Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts.

Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.

Spatiotemporal Trends Spanning Three Decades Show Toxic Levels of Chemical Contaminants in Marine Mammals.

Despite their ban and restriction under the 2001 Stockholm Convention, persistent organic pollutants (POPs) are still widespread and pervasive in the environment. Releases of these toxic and bioaccumulative chemicals are ongoing, and their contribution to population declines of marine mammals is of global concern. To safeguard their survival, it is of paramount importance to understand the effectiveness of mitigation measures. Using one of the world's largest marine mammals strandings data sets, we combine published and unpublished data to examine pollutant concentrations in 11 species that stranded along the coast of Great Britain to quantify spatiotemporal trends over three decades and identify species and regions where pollutants pose the greatest threat. We find that although levels of pollutants have decreased overall, there is significant spatial and taxonomic heterogeneity such that pollutants remain a threat to biodiversity in several species and regions. Of individuals sampled within the most recent five years (2014-2018), 48% of individuals exhibited a concentration known to exceed toxic thresholds. Notably, pollutant concentrations are highest in long-lived, apex odontocetes (e.g., killer whales (Orcinus orca), bottlenose dolphins (Tursiops truncatus), and white-beaked dolphins (Lagenorhynchus albirostris)) and were significantly higher in animals that stranded on more industrialized coastlines. At the present concentrations, POPs are likely to be significantly impacting marine mammal health. We conclude that more effective international elimination and mitigation strategies are urgently needed to address this critical issue for the global ocean health.

Development of Mercury Analysis by NanoSIMS for the Localization of Mercury-Selenium Particles in Whale Liver.

Nanoscale secondary ion mass spectrometry (NanoSIMS) is a dynamic SIMS technique, which offers high spatial resolution allowing the mapping of chemical elements at the nanometer scale combined with high sensitivity. However, SIMS for mercury analysis is a challenging issue due to the low secondary ion yield and has never been done on NanoSIMS. The introduction of an rf plasma oxygen primary ion source on NanoSIMS enabled higher lateral resolution and higher sensitivity for electropositive elements such as most metals. In this paper, for the first time, mercury analysis by NanoSIMS was developed applying the new rf plasma O- ion source. All mercury isotopes could be detected as Hg+ secondary ions and the isotopic pattern corresponded to their natural isotopic abundances. Furthermore, Hg+ detection in HgSe nanocrystals has been investigated where polyatomic interferences from selenium clusters were identified and separated by high mass resolution (ΔM/M ≥ 3200). However, in the presence of selenium a strong matrix effect was observed, decreasing the Hg+ secondary ion yield. In addition, a detection of Se+ ions was possible, too. The newly developed method was successfully applied to nanoscale localization by chemical imaging of HgSe particles accumulated in the liver tissue of sperm whale (Physeter macrocephalus). This demonstrated the applicability of NanoSIMS not only for mercury detection in surface analysis but also for mercury mapping in biological samples.

Runs of homozygosity in killer whale genomes provide a global record of demographic histories.

Runs of homozygosity (ROH) occur when offspring inherit haplotypes that are identical by descent from each parent. Length distributions of ROH are informative about population history; specifically, the probability of inbreeding mediated by mating system and/or population demography. Here, we investigated whether variation in killer whale (Orcinus orca) demographic history is reflected in genome-wide heterozygosity and ROH length distributions, using a global data set of 26 genomes representative of geographic and ecotypic variation in this species, and two F1 admixed individuals with Pacific-Atlantic parentage. We first reconstructed demographic history for each population as changes in effective population size through time using the pairwise sequential Markovian coalescent (PSMC) method. We found a subset of populations declined in effective population size during the Late Pleistocene, while others had more stable demography. Genomes inferred to have undergone ancestral declines in effective population size, were autozygous at hundreds of short ROH (<1 Mb), reflecting high background relatedness due to coalescence of haplotypes deep within the pedigree. In contrast, longer and therefore younger ROH (>1.5 Mb) were found in low latitude populations, and populations of known conservation concern. These include a Scottish killer whale, for which 37.8% of the autosomes were comprised of ROH >1.5 Mb in length. The fate of this population, in which only two adult males have been sighted in the past five years, and zero fecundity over the last two decades, may be inextricably linked to its demographic history and consequential inbreeding depression.

