Diverse papillomaviruses identified from Antarctic fur seals, leopard seals and Weddell seals from the Antarctic.

Papillomaviruses (family Papillomaviridae) are non-enveloped, circular, double-stranded DNA viruses known to infect squamous and mucosal epithelial cells. In the family Papillomaviridae there are 53 genera and 133 viral species whose members infect a variety of mammalian, avian, reptilian, and fish species. Within the Antarctic context, papillomaviruses (PVs) have been identified in Adélie penguins (Pygoscelis adeliae, 2 PVs), Weddell seals (Leptonychotes weddellii, 7 PVs), and emerald notothen (Trematomus bernacchii, 1 PV) in McMurdo Sound and Ross Island in eastern Antarctica. Here we identified 13 diverse PVs from buccal swabs of Antarctic fur seals (Arctocephalus gazella, 2 PVs) and leopard seal (Hydrurga leptonyx, 3 PVs) in western Antarctica (Antarctic Peninsula), and vaginal and nasal swabs of Weddell seals (8 PVs) in McMurdo Sound. These PV genomes group into four genera representing 11 new papillomavirus types, of which five are from two Antarctic fur seals and a leopard seal and six from Weddell seals.

Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein.

Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between ß-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.

An enigmatic pelagic fish with internalized red muscle: A future regional endotherm or forever an ectotherm?

Ectothermy and endothermy in extant fishes are defined by distinct integrated suites of characters. Although only ⁓0.1% of fishes are known to have endothermic capacity, recent discoveries suggest that there may still be uncommon pelagic fish species with yet to be discovered endothermic traits. Among the most rarely encountered marine fishes, the louvar Luvarus imperialis is a remarkable example of adaptive evolution as the only extant pelagic species in the order Acanthuriformes (including surgeonfishes, tangs, unicornfishes and Moorish idol). Magnetic resonance imaging and gross necropsy did not yield evidence of cranial or visceral endothermy but revealed a central-posterior distribution of myotomal red muscle that is a mixture of the character states typifying ectotherms (lateral-posterior) and red muscle endotherms (central-anterior). Dissection of a specimen confirmed, and an osteological proxy supported, that L. imperialis has not evolved the vascular rete that is vital to retaining heat in the red muscle. The combination of presumably relying on caudal propulsion while exhibiting internal red muscle without associated retia is unique to L. imperialis among all extant fishes, raising the macroevolutionary question of whether this species - in geologic timescales - will remain an ectotherm or evolve red muscle endothermy.

Non-invasive measurements of respiration and heart rate across wildlife species using Eulerian Video Magnification of infrared thermal imagery.

BACKGROUND: An animal's metabolic rate, or energetic expenditure, both impacts and is impacted by interactions with its environment. However, techniques for obtaining measurements of metabolic rate are invasive, logistically difficult, and costly. Red-green-blue (RGB) imaging tools have been used in humans and select domestic mammals to accurately measure heart and respiration rate, as proxies of metabolic rate. The purpose of this study was to investigate if infrared thermography (IRT) coupled with Eulerian video magnification (EVM) would extend the applicability of imaging tools towards measuring vital rates in exotic wildlife species with different physical attributes. RESULTS: We collected IRT and RGB video of 52 total species (39 mammalian, 7 avian, 6 reptilian) from 36 taxonomic families at zoological institutions and used EVM to amplify subtle changes in temperature associated with blood flow for respiration and heart rate measurements. IRT-derived respiration and heart rates were compared to 'true' measurements determined simultaneously by expansion of the ribcage/nostrils and stethoscope readings, respectively. Sufficient temporal signals were extracted for measures of respiration rate in 36 species (85% success in mammals; 50% success in birds; 100% success in reptiles) and heart rate in 24 species (67% success in mammals; 33% success in birds; 0% success in reptiles) using IRT-EVM. Infrared-derived measurements were obtained with high accuracy (respiration rate, mean absolute error: 1.9 breaths per minute, average percent error: 4.4%; heart rate, mean absolute error: 2.6 beats per minute, average percent error: 1.3%). Thick integument and animal movement most significantly hindered successful validation. CONCLUSION: The combination of IRT with EVM analysis provides a non-invasive method to assess individual animal health in zoos, with great potential to monitor wildlife metabolic indices in situ.

Seasonal habitat preference and foraging behaviour of post-moult Weddell seals in the western Ross Sea.

Weddell seals (Leptonychotes weddellii) are important predators in the Southern Ocean and are among the best-studied pinnipeds on Earth, yet much still needs to be learned about their year-round movements and foraging behaviour. Using biologgers, we tagged 62 post-moult Weddell seals in McMurdo Sound and vicinity between 2010 and 2012. Generalized additive mixed models were used to (i) explain and predict the probability of seal presence and foraging behaviour from eight environmental variables, and (ii) examine foraging behaviour in relation to dive metrics. Foraging probability was highest in winter and lowest in summer, and foraging occurred mostly in the water column or just above the bottom; across all seasons, seals preferentially exploited the shallow banks and deeper troughs of the Ross Sea, the latter providing a pathway for Circumpolar Deep Water to flow onto the shelf. In addition, the probability of Weddell seal occurrence and foraging increased with increasing bathymetric slope and where water depth was typically less than 600 m. Although the probability of occurrence was higher closer to the shelf break, foraging was higher in areas closer to shore and over banks. This study highlights the importance of overwinter foraging for recouping body mass lost during the previous summer.

Iron mobilization during lactation reduces oxygen stores in a diving mammal.

The profound impacts that maternal provisioning of finite energy resources has on offspring survival have been extensively studied across mammals. This study shows that in addition to calories, high hemoprotein concentrations in diving mammals necessitates exceptional female-to-pup iron transfer. Numerous indices of iron mobilization (ferritin, serum iron, total-iron-binding-capacity, transferrin saturation) were significantly elevated during lactation in adult female Weddell seals (Leptonychotes weddellii), but not in skip-breeders. Iron was mobilized from endogenous stores for incorporation into the Weddell seal's milk at concentrations up to 100× higher than terrestrial mammals. Such high rates of iron offload to offspring drew from the female's own heme stores and led to compromised physiologic dive capacities (hemoglobin, myoglobin, and total body oxygen stores) after weaning their pups, which was further reflected in shorter dive durations. We demonstrate that lactational iron transfer shapes physiologic dive thresholds, identifying a cost of reproduction to a marine mammal.

Circoviruses and cycloviruses identified in Weddell seal fecal samples from McMurdo Sound, Antarctica.

Circoviridae is a family of circular single-stranded DNA viruses whose members infect a wide variety of hosts. While well characterized in avian and mammalian hosts, little is known about circoviruses associated with Antarctic animals. From 48 Weddell seal (Leptonychotes weddellii) fecal samples collected on the sea ice in McMurdo between Nov 2014 and Dec 2014, we identified and determined the genomes of novel viruses that fall within two genera of the family Circoviridae, i.e. Circovirus (n = 7) and Cyclovirus (n = 45). We named these viruses as werosea circovirus (WerCV) and werosea cyclovirus (WerCyV). The genomes of WerCV and WerCyV share ~63-64% genome-wide pairwise identity with classified circoviruses and cycloviruses, respectively. Based on the species demarcation threshold of 80% for members of the Circoviridae, the genomes of WerCV and WerCyV represent new species in their respective genera. Evidence indicated recombination in five of the 45 WerCyV genomes identified in this study. These are the first circoviruses found associated with Antarctic pinnipeds, adding to those recently identified associated with Adélie (Pygoscelis adeliae) and chinstrap penguins (P. antarcticus).

Links between muscle phenotype and life history: differentiation of myosin heavy chain composition and muscle biochemistry in precocial and altricial pinniped pups.

In marine mammals, muscular development has been identified as a rate-limiting factor in achieving adult dive capacities. This study investigates the rate that myosin heavy chain (MHC) composition matures in a postural and locomotor skeletal muscle for four pinniped species with different lactation lengths: hooded seals, Cystophora cristata; harp seals, Pagophilus groenlandicus; northern fur seals, Callorhinus ursinus, and Steller sea lions, Eumetopias jubatus. The ontogeny of MHC isoform expression was compared with developmental rates of myoglobin concentrations, and aerobic (citrate synthase, ß-hydroxyacyl-CoA dehydrogenase) and anaerobic (lactate dehydrogenase) enzyme activities. Within taxonomic families, species with shorter lactation periods had more mature muscles biochemically at birth, and fiber types differentiated earlier during ontogeny (Phocidae: hooded > harp seals, Otariidae: northern fur seals > Steller sea lions). Northern fur seal neonates had the most phenotypically-mature muscles in this study, with no immature MHC isoforms. The relationship between muscle biochemistry and MHC composition became more pronounced with age, and developed to reflect swimming mode and activity levels. In adults, phocids had more slow-twitch oxidative protein in their primary locomotor muscle, the Longissimus dorsi (LD), than otariids which likely reflects oxygen-sparing strategies for the phocids' longer dives. Conversely, northern fur seal muscles had higher proportions of fast-twitch MHCs in the Pectoralis and LD, likely indicative of this species' smaller size and higher mass-specific metabolic rates. Thus, muscle phenotype is linked with species life history, and a mismatch between muscle biochemistry and MHC composition at weaning has important implications for the first year of independent foraging in pinniped pups.

Diverse papillomaviruses identified in Weddell seals.

Papillomaviridae is a diverse family of circular, double-stranded DNA (dsDNA) viruses that infect a broad range of mammalian, avian and fish hosts. While papillomaviruses have been characterized most extensively in humans, the study of non-human papillomaviruses has contributed greatly to our understanding of their pathogenicity and evolution. Using high-throughput sequencing approaches, we identified 7 novel papillomaviruses from vaginal swabs collected from 81 adult female Weddell seals (Leptonychotes weddellii) in the Ross Sea of Antarctica between 2014-2017. These seven papillomavirus genomes were amplified from seven individual seals, and six of the seven genomes represented novel species with distinct evolutionary lineages. This highlights the diversity of papillomaviruses among the relatively small number of Weddell seal samples tested. Viruses associated with large vertebrates are poorly studied in Antarctica, and this study adds information about papillomaviruses associated with Weddell seals and contributes to our understanding of the evolutionary history of papillomaviruses.

Temporal changes in Weddell seal dive behavior over winter: Are females increasing foraging effort to support gestation?

In capital-breeding marine mammals, prey acquisition during the foraging trip coinciding with gestation must provide energy to meet the immediate needs of the growing fetus and also a store to meet the subsequent demands of lactation. Weddell seals (Leptonychotes weddellii) that give birth following the gestational (winter) foraging period gain similar proportions of mass and lipid as compared to females that fail to give birth. Therefore, any changes in foraging behavior can be attributed to gestational costs. To investigate differences in foraging effort associated with successful reproduction, twenty-three satellite tags were deployed on post-molt female Weddell seals in the Ross Sea. Of the 20 females that returned to the area the following year, 12 females gave birth and eight did not. Females that gave birth the following year began the winter foraging period with significantly longer and deeper dives, as compared to non-reproductive seals. Mid- to late winter, reproductive females spent a significantly greater proportion of the day diving, and either depressed their diving metabolic rates (DMR), or exceeded their calculated aerobic dive limit (cADL) more frequently than females that returned without a pup. Moreover, non-reproductive females organized their dives into 2-3 short bouts per day on average (BOUTshort; 7.06 ± 1.29 hr; mean ± 95% CI), whereas reproductive females made 1-2 BOUTshort per day (10.9 ± 2.84 hr), comprising one long daily foraging bout without rest. The magnitude of the increase in dive activity budgets and depression in calculated DMR closely matched the estimated energetic requirements of supporting a fetus. This study is one of the first to identify increases in foraging effort that are associated with successful reproduction in a top predator and indicates that reproductive females must operate closer to their physiological limits to support gestational costs.

Pairing ultrasonography with endocrinology to elucidate underlying mechanisms of successful pregnancy in the northern fur seal (Callorhinus ursinus).

Reproductive success is one of the central tenets of conservation management programs, yet the inability to study underlying physiological processes in a minimally-invasive manner and the unpredictable nature of wild animal populations leaves large gaps in our knowledge of factors critical to successful reproduction in wild species. This study integrated ultrasonography of the reproductive tract and analysis of reproductive hormones in 172 northern fur seals (Callorhinus ursinus) to identify intrinsic factors associated with reinitiating embryonic growth at the end of diapause. Within the first 3-4 weeks of active gestation, pregnant fur seals (n = 126) had a larger corpus luteum and fewer antral follicles than non-pregnant fur seals, or those still in diapause (n = 46). This suggests that the conceptus drives changes in ovarian status to convey its presence to the female. Morphological changes in the reproductive tract associated with pregnancy were not reflected in differences in endocrine profiles (estradiol, estrone, progesterone, and relaxin) between pregnant and non-pregnant individuals. Hormone concentrations correlated more strongly with calendar date than with the presence or size of the conceptus, demonstrating that none of these reproductive hormones were reliable markers for early pregnancy diagnosis. Instead, the northern fur seal's long diestrus may serve to reduce the probability of a temporal mismatch between corpus luteum regression and embryo implantation. Indeed, conception rates were high and confirmed rates of pregnancy loss were relatively low (11%). In this study, minimally-invasive ultrasonography was used in wild pinnipeds to detect very early pregnancy (embryonic vesicles >2 mm) in combination with ovarian and endocrine dynamics at the time of embryo implantation, shedding light on mechanisms for maternal recognition of pregnancy. This study is also the first to track whether these same animals carried the embryo to term, by observing fur seals during the birthing season the following year. Data do not support the notion that decreased pregnancy rates or higher pregnancy loss rates are major contributing factors to the northern fur seal's population decline.

Diverse and highly recombinant anelloviruses associated with Weddell seals in Antarctica.

The viruses circulating among Antarctic wildlife remain largely unknown. In an effort to identify viruses associated with Weddell seals (Leptonychotes weddellii) inhabiting the Ross Sea, vaginal and nasal swabs, and faecal samples were collected between November 2014 and February 2015. In addition, a Weddell seal kidney and South Polar skua (Stercorarius maccormicki) faeces were opportunistically sampled. Using high throughput sequencing, we identified and recovered 152 anellovirus genomes that share 63-70% genome-wide identities with other pinniped anelloviruses. Genome-wide pairwise comparisons coupled with phylogenetic analysis revealed two novel anellovirus species, tentatively named torque teno Leptonychotes weddellii virus (TTLwV) -1 and -2. TTLwV-1 (n = 133, genomes encompassing 40 genotypes) is highly recombinant, whereas TTLwV-2 (n = 19, genomes encompassing three genotypes) is relatively less recombinant. This study documents ubiquitous TTLwVs among Weddell seals in Antarctica with frequent co-infection by multiple genotypes, however, the role these anelloviruses play in seal health remains unknown.

Field use of ultrasonography to characterize the reproductive tract and early pregnancy in a phocid, the Weddell seal (Leptonychotes weddellii).

The utility of transrectal ultrasonography was tested in a field setting to characterize the reproductive tract and detect early pregnancy (embryonic vesicles < 3 mm in diameter) in 17 multiparous female Weddell seals (Leptonychotes weddellii). Female Weddell seals give birth in October/November each year, followed by the breeding season (December) and embryonic diapause. Transrectal ultrasonography was attempted in January/February 2014 to examine the entire reproductive tract (uterine horns and body, ovaries with follicles and corpora lutea) using a 5-10 MHz linear-array probe with a 70 cm-long extension. A single pregnancy was detected in 14 of 17 seals (82.4%) as a circular or guitar-pick shaped nonechogenic (black) vesicle with a clearly visible echogenic border within the lumen of the uterus. The stage of embryonic development (ostensibly the gestational age) varied markedly among individuals, ranging from a vesicle with no embryo proper to a large fetus with an ocular orbit, nose/mouth, limb buds, spinal column, umbilical cord, and prominent vasculature. Two of the pregnant seals were re-examined 3-6 days after the initial examination to obtain longitudinal growth rates. Images of one or both ovaries were obtained in nine and seven of the 19 examinations, respectively. Numerous ovarian follicles (3 to 12 mm diameter) were detected and animals typically had a single well-perfused corpus luteum (determined by Doppler color-flow) ipsilateral to the uterine horn containing the pregnancy. We conclude that real-time transrectal ultrasonography is an effective tool for characterizing reproductive events in phocids including ovarian dynamics, and for elucidating the nature of embryonic diapause.

Scaling matters: incorporating body composition into Weddell seal seasonal oxygen store comparisons reveals maintenance of aerobic capacities.

Adult Weddell seals (Leptonychotes weddellii) haul-out on the ice in October/November (austral spring) for the breeding season and reduce foraging activities for ~4 months until their molt in the austral fall (January/February). After these periods, animals are at their leanest and resume actively foraging for the austral winter. In mammals, decreased exercise and hypoxia exposure typically lead to decreased production of O2-carrying proteins and muscle wasting, while endurance training increases aerobic potential. To test whether similar effects were present in marine mammals, this study compared the physiology of 53 post-molt female Weddell seals in the austral fall to 47 pre-breeding females during the spring in McMurdo Sound, Antarctica. Once body mass and condition (lipid) were controlled for, there were no seasonal changes in total body oxygen (TBO2) stores. Within each season, hematocrit and hemoglobin values were negatively correlated with animal size, and larger animals had lower mass-specific TBO2 stores. But because larger seals had lower mass-specific metabolic rates, their calculated aerobic dive limit was similar to smaller seals. Indicators of muscular efficiency, myosin heavy chain composition, myoglobin concentrations, and aerobic enzyme activities (citrate synthase and ß-hydroxyacyl CoA dehydrogenase) were likewise maintained across the year. The preservation of aerobic capacity is likely critical to foraging capabilities, so that following the molt Weddell seals can rapidly regain body mass at the start of winter foraging. In contrast, muscle lactate dehydrogenase activity, a marker of anaerobic metabolism, exhibited seasonal plasticity in this diving top predator and was lowest after the summer period of reduced activity.

Improving the precision of our ecosystem calipers: a modified morphometric technique for estimating marine mammal mass and body composition.

Mass and body composition are indices of overall animal health and energetic balance and are often used as indicators of resource availability in the environment. This study used morphometric models and isotopic dilution techniques, two commonly used methods in the marine mammal field, to assess body composition of Weddell seals (Leptonychotes weddellii, N = 111). Findings indicated that traditional morphometric models that use a series of circular, truncated cones to calculate marine mammal blubber volume and mass overestimated the animal's measured body mass by 26.9±1.5% SE. However, we developed a new morphometric model that uses elliptical truncated cones, and estimates mass with only -2.8±1.7% error (N = 10). Because this elliptical truncated cone model can estimate body mass without the need for additional correction factors, it has the potential to be a broadly applicable method in marine mammal species. While using elliptical truncated cones yielded significantly smaller blubber mass estimates than circular cones (10.2±0.8% difference; or 3.5±0.3% total body mass), both truncated cone models significantly underestimated total body lipid content as compared to isotopic dilution results, suggesting that animals have substantial internal lipid stores (N = 76). Multiple linear regressions were used to determine the minimum number of morphometric measurements needed to reliably estimate animal mass and body composition so that future animal handling times could be reduced. Reduced models estimated body mass and lipid mass with reasonable accuracy using fewer than five morphometric measurements (root-mean-square-error: 4.91% for body mass, 10.90% for lipid mass, and 10.43% for % lipid). This indicates that when test datasets are available to create calibration coefficients, regression models also offer a way to improve body mass and condition estimates in situations where animal handling times must be short and efficient.

Development of the aerobic dive limit and muscular efficiency in northern fur seals (Callorhinus ursinus).

Northern fur seal (Callorhinus ursinus; NFS) populations have been declining, perhaps due to limited foraging ability of pups. Because a marine mammal's proficiency at exploiting underwater prey resources is based on the ability to store large amounts of oxygen (O(2)) and to utilize these reserves efficiently, this study was designed to determine if NFS pups had lower blood, muscle, and total body O(2) stores than adults. Pups (<1-month old) had a calculated aerobic dive limit only ~40% of adult females due to lower blood and, to a much greater extent, muscle O(2) stores. Development of the Pectoralis (Pec) and Longissimus dorsi (LD) skeletal muscles was further examined by determining their myosin heavy chain (MHC) composition and enzyme activities. In all animals, the slow MHC I and fast-twitch IIA proteins typical of oxidative fiber types were dominant, but adult muscles contained more (Pec ~50%; LD ~250% higher) fast-twitch MHC IID/X protein characteristic of glycolytic muscle fibers, than pup muscles. This suggests that adults have greater ability to generate muscle power rapidly and/or under anaerobic conditions. Pup muscles also had lower aerobic and anaerobic ATP production potential, as indicated by lower metabolically scaled citrate synthase, ß-hydroxyacyl CoA dehydrogenase, and lactate dehydrogenase activities (all P values ≤0.001). In combination, these findings indicate that pups are biochemically and physiologically limited in their diving capabilities relative to adults. This may contribute to lower NFS first year survival.

Platelet kainate receptor signaling promotes thrombosis by stimulating cyclooxygenase activation.

RATIONALE: Glutamate is a major signaling molecule that binds to glutamate receptors including the ionotropic glutamate receptors; kainate (KA) receptor (KAR), the N-methyl-d-aspartate receptor, and the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor. Each is well characterized in the central nervous system, but glutamate has important signaling roles in peripheral tissues as well, including a role in regulating platelet function. OBJECTIVE: Our previous work has demonstrated that glutamate is released by platelets in high concentrations within a developing thrombus and increases platelet activation and thrombosis. We now show that platelets express a functional KAR that drives increased agonist induced platelet activation. METHODS AND RESULTS: KAR induced increase in platelet activation is in part the result of activation of platelet cyclooxygenase in a mitogen-activated protein kinase-dependent manner. Platelets derived from KAR subunit knockout mice (GluR6(-/-)) are resistant to KA effects and have a prolonged time to thrombosis in vivo. Importantly, we have also identified polymorphisms in KAR subunits that are associated with phenotypic changes in platelet function in a large group of whites and blacks. CONCLUSIONS: Our data demonstrate that glutamate regulation of platelet activation is in part cyclooxygenase-dependent and suggest that the KAR is a novel antithrombotic target.