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The Antarctic fur seal (Arctocephalus gazella) is an important top predator and indicator of the health of the Southern Ocean ecosystem. Although abundant, this species narrowly escaped extinction due to historical sealing and is currently declining as a consequence of climate change. Genomic tools are essential for understanding these anthropogenic impacts and for predicting long-term viability. However, the current reference genome ("arcGaz3") shows considerable room for improvement in terms of both completeness and contiguity. We therefore combined PacBio sequencing, haplotype-aware HiRise assembly, and scaffolding based on Hi-C information to generate a refined assembly of the Antarctic fur seal reference genome ("arcGaz4_h1"). The new assembly is 2.53 Gb long, has a scaffold N50 of 55.6 Mb and includes 18 chromosome-sized scaffolds, which correspond to the 18 chromosomes expected in otariids. Genome completeness is greatly improved, with 23,408 annotated genes and a Benchmarking Universal Single-Copy Orthologs score raised from 84.7% to 95.2%. We furthermore included the new genome in a reference-free alignment of the genomes of 11 pinniped species to characterize evolutionary conservation across the Pinnipedia using genome-wide Genomic Evolutionary Rate Profiling. We then implemented Gene Ontology enrichment analyses to identify biological processes associated with those genes showing the highest levels of either conservation or differentiation between the 2 major pinniped families, the Otariidae and Phocidae. We show that processes linked to neuronal development, the circulatory system, and osmoregulation are overrepresented both in conserved as well as in differentiated regions of the genome. [ABSTRACT FROM AUTHOR]

The article discusses the threat of avian influenza H5N1 to krill-dependent predators in Antarctica, specifically pinnipeds such as seals and sea lions. The virus has spread globally and can be transmitted from birds to pinnipeds with low barriers. It has caused mass die-offs in seabirds and pinnipeds in South America and has now been confirmed in several locations on the Antarctic Peninsula. The risk to Antarctic pinnipeds, such as Antarctic fur seals, is extremely high. The article recommends adopting conservation measures, enhanced surveillance and testing, and proper disposal of infected carcasses to mitigate the impact of the virus. The list of references provides additional scientific articles that discuss the detection and spread of H5N1 in marine mammals, seabirds, and pinnipeds, emphasizing the need for risk assessment and management strategies to protect wildlife populations. [Extracted from the article]

In the marine environment, many animals use sound to interact and communicate with their conspecifics or other species. Over the last decades, the development of sound recording systems has allowed a significant advance in our knowledge of sound production in marine animals. We deployed miniature sound and movement tags on Antarctic fur seals (AFS), a small otariid foraging on mesopelagic fish, to uncover potential underwater vocalizations in this species. Tags recorded underwater sounds synchronously with high‐resolution AFS movements and diving behavior, allowing us to investigate the behavioral context of vocalizations in the natural environment. We provide evidence of underwater vocalizations in foraging female AFS in a context of foraging at sea. AFS produced stereotyped calls made of low‐frequency pulses produced in series, exclusively during foraging dives. We hypothesized that these acoustic pulse series could be used as an acoustic lure to confuse or attract fish prey, however, a larger sample size is needed to study the adaptive significance of these underwater vocalizations. [ABSTRACT FROM AUTHOR]

The response to climate change in highly dimorphic species can be hindered by differences between sexes in habitat preferences and movement patterns. The Antarctic fur seal, Arctocephalus gazella, is the most abundant pinniped in the Southern Hemisphere, and one of the main consumers of Antarctic krill, Euphausia superba, in the Southern Ocean. However, the populations breeding in the Atlantic Southern Ocean are decreasing, partly due to global warming. Male and female Antarctic fur seals differ greatly in body size and foraging ecology, and little is known about their sex‐specific responses to climate change. We used satellite tracking data and Earth System Models to predict changes in habitat suitability for male and female Antarctic fur seals from the Western Antarctic Peninsula under different climate change scenarios. Under the most extreme scenario (SSP5‐8.5; global average temperature +4.4°C projected by 2100), suitable habitat patches will shift southward during the non‐breeding season, leading to a minor overall habitat loss. The impact will be more pronounced for females than for males. The reduction of winter foraging grounds might decrease the survival of post‐weaned females, reducing recruitment and jeopardizing population viability. During the breeding season, when males fast on land, suitable foraging grounds for females off the South Shetland Islands will remain largely unmodified, and new ones will emerge in the Bellingshausen Sea. As Antarctic fur seals are income breeders, the foraging grounds of females should be reasonably close to the breeding colony. As a result, the new suitable foraging grounds will be useful for females only if nearby beaches currently covered by sea ice emerge by the end of the century. Furthermore, the colonization of these new, ice‐free breeding locations might be limited by strong female philopatry. These results should be considered when managing the fisheries of Antarctic krill in the Southern Ocean. [ABSTRACT FROM AUTHOR]

Antarctic fur seals (Arctocephalus gazella) are an iconic marine mammal, an important component of Antarctic ecosystems, and a key indicator species for regional fisheries management. Recent studies have demonstrated Arctocephalus gazella is composed of at least four distinct subpopulations, including one breeding on the South Shetland Islands. These South Shetland Antarctic fur seals (SSAFS) are the highest latitude population of otariids in the world. As such, this subpopulation faces a unique array of environmental and ecological challenges, harbours a disproportionately large reservoir of genetic diversity for the species, and has experienced catastrophic population decline in the last 15 years (2008–2023).We review the array of current and potential threats to the successful recovery of SSAFS.If decision makers wish to promote resilience and support a robust population of this species with future recovery potential, actions are needed to address threats ranging from uncertain to critical, including debris entanglement, climate change, incidental mortality, and resource competition with the krill fishery.In particular, the risks associated with overlap in the spatial and temporal distribution of the young of the year and the krill fishery should be addressed carefully.There is an urgent need for updated population estimates for all Antarctic fur seal subpopulations, analysis on the population viability of the SSAFS, and further characterising summer and winter foraging behaviours to better inform potential conservation actions. [ABSTRACT FROM AUTHOR]

With environmental change, understanding how species recover from overharvesting and maintain viable populations is central to ecosystem restoration. Here, we reconstruct 90 years of recovery trajectory of the Antarctic fur seal at South Georgia (S.W. Atlantic), a key indicator species in the krill‐based food webs of the Southern Ocean. After being harvested to commercial extinction by 1907, this population rebounded and now constitutes the most abundant otariid in the World. However, its status remains uncertain due to insufficient and conflicting data, and anthropogenic pressures affecting Antarctic krill, an essential staple for millions of fur seals and other predators. Using integrated population models, we estimated simultaneously the long‐term abundance for Bird Island, northwest South Georgia, epicentre of recovery of the species after sealing, and population adjustments for survey counts with spatiotemporal applicability. Applied to the latest comprehensive survey data, we estimated the population at South Georgia in 2007–2009 as 3,510,283 fur seals [95% CI: 3,140,548–3,919,604] (ca. 98% of global population), after 40 years of maximum growth and range expansion owing to an abundant krill supply. At Bird Island, after 50 years of exponential growth followed by 25 years of slow stable growth, the population collapsed in 2009 and has thereafter declined by −7.2% [−5.2, −9.1] per annum, to levels of the 1970s. For the instrumental record, this trajectory correlates with a time‐varying relationship between coupled climate and sea surface temperature cycles associated with low regional krill availability, although the effects of increasing krill extraction by commercial fishing and natural competitors remain uncertain. Since 2015, fur seal longevity and recruitment have dropped, sexual maturation has retarded, and population growth is expected to remain mostly negative and highly variable. Our analysis documents the rise and fall of a key Southern Ocean predator over a century of profound environmental and ecosystem change. [ABSTRACT FROM AUTHOR]

The energetic costs of lactation have been studied in many marine mammals, but little is known about the behavioral adjustments needed to cope with this event. By simultaneously measuring foraging behavior of lactating and nonlactating Antarctic fur seal females, we estimate the behavioral changes necessary to cope with the constraints of lactation and include the first comparative record of dive behavior between lactating and nonlactating female otariids. Nonlactating females exhibited highly variable foraging trip durations and spent long times onshore between trips. In contrast, lactating females exhibited consistently shorter trips and spent half the time hauled‐out compared to nonlactating females likely to maximize offspring provisioning. Lactating females show a reduced mean time per dive but greater percentage of time per trip spent diving compared to nonlactating animals. The reduction in time onshore and trip duration, together with modifications in dive performance suggests additional effort of lactating females to compensate for the constraints of rearing a pup, which has not been observed previously due to the lack of simultaneous comparison of lactating and nonlactating individuals. When possible, future studies of maternal investment should also include nonlactating individuals, since lactation may have a strong synergistic effect with other aspects shaping foraging behavior. [ABSTRACT FROM AUTHOR]

Abstract Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, Arctocephalus gazella, are particularly interesting in this regard, as they are concomitantly reliant on both ice‐associated prey and ice‐free coastal breeding areas. We reconstructed the history of this species through the Last Glacial Maximum (LGM) using genomic sequence data from seals across their range. Population size trends and divergence events were investigated using continuous‐time size estimation analysis and divergence time estimation models. The combined results indicated that a panmictic population present prior to the LGM split into two small refugial populations during peak ice extent. Following ice decline, the western refugial population founded colonies at the South Shetlands, South Georgia, and Bouvetøya, while the eastern refugial population founded the colