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Diet is a primary driver of the composition of gut microbiota and is considered one of the main routes of microbial colonization. Prey identification is fundamental for correlating the diet with the presence of particular microbial groups. The present study examined how diet influenced the composition and function of the gut microbiota of the Pacific harbor seal (Phoca vitulina richardii) in order to better understand the role of prey consumption in shaping its microbiota. This species is a good indicator of the quality of the local environment due to both its foraging and haul-out site fidelity. DNA was extracted from 20 fecal samples collected from five harbor seal colonies located in Baja California, Mexico. The V4 region of 16S rRNA gene was amplified and sequenced using the Illumina technology. Results showed that the gut microbiota of the harbor seals was dominated by the phyla Firmicutes (37%), Bacteroidetes (26%) and Fusobacteria (26%) and revealed significant differences in its composition among the colonies. Funtional analysis using the PICRUSt software suggests a high number of pathways involved in the basal metabolism, such as those for carbohydrates (22%) and amino acids (20%), and those related to the degradation of persistent environmental pollutants. In addition, a DNA metabarcoding analysis of the same samples, via the amplification and sequencing of the mtRNA 16S and rRNA 18S genes, was used to identify the prey consumed by harbor seals revealing the consumption of prey with mainly demersal habits. Functional redundancy in the seal gut microbiota was observed, irrespective of diet or location. Our results indicate that the frequency of occurrence of specific prey in the harbor seal diet plays an important role in shaping the composition of the gut microbiota of harbor seals by influencing the relative abundance of specific groups of gut microorganisms. A significant relationship was found among diet, gut microbiota composition and OTUs assigned to a particular metabolic pathway. [ABSTRACT FROM AUTHOR]

Community marine reserves are geographical areas closed to fishing activities, implemented and enforced by the same fishermen that fish around them. Their main objective is to recover commercial stocks of fish and invertebrates. While marine reserves have proven successful in many parts of the world, their success near important marine predator colonies, such as the California sea lion (Zalophus californianus) and the Pacific harbor seal (Phoca vitulina richardii), is yet to be analyzed. In response to the concerns expressed by local fishermen about the impact of the presence of pinnipeds on their communities’ marine reserves, we conducted underwater surveys around four islands in the Pacific west of the Baja California Peninsula: two without reserves (Todos Santos and San Roque); one with a recently established reserve (San Jeronimo); and, a fourth with reserves established eight years ago (Natividad). All these islands are subject to similar rates of exploitation by fishing cooperatives with exclusive rights. We estimated fish biomass and biodiversity in the seas around the islands, applying filters for potential California sea lion and harbor seal prey using known species from the literature. Generalized linear mixed models revealed that the age of the reserve has a significant positive effect on fish biomass, while the site (inside or outside of the reserve) did not, with a similar result found for the biomass of the prey of the California sea lion. Fish biodiversity was also higher around Natividad Island, while invertebrate biodiversity was higher around San Roque. These findings indicate that marine reserves increase overall fish diversity and biomass, despite the presence of top predators, even increasing the numbers of their potential prey. Community marine reserves may help to improve the resilience of marine mammals to climate-driven phenomena and maintain a healthy marine ecosystem for the benefit of both pinnipeds and fishermen. [ABSTRACT FROM AUTHOR]

Investigation of marine mammal dive-by-dive blood distribution and oxygenation has been limited by a lack of noninvasive technology for use in freely diving animals. Here, we developed a noninvasive near-infrared spectroscopy (NIRS) device to measure relative changes in blood volume and haemoglobin oxygenation continuously in the blubber and brain of voluntarily diving harbour seals. Our results show that seals routinely exhibit preparatory peripheral vasoconstriction accompanied by increased cerebral blood volume approximately 15 s before submersion. These anticipatory adjustments confirm that blood redistribution in seals is under some degree of cognitive control that precedes the mammalian dive response. Seals also routinely increase cerebral oxygenation at a consistent time during each dive, despite a lack of access to ambient air. We suggest that this frequent and reproducible reoxygenation pattern, without access to ambient air, is underpinned by previously unrecognised changes in cerebral drainage. The ability to track blood volume and oxygenation in different tissues using NIRS will facilitate a more accurate understanding of physiological plasticity in diving animals in an increasingly disturbed and exploited environment. [ABSTRACT FROM AUTHOR]

Unihemispheric slow wave sleep (USWS) is a unique form of sleep in which one brain hemisphere maintains low voltage electrical activity indicative of waking while the opposite exhibits slow wave electrical activity indicative of sleep. USWS is present in several marine mammals and in some species of birds. One proposed biological function of USWS is to enable the animal to monitor the environment to detect predators or conspecifics. While asymmetrical eye state was often observed during behavioral sleep in birds and marine mammals, electrophysiological (electroencephalogram, EEG) correlates between the asymmetry of eye state and EEG of two cortical hemispheres have not been reliably established. This study examined the association between eye state and EEG activity during aquatic sleep in two subadult northern fur seals (Callorhinus ursinus), taking advantage of the simultaneous visibility of both eyes when the seals were in the prone position. We found that during USWS the eye contralateral to the sleeping hemisphere was closed on average 99.4±0.1% of the recording time. The eye contralateral to the waking hemisphere opened briefly for on average 1.9±0.1 sec with a rate of 8.2±1.0 per min. This eye was open on average 24.8±2.5% of the USWS time and it was closed no longer than 3 sec, on average 39.4±5.6% of the time. These data indicate that fur seals sleep in seawater by having intermittent visual monitoring. Our findings document the extent of visual monitoring of both eyes during USWS and support the idea that USWS allows intermittent visual vigilance. Thus, USWS serves two functions in the fur seal, facilitating movement and visual vigilance, which may also be the case in cetaceans. [ABSTRACT FROM AUTHOR]

The pelagic ecosystems of the Western Antarctic Peninsula are dynamic and changing rapidly in the face of sustained warming. There is already evidence that warming may be impacting the food web. Antarctic krill, Euphausia superba, is an ice-associated species that is both an important prey item and the target of the only commercial fishery operating in the region. The goal of this study is to develop a dynamic trophic model for the region that includes the impact of the sea-ice regime on krill and krill predators. Such a model may be helpful to fisheries managers as they develop new management strategies in the face of continued sea-ice loss. A mass balanced food-web model (Ecopath) and time dynamic simulations (Ecosim) were created. The Ecopath model includes eight currently monitored species as single species to facilitate its future development into a model that could be used for marine protected area planning in the region. The Ecosim model is calibrated for the years 1996–2012. The successful calibration represents an improvement over existing Ecopath models for the region. Simulations indicate that the role of sea ice is both central and complex. The simulations are only able to recreate observed biomass trends for the monitored species when metrics describing the sea-ice regime are used to force key predator-prey interactions, and to drive the biomasses of Antarctic krill and the fish species Gobionotothen gibberifrons. This model is ready to be used for exploring results from sea-ice scenarios or to be developed into a spatial model that informs discussions regarding the design of marine protected areas in the region. [ABSTRACT FROM AUTHOR]

Reliable population estimates are fundamental to the conservation of endangered species. We evaluate here the use of photo-identification (photo-ID) and mark-recapture techniques for estimating the population size of the endangered Saimaa ringed seal (Phoca hispida saimensis). Photo-ID data based on the unique pelage patterns of individuals were collected by means of camera traps and boat-based surveys during the molting season in two of the species' main breeding areas, over a period of five years in the Pihlajavesi basin and eight years in the Haukivesi basin. An open model approach provided minimum population estimates for these two basins. The results indicated high survival rates and site fidelity among the adult seals. More accurate estimates can be obtained in the future by increasing the surveying effort both spatially and temporally. The method presented here proved effective for evaluating population size objectively, whereas the results of the current snow lair censuses are dependent on varying winter conditions, for instance. We therefore suggest that a photo-ID-based non-invasive mark-recapture method should be used for estimating Saimaa ringed seal abundances in order to ensure reliable, transparent population monitoring under changing climatic conditions. [ABSTRACT FROM AUTHOR]

