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.

The Genome Assembly and Annotation of the Southern Elephant Seal Mirounga leonina.

The southern elephant seal Mirounga leonina is the largest phocid seal and one of the two species of elephant seals. They are listed as 'least concern' by the International Union for Conservation of Nature (IUCN) Red List of Threatened Species 2015. Here, we have assembled the reference genome for M. leonina using the 10× chromium sequencing platform. The final genome assembly of M. leonina was 2.42 Gb long, with a contig N50 length of 54 Mb and a maximum length of 111.6 Mb. The M. leonina genome contained 20,457 predicted protein-coding genes and possessed 41.51% repeated sequences. The completeness of the M. leonina genome was evaluated using benchmarking universal single-copy orthologous genes (BUSCOs): the assembly was highly complete, containing 95.6% of the core set of mammalian genes. The high-quality genomic information on M. leonina will be essential for further understanding of adaptive metabolism upon repeated breath-hold dives and the exploration of molecular mechanisms contributing to its unique biochemical and physiological characteristics. The southern elephant seal genome project was deposited at NCBI (National Center for Biotechnology Information) under BioProject number PRJNA587380.

Complementary methods assessing short and long-term prey of a marine top predator ‒ Application to the grey seal-fishery conflict in the Baltic Sea.

The growing grey seal (Halichoerus grypus) population in the Baltic Sea has created conflicts with local fisheries, comparable to similar emerging problems worldwide. Adequate information on the foraging habits is a requirement for responsible management of the seal population. We investigated the applicability of available dietary assessment methods by comparing morphological analysis and DNA metabarcoding of gut contents (short-term diet; n = 129/125 seals, respectively), and tissue chemical markers i.e. fatty acid (FA) profiles of blubber and stable isotopes (SIs) of liver and muscle (mid- or long-term diet; n = 108 seals for the FA and SI markers). The methods provided complementary information. Short-term methods indicated prey species and revealed dietary differences between age groups and areas but for limited time period. In the central Baltic, herring was the main prey, while in the Gulf of Finland percid and cyprinid species together comprised the largest part of the diet. Perch was also an important prey in the western Baltic Proper. The DNA analysis provided firm identification of many prey species, which were neglected or identified only at species group level by morphological analysis. Liver SIs distinguished spatial foraging patterns and identified potentially migrated individuals, whereas blubber FAs distinguished individuals frequently utilizing certain types of prey. Tissue chemical markers of adult males suggested specialized feeding to certain areas and prey, which suggest that these individuals are especially prone to cause economic losses for fisheries. We recommend combined analyses of gut contents and tissue chemical markers as dietary monitoring methodology of aquatic top predators to support an optimal ecosystem-based management.

Underwater vocal complexity of Arctic seal Erignathus barbatus in Kongsfjorden (Svalbard).

In this study the description of underwater vocal repertoire of bearded seal in Svalbard (Norway) was extended. Two autonomous passive acoustic recorders were deployed for one year (August 2014-July 2015) in the inner and outer parts of the Kongsfjorden, and 1728 h were recorded and 17 220 vocalizations were found. Nine different vocalization classes were identified and characterized using ten acoustic parameters. The calls showed heterogeneous spectral features, but share the descending trend of frequency modulation. The different classes emerged were discriminated primarily by bandwidth and duration, and then by minimum frequency, central frequency, and maximum frequency in this order. This study represents a step forward to improve the understanding of the acoustic behaviour and the social function of these calls, and identified long passive acoustic monitoring as an effective method to assess vocal complexity and the ecology of marine species producing sounds.

Shift of grey seal subspecies boundaries in response to climate, culling and conservation.

Identifying the processes that drive changes in the abundance and distribution of natural populations is a central theme in ecology and evolution. Many species of marine mammals have experienced dramatic changes in abundance and distribution due to climatic fluctuations and anthropogenic impacts. However, thanks to conservation efforts, some of these species have shown remarkable population recovery and are now recolonizing their former ranges. Here, we use zooarchaeological, demographic and genetic data to examine processes of colonization, local extinction and recolonization of the two northern European grey seal subspecies inhabiting the Baltic Sea and North Sea. The zooarchaeological and genetic data suggest that the two subspecies diverged shortly after the formation of the Baltic Sea approximately 4200 years bp, probably through a gradual shift to different breeding habitats and phenologies. By comparing genetic data from 19th century pre-extinction material with that from seals currently recolonizing their past range, we observed a marked spatiotemporal shift in subspecies boundaries, with increasing encroachment of North Sea seals on areas previously occupied by the Baltic Sea subspecies. Further, both demographic and genetic data indicate that the two subspecies have begun to overlap geographically and are hybridizing in a narrow contact zone. Our findings provide new insights into the processes of colonization, extinction and recolonization and have important implications for the management of grey seals across northern Europe.

