Search

With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32-36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.

Ross seals Ommatophoca rossii are one of the least studied marine mammals, with little known about their foraging ecology. Research to date using bulk stable isotope analysis suggests that Ross seals have a trophic position intermediate between that of Weddell Leptonychotes weddellii and crabeater Lobodon carcinophaga seals. However, consumer bulk stable isotope values not only reflect trophic dynamics, but also variations in baseline isotope values, which can be substantial. We used compound-specific isotope analysis of amino acids (CSI-AA) to separate isotopic effects of a shifting baseline versus trophic structure on the foraging ecology of these ecologically important Antarctic pinnipeds. We found that Ross seals forage in an open ocean food web, while crabeater and Weddell seals forage within similar food webs closer to shore. However, isotopic evidence suggests that crabeater seals are likely following sea ice, while Weddell seals target productive areas of the continental shelf of West Antarctica. Our CSI-AA data indicate that Ross seals have a high trophic position equivalent to that of Weddell seals, contrary to prior conclusions from nitrogen isotope results on bulk tissues. CSI-AA indicates that crabeater seals are at a trophic position lower than that of Ross and Weddell seals, consistent with a krill-dominated diet. Our results redefine the view of the trophic dynamics and foraging ecology of the Ross seal, and also highlight the importance of quantifying baseline isotope variations in foraging studies.

Background Resolving the preferred prey items and dietary proportions of leopard seals is central to understanding food-web dynamics in the rapidly-warming Antarctic Peninsula region. Previous studies have identified a wide range of prey items; however, due to anecdotal or otherwise limited information, leopard seal diets remain unresolved by seal sex, individual, body size, region, and season. Over the 2013, 2014, and 2017 field seasons we collected scat, tissue samples (red blood cells and plasma; n = 23) for stable isotope analyses, and previously-reported animal-borne video from 19 adult leopard seals foraging near mesopredator breeding colonies at Cape Shirreff, Livingston Island. We summarized a priori diet information from scat and video analysis and applied a three-isotope (δ13C, δ15N, δ34S), four-source (fish, fur seal, krill, penguin) Bayesian mixing model to examine temporal variability in both prey sources and leopard seal tissues. Results The austral spring diets of males and females focused on Antarctic krill (31.7–38.0%), notothen fish (31.6–36.5%), and penguin (24.4–26.9%) and were consistent across all 3 years. Several lines of evidence suggest the transition to summer foraging was distinct for males and females. Female diets transitioned rapidly to higher δ15N values (+2.1‰), indicating increased consumption of penguin (29.5–46.2%) and energy-dense Antarctic fur seal pup (21.3–37.6%). Conclusions The seasonal increase in leopard seal δ15N values, and thus fur seal in their diet, was predictably related to larger body size; it may also be forcing reductions to the largest Antarctic fur seal colony in the Antarctic Peninsula. Our ensemble sampling approach reduces historical biases in monitoring marine apex predator diets. Further, our results are necessary to best inform regional fisheries management planning.

International audience; Southern Ocean ecosystems are under pressure from resource exploitation and climate change1,2. Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40°S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.

To understand and predict current and future distributions of animals under a changing climate it is essential to establish historical ranges as baselines against which distribution shifts can be assessed. Management approaches also require comprehension of temporal variability in spatial distributions that can occur over shorter time scales, such as inter-annually or seasonally. Focussing on the Southern Ocean, one of the most rapidly changing environments on Earth, we used Species Distribution Models (SDMs) and satellite ocean data to reconstruct the likely historical foraging habitats of Antarctic fur seals (Arctocephalus gazella) from three populations during the non-breeding winter (Marion Island, Bird Island and Cape Shirreff), to assess whether habitat quality has changed in recent decades. We then quantified temporal variability in distributions to assess overlap with management areas (CCAMLR – Commission for the Conservation of Antarctic Marine Living Resources) and the potential for competition with fisheries. Despite notable physical ocean changes, the quality of foraging habitat during the non-breeding season has remained relatively consistent over 20 years at Marion and Bird Islands, but less so at Cape Shirreff, where reduced sea ice cover has improved habitat accessibility. Spatio-temporally explicit SDMs identified variability in habitats across the winter. Some areas overlapped significantly with fisheries activities, suggesting a potential for competition for prey resources at several key periods. A significant component of core habitat at all populations was not within the CCAMLR Convention Area. Although organisations such as CCAMLR adopt a precautionary, ecosystem-based approach to fisheries management, changes to the physical environment and developments in the fishing industry can affect how dependant species are impacted. The hindcasting of historical spatial distributions shown here are baselines against which future changes can be assessed. Given recent proposals for a system of marine protected areas (MPAs) in the Southern Ocean, our results can be used in the design and evaluation of MPAs, be they static or dynamic. Our study also demonstrates that the core habitat of species may fall outside of areas of active management, providing an important context for the interpretation of monitoring programs and management efforts.