In marine ecosystems, maximum sustainable yield considerations are affected by any substantial changes that occur in the top and bottom compartments of the food-web. This study explores how the southern North Sea’s fisheries may need to adjust their fishing efforts to maintain optimum yields of sole, plaice, cod and brown shrimps under increased marine mammal populations and a reduced primary productivity. We constructed plausible scenarios of ongoing food-web changes using the results of Bayesian age-structured population models to estimate carrying capacities of harbour porpoises (Phocoena phocoena) and grey seals (Halichoerus grypus). Losses in primary productivity were predicted by lower trophic level ecosystem models. These scenarios were implemented in a food-web model of the southern North Sea. For each scenario, we sought mixed-fleet fishing efforts that would deliver maximum yields of sole, plaice, cod and brown shrimp combined. We also did so for a baseline run with unaltered mammal and primary production, and compared the differences in optimal fishing strategies, predicted yields, and states of the stocks between the scenarios. We found stocks and yields to be far more sensitive to changes in primary productivity than to increased marine mammal predation. The latter predominantly impacted cod, and even benefitted brown shrimps compared to the baseline run. Under 30% reduced primary productivity, fishing efforts had to be reduced by 50% to still provide maximum yields, whereas the marine mammal scenario induced no need to adjust the fishing regime. This draws attention to the potential gains of incorporating bottom-up processes into long-term management considerations, while marine mammal predation may be less of a concern, in particular for flatfish fisheries in the North Sea, and may even benefit shrimp trawlers because of reduced predation on shrimp from fish predators. [ABSTRACT FROM AUTHOR]

Seabirds and pinnipeds play an important role in biogeochemical cycling by transferring nutrients from aquatic to terrestrial environments. Indeed, soils rich in animal depositions have generally high organic carbon, nitrogen and phosphorus contents. Several studies have assessed bacterial diversity in Antarctic soils influenced by marine animals; however most have been conducted in areas with significant human impact. Thus, we chose Cape Shirreff, Livingston Island, an Antarctic Specially Protected Area designated mainly to protect the diversity of marine vertebrate fauna, and selected sampling sites with different types of animals coexisting in a relatively small space, and where human presence and impact are negligible. Using 16S rRNA gene analyses through massive sequencing, we assessed the influence of animal concentrations, via their modification of edaphic characteristics, on soil bacterial diversity and composition. The nutrient composition of soils impacted by Antarctic fur seals and kelp gulls was more similar to that of control soils (i.e. soils without visible presence of plants or animals), which may be due to the more active behaviour of these marine animals compared to other species. Conversely, the soils from concentrations of southern elephant seals and penguins showed greater differences in soil nutrients compared to the control. In agreement with this, the bacterial communities of the soils associated with these animals were most different from those of the control soils, with the soils of penguin colonies also possessing the lowest bacterial diversity. However, all the soils influenced by the presence of marine animals were dominated by bacteria belonging to Gammaproteobacteria, particularly those of the genus Rhodanobacter. Therefore, we conclude that the modification of soil nutrient composition by marine vertebrates promotes specific groups of bacteria, which could play an important role in the recycling of nutrients in terrestrial Antarctic ecosystems. [ABSTRACT FROM AUTHOR]

Climate change, together with increasing human activity, poses a threat to the breeding success of endangered landlocked ringed seals (Phoca hispida saimensis). In this study, we estimated the spatial ecology of Saimaa ringed seals during the breeding season in the ice-covered period of December-April. The telemetry data on tagged seals (n = 20), with a total of 25 separate tracking periods and birth lair locations (n = 59) of non-tagged seals, were studied to estimate the movement ecology and breeding density. The movements of the ringed seals were more restricted during the ice-covered season; the total home range size (average 7.4 km2) in winter was 13 times smaller than that in summer. Individual tagged seals occupied an average of 5 ± 3 SD subnivean haul outs (snow lairs or ice cavities), and the mean distance between the haul outs was 1.6 ± 1.1 SD km (range 0.2–5.9 km). Moreover, our data indicated that ringed seal females likely exhibited breeding time avoidance of each other’s core areas, which may indicate some degree of territoriality. This was supported by the findings that the core areas (mean 1.2 km2) of tagged adult females (n = 9), did not overlap with each other. Also data on non-tagged seals showed that females did not give birth to pups within the core area radius of other parturient females. This study, together with earlier findings on the home ranges of nursed pups and perinatal mortality rates, has implications into land usage planning in Lake Saimaa by highlighting the need of undisturbed area between seal lairs and anthropogenic disturbances. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In ecological studies it is often assumed that predator foraging strategies and resource use are geographically and seasonally homogeneous, resulting in relatively static trophic relationships. However, certain centrally placed foragers (e.g. seals) often have terrestrial sites for breeding, resting, and moulting that are geographically distinct, and associated with different habitat types. Therefore, accurate estimations of predator diet at relevant spatial and temporal scales are key to understanding energetic requirements, predator-prey interactions and ecosystem structure. We investigate geographic variation in the diet of grey seals (Halichoerus grypus), a relatively abundant and widely distributed central place forager, to provide insights into geographic variation in resource use. Prey composition was identified using scat samples collected over concurrent timescales and a multivariate approach was used to analyse diet from two contrasting habitats. Regional differences in prey assemblages occurred within all years (2011–2013) and all seasons (ANOSIM, all p<0.05), apart from in winter. Telemetry data were used to identify core foraging areas and habitats most likely associated with scat samples collected at the two haul-out sites. Regional differences in the diet appear to reflect regional differences in the physical habitat features, with seals foraging in deeper waters over sandy substrates showing a higher prevalence of pelagic and bentho-pelagic prey species such as blue whiting and sandeels. Conversely, seals foraging in comparatively shallow waters had a greater contribution of demersal and groundfish species such as cephalopods and flatfish in their diet. We suggest that shallower waters enable seals to spend more time foraging along the benthos while remaining within aerobic dive limits, resulting in more benthic species in the diet. In contrast, the diet of seals hauled-out in areas adjacent to deeper waters indicates that either seals engage in a more pelagic foraging strategy, or that seals can spend less time at the benthos, resulting in comparatively more pelagic prey recovered in the diet. The substantial differences in prey assemblages over a small spatial scale (<300 km) demonstrates the importance of using regionally-specific diet information in ecosystem-based models to better account for different trophic interactions. [ABSTRACT FROM AUTHOR]

Killer whales have a cosmopolitan distribution and as a species are generalists, feeding on a variety of prey. However, local populations tend to specialise on specific prey types. In Icelandic waters, killer whales are generally associated with herring and, thus, have been presumed to be herring specialists. However, recent studies suggest a more complex foraging ecology, possibly including a mosaic of strategies. With increased observational effort in recent years due to research and whale-watching activities, there have been several reports of interactions with different prey, including confirmed predation events. In this study we aimed to summarise the range of potential prey of killer whales observed in Icelandic waters. We report on 12 previously unpublished accounts and review 15 accounts published in the scientific literature or local newspapers, making a total of 27 events where killer whales were observed interacting with actual or potential prey. Thirteen different species, including birds (n = 1), cephalopods (n = 1), fish (n = 5) and marine mammals (n = 6), are reported, although herring is by far the species that killer whales are most often observed interacting with. This study provides the first summary of actual and suspected killer whale prey in Icelandic waters, and contributes towards our understanding of this population’s prey preferences. However, describing the diet of individuals/groups was not possible and this study points to a need for continued monitoring to understand the intricacies of killer whale foraging behaviour in this area. [ABSTRACT FROM AUTHOR]

Brucella are highly infectious bacterial pathogens responsible for a severely debilitating zoonosis called brucellosis. Half of the human population worldwide is considered to live at risk of exposure, mostly in the poorest rural areas of the world. Prompt diagnosis of brucellosis is essential to prevent complications and to control epidemiology outbreaks, but identification of Brucella isolates may be hampered by the lack of rapid and cost-effective methods. Nowadays, many clinical microbiology laboratories use Matrix-Assisted Laser Desorption Ionization–Time Of Flight mass spectrometry (MALDI-TOF MS) for routine identification. However, lack of reference spectra in the currently commercialized databases does not allow the identification of Brucella isolates. In this work, we constructed a Brucella MALDI-TOF MS reference database using VITEK MS. We generated 590 spectra from 84 different strains (including rare or atypical isolates) to cover this bacterial genus. We then applied a novel biomathematical approach to discriminate different species. This allowed accurate identification of Brucella isolates at the genus level with no misidentifications, in particular as the closely related and less pathogenic Ochrobactrum genus. The main zoonotic species (B. melitensis, B. abortus and B. suis) could also be identified at the species level with an accuracy of 100%, 92.9% and 100%, respectively. This MALDI-TOF reference database will be the first Brucella database validated for diagnostic and accessible to all VITEK MS users in routine. This will improve the diagnosis and control of brucellosis by allowing a rapid identification of these pathogens. [ABSTRACT FROM AUTHOR]

Pinniped vibrissae provide information on changes in diet at seasonal and annual scales; however, species-specific growth patterns must first be determined in order to interpret these data. In this study, a simple linear model was used to estimate the growth rate of vibrissae from adult female California sea lions (Zalophus californianus) from San Esteban Island in the Gulf of California, Mexico. The δ15N and δ13C values do not display a marked oscillatory pattern that would permit direct determination of the time period contained in each vibrissa; thus, time (age) was calculated in two ways: 1) based on the correlation between the observed number of peaks (Fourier series) in the δ15N profile and the length of each vibrissa, and 2) through direct comparison with the observed number of peaks in the δ15N profile. Cross-correlation confirmed that the two peaks in the δ15N profile reflected the two peaks in the chlorophyll-a concentration recorded annually around the island. The mean growth rate obtained from the correlation was 0.08 ± 0.01 mm d-1, while that calculated based on the observed number of peaks was 0.10 ± 0.05 mm d-1. Both are consistent with the rates reported for adult females of other otariid species (0.07 to 0.11 mm d-1). Vibrissa growth rates vary by individual, age, sex, and species; moreover, small differences in the growth rate can result in significant differences over the time periods represented by the isotopic signal. Thus, it is important to assess this parameter on a species-by-species basis. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Effective ecosystem-based management requires estimates of abundance and population trends of species of interest. Trend analyses are often limited due to sparse or short-term abundance estimates for populations that can be logistically difficult to monitor over time. Therefore it is critical to assess regularly the quality of the metrics in long-term monitoring programs. For a monitoring program to provide meaningful data and remain relevant, it needs to incorporate technological improvements and the changing requirements of stakeholders, while maintaining the integrity of the data. In this paper we critically examine the monitoring program for the Australian fur seal (AFS) Arctocephalus pusillus doriferus as an example of an ad-hoc monitoring program that was co-ordinated across multiple stakeholders as a range-wide census of live pups in the Austral summers of 2002, 2007 and 2013. This 5-yearly census, combined with historic counts at individual sites, successfully tracked increasing population trends as signs of population recovery up to 2007. The 2013 census identified the first reduction in AFS pup numbers (14,248 live pups, -4.2% change per annum since 2007), however we have limited information to understand this change. We analyse the trends at breeding colonies and perform a power analysis to critically examine the reliability of those trends. We then assess the gaps in the monitoring program and discuss how we may transition this surveillance style program to an adaptive monitoring program than can evolve over time and achieve its goals. The census results are used for ecosystem-based modelling for fisheries management and emergency response planning. The ultimate goal for this program is to obtain the data we need with minimal cost, effort and impact on the fur seals. In conclusion we identify the importance of power analyses for interpreting trends, the value of regularly assessing long-term monitoring programs and proper design so that adaptive monitoring principles can be applied. [ABSTRACT FROM AUTHOR]

The growing seal populations of the Baltic have led to more frequent interactions with coastal fisheries. The motivation for seals to interact with fishing gear is high. It provides high densities of fish. A successful means of mitigating the conflict is the pontoon trap. Seal visits here have been frequent. Seals have access to most parts of the trap system including the middle chamber, which is an overhead environment. Concerns have been raised about seals possible entanglement in this specific part of the trap. As a means of keeping seals from entering the middle chamber, two different Seal Exclusion Devices (SEDs) were tested. A diamond mesh SED and a square mesh SED, which was rotated 45°. The aim was to compare the functionality of the different SEDs with respect to seal deterrent abilities and catch composition. The hypothesis tested were (i) that seals would not be able to enter the middle chamber, (ii) that the catch would increase and (iii) that the SED would deter larger fish from swimming into the middle chamber. Catch data and underwater film were collected. Larger salmons were caught in traps equipped with SEDs. The SEDs did not affect the number of caught fish or the total catch per soak day. [ABSTRACT FROM AUTHOR]

Big data offer a great opportunity for nature-based recreation (NbR) mapping and evaluation. However, it is important to determine when and how it is appropriate to use this resource. We used Scotland as a case study to validate the use of data from Flickr as an indicator of NbR on a national scale and at several regional spatial and temporal resolutions. We compared Flickr photographs to visitor statistics in the Cairngorms National Park (CNP) and determined whether temporal variability in photo counts could be explained by known annual estimates of CNP visitor numbers. We then used a unique recent national survey of nature recreation in Scotland to determine whether the spatial distribution of Flickr photos could be explained by known spatial variability in nature use. Following this validation work, we used Flickr data to identify hotspots of wildlife watching in Scotland and investigated how they changed between 2005 and 2015. We found that spatial and temporal patterns in Flickr count are explained by measures of visitation obtained through surveys and that this relationship is reliable down to a 10 Km scale resolution. Our findings have implications for planning and management of NbR as they suggest that photographs uploaded on Flickr reflect patterns of NbR at spatial and temporal scales that are relevant for ecosystem management. [ABSTRACT FROM AUTHOR]

Chemical cues are arguably the most fundamental means of animal communication and play an important role in mate choice and kin recognition. Consequently, there is growing interest in the use of gas chromatography (GC) to investigate the chemical basis of eco-evolutionary interactions. Both GC-MS (mass spectrometry) and FID (flame ionization detection) are commonly used to characterise the chemical composition of biological samples such as skin swabs. The resulting chromatograms comprise peaks that are separated according to their retention times and which represent different substances. Across chromatograms of different samples, homologous substances are expected to elute at similar retention times. However, random and often unavoidable experimental variation introduces noise, making the alignment of homologous peaks challenging, particularly with GC-FID data where mass spectral data are lacking. Here we present , a user-friendly R package for aligning GC-FID data based on retention times. The package was developed specifically for ecological and evolutionary studies that seek to investigate similarity patterns across multiple and often highly variable biological samples, for example representing different sexes, age classes or reproductive stages. The package also implements dynamic visualisations to facilitate inspection and fine-tuning of the resulting alignments and can be integrated within a broader workflow in R to facilitate downstream multivariate analyses. We demonstrate an example workflow using empirical data from Antarctic fur seals and explore the impact of user-defined parameter values by calculating alignment error rates for multiple datasets. The resulting alignments had low error rates for most of the explored parameter space and we could also show that performed equally well or better than other available software. We hope that will help to simplify the processing of chemical datasets and improve the standardization and reproducibility of chemical analyses in studies of animal chemical communication and related fields. [ABSTRACT FROM AUTHOR]

Leopard seals are an important Antarctic apex predator that can affect marine ecosystems through local predation. Here we report on the successful use of micro geolocation logging sensor tags to track the movements, and activity, of four leopard seals for trips of between 142–446 days including one individual in two separate years. Whilst the sample size is small the results represent an advance in our limited knowledge of leopard seals. We show the longest periods of tracking of leopard seals’ migratory behaviour between the pack ice, close to the Antarctic continent, and the sub-Antarctic island of South Georgia. It appears that these tracked animals migrate in a directed manner towards Bird Island and, during their residency, use this as a central place for foraging trips as well as exploiting the local penguin and seal populations. Movements to the South Orkney Islands were also recorded, similar to those observed in other predators in the region including the krill fishery. Analysis of habitat associations, taking into account location errors, indicated the tracked seals had an affinity for shallow shelf water and regions of sea ice. Wet and dry sensors revealed that seals hauled out for between 22 and 31% of the time with maximum of 74 hours and a median of between 9 and 11 hours. The longest period a seal remained in the water was between 13 and 25 days. Fitting GAMMs showed that haul out rates changed throughout the year with the highest values occurring during the summer which has implications for visual surveys. Peak haul out occurred around midday for the months between October and April but was more evenly spread across the day between May and September. The seals’ movements between, and behaviour within, areas important to breeding populations of birds and other seals, coupled with the dynamics of the region’s fisheries, shows an understanding of leopard seal ecology is vital in the management of the Southern Ocean resources. [ABSTRACT FROM AUTHOR]

