks threaten seabird species on Amsterdam Island

Infectious diseases may be particularly critical for the conservation of endangered species. A striking example is the recurrent outbreaks that have been occurring in seabirds on Amsterdam Island for the past 30 years, threatening populations of three Endangered seabird species and of the endemic, Critically Endangered Amsterdam albatross Diomedea amsterdamensis. The bacteria Pasteurella multocida (avian cholera causative agent), and to a lesser extent Erysipelothrix rhusiopathiae (erysipelas causative agent), were both suspected to be responsible for these epidemics. Despite this critical situation, demographic trends were not available for these threatened populations, and the occurrence and characterization of potential causative agents of epizootics remain poorly known. The aims of the current study were to (i) provide an update of population trends for four threatened seabird species monitored on Amsterdam Island, (ii) assess the occurrence of P. multocida, and E. rhusiopathiae in live birds from five species, (iii) search for other infectious agents in these samples and, (iv) isolate and genotype the causative agent(s) of epizooties from dead birds. Our study shows that the demographic situation has worsened substantially in three seabird species during the past decade, with extremely low reproductive success and declining populations for Indian yellow-nosed albatrosses Thalassarche carteri, sooty albatrosses Phoebetria fusca, and northern rockhopper penguins Eudyptes moseleyi. Pasteurella multocida or E. rhusiopathiae were detected by PCR in live birds of all five investigated species, while results were negative for eight additional infectious agents. A single strain of P. multocida was repeatedly cultured from dead birds, while no E. rhusiopathiae could be isolated. These results highlight the significance of P. multocida in this particular eco-epidemiological system as the main agent responsible for epizootics. The study stresses the urgent need to implement mitigation measures to alter the course of avian cholera outbreaks threatening the persistence of seabird populations on Amsterdam Island.

Osteoarthritis of the temporomandibular joint in the Eastern Atlantic harbour seal (Phoca vitulina vitulina) from the German North Sea: a study of the lesions seen in dry bone

BACKGROUND

Pathological changes and resulting functional impairment of the temporomandibular joint (TMJ) can substantially affect physical condition, morbidity, and mortality of wildlife species. Analysis of TMJ disorders is therefore of interest for the characterization of the health status of populations of wild mammals. This paper, for the first time, analyses the prevalence of TMJ osteoarthritis (TMJ-OA) and the spectrum of osteoarthritic bone lesions of the TMJ in the Eastern Atlantic harbour seal (Phoca vitulina vitulina), applying a standardized scoring system. Dry skulls of 1872 individuals from the German North Sea, collected between 1961 and 1994, were examined for lesions consistent with a diagnosis of TMJ-OA. Of the skulls, 913 (48.8%) were from male, 959 (51.2%) from female seals, with age at death ranging from 2 weeks to 25 years. Possible associations of TMJ-OA with dental or periodontal disorders were also analysed.

RESULTS

Lesions consistent with TMJ-OA were found in 963 (53.9%) of the 1787 juvenile/subadult (5 weeks to 5 years of age) and adult (> 5 years) specimens, the condition mostly (95.0% of affected individuals) occurring in a bilateral fashion. Males were affected more frequently than females (p < 0.001), while lesion severity tended to be higher in females (p < 0.05). Severity of TMJ-OA lesions was positively correlated with age (p < 0.001). Lesion severity was also weakly positively correlated with the number of fractured teeth (p < 0.05) and of intravitally lost teeth (p < 0.01), when controlling for age at death as a confounder.

CONCLUSIONS

TMJ-OA is a common disorder in the Eastern Atlantic harbour seal. The more pronounced severity of the lesions in females compared to males is basically attributed to the higher average age of the female subsample. The causes underlying the high prevalence of TMJ-OA in the studied assemblage remain unknown. Most of the specimens (75.3%) analysed in the present study were found dead during the first phocine distemper virus epizootic in 1988. Therefore, it is assumed that, contrary to other museum collections, only little overrepresentation of pathological skeletal conditions is present in this death sample compared with the population from which it originated.

T lymphocyte-proliferative responses of harbor seal (Phoca vitulina) peripheral blood mononuclear cells (PBMCs) exposed to pharmaceuticals in vitro

The ubiquity of pharmaceuticals in the aquatic environment and the accumulation in organisms of lower trophic levels have been documented. The immunotoxicity of these xenobiotics has however been little investigated. This study assessed the effects of pharmaceuticals on the immune responses of harbor seal lymphocytes. Peripheral blood mononuclear cells isolated from harbor seal pups were exposed to varying concentrations of 17α-ethinyl estradiol (250-50,000μg/L), naproxen (500-100,000μg/L), carbamazepine (500-100,000μg/L), erythromycin (750-150,000μg/L) and binary mixtures thereof in vitro. All individual compounds and mixtures inhibited lymphocyte proliferation. Mixture effects were non-additive and predictive values overestimated the inhibition of proliferation. Male pups were more sensitive to erythromycin exposure. Comparison with the sensitivity of the 11B7501 cell line showed a higher sensitivity of pups to individual compounds and the inverse trend for mixtures. Based on our results, we hypothesize that pharmaceuticals may have the potential to interrupt immune functions in harbor seals.