Quantification of the physical and biological environmental factors that influence the spatial distribution of higher trophic species is central to inform management and develop ecosystem models, particularly in light of ocean changes. We used tracking data from 184 female Antarctic fur seals (Arctocephalus gazella) to develop habitat models for three breeding colonies for the poorly studied Southern Ocean winter period. Models were used to identify and predict the broadly important winter foraging habitat and to elucidate the environmental factors influencing these areas. Model predictions closely matched observations and several core areas of foraging habitat were identified for each colony, with notable areas of inter-colony overlap suggesting shared productive foraging grounds. Seals displayed clear choice of foraging habitat, travelling through areas of presumably poorer quality to access habitats that likely offer an energetic advantage in terms of prey intake. The relationships between environmental predictors and foraging habitat varied between colonies, with the principal predictors being wind speed, sea surface temperature, chlorophyll a concentration, bathymetry and distance to the colony. The availability of core foraging areas was not consistent throughout the winter period. The habitat models developed in this study not only reveal the core foraging habitats of Antarctic fur seals from multiple colonies, but can facilitate the hindcasting of historical foraging habitats as well as novel predictions of important habitat for other major colonies currently lacking information of the at-sea distribution of this major Southern Ocean consumer.

Quantifying metabolic rates and the factors that influence them is key to wildlife conservation efforts because anthropogenic activities and habitat alteration can disrupt energy balance, which is critical for reproduction and survival. We investigated the effect of diving behaviour, diet and season on field metabolic rates (FMR) and foraging success of lactating northern fur seals (Callorhinus ursinus) from the Pribilof Islands during a period of population decline. Variation in at-sea FMR was in part explained by season and trip duration, with values that ranged from 5.18 to 9.68 W kg−1 (n = 48). Fur seals experienced a 7.2% increase in at-sea FMR from summer to fall and a 1.9% decrease in at-sea FMR for each additional day spent at sea. There was no effect of foraging effort, dive depth or diet on at-sea FMR. Mass gains increased with trip duration and were greater in the fall compared with summer, but were unrelated to at-sea FMR, diving behaviour and diet. Seasonal increases in at-sea FMR may have been due to costs associated with the annual molt but did not appear to adversely impact the ability of females to gain mass on foraging trips. The overall high metabolic rates in conjunction with the lack of any diet-related effects on at-sea FMR suggests that northern fur seals may have reached a metabolic ceiling early in the population decline. This provides indirect evidence that food limitation may be contributing to the low pup growth rates observed in the Pribilof Islands, as a high metabolic overhead likely results in less available energy for lactation. The limited ability of female fur seals to cope with changes in prey availability through physiological mechanisms is particularly concerning given the recent and unprecedented environmental changes in the Bering Sea that are predicted to have ecosystem-level impacts., Lay summary: We measured metabolic rates of northern fur seals from a declining population and examined the influence of season and foraging behavior on energy expenditure. Our results are relevant for bioenergetic modelling efforts and provide insight into the potential role of prey availability in the population decline.

Antarctic fur seals ( Arctocephalus gazella ) are polygynous and both sexes are typically faithful to a breeding site. These characteristics could promote remating among individuals over time, leading to increased relatedness levels and negatively affecting genetic diversity. To examine this issue, the reproductive output of 55 females was monitored annually for 12 years and their pups were sampled (n = 280) and genotyped using 17 microsatellite markers. A full likelihood pedigree inference method was used to confirm maternities inferred in the field and estimate the number of full sibling pups born across years. Relatedness coefficients were estimated for pairs of individuals in the pedigree and compared to simulated values for each relationship category. There were nine cases where a female mated with the same male twice and one case where a female mated with the same male three times over the study period. The observed relatedness coefficients estimated among the sampled pups matched the simulated distribution for half-siblings. In addition, no first order relatives were found among the fur seal mothers studied, nor did observed relatedness coefficient distributions differ significantly from simulated values. Together, these results suggest a low remating rate and a negligible effect of remating on pair-wise relatedness. Territorial male replacement over time as well as female small-scale movements, driven by suitable pupping habitat, likely contribute to the low remating frequency observed in Antarctic fur seals.