Canine distemper virus (CDV), Leptospira interrogans, and Toxoplasma gondii are potentially lethal pathogens associated with decline in marine mammal populations. The Caspian Sea is home for the endangered Caspian seal (Pusa caspica). In the late 1990s and early 2000s, CDV caused a series of mortality events involving at least several thousand Caspian seals. To assess current infection status in Caspian seals, we surveyed for antibodies to three pathogens with potential to cause mortality in marine mammals. During 2015–2017, we tested serum samples from 36, apparently healthy, Caspian seals, accidentally caught in fishing nets in the Caspian Sea off Northern Iran, for antibodies to CDV, L. interrogans, and T. gondii, by virus neutralization, microscopic agglutination, and modified agglutination, respectively. Twelve (33%), 6 (17%), and 30 (83%) samples were positive for CDV, L. interrogans and T. gondii antibodies, respectively. The highest titers of CDV, L. interrogans, and T. gondii antibodies were 16, 400, and 50, respectively. Frequencies of antibody to these pathogens were higher in seals >1 year old compared to seals <1 year old. Two serovars of L. interrogans (Pomona and Canicola) were detected. Our results suggest a need for additional studies to clarify the impact of these pathogens on Caspian seal population decline and the improvement of management programs, including systematic screening to detect and protect the remaining population from disease outbreaks. [ABSTRACT FROM AUTHOR]

The first year of life is typically the most critical to a pinniped’s survival, especially for Arctic phocids which are weaned at only a few weeks of age and left to locate and capture prey on their own. Their seasonal movements and habitat selection are therefore important factors in their survival. During a cooperative effort between scientists and subsistence hunters in October 2004, 2005, and 2006, 13 female and 13 male young (i.e., age <2) bearded seals (Erignathus barbatus) were tagged with satellite-linked dive recorders (SDRs) in Kotzebue Sound, Alaska. Shortly after being released, most seals moved south with the advancing sea-ice through the Bering Strait and into the Bering Sea where they spent the winter and early spring. The SDRs of 17 (8 female and 9 male) seals provided frequent high-quality positions in the Bering Sea; their data were used in our analysis. To investigate habitat selection, we simulated 20 tracks per seal by randomly selecting from the pooled distributions of the absolute bearings and swim speeds of the tagged seals. For each point in the observed and simulated tracks, we obtained the depth, sea-ice concentration, and the distances to sea-ice, open water, the shelf break and coastline. Using logistic regression with a stepwise model selection procedure, we compared the simulated tracks to those of the tagged seals and obtained a model for describing habitat selection. The regression coefficients indicated that the bearded seals in our study selected locations near the ice edge. In contrast, aerial surveys of the bearded seal population, predominantly composed of adults, indicated higher abundances in areas farther north and in heavier pack ice. We hypothesize that this discrepancy is the result of behavioral differences related to age. Ice concentration was also shown to be a statistically significant variable in our model. All else being equal, areas of higher ice concentration are selected for up to about 80%. The effects of sex and bathymetry were not statistically significant. The close association of young bearded seals to the ice edge in the Bering Sea is important given the likely effects of climate warming on the extent of sea-ice and subsequent changes in ice edge habitat. [ABSTRACT FROM AUTHOR]

Gray seals (Halichoerus grypus) have been rapidly recolonizing the Northeast US coast, eliciting concern from the fishing industry. However, the ecological effect of this recovery is still unknown and as such, research is needed to better understand how the diet composition of gray seals in US waters will contribute to the ecological impact. While previous research on seal diets has focused on the analysis of hard prey remains, stable isotope analysis presents an alternative method that can be used to describe marine mammal diets when direct observation is impossible. To address this issue, we used stable isotope analysis of gray seal pup vibrissae and lanugo from Monomoy Island, Cape Cod, MA during the 2015/2016 winter breeding season to estimate adult female diet composition during pregnancy. Stable isotope mixing models (SIMM) suggested adult female gray seals were consuming greater amounts of cephalopod prey and less sand lance than previously indicated from analysis of hard prey remains. However, using SIMMs to estimate the diet composition of gray seals remains difficult due to the large number of isotopically similar prey species and uncertainty in tissue-specific, stable isotope trophic enrichment factors. Even so, by combining prey sources into ecologically informative groups and integrating prior information into SIMMs it is possible to obtain additional insights into the diet of this generalist predator. [ABSTRACT FROM AUTHOR]

The Earth′s climate is warming, especially in the mid- and high latitudes of the Northern Hemisphere. The northern elephant seal (Mirounga angustirostris) breeds and haul-outs on islands and the mainland of Baja California, Mexico, and California, U.S.A. At the beginning of the 21st century, numbers of elephant seals in California are increasing, but the status of Baja California populations is unknown, and some data suggest they may be decreasing. We hypothesize that the elephant seal population of Baja California is experiencing a decline because the animals are not migrating as far south due to warming sea and air temperatures. Here we assessed population trends of the Baja California population, and climate change in the region. The numbers of northern elephant seals in Baja California colonies have been decreasing since the 1990s, and both the surface waters off Baja California and the local air temperatures have warmed during the last three decades. We propose that declining population sizes may be attributable to decreased migration towards the southern portions of the range in response to the observed temperature increases. Further research is needed to confirm our hypothesis; however, if true, it would imply that elephant seal colonies of Baja California and California are not demographically isolated which would pose challenges to environmental and management policies between Mexico and the United States. [ABSTRACT FROM AUTHOR]

In this study, we used relatively large number of samples (n = 178) and control region of mtDNA (454bp) to clearify the divergence history of Japanese harbour seals (Phoca vitulina stejnegeri) and phylogenetic relationship between the seals in Japan and other countries. Our results suggested that Japanese harbour seals possibly consisted of more than two lineages and secondary contact of populations after a long isolation. Furthermore, one of the lineage was made only by Japanese harbour seals (Group P1). The proportion of Group P1 was the highest at the South West and gradually decreased towards the North East of Hokkaido, Japan. On the other hand, the haplotypes do not belonged to Group P1 showed close relationship to the seals in the North Pacific. Based on the fossil record of harbour seal in Japan and the range of sea ice during the Last Glacial Maximum (LGM), Group P1 might have entered Japan before the LGM and became isolated due to the geographical boundary, and gradually extended its range from the South West towards the North East of Hokkaido after the disappearance of the sea ice, while the seals which are not in Group P1 immigrated into Japan from the North Pacific. [ABSTRACT FROM AUTHOR]

Body mass dynamics of animals can indicate critical associations between extrinsic factors and population vital rates. Photogrammetry can be used to estimate mass of individuals in species whose life histories make it logistically difficult to obtain direct body mass measurements. Such studies typically use equations to relate volume estimates from photogrammetry to mass; however, most fail to identify the sources of error between the estimated and actual mass. Our objective was to identify the sources of error that prevent photogrammetric mass estimation from directly predicting actual mass, and develop a methodology to correct this issue. To do this, we obtained mass, body measurements, and scaled photos for 56 sedated Weddell seals (Leptonychotes weddellii). After creating a three-dimensional silhouette in the image processing program PhotoModeler Pro, we used horizontal scale bars to define the ground plane, then removed the below-ground portion of the animal’s estimated silhouette. We then re-calculated body volume and applied an expected density to estimate animal mass. We compared the body mass estimates derived from this silhouette slice method with estimates derived from two other published methodologies: body mass calculated using photogrammetry coupled with a species-specific correction factor, and estimates using elliptical cones and measured tissue densities. The estimated mass values (mean ± standard deviation 345±71 kg for correction equation, 346±75 kg for silhouette slice, 343±76 kg for cones) were not statistically distinguishable from each other or from actual mass (346±73 kg) (ANOVA with Tukey HSD post-hoc, p>0.05 for all pairwise comparisons). We conclude that volume overestimates from photogrammetry are likely due to the inability of photo modeling software to properly render the ventral surface of the animal where it contacts the ground. Due to logistical differences between the “correction equation”, “silhouette slicing”, and “cones” approaches, researchers may find one technique more useful for certain study programs. In combination or exclusively, these three-dimensional mass estimation techniques have great utility in field studies with repeated measures sampling designs or where logistic constraints preclude weighing animals. [ABSTRACT FROM AUTHOR]

Terrestrial and marine wildlife populations have been severely reduced by hunting, fishing and habitat destruction, especially in the last centuries. Although management regulations have led to the recovery of some populations, the underlying processes are not always well understood. This study uses a 40-year time series of counts of harbour seals (Phoca vitulina) in the Wadden Sea to study these processes, and demonstrates the influence of historical regional differences in management regimes on the recovery of this population. While the Wadden Sea is considered one ecologically coupled zone, with a distinct harbour seal population, the area is divided into four geo-political regions i.e. the Netherlands, Lower Saxony including Hamburg, Schleswig-Holstein and Denmark. Gradually, seal hunting was banned between 1962 and 1977 in the different regions. Counts of moulting harbour seals and pup counts, obtained during aerial surveys between 1974 and 2014, show a population growth from approximately 4500 to 39,000 individuals. Population growth models were developed to assess if population growth differed between regions, taking into account two Phocine Distemper Virus (PDV) epizootics, in 1988 and 2002 which seriously affected the population. After a slow start prior to the first epizootic, the overall population grew exponentially at rates close to assumed maximum rates of increase in a harbour seal population. Recently, growth slowed down, potentially indicative of approaching carrying capacity. Regional differences in growth rates were demonstrated, with the highest recovery in Netherlands after the first PDV epizootic (i.e. 17.9%), suggesting that growth was fuelled by migration from the other regions, where growth remained at or below the intrinsic growth rate (13%). The seals’ distribution changed, and although the proportion of seals counted in the German regions declined, they remained by far the most important pupping region, with approximately 70% of all pups being born there. It is hypothesised that differences in hunting regime, preceding the protection in the 1960’s and 1970’s, created unbalance in the distribution of breeding females throughout the Wadden Sea, which prevailed for decades. Breeding site fidelity promoted the growth in pup numbers at less affected breeding sites, while recolonisation of new breeding areas would be suppressed by the philopatry displayed by the animals born there. This study shows that for long-lived species, variable management regimes in this case hunting regulations, across a species’ range can drive population dynamics for several generations. [ABSTRACT FROM AUTHOR]

Identifying environmental characteristics that define the ecological niche of a species is essential to understanding how changes in physical conditions might affect its distribution and other aspects of its ecology. The present study used satellite relay data loggers (SRDLs) to study habitat use by Northeast Atlantic hooded seals (N = 20; 9 adult females, 3 adult males, and 8 juveniles). Three different methods were used in combination to achieve maximum insight regarding key foraging areas for hooded seals in this region, which have decline by 85% in recent decades: 1) first passage time (FPT); 2) vertical transit rate and; 3) change in dive drift rate. Generalized additive mixed models (GAMM) were applied to each method to determine whether specific habitat characteristics were associated with foraging. Separate models were run for the post-molting and the post-breeding seasons; sex and age classes were included in the GAMMs. All three methods highlighted a few common geographic areas as being important foraging zones; however, there were also some different areas identified by the different methods, which highlights the importance of using multiple indexes when analyzing tracking and diving data to study foraging behavior. Foraging occurred most commonly in relatively shallow areas with high Sea Surface Temperatures (SST), corresponding to continental shelf areas with Atlantic Water masses. All age and sex classes overlapped spatially to some extent, but the different age and sex groups showed differences in the bathymetry of their foraging areas as well as in their vertical use of the water column. When foraging, pups dove in the upper part of the water column in relatively deep areas. Adult females foraged relatively shallowly in deep water areas too, though in shallower areas than pups. Adult males foraged close to the bottom in shallower areas. [ABSTRACT FROM AUTHOR]

Measurements of body size and mass are fundamental to pinniped population management and research. Manual measurements tend to be accurate but are invasive and logistically challenging to obtain. Ground-based photogrammetric techniques are less invasive, but inherent limitations make them impractical for many field applications. The recent proliferation of unmanned aerial systems (UAS) in wildlife monitoring has provided a promising new platform for the photogrammetry of free-ranging pinnipeds. Leopard seals (Hydrurga leptonyx) are an apex predator in coastal Antarctica whose body condition could be a valuable indicator of ecosystem health. We aerially surveyed leopard seals of known body size and mass to test the precision and accuracy of photogrammetry from a small UAS. Flights were conducted in January and February of 2013 and 2014 and 50 photogrammetric samples were obtained from 15 unrestrained seals. UAS-derived measurements of standard length were accurate to within 2.01 ± 1.06%, and paired comparisons with ground measurements were statistically indistinguishable. An allometric linear mixed effects model predicted leopard seal mass within 19.40 kg (4.4% error for a 440 kg seal). Photogrammetric measurements from a single, vertical image obtained using UAS provide a noninvasive approach for estimating the mass and body condition of pinnipeds that may be widely applicable. [ABSTRACT FROM AUTHOR]

White sharks (Carcharodon carcharias) are apex predators that play an important role in the structure and stability of marine ecosystems. Despite their ecological importance and protected status, white sharks are still subject to lethal control to reduce the risk of shark bites for recreational water users. The Shark Spotters program, pioneered in Cape Town, South Africa, provides a non-lethal alternative for reducing the risk of human-shark conflict. In this study we assessed the efficacy of the Shark Spotters program in reducing overlap between water users and white sharks at two popular beaches in False Bay, South Africa. We investigated seasonal and diel patterns in water use and shark presence at each beach, and thereafter quantified the impact of different shark warnings from shark spotters on water user abundance. We also assessed the impact of a fatal shark incident on patterns of water use. Our results revealed striking diel and seasonal overlap between white sharks and water users at both beaches. Despite this, there was a low rate of shark-human incidents (0.5/annum) which we attribute partly to the success of the Shark Spotters program. Shark spotters use visual (coloured flags) and auditory (siren) cues to inform water users of risk associated with white shark presence in the surf zone. Our results showed that the highest risk category (denoted by a white flag and accompanying siren) caused a significant reduction in water user abundance; however the secondary risk category (denoted by a red flag with no siren) had no significant effect on water users. A fatal shark incident was shown to negatively impact the number of water users present for at least three months following the incident. Our results indicate that the Shark Spotters program effectively reduces spatial overlap between white sharks and water users when the risk of conflict is highest. [ABSTRACT FROM AUTHOR]

Extension of known ecological niches of Brucella has included the description of two novel species from marine mammals. Brucella pinnipedialis is associated predominantly with seals, while two major Brucella ceti clades, most commonly associated with porpoises or dolphins respectively, have been identified. To date there has been limited characterisation of Brucella isolates obtained from marine mammals outside Northern European waters, including North American waters. To address this gap, and extend knowledge of the global population structure and host associations of these Brucella species, 61 isolates from marine mammals inhabiting North American waters were subject to molecular and phenotypic characterisation enabling comparison with existing European isolates. The majority of isolates represent genotypes previously described in Europe although novel genotypes were identified in both B. ceti clades. Harp seals were found to carry B. pinnipedialis genotypes previously confined to hooded seals among a diverse repertoire of sequence types (STs) associated with this species. For the first time Brucella isolates were characterised from beluga whales and found to represent a number of distinct B. pinnipedialis genotypes. In addition the known host range of ST27 was extended with the identification of this ST from California sea lion samples. Finally the performance of the frequently used diagnostic tool Bruce-ladder, in differentiating B. ceti and B. pinnipedialis, was critically assessed based on improved knowledge of the global population structure of Brucella associated with marine mammals. [ABSTRACT FROM AUTHOR]

Carcasses of wild animals are often visited by different scavengers. However, determining which scavenger caused certain types of bite marks is particularly difficult and knowledge thereof is lacking. Therefore, a loop-mediated isothermal amplification (LAMP) assay (target sequence cytochrome b) was developed to detect red fox DNA in carcasses of harbour porpoises. The MSwab™ method for direct testing without prior DNA isolation was validated. As a detection device, the portable real-time fluorometer Genie® II was used, which yields rapid results and can be used in field studies without huge laboratory equipment. In addition to in vitro evaluation and validation, a stranded and scavenged harbour porpoise carcass was successfully examined for red fox DNA residues. The developed LAMP method is a valuable diagnostic tool for confirming presumable red fox bite wounds in harbour porpoises without further DNA isolation steps. [ABSTRACT FROM AUTHOR]

In this paper, we studied the genetic variability in Weddell seal from colonies in Terra Nova Bay and Wood Bay, both sites located in the Ross Sea area, Antarctica. Two mitochondrial genes and one nuclear gene, with different mutation rates, were sequenced to investigate the haplotype diversity of the colonies and to test for a possible recent expansion. Fifteen microsatellites were used to analyze their genetic structure. Sequenced genes and microsatellites were also used to estimate the effective population size of the studied colonies and the Ross Sea seal population. The Ross Sea has a high density population of Weddel seals, with an estimated effective number of 50,000 females, and 1,341 individuals for the sampling area, possibly due to its high primary production. The colonies showed high diversity (Hd > 0.90) and many exclusive haplotypes (> 75%), likely a consequence of the surprisingly high site fidelity of Weddell seals, despite the proximity of the colonies. Nevertheless, there was low microsatellite differentiation between colonies, suggesting that they are part of a single larger population. Their expansion seemed to have started during the last glacial cycle (around 58,000 years ago), indicating that the Ross Sea seal populations have been present in the area for long time, probably due to the lack of hunting by humans and terrestrial predation. As a top predator, the role of Weddell seals in the Ross Sea ecology is crucial, and its demographic dynamics should be monitored to follow the future changes of such an important ecosystem. [ABSTRACT FROM AUTHOR]

Sealing log books from 75 out of 79 commercial harvest cruises carried out between 1972 and 1994 in the Sea of Okhotsk, Russia, were analyzed to describe spatial and temporal allocation of ice-associated seal harvest effort, species composition of catches, total harvest rates, and related parameters for species including ringed (Pusa hispida), ribbon (Histriophoca fasciata), bearded (Erignathus barbatus) and spotted (Phoca largha) seal. Variations in catch per unit effort were explored in relation to year, sea ice conditions, day of the year, and geographic location. In most years, the harvest was predominantly represented by ringed seals (mean = 0.43, range 0.25–0.67), followed by ribbon (mean = 0.31, range 0.15–0.43), spotted (mean = 0.19, range 0.11–0.35) and bearded seals (mean = 0.07, range 0.03–0.14). The struck-and-lost percentages were as high as 30–35% for ringed, bearded and spotted seals and 15–20% for ribbon seals. Catch per unit effort (number of seals/skiff*day) for ringed, ribbon, and spotted seals had a similar seasonal pattern with a distinct spike in catches for spotted seals in the first week of May, for ribbon seals in the last week of May, and for ringed seals in the second week of June. Catches of bearded seals showed a less pronounced temporal structure with a gradual increase toward the end of the harvest season in the majority of years. Spatial distribution of harvest effort followed closely with seal distribution obtained from aerial surveys. These data could be used as a source of information on seal herd location throughout the breeding and molting seasons and for more complex demographic or life-table models. We did not find any evidence of the decline of catch per unit effort over the study period. Timely introduction of state regulations and efficient harvest management apparently prevented severe depletion of ice-associated seal populations in the Sea of Okhotsk during the periods of their intense exploitation. [ABSTRACT FROM AUTHOR]

Killer whales (Orcinus orca) have been documented preying on either fish or marine mammals in several regions, suggesting that this odontocete species has the ability to specialize on different types of prey. Off Norway, killer whales have been shown to rely on the Atlantic herring (Clupea harengus) as a main prey resource. Infrequent observations have revealed seals as an additional component of their diet, yet the extent of predation on marine mammals has remained largely unknown. Here, we present the findings of 29 years of photographic and observational data on seal-feeding killer whale groups identified in Norwegian coastal waters. Four groups have been observed preying and feeding on seals over several years, taking both harbor (Phoca vitulina) and grey (Halichoerus grypus) seals. These stable groups are shown to adopt small group sizes, were typically observed in near-shore areas and were not encountered on herring wintering grounds. Behavioral and social traits adopted by these groups are similar to those of pinniped-feeding killer whales from other regions. The potential ecological reasons and the extent of such prey specializations are discussed. [ABSTRACT FROM AUTHOR]

Information on drivers of dispersal is critical for wildlife conservation but is rare for long-lived marine mammal species with large geographic ranges. We fit multi-state mark-recapture models to resighting data of 369 known-aged Steller sea lion (Eumetopias jubatus) females marked as pups on their natal rookeries in southeastern Alaska from 1994–2005 and monitored from 2001–15. We estimated probabilities of females being first observed parous at their natal site (natal philopatry), and of not moving breeding sites among years (breeding philopatry) at large (> 400 km, all five rookeries in southeastern Alaska) and small (< 4 km, all islands within the largest rookery, Forrester Island Complex, F) spatial scales. At the rookery scale, natal philopatry was moderately high (0.776–0.859) for most rookeries and breeding philopatry was nearly 1, with < 3% of females switching breeding rookeries between years. At more populous islands at F, natal philopatry was 0.500–0.684 versus 0.295–0.437 at less populous islands, and breeding philopatry was 0.919–0.926 versus 0.604–0.858. At both spatial scales, the probability of pupping at a non-natal site increased with population size of, and declined with distance from, the destination site. Natal philopatry of < 1 would increase gene flow, improve population resilience, and promote population recovery after decline in a heterogeneous environment. Very high breeding philopatry suggests that familiarity with neighboring females and knowledge of the breeding site (the topography of pupping sites and nearby foraging locations) may be a critical component to reproductive strategies of sea lions. [ABSTRACT FROM AUTHOR]

Following heavy precipitation, we observed an intense algal bloom in the St. Lawrence Estuary (SLE) that coincided with an unusually high mortality of several species of marine fish, birds and mammals, including species designated at risk. The algal species was identified as Alexandrium tamarense and was determined to contain a potent mixture of paralytic shellfish toxins (PST). Significant levels of PST were found in the liver and/or gastrointestinal contents of several carcasses tested as well as in live planktivorous fish, molluscs and plankton samples collected during the bloom. This provided strong evidence for the trophic transfer of PST resulting in mortalities of multiple wildlife species. This conclusion was strengthened by the sequence of mortalities, which followed the drift of the bloom along the coast of the St. Lawrence Estuary. No other cause of mortality was identified in the majority of animals examined at necropsy. Reports of marine fauna presenting signs of neurological dysfunction were also supportive of exposure to these neurotoxins. The event reported here represents the first well-documented case of multispecies mass mortality of marine fish, birds and mammals linked to a PST-producing algal bloom. [ABSTRACT FROM AUTHOR]