Source levels of the underwater calls of a male leopard seal.

Leopard seals (Hydrurga leptonyx) are top predators in the Antarctic ecosystem. They produce stereotyped calls as part of a stylized underwater vocal display. Understanding of their acoustic behavior is improved by identifying the amplitude of their calls. The amplitude of five types of calls (n = 50) from a single male seal were measured as broadband source levels and ranged from 153 to 177 dB re 1 µPa at 1 m. The mean source levels differed between call types, the lower frequency calls (L, D, and O) tended to have source levels 10 dB higher than the higher frequency calls (H and M). Information on call-type source levels is important to take into account for passive acoustic studies investigating repertoire usage as calls produced with greater amplitudes are likely to have larger acoustic ranges, especially when these are also the calls with lower frequencies, such as is the case in leopard seals.

Diet and phylogeny shape the gut microbiota of Antarctic seals: a comparison of wild and captive animals.

The gut microbiota of mammals underpins the metabolic capacity and health of the host. Our understanding of what influences the composition of this community has been limited primarily to evidence from captive and terrestrial mammals. Therefore, the gut microbiota of southern elephant seals, Mirounga leonina, and leopard seals, Hydrurga leptonyx, inhabiting Antarctica were compared with captive leopard seals. Each seal exhibited a gut microbiota dominated by four phyla: Firmicutes (41.5 ± 4.0%), Fusobacteria (25.6 ± 3.9%), Proteobacteria (17.0 ± 3.2%) and Bacteroidetes (14.1 ± 1.7%). Species, age, sex and captivity were strong drivers of the composition of the gut microbiota, which can be attributed to differences in diet, gut length and physiology and social interactions. Differences in particular prey items consumed by seal species could contribute to the observed differences in the gut microbiota. The longer gut of the southern elephant seal provides a habitat reduced in available oxygen and more suitable to members of the phyla Bacteroidetes compared with other hosts. Among wild seals, 16 'core' bacterial community members were present in the gut of at least 50% of individuals. As identified between southern elephant seal mother-pup pairs, 'core' members are passed on via vertical transmission from a young age and persist through to adulthood. Our study suggests that these hosts have co-evolved with their gut microbiota and core members may provide some benefit to the host, such as developing the immune system. Further evidence of their strong evolutionary history is provided with the presence of 18 shared 'core' members in the gut microbiota of related seals living in the Arctic. The influence of diet and other factors, particularly in captivity, influences the composition of the community considerably. This study suggests that the gut microbiota has co-evolved with wild mammals as is evident in the shared presence of 'core' members.

Amalgamating source trees with different taxonomic levels.

Supertree methods combine a collection of source trees into a single parent tree or supertree. For almost all such methods, the terminal taxa across the source trees have to be non-nested for the output supertree to make sense. Motivated by Page, the first supertree method for combining rooted source trees where the taxa can be hierarchically nested is called AncestralBuild. In addition to taxa labeling the leaves, this method allows the rooted source trees to have taxa labeling some of the interior nodes at a higher taxonomic level than their descendants (e.g., genera vs. species). However, the utility of AncestralBuild is somewhat restricted as it is mostly intended to decide if a collection of rooted source trees is compatible. If the initial collection is not compatible, then no tree is returned. To overcome this restriction, we introduce here the MultiLevelSupertree (MLS) supertree method whose input is the same as that for AncestralBuild, but which accommodates incompatibilities among rooted source trees using a MinCut-like procedure. We show that MLS has several desirable properties including the preservation of common subtrees among the source trees, the preservation of ancestral relationships whenever they are compatible, as well as running in polynomial time. Furthermore, application to a small test data set (the mammalian carnivore family Phocidae) indicates that the method correctly places nested taxa at different taxonomic levels (reflecting vertical signal), even in cases where the input trees harbor a significant level of conflict between their clades (i.e., in their horizontal signal).

Multiple markers and multiple individuals refine true seal phylogeny and bring molecules and morphology back in line.

Despite decades of study, some aspects of Phocidae (Pinnipedia, Carnivora) phylogeny still remain unresolved. Using the largest novel dataset to date, including all extant phocids and comprising 15 nuclear and 13 mitochondrial genes, we illustrate the utility of including multiple individuals per species in resolving rapid radiations, and provide new insight into phocid phylogeny. In line with longstanding morphological views, Pusa is recovered as monophyletic for the first time with genetic data. The data are also used to explore the relationship between genetic distance and taxonomic rank. Intraspecific sampling also highlights the discrepancy between molecular and morphological rates of evolution within Phocidae.