Leopard seals are conspicuous apex predators in Antarctic coastal ecosystems, yet their foraging ecology is poorly understood. Historically, the ecology of diving vertebrates has been studied using high-resolution time-depth records; however, to date such data have not been available for leopard seals. Twenty-one time-depth recorders were deployed on seasonally resident adult females in January and February between 2008 and 2014. The average deployment length was 13.65 ± 11.45 d and 40,308 postfilter dives were recorded on 229 foraging trips. Dive durations averaged 2.20 ± 1.23 min. Dives were shallow with 90.1% measuring 30 m or less, and a mean maximum dive depth of 16.60 ± 10.99 m. Four dive types were classified using a k-means cluster analysis and compared with corresponding animal-borne video data. Dive activity (number of dives/hour) was concentrated at night, including crepuscular periods. Haul-out probabilities were highest near midday and were positively correlated with available daylight. Visual observations and comparisons of diving activity between and within years suggest individual-based differences of foraging effort by time of day. Finally, dive and video data indicate that in addition to at-surface hunting, benthic searching and facultative scavenging are important foraging strategies for leopard seals near coastal mesopredator breeding colonies.

The large-scale spatial patterns and primary drivers of food web dynamics across seascapes can be investigated using isotope ratios in marine consumers. However, interpreting complex signatures from mobile animals can require good knowledge of spatial isotopic variations in the environment. This is particularly true in the Southern Ocean where regional differences in the physical environment affect habitat predictability and predator foraging. We applied a retrospective-isotope approach integrated with tracking locations for a model species, the Antarctic fur seal (Arctocephalus gazella), to generate large-scale spatially-explicit predictions of isotopic gradients (“isoscapes”) across the Southern Ocean. Vibrissae and blood samples were collected during post- and pre-breeding periods from both Antarctic and sub-Antarctic breeding environments. Stable isotope values from vibrissae growth and serially sampled blood enabled the reconstruction of an isotopic time-series that could be directly related to feeding locations at sea. Tracked seals were widely distributed in the southern Atlantic and Indian Oceans, with important foraging activity centred on productive upwelling areas, oceanic frontal zones and shelf environments. Corresponding seal δ13C and δ15N values were positively correlated to the Southern Ocean latitudes at which the tracked individuals foraged. Breeding site, bi-monthly foraging period and foraging location all explained significant variation in isotopic values during migration. Isotopic variation was largely driven by the latitudinal and inshore/offshore gradient in δ13C and δ15N at the base of the food web in neritic and oceanic waters. These delineate the spatio-temporal isotopic variability of important foraging habitats, providing a valuable perspective on the spatial and seasonal distribution of predators and forage availability. Differences in inferred predator distribution within and between breeding locations have implications for relative exposure to anthropogenic threats from fisheries interactions and climate change. This study demonstrates that isotope tracers in archival tissues are useful indicators of resource partitioning by marine consumers to directly inform spatial conservation planning and ecosystem management strategies at the cross-basin scale.

Recent advances in high throughput sequencing have transformed the study of wild organisms by facilitating the generation of high quality genome assemblies and dense genetic marker datasets. These resources have the potential to significantly advance our understanding of diverse phenomena at the level of species, populations and individuals, ranging from patterns of synteny through rates of linkage disequilibrium (LD) decay and population structure to individual inbreeding. Consequently, we used PacBio sequencing to refine an existing Antarctic fur seal (Arctocephalus gazella) genome assembly and genotyped 83 individuals from six populations using restriction site associated DNA (RAD) sequencing. The resulting hybrid genome comprised 6,169 scaffolds with an N50 of 6.21 Mb and provided clear evidence for the conservation of large chromosomal segments between the fur seal and dog (Canis lupus familiaris). Focusing on the most extensively sampled population of South Georgia, we found that LD decayed rapidly, reaching the background level ofr2= 0.09 by around 26 kb, consistent with other vertebrates but at odds with the notion that fur seals experienced a strong historical bottleneck. We also found evidence for population structuring, with four main Antarctic island groups being resolved. Finally, appreciable variance in individual inbreeding could be detected, reflecting the strong polygyny and site fidelity of the species. Overall, our study contributes important resources for future genomic studies of fur seals and other pinnipeds while also providing a clear example of how high throughput sequencing can generate diverse biological insights at multiple levels of organisation.

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.

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.

We demonstrate the first use of marine mammal dive-depth data to improve maps of bathymetry in poorly sampled regions of the continental shelf. A group of 57 instrumented elephant seals made on the order of 2 x 10(5) dives over and near the continental shelf on the western side of the Antarctic Peninsula during five seasons, 2005-2009. Maximum dive depth exceeded 2000 m. For dives made near existing ship tracks with measured water depths H

Polar regions are particularly sensitive to climate change, with the potential for significant feedbacks between ocean circulation, sea ice, and the ocean carbon cycle. However, the difficulty in obtaining in situ data means that our ability to detect and interpret change is very limited, especially in the Southern Ocean, where the ocean beneath the sea ice remains almost entirely unobserved and the rate of sea-ice formation is poorly known. Here, we show that southern elephant seals ( Mirounga leonina ) equipped with oceanographic sensors can measure ocean structure and water mass changes in regions and seasons rarely observed with traditional oceanographic platforms. In particular, seals provided a 30-fold increase in hydrographic profiles from the sea-ice zone, allowing the major fronts to be mapped south of 60°S and sea-ice formation rates to be inferred from changes in upper ocean salinity. Sea-ice production rates peaked in early winter (April–May) during the rapid northward expansion of the pack ice and declined by a factor of 2 to 3 between May and August, in agreement with a three-dimensional coupled ocean–sea-ice model. By measuring the high-latitude ocean during winter, elephant seals fill a “blind spot” in our sampling coverage, enabling the establishment of a truly global ocean-observing system.

Responses by marine top predators to environmental variability have previously been almost impossible to observe directly. By using animal-mounted instruments simultaneously recording movements, diving behavior, and in situ oceanographic properties, we studied the behavioral and physiological responses of southern elephant seals to spatial environmental variability throughout their circumpolar range. Improved body condition of seals in the Atlantic sector was associated with Circumpolar Deep Water upwelling regions within the Antarctic Circumpolar Current, whereas High-Salinity Shelf Waters or temperature/salinity gradients under winter pack ice were important in the Indian and Pacific sectors. Energetic consequences of these variations could help explain recently observed population trends, showing the usefulness of this approach in examining the sensitivity of top predators to global and regional-scale climate variability.

SUMMARYInterpolation of geolocation or Argos tracking data is a necessity for habitat use analyses of marine vertebrates. In a fluid marine environment,characterized by curvilinear structures, linearly interpolated track data are not realistic. Based on these two facts, we interpolated tracking data from albatrosses, penguins, boobies, sea lions, fur seals and elephant seals using six mathematical algorithms. Given their popularity in mathematical computing,we chose Bézier, hermite and cubic splines, in addition to a commonly used linear algorithm to interpolate data. Performance of interpolation methods was compared with different temporal resolutions representative of the less-precise geolocation and the more-precise Argos tracking techniques. Parameters from interpolated sub-sampled tracks were compared with those obtained from intact tracks. Average accuracy of the interpolated location was not affected by the interpolation method and was always within the precision of the tracking technique used. However, depending on the species tested, some curvilinear interpolation algorithms produced greater occurrences of more accurate locations, compared with the linear interpolation method. Total track lengths were consistently underestimated but were always more accurate using curvilinear interpolation than linear interpolation. Curvilinear algorithms are safe to use because accuracy, shape and length of the tracks are either not different or are slightly enhanced and because analyses always remain conservative. The choice of the curvilinear algorithm does not affect the resulting track dramatically so it should not preclude their use. We thus recommend using curvilinear interpolation techniques because of the more realistic fluid movements of animals. We also provide some guidelines for choosing an algorithm that is most likely to maximize track quality for different types of marine vertebrates.

Leopard seals are apex predators that can alter the community structure of Antarctic coastal ecosystems. Previous behavioral studies were limited to land-based, daytime observations of foraging leopard seals. Consequently, foraging tactics, social behaviors, and indirect ecosystem impacts are poorly understood. Here, we present the first analysis of animal-borne HD video footage for foraging leopard seals. Each CRITTERCAM was deployed with Fastloc GPS and time-depth recorder instruments providing fine-scale habitat context for observed foraging behavior. We analyzed seven deployments obtained in January and February of 2013 and 2014 from adult female leopard seals near mesopredator breeding colonies on Livingston Island, Antarctica. The average deployment length was 4.80 ± 2.45 (range 0.86–9.12) days, which covered a total of 16 foraging trips. Habitat use, along with 39 prey capture attempts, and 11 leopard seal social encounters were scored from 50.3 h of video data. We obtained 3,833 post-filter GPS positions, accurate to within 70 m, and the mean dive depth was 14.84 ± 8.98 m. Leopard seal foraging focused on four prey items: Antarctic fur seals, Antarctic fur seal pups, pygoscelid penguins, and demersal notothen fishes. Ambush tactics used only by a subset of leopard seals drove high capture success rates of fur seal pups. We identified novel prey-specific foraging tactics including stalking and flushing notothen fishes. Leopard seals have been described as generalist apex predators; however, video and movement data suggest that leopard seals employ specialized prey-specific hunting tactics. Although preliminary, our findings indicate that leopard seals can affect coastal ecosystems through pathways beyond direct predation, including intraspecific kleptoparasitism and facultative scavenging/food caching. Our results suggest that position-integrated video data will be vital in quantifying the ecological impact of this abundant and versatile apex predator.