The efficiency with which individuals extract energy from their environment defines their survival and reproductive success, and thus their selective contribution to the population. Individuals that forage more efficiently (i.e., when energy gained exceeds energy expended) are likely to be more successful at raising viable offspring than individuals that forage less efficiently. Our goal was to test this prediction in large long-lived mammals under free-ranging conditions. To do so, we equipped 20 lactating Antarctic fur seals (Arctocephalus gazella) breeding on Kerguelen Island in the Southern Ocean with tags that recorded GPS locations, depth and tri-axial acceleration to determine at-sea behaviours and detailed time-activity budgets during their foraging trips. We also simultaneously measured energy spent at sea using the doubly-labeled water (DLW) method, and estimated the energy acquired while foraging from 1) type and energy content of prey species present in scat remains, and 2) numbers of prey capture attempts determined from head acceleration. Finally, we followed the growth of 36 pups from birth until weaning (of which 20 were the offspring of our 20 tracked mothers), and used the relative differences in body mass of pups at weaning as an index of first year survival and thus the reproductive success of their mothers. Our results show that females with greater foraging efficiencies produced relatively bigger pups at weaning. These mothers achieved greater foraging efficiency by extracting more energy per minute of diving rather than by reducing energy expenditure. This strategy also resulted in the females spending less time diving and less time overall at sea, which allowed them to deliver higher quality milk to their pups, or allowed their pups to suckle more frequently, or both. The linkage we demonstrate between reproductive success and the quality of individuals as foragers provides an individual-based quantitative framework to investigate how changes in the availability and accessibility of prey can affect fitness of animals. [ABSTRACT FROM AUTHOR]

The native groups of Patagonia have relied on a hunter-gatherer economy well after the first Europeans and North Americans reached this part of the world. The large exploitation of marine mammals (i.e., seals) by such allochthonous groups has had a strong impact on the local ecology in a way that might have forced the natives to adjust their subsistence strategies. Similarly, the introduction of new foods might have changed local diet. These are the premises of our isotopic-based analysis. There is a large set of paleonutritional investigations through isotopic analysis on Fuegians groups, however a systematic exploration of food practices across time in relation to possible pre- and post-contact changes is still lacking. In this paper we investigate dietary variation in hunter-gatherer groups of Tierra del Fuego in a diachronic perspective, through measuring the isotopic ratio of carbon (∂13C) and nitrogen (∂15N) in the bone collagen of human and a selection of terrestrial and marine animal samples. The data obtained reveal an unexpected isotopic uniformity across prehistoric and recent groups, with little variation in both carbon and nitrogen mean values, which we interpret as the possible evidence of resilience among these groups and persistence of subsistence strategies, allowing inferences on the dramatic contraction (and extinction) of Fuegian populations. [ABSTRACT FROM AUTHOR]

In response to climate warming, a southward shift in productive frontal systems serving as the main foraging sites for many top predator species is likely to occur in Subantarctic areas. Central place foragers, such as seabirds and pinnipeds, are thus likely to cope with an increase in the distance between foraging locations and their land-based breeding colonies. Understanding how central place foragers should modify their foraging behavior in response to changes in prey accessibility appears crucial. A spatially explicit individual-based simulation model (Marine Central Place Forager Simulator (MarCPFS)), including bio-energetic components, was built to evaluate effects of possible changes in prey resources accessibility on individual performances and breeding success. The study was calibrated on a particular example: the Antarctic fur seal (Arctocephalus gazella), which alternates between oceanic areas in which females feed and the land-based colony in which they suckle their young over a 120 days rearing period. Our model shows the importance of the distance covered to feed and prey aggregation which appeared to be key factors to which animals are highly sensitive. Memorization and learning abilities also appear to be essential breeding success traits. Females were found to be most successful for intermediate levels of prey aggregation and short distance to the resource, resulting in optimal female body length. Increased distance to resources due to climate warming should hinder pups’ growth and survival while female body length should increase. [ABSTRACT FROM AUTHOR]

Humans have devised fishing technologies that compete with marine predators for fish resources world-wide. One such fishery for the Patagonian toothfish (Dissostichus eleginoides) has developed interactions with a range of predators, some of which are marine mammals capable of diving to extreme depths for extended periods. A deep-sea camera system deployed within a toothfish fishery operating in the Southern Ocean acquired the first-ever video footage of an extreme-diver, the southern elephant seal (Mirounga leonina), depredating catch from longlines set at depths in excess of 1000m. The interactions recorded were non-lethal, however independent fisheries observer reports confirm elephant seal-longline interactions can be lethal. The seals behaviour of depredating catch at depth during the line soak-period differs to other surface-breathing species and thus presents a unique challenge to mitigate their by-catch. Deployments of deep-sea cameras on exploratory fishing gear prior to licencing and permit approvals would gather valuable information regarding the nature of interactions between deep diving/dwelling marine species and longline fisheries operating at bathypelagic depths. Furthermore, the positive identification by sex and age class of species interacting with commercial fisheries would assist in formulating management plans and mitigation strategies founded on species-specific life-history strategies. [ABSTRACT FROM AUTHOR]

Mitigating direct and indirect interactions between marine predators and fisheries is a motivating factor for ecosystem-based fisheries management (EBFM), especially where predators and fisheries compete for a shared resource. One difficulty in advancing EBFM is parameterizing clear functional responses of predators to indices of prey availability. Alternative characterizations of fishery-predator interactions may therefore benefit the implementation of EBFM. Telemetry data identify foraging areas used by predators and, therefore, represent critical information to mitigate potential competition between predators and fisheries. We analyzed six years (2009–2014) of telemetry data collected at Cape Shirreff, Livingston Island and Admiralty Bay, King George Island, Antarctica, on three species of Pygoscelid penguins and female Antarctic fur seals. In this region, all four species are primarily dependent on Antarctic krill. The tracking data demonstrate local movements near breeding colonies during the austral summer and dispersal from breeding colonies during the winter. We then assessed overlap between predators and the Antarctic krill fishery on a suite of spatiotemporal scales to examine how different data aggregations affect the extent and location of overlap. Concurrent overlap was observed on all spatiotemporal scales considered throughout the Antarctic Peninsula and South Orkney Islands region, including near tagging locations and in distant areas where recent fishing activity has concentrated. Overlap occurred at depths where mean krill densities were relatively high. Our results demonstrate that direct overlap of krill-dependent predators with the krill fishery on small spatiotemporal scales is relatively common throughout the Antarctic Peninsula region. As the krill fishery continues to develop and efforts to implement ecosystem-based management mature, indices of overlap may provide a useful metric for indicating where the risks of fishing are highest. A precautionary approach to allocating krill catches in space would be to avoid large increases in catch where overlap on small spatiotemporal scales is common. [ABSTRACT FROM AUTHOR]

The brain of diving mammals tolerates low oxygen conditions better than the brain of most terrestrial mammals. Previously, it has been demonstrated that the neurons in brain slices of the hooded seal (Cystophora cristata) withstand hypoxia longer than those of mouse, and also tolerate reduced glucose supply and high lactate concentrations. This tolerance appears to be accompanied by a shift in the oxidative energy metabolism to the astrocytes in the seal while in terrestrial mammals the aerobic energy production mainly takes place in neurons. Here, we used RNA-Seq to compare the effect of hypoxia and reoxygenation in vitro on brain slices from the visual cortex of hooded seals. We saw no general reduction of gene expression, suggesting that the response to hypoxia and reoxygenation is an actively regulated process. The treatments caused the preferential upregulation of genes related to inflammation, as found before e.g. in stroke studies using mammalian models. Gene ontology and KEGG pathway analyses showed a downregulation of genes involved in ion transport and other neuronal processes, indicative for a neuronal shutdown in response to a shortage of O2 supply. These differences may be interpreted in terms of an energy saving strategy in the seal's brain. We specifically analyzed the regulation of genes involved in energy metabolism. Hypoxia and reoxygenation caused a similar response, with upregulation of genes involved in glucose metabolism and downregulation of the components of the pyruvate dehydrogenase complex. We also observed upregulation of the monocarboxylate transporter Mct4, suggesting increased lactate efflux. Together, these data indicate that the seal brain responds to the hypoxic challenge by a relative increase in the anaerobic energy metabolism. [ABSTRACT FROM AUTHOR]

Constructing activity budgets for marine animals when they are at sea and cannot be directly observed is challenging, but recent advances in bio-logging technology offer solutions to this problem. Accelerometers can potentially identify a wide range of behaviours for animals based on unique patterns of acceleration. However, when analysing data derived from accelerometers, there are many statistical techniques available which when applied to different data sets produce different classification accuracies. We investigated a selection of supervised machine learning methods for interpreting behavioural data from captive otariids (fur seals and sea lions). We conducted controlled experiments with 12 seals, where their behaviours were filmed while they were wearing 3-axis accelerometers. From video we identified 26 behaviours that could be grouped into one of four categories (foraging, resting, travelling and grooming) representing key behaviour states for wild seals. We used data from 10 seals to train four predictive classification models: stochastic gradient boosting (GBM), random forests, support vector machine using four different kernels and a baseline model: penalised logistic regression. We then took the best parameters from each model and cross-validated the results on the two seals unseen so far. We also investigated the influence of feature statistics (describing some characteristic of the seal), testing the models both with and without these. Cross-validation accuracies were lower than training accuracy, but the SVM with a polynomial kernel was still able to classify seal behaviour with high accuracy (>70%). Adding feature statistics improved accuracies across all models tested. Most categories of behaviour -resting, grooming and feeding—were all predicted with reasonable accuracy (52–81%) by the SVM while travelling was poorly categorised (31–41%). These results show that model selection is important when classifying behaviour and that by using animal characteristics we can strengthen the overall accuracy. [ABSTRACT FROM AUTHOR]

Understanding the diving behaviour of diving predators in relation to concomitant prey distribution could have major practical applications in conservation biology by allowing the assessment of how changes in fine scale prey distribution impact foraging efficiency and ultimately population dynamics. The southern elephant seal (Mirounga leonina, hereafter SES), the largest phocid, is a major predator of the southern ocean feeding on myctophids and cephalopods. Because of its large size it can carry bio-loggers with minimal disturbance. Moreover, it has great diving abilities and a wide foraging habitat. Thus, the SES is a well suited model species to study predator diving behaviour and the distribution of ecologically important prey species in the Southern Ocean. In this study, we examined how SESs adjust their diving behaviour and horizontal movements in response to fine scale prey encounter densities using high resolution accelerometers, magnetometers, pressure sensors and GPS loggers. When high prey encounter rates were encountered, animals responded by (1) diving and returning to the surface with steeper angles, reducing the duration of transit dive phases (thus improving dive efficiency), and (2) exhibiting more horizontally and vertically sinuous bottom phases. In these cases, the distance travelled horizontally at the surface was reduced. This behaviour is likely to counteract horizontal displacement from water currents, as they try to remain within favourable prey patches. The prey encounter rate at the bottom of dives decreased with increasing diving depth, suggesting a combined effect of decreased accessibility and prey density with increasing depth. Prey encounter rate also decreased when the bottom phases of dives were spread across larger vertical extents of the water column. This result suggests that the vertical aggregation of prey can regulate prey density, and as a consequence impact the foraging success of SESs. To our knowledge, this is one of only a handful of studies showing how the vertical distributions and structure of prey fields influence the prey encounter rates of a diving predator. [ABSTRACT FROM AUTHOR]

The biliary trematode Pseudamphistomum truncatum parasitizes a wide range of fish-eating mammals, including humans. Here we report the emergence of this parasite in grey seals (Halichoerus grypus) in the Baltic Sea. One hundred eighty-three of 1 554 grey seals (11.9%) examined from 2002–2013 had detectable hepatobiliary trematode infection. Parasite identification was confirmed as P. truncatum by sequencing the ITS2 region of a pool of five to 10 trematodes from each of ten seals collected off the coast of seven different Swedish counties. The proportion of seals parasitized by P. truncatum increased significantly over time and with increasing age of seals. Males were 3.1 times more likely to be parasitized than females and animals killed in fishery interactions were less likely to be parasitized than animals found dead or hunted. There was no significant difference in parasitism of seals examined from the Gulf of Bothnia versus those examined from the Baltic Proper. Although the majority of infections were mild, P. truncatum can cause severe hepatobiliary disease and resulted in liver failure in at least one seal. Because cyprinid fish are the second intermediate host for opisthorchiid trematodes, diets of grey seals from the Baltic Sea were analysed regarding presence of cyprinids. The proportion of gastrointestinal tracts containing cyprinid remains was ten times higher in seals examined from 2008 to 2013 (12.2%) than those examined from 2002 to 2007 (1.2%) and coincided with a general increase of trematode parasitism in the host population. The emergence and relatively common occurrence of P. truncatum in grey seals signals the presence of this parasite in the Baltic Sea ecosystem and demonstrates how aquatic mammals can serve as excellent sentinels of marine ecosystem change. Investigation of drivers behind P. truncatum emergence and infection risk for other mammals, including humans, is highly warranted. [ABSTRACT FROM AUTHOR]

Seals and humans often target the same food resource, leading to competition. This is of mounting concern with fish stocks in global decline. Grey seals were tracked from southeast Ireland, an area of mixed demersal and pelagic fisheries, and overlap with fisheries on the Celtic Shelf and Irish Sea was assessed. Overall, there was low overlap between the tagged seals and fisheries. However, when we separate active (e.g. trawls) and passive gear (e.g. nets, lines) fisheries, a different picture emerged. Overlap with active fisheries was no different from that expected under a random distribution, but overlap with passive fisheries was significantly higher. This suggests that grey seals may be targeting the same areas as passive fisheries and/or specifically targeting passive gear. There was variation in foraging areas between individual seals suggesting habitat partitioning to reduce intra-specific competition or potential individual specialisation in foraging behaviour. Our findings support other recent assertions that seal/fisheries interactions in Irish waters are an issue in inshore passive fisheries, most likely at the operational and individual level. This suggests that seal population management measures would be unjustifiable, and mitigation is best focused on minimizing interactions at nets. [ABSTRACT FROM AUTHOR]

Pathology has not been observed in true seals infected with Brucella pinnipedialis. A lack of intracellular survival and multiplication of B. pinnipedialis in hooded seal (Cystophora cristata) macrophages in vitro indicates a lack of chronic infection in hooded seals. Both epidemiology and bacteriological patterns in the hooded seal point to a transient infection of environmental origin, possibly through the food chain. To analyse the potential role of fish in the transmission of B. pinnipedialis, Atlantic cod (Gadus morhua) were injected intraperitoneally with 7.5 x 107 bacteria of a hooded seal field isolate. Samples of blood, liver, spleen, muscle, heart, head kidney, female gonads and feces were collected on days 1, 7, 14 and 28 post infection to assess the bacterial load, and to determine the expression of immune genes and the specific antibody response. Challenged fish showed an extended period of bacteremia through day 14 and viable bacteria were observed in all organs sampled, except muscle, until day 28. Neither gross lesions nor mortality were recorded. Anti-Brucella antibodies were detected from day 14 onwards and the expression of hepcidin, cathelicidin, interleukin (IL)-1β, IL-10, and interferon (IFN)-γ genes were significantly increased in spleen at day 1 and 28. Primary mononuclear cells isolated from head kidneys of Atlantic cod were exposed to B. pinnipedialis reference (NCTC 12890) and hooded seal (17a-1) strain. Both bacterial strains invaded mononuclear cells and survived intracellularly without any major reduction in bacterial counts for at least 48 hours. Our study shows that the B. pinnipedialis strain isolated from hooded seal survives in Atlantic cod, and suggests that Atlantic cod could play a role in the transmission of B. pinnipedialis to hooded seals in the wild. [ABSTRACT FROM AUTHOR]

Large numbers of dead seals with characteristic spiral lesions have been washing ashore around the North Atlantic over the past two decades. Interactions with ship propellers and shark predation have been suggested as the likely causal mechanisms. However, new evidence points towards a more likely candidate: grey seal predation. An adult male grey seal was observed and recorded catching, killing and eating five weaned grey seal pups over a period of one week on the Isle of May, Scotland. A further 9 carcasses found in the same area exhibited similar injuries. Post mortem analysis of lesions indicated the wound characteristics were similar to each other and in 12 of the 14 carcasses analysed, were indistinguishable from carcasses previously attributed to propeller interaction. We therefore propose that most of the seal carcasses displaying spiral lacerations in the UK are caused by grey seal predation. Cases in other locations should be re-evaluated using the scoring system presented here to identify whether grey seal predation is a major cause of mortality in phocid seals. [ABSTRACT FROM AUTHOR]