Extremely low genetic diversity in the endangered Hawaiian monk seal (Monachus schauinslandi).

Hunted to near extinction in the late 19th century, the endangered and endemic Hawaiian monk seal (Monachus schauinslandi) exhibits low variation at all molecular markers tested to date. Here we confirm extreme paucity of genetic diversity, finding polymorphisms at only 8 of 154 microsatellite loci tested (143 novel species-specific loci, 10 loci from Antarctic seals, and 1 previously characterized locus). This screening revealed unprecedentedly low levels of allelic diversity and heterozygosity (A = 1.1, H(e) = 0.026). Subsequent analyses of 2409 Hawaiian monk seals at the 8 polymorphic loci provide evidence for a bottleneck (P = 0.002), but simulations indicate low genetic diversity (H(e) < 0.09) prior to recorded human influence. There is little indication of contemporary inbreeding (F(IS) = 0.018) or population structure (K = 1 population). Minimal genetic variation did not prevent partial recovery by the late 1950s and may not be driving the current population decline to approximately 1200 seals. Nonetheless, genotyping nearly every individual living during the past 25 years sets a new benchmark for low genetic diversity in an endangered species.

Trace element analysis in the serum and hair of Antarctic leopard seal, Hydrurga leptonyx, and Weddell seal, Leptonychotes weddellii.

Leopard seal, Hydrurga leptonyx, and Weddell seal, Leptonychotes weddellii, occupy an upper trophic level within the Antarctic ecosystem and are useful indicator species in the Southern Ocean of trace element concentrations. Reference values for the concentration of 19 trace elements were determined in the serum and hair of leopard and Weddell seals sampled in Eastern Antarctica. These reference values can be used as 'baseline' levels for monitoring trace element concentrations in these species. Greater trace element concentrations were determined in hair compared to serum, indicating different time scales of trace element accumulation in these samples. For the majority of trace elements, except for Se in the leopard seal samples and Cr in the Weddell seal samples, significant regression relationships for trace element concentrations in hair and serum were not elucidated. Significant differences were determined in the concentrations of seven out of 15 elements with hair type, moult and new, in the leopard seal; concentrations in moult hair were determined to be greater than in new hair for all elements except Zn. Hair analysis was determined to be useful for monitoring exposure to trace elements and when collected off the ice from moulting seals, hair can be employed as a non-invasive sample for trace element analysis in leopard and Weddell seals.

Population structure of ice-breeding seals.

The development of population genetic structure in ice-breeding seal species is likely to be shaped by a combination of breeding habitat and life-history characteristics. Species that return to breed on predictable fast-ice locations are more likely to exhibit natal fidelity than pack-ice-breeding species, which in turn facilitates the development of genetic differentiation between subpopulations. Other aspects of life history such as geographically distinct vocalizations, female gregariousness, and the potential for polygynous breeding may also facilitate population structure. Based on these factors, we predicted that fast-ice-breeding seal species (the Weddell and ringed seal) would show elevated genetic differentiation compared to pack-ice-breeding species (the leopard, Ross, crabeater and bearded seals). We tested this prediction using microsatellite analysis to examine population structure of these six ice-breeding species. Our results did not support this prediction. While none of the Antarctic pack-ice species showed statistically significant population structure, the bearded seal of the Arctic pack ice showed strong differentiation between subpopulations. Again in contrast, the fast-ice-breeding Weddell seal of the Antarctic showed clear evidence for genetic differentiation while the ringed seal, breeding in similar habitat in the Arctic, did not. These results suggest that the development of population structure in ice-breeding phocid seals is a more complex outcome of the interplay of phylogenetic and ecological factors than can be predicted on the basis of breeding substrate and life-history characteristics.

A phylogeny of the extant Phocidae inferred from complete mitochondrial DNA coding regions.