Meningoencephalitis in a common minke whale Balaenoptera acutorostrata associated with Brucella pinnipedialis and gamma-herpesvirus infection.

Fatal marine Brucella infections with histologic lesions specific to the central nervous system (CNS), known as neurobrucellosis, have been described in 5 species of odontocete cetaceans in the UK: striped dolphins Stenella coeruleoalba, Atlantic white-sided dolphins Lagenorhynchus acutus, short-beaked common dolphins Delphinus delphis, long-finned pilot whale Globicephala melas and Sowerby's beaked whale Mesoplodon bidens. To date, these CNS lesions have only been associated with Brucella ceti ST26 and not with B. pinnipedialis, which is rarely isolated from cetaceans and, although commonly found in various seal species, has never been associated with any pathology. This paper describes the first report of neurobrucellosis in a common minke whale Balaenoptera acutorostrata which was associated with the isolation of Brucella pinnipedialis ST24 and co-infection with Balaenoptera acutorostrata gamma-herpesvirus 2. This is the first report of neurobrucellosis in any species of mysticete and the first report of Brucella pinnipedialis in association with any pathology in any species of marine mammal, which may be due to co-infection with a herpesvirus, as these are known to be associated with immunosuppression.

First confirmed reports of the isolation of Brucella ceti from a Risso's dolphin Grampus griseus and a killer whale Orcinus orca.

Brucella ceti has been recovered from a number species of cetaceans worldwide over the last 25 yr. Here we report, for the first time, the recovery of B. ceti from a Risso's dolphin Grampus griseus and a killer whale Orcinus orca. Recovery from an abdominal mass in the dolphin provides further evidence of the systemic pathogenic potential for B. ceti infection in cetaceans. The isolation of B. ceti ST23 (porpoise cluster) from a killer whale from a group known to eat other marine mammals raises the possibility of infection via ingestion. This report takes the number of cetacean species in UK coastal waters from which B. ceti has been isolated to 11 and highlights the value of routine, comprehensive and specific screening for significant pathogens such as Brucella sp. by strandings networks.

Levels of Polychlorinated Biphenyls Are Still Associated with Toxic Effects in Harbor Porpoises (Phocoena phocoena) Despite Having Fallen below Proposed Toxicity Thresholds.

Polychlorinated biphenyls (PCBs) are toxic, persistent, and lipophilic chemical compounds that accumulate to high levels in harbor porpoises (Phocoena phocoena) and other cetaceans. It is important to monitor PCBs in wildlife, particularly in highly exposed populations to understand if concentrations are declining and how levels relate to toxicological thresholds and indices of health like infectious disease mortality. Here we show, using generalized additive models and tissue samples of 814 U.K.-stranded harbor porpoises collected between 1990 and 2017, that mean blubber PCB concentrations have fallen below the proposed thresholds for toxic effects. However, we found they are still associated with increased rates of infectious disease mortality such that an increase in PCB blubber concentrations of 1 mg kg-1 lipid corresponds with a 5% increase in risk of infectious disease mortality. Moreover, rates of decline and levels varied geographically, and the overall rate of decline is slow in comparison to other pollutants. We believe this is evidence of long-term preservation in the population and continued environmental contamination from diffuse sources. Our findings have serious implications for the management of PCB contamination in the U.K. and reinforce the need to prevent PCBs entering the marine environment to ensure that levels continue to decline.

Campylobacter pinnipediorum subsp. caledonicus and C. pinnipediorum subsp. pinnipediorum recovered from abscesses in pinnipeds.

Campylobacter pinnipediorum was described recently for isolates recovered from pinnipeds. The novel species was further split into 2 subspecies based on host and geography, with C. pinnipediorum subsp. pinnipediorum recovered from otariid seals in California (USA) and C. pinnipediorum subsp. caledonicus recovered from phocid seals in Scotland. We report details of the infections of 7 pinnipeds from which C. pinnipediorum was isolated: C. pinnipediorum subsp. caledonicus was isolated from 2 harbour seals Phoca vitulina and a single grey seal Halichoerus grypus, and C. pinnipediorum subsp. pinnipediorum was isolated from California sea lions Zalophus californianus. Six of the isolates were recovered from samples collected at post-mortem investigation. In 2 of the Scottish seals and in 3 of the California seals, C. pinnipediorum was the sole bacterial isolate recovered from abscesses present and suggests they may have resulted from conspecific or intraspecific bite wounds.

Killer whale genomes reveal a complex history of recurrent admixture and vicariance.

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global data set of killer whale genomes in a rare attempt to elucidate global population structure in a nonhuman species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during postglacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

Postglacial Colonization of Northern Coastal Habitat by Bottlenose Dolphins: A Marine Leading-Edge Expansion?

Oscillations in the Earth's temperature and the subsequent retreating and advancing of ice-sheets around the polar regions are thought to have played an important role in shaping the distribution and genetic structuring of contemporary high-latitude populations. After the Last Glacial Maximum (LGM), retreating of the ice-sheets would have enabled early colonizers to rapidly occupy suitable niches to the exclusion of other conspecifics, thereby reducing genetic diversity at the leading-edge. Bottlenose dolphins (genus Tursiops) form distinct coastal and pelagic ecotypes, with finer-scale genetic structuring observed within each ecotype. We reconstruct the postglacial colonization of the Northeast Atlantic (NEA) by bottlenose dolphins using habitat modeling and phylogenetics. The AquaMaps model hindcasted suitable habitat for the LGM in the Atlantic lower latitude waters and parts of the Mediterranean Sea. The time-calibrated phylogeny, constructed with 86 complete mitochondrial genomes including 30 generated for this study and created using a multispecies coalescent model, suggests that the expansion to the available coastal habitat in the NEA happened via founder events starting ~15 000 years ago (95% highest posterior density interval: 4 900-26 400). The founders of the 2 distinct coastal NEA populations comprised as few as 2 maternal lineages that originated from the pelagic population. The low effective population size and genetic diversity estimated for the shared ancestral coastal population subsequent to divergence from the pelagic source population are consistent with leading-edge expansion. These findings highlight the legacy of the Late Pleistocene glacial cycles on the genetic structuring and diversity of contemporary populations.

First isolation of Brucella pinnipedialis and detection of Brucella antibodies from bearded seals Erignathus barbatus.

Brucella species infecting marine mammals was first reported in 1994 and in the years since has been documented in various species of pinnipeds and cetaceans. While these reports have included species that inhabit Arctic waters, the few available studies on bearded seals Erignathus barbatus have failed to detect Brucella infection to date. We report the first isolation of Brucella pinnipedialis from a bearded seal. The isolate was recovered from the mesenteric lymph node of a bearded seal that stranded in Scotland and typed as ST24, a sequence type associated typically with pinnipeds. Furthermore, serological studies of free-ranging bearded seals in their native waters detected antibodies to Brucella in seals from the Chukchi Sea (1990-2011; 19%) and Svalbard (1995-2007; 8%), whereas no antibodies were detected in bearded seals from the Bering Sea or Bering Strait or from captive bearded seals.

Exposure of harbour seals Phoca vitulina to Brucella in declining populations across Scotland.

Since 2000 there has been a major decline in the abundance of Scottish harbour seals Phoca vitulina. The causes of the decline remain uncertain. The aim of this study was to establish the extent to which the seals in the regions of greatest decline have been exposed to Brucella, a bacterial pathogen that causes reproductive failure in terrestrial mammalian hosts. Tissues from dead seals collected between 1992 and 2013 were cultured for Brucella (n = 150). Serum samples collected from live capture-released seals (n = 343) between 1997 and 2012 were tested for Brucella antibodies using the Rose Bengal plate agglutination test (RBT) and a competitive enzyme-linked immunosorbent assay (cELISA). In total, 16% of seals cultured had Brucella isolated from one or more tissues, but there were no pathological signs of infection. The cELISA results were more sensitive than the RBT results, showing that overall 25.4% of seals were seropositive, with the highest seroprevalence in juveniles. As there was no evidence of either a higher seroprevalence or higher circulating antibody levels in seropositive animals in the areas with the greatest declines, it was concluded that Brucella infection is likely not a major contributing factor to recent declines. However, the consistently high proportion of seals exposed to Brucella indicates possible endemicity in these populations, likely due to B. pinnipedialis, which has demonstrated a preference for pinniped hosts. Importantly, given the close proximity between seals, humans and livestock in many areas, there is the potential for cross-species infections.

Direct online HPLC-CV-AFS method for traces of methylmercury without derivatisation: a matrix-independent method for urine, sediment and biological tissue samples.

Mercury (Hg) is a global pollutant which occurs in different species, with methylmercury (MeHg) being the critical compound due to its neurotoxicity and bioaccumulation through the food chain. Methods for trace speciation of MeHg are therefore needed for a vast range of sample matrices, such as biological tissues, fluids, soils or sediments. We have previously developed an ultra-trace speciation method for methylmercury in water, based on a preconcentration HPLC cold vapour atomic fluorescence spectrometry (HPLC-CV-AFS) method. The focus of this work is mercury speciation in a variety of sample matrices to assess the versatility of the method. Certified reference materials were used where possible, and samples were spiked where reference materials were not available, e.g. human urine. Solid samples were submitted for commonly used digestion or extraction processes to obtain a liquid sample for injection into the analytical system. For MeHg in sediment samples, an extraction procedure was adapted to accommodate MeHg separation from high amounts of Hg(2+) to avoid an overload of the column. The recovery for MeHg determination was found to be in the range of 88-104% in fish reference materials (DOLT-2, DOLT-4, DORM-3), lobster (TORT-2), seaweed (IAEA-140/TM), sediments (ERM(®)-CC580) and spiked urine and has been proven to be robust, reliable, virtually matrix-independent and relatively cost-effective. Applications in the ultra-trace concentration range are possible using the preconcentration up to 200 mL, while for higher MeHg-containing samples, lower volumes can be applied. A comparison was carried out between species-specific isotope dilution gas chromatography inductively coupled plasma mass spectrometry (SSID-GC-ICP-MS) as the gold standard and HPLC-CV-AFS for biological tissues (liver, kidney and muscle of pilot whales), showing a slope of 1.008 and R (2) = 0.97, which indicates that the HPLC-CV-AFS method achieves well-correlated results for MeHg in biological tissues.

First report of Brucella ceti-associated meningoencephalitis in a long-finned pilot whale Globicephala melas.

Fatal Brucella ceti infection with histological lesions specific to the central nervous system has been described in only 3 species of cetaceans: striped dolphins Stenella coeruleoalba, Atlantic white-sided dolphins Lagenorhynchus acutus and short-beaked common dolphins Delphinus delphis. This paper describes the first report of a B. ceti-associated meningoencephalitis in a long-finned pilot whale Globicephala melas, showing the increasing range of species susceptibility. Brucella was recovered in larger numbers from cerebrospinal fluid than from brain tissue and is the sample of choice for isolation.

Habitat-driven population structure of bottlenose dolphins, Tursiops truncatus, in the North-East Atlantic.

Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. 'coastal' and 'pelagic') have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.

An optimized computed tomography protocol for metallic gunshot head trauma in a seal model.

Computed tomography (CT) is commonly used to assess animals with head trauma. However, strongly attenuating objects such as metallic gunshot cause artifacts that may make accurate localization of shrapnel pieces difficult. The purpose of this study was to develop an optimized CT protocol for minimizing metal artifacts in an animal model of gunshot head trauma. A cadaver head of a stranded Gray seal (Halichoerus grypus) was shot post-mortem with a 0.223-inch caliber rifle. The head was frozen, thawed, and scanned using a multislice CT scanner and protocols with varying acquisition and reconstruction parameters. Scans were acquired with and without use of the scanner's proprietary Extended CT Scale (ECTS) mode and beam hardening reduction (Posterior Fossa Optimization [PFO]) filter. Window/level display settings were also varied. For each protocol and each of five selected metallic shrapnel pieces, a single observer measured combined metal halo artifact and shrapnel area using a hand-traced region of interest. The number of hypo- and hyper-attenuating streak artifacts was also recorded. Measurements were repeated for three different reading sessions. Metal CT artifacts were minimized with a high-frequency image reconstruction algorithm and a wide window setting. Further artifact reduction was achieved with a proprietary ECTS raw data reconstruction technique and a very wide window. This enabled a more confident evaluation of surrounding bone. On the other hand, these techniques are unfortunately not effective under conditions of soft tissue evaluation. Increasing tube voltage and use of a proprietary PFO filter did not yield a significant reduction in metal artifacts.

Intravascular central nervous system T-cell lymphoma in a common dolphin (Delphinus delphis) with cerebral infarction.

Lymphoid and haematopoietic neoplasms are rare in cetaceans. This report describes intravascular lymphoma in an adult common dolphin that presented with neurological signs prior to stranding. Intravascular lymphoma is a rare neoplasm previously recorded in humans, dogs, a cat and a horse. The condition is characterized by intravascular neoplastic lymphocytic proliferation, the sequelae of which are dependent on the organ affected. Key pathological findings in this case included multifocal cerebrocortical malacia secondary to vascular occlusion associated with intravascular neoplastic lymphocytic proliferation. Immunohistochemistry supported a T-cell phenotype similar to that observed in dogs. The neurological presentation was consistent with that seen in other species in which the central nervous system is involved. The aetiology and pathogenesis have not been established in other species and although no further investigations were made in this common dolphin, this report adds to the short list of species affected by this rare neoplasm.

Toxic arsenolipids bioaccumulate in the developing brain of pilot whales.

Arsenic-containing hydrocarbons (AsHC), a subclass of arsenolipids (AsL), have been proven to exert neuro- and cytotoxic effects in in-vitro and in-vivo studies and were shown to pass through biological barriers like the blood-brain barrier. However, there has been no connection as to the environmental relevance of these findings, meaning there is no study based on samples from free living animals that are exposed to these compounds. Here, we report the identification of two AsHC as well as 3 arsenosugar phospholipids (AsPL) in the brains of a pod of stranded long-finned pilot whales (Globicephala melas) as well as the absence of arsenobetaine (AsB) which is often found to be a dominant As species in fish. We show data which suggests that there is an age-dependent accumulation of AsL in the brains of the animals. The results show that, in contrast to other organs, total arsenic as well as arsenolipids accumulate in an asymptotic pattern in the brains of the animals. Total As concentrations were found to range from 87 to 260 µg As/kg wet weight and between 0.6 and 27.6 µg As/kg was present in the form of AsPL958 in the brains of stranded pilot whales which was the most dominant lipophilic species present. The asymptotic relationship between total As, as well as AsPL, concentration in the brain and whale age may suggest that the accumulation of these species takes place prior to the full development of the blood-brain barrier in young whales. Finally, comparison between the organs of local squid, a common source of food for pilot whales, highlighted a comparable AsL profile which indicates a likely bioaccumulation pathway through the food chain.

High resolution visualisation of tiemannite microparticles, essential in the detoxification process of mercury in marine mammals.

The North Sea is an ecologically rich habitat for marine wildlife which has also been impacted by industrial developments and anthropogenic emissions of contaminants such as mercury. Marine mammals are particularly susceptible to mercury exposure, due to their trophic position, long lifespan, and dependence on (increasingly contaminated) aquatic prey species. To mitigate impact, marine mammals can detoxify methylmercury by binding it to selenium-containing biomolecules, creating insoluble mercury selenide granules. Here, liver, kidney, muscle, and brain samples from an adult male bottlenose dolphin (Tursiops truncatus) with known elevated mercury concentrations were analysed through scanning electron microscopy (SEM). Tiemannite (HgSe) deposits were identified in all organs, ranging from 400 nm to 5 µm in diameter, with particle size being organ-dependent. Although reported in other studies, this is the first time that the three-dimensional nature of tiemannite is captured in marine mammal tissue.