Despite extensive interest in the systematics of Pinnipedia, questions remain concerning phylogenetic relationships within the Phocidae or "true" seals. Relationships within the phocids and their placement relative to the remaining pinnipeds and major lineages of arctoid carnivores were examined using a large molecular data set consisting of 12 mitochondrial protein coding genes. Phylogenetic analysis including 15 extant species of the Phocidae, and representatives of the Otariidae, Odobenidae, Ursidae, Mustelidae, Canidae, and Felidae confirmed the monophyletic origins of the Pinnipedia within the Arctoidea. Slightly more support was found for an ursid affinity of the pinnipeds, however, this relationship remains contentious. The Phocidae were placed as the sister group to a common odobenid-otariid clade. Within the family Phocidae, strong support for the traditionally accepted subfamilies Phocinae (northern seals), and Monachinae (southern seals plus monk seals) was found. In contrast to recent suggestions, a monophyletic Monachus was strongly supported and was placed in a deep branching position within the Monachinae. Evidence from sequence divergence under a maximum likelihood model illustrated that the rarely used tribal distinction within the Monachinae are comparable, in terms of evolutionary distance, to accepted tribal distinctions within the Phocinae. In addition, results suggest that Pagophilus should be accepted as a genus within the Phocini. Sequence divergence between Phoca, Pusa, and Halichoerus is minimal, supporting a taxonomic reclassification of the three genera into an emended genus Phoca, without subgeneric distinctions.

Vertical stratification of fatty acids in the blubber of southern elephant seals (Mirounga leonina): implications for diet analysis.

Fatty acid signature analysis (FASA) is a powerful ecological tool that uses essential fatty acids (FA) from the tissues of animals to indicate aspects of diet. However, the presence of vertical stratification in FA distribution throughout blubber complicates the application of FASA to marine mammals. Blubber biopsy samples were collected from adult female southern elephant seals (Mirounga leonina) from Macquarie Island (n=11), and blubber cores were divided into inner and outer sections to determine the degree to which the blubber layer was stratified in FA composition, we found 19 FA from both blubber layers in greater than trace amounts (>0.5%). The inner and outer blubber layers could be separated using principal components analysis based on the relative proportion of FA in each layer. Dietary polyunsaturated fatty acids (PUFA) were also observed in significantly higher proportions in the inner blubber layer. Due to the degree of FA stratification in southern elephant seals, we concur with other marine mammal studies that sampling only the outer blubber layer will result in a loss of recently accumulated information regarding diet structure (as indicated by 'surplus' PUFA from the diet). This finding suggests that differential mobilization/deposition of certain FA may result in a modified signature from prey to predator. Thus, sampling animals to recover the inner blubber layer is important for studies attempting to describe aspects of marine mammal diet. This can be achieved in animals such as pinnipeds where the whole blubber layer can be readily sampled.

The trouble with sealworms (Pseudoterranova decipiens species complex, Nematoda): a review.

Sealworms or codworms, larvae of ascaridoid nematodes belonging to the Pseudoterranova decipiens species complex, infect the flesh of numerous species of marine and euryhaline fish, and have proven a chronic and costly cosmetic problem for seafood processors. Moreover, the parasite may cause abdominal discomfort in humans when consumed in raw, undercooked or lightly marinated fish. In this review, the phylogeny, life cycle and distributions of sealworms are discussed along with biotic and abiotic factors which may influence distributions of these parasites in their intermediate and final hosts. Also considered here are efforts to control the problem through commercial fishing practices, fish processing technology, and the reduction of infection parameters in marine fish populations by biological means. Ironically, concern over sealworm problem has subsided in some fisheries in recent years, not as a result of falling infection parameters in fish stocks or innovations in processing technology, but as a consequence of declines in abundance and size of groundfish.

Accumulation of silver in the liver of three species of pinnipeds.

Silver in the three species of pinnipeds [northern fur seal (Callorhinus ursinus), Steller sea lion (Eumetopias jubatus), and harbor seal (Phoca vitulina)] caught in the North Pacific Ocean were analyzed using inductively coupled plasma-mass spectrometry, in order to understand accumulation and distribution of silver in pinnipeds. In northern fur seals, relatively high concentrations of silver were observed in the liver and body hair. Some 70% of the silver burden was concentrated in the liver. Hepatic silver concentrations were significantly correlated to age in northern fur seals (r = 0.766, P < 0.001, n = 49) and Steller sea lions (r = 0.496, P < 0.01, n = 28). Levels of silver concentrations per wet weight (microgram g-1) in the three pinnipeds ranged from 0.04 to 0.55 for northern fur seals, from 0.1 to 1.04 for Steller sea lions and from 0.03 to 0.83 for harbor seals. Silver concentrations in liver for all pinnipeds were significantly correlated with mercury, and selenium (P < 0.001). Molar ratios between silver to selenium approximated 1:180 in northern fur seals, 1:120 in Steller sea lions, and 1:60 in harbor seals. The silver-mercury molar ratios were approximately 1:170 in northern fur seals, and 1:80 both in the other species. Increase in silver accumulation in the liver was caused by the retention in nuclei and mitochondria fraction together with mercury and selenium in the cells of northern fur seals.

Renal lesions in Baltic grey seals (Halichoerus grypus) and ringed seals (Phoca hispida botnica).

A severe reduction in the populations of grey and ringed seals in the Baltic occurred during the 1960s and 1970s. Adult animals showed (and still show) a series of lesions inter alia in the female reproductive organs, intestines, integument, kidneys, adrenals, and skulls (the Baltic seal disease complex). The morphology and prevalence of light microscopic changes in the kidneys of 76 grey seals and 29 ringed seals collected in the Baltic proper and the Gulf of Bothnia during 1977-1996 are presented in this report. Specific changes in the glomeruli were diffuse thickening of the capillary walls and the presence of large, rounded, hyaline bodies in the capillary or capsular walls. Specific changes in the distal convoluted tubules and the collecting ducts included focal replacement of the normal epithelium by multilayered cell proliferations. The prevalence and extent of the changes were age-related and thus correlated with the time of exposure to environmental toxicants. The lesions were more conspicuous in Baltic grey seals than in Baltic ringed seals. Similar findings were recorded in 5 grey seals from Swedish zoological gardens. These animals had been fed Baltic fish for most of their lives. Electron microscopy was performed on 5 of the Baltic grey seals and on one of the grey seals from zoological gardens. Electron microscopy results mainly based on findings in one of the Baltic grey seals, included mesangial inter-position in the glomerular capillary walls and the characteristics of intercalated cells in cell proliferations in the distal parts of the nephrons. Eleven grey seals from the Scottish coast and 23 ringed seals from Svalbard served as reference material. None of the reference seals showed the specific lesions described above. The authors propose that organochlorine pollution of the Baltic environment is a factor in the cause of these kidney changes.

Amoxicillin pharmacokinetics in harbor seals (Phoca vitulina) and northern elephant seals (Mirounga angustirostris) following single dose intravenous administration: implications for interspecific dose scaling.

The pharmacokinetics of sodium amoxicillin after a single intravenous dose of 20 mg/kg were determined in ten harbor seals (Phoca vitulina) and ten northern elephant seals (Mirounga angustirostris). The seals ranged in age from 1 to 6 months and the mean weights were 11.7 kg (range, 9.5-18.5 kg) for harbor seals and 47.1 kg (range, 39.5-61.4 kg) for elephant seals. The median half-life of amoxicillin (quartiles) in harbor seals, 1.5 (1.0-3.1) h. was not statistically different from that of elephant seals, 2.0 (1.4-3.8) h, nor were the differences between the terminal elimination rate constants between the two species. The only statistically significant differences between species were for area-under-the-curve (AUC), and total systemic clearance. The lack of statistical significance for differences in the volume of distribution at steady-state (Vss) may have been due to minor differences in the time frame of data collection and dose administered between the two groups. A true physiologic difference in drug handling, possibly related to renal perfusion or tubal secretory efficiency could affect amoxicillin kinetics in these species, and longer administration intervals may be appropriate for elephant seals as compared to harbor seals when administering multiple dose amoxicillin therapy at 20 mg/kg.

Patterns of extensive genetic differentiation and variation among European harbor seals (Phoca vitulina vitulina) revealed using microsatellite DNA polymorphisms.

The harbor seal (Phoca vitulina) has the most extensive distribution of any phocid seal species. An analysis of population structure in this species across its European range was made using 7 phocid derived microsatellites in a sample of 1,029 individuals from 12 separate geographic areas. Despite the species potential for long-distance movement, significant genetic differentiation between areas was observed using an unbiased estimator of RST. Six distinct population units were identified: Ireland-Scotland, English east coast, Waddensea, western Scandinavia (Norway-Kattegat-Skagerrak-west Baltic), east Baltic, and Iceland. Little local substructuring is present along coastlines with a continuous distribution of breeding animals, but differentiation does increase with geographic distance. The degree of differentiation is greater over equivalent distances where the distribution is discontinuous, such as along coasts where breeding colonies are separated by large distances or by stretches of open sea. Patterns of population differentiation derived from microsatellites are very similar to those obtained from previous mitochondrial DNA analysis and suggest that philopatry in harbor seals operates over 300-500 km. In Europe, harbor seals have experienced a complex demographic history and patterns of population structure are likely to have been affected by natural environmental influences such as Pleistocene glaciations and epizootics. Comparison of Nm values from an unbiased estimator of RST, GST, and theta are consistent and, in some cases, may indicate populations where conditions deviate from the expectations of the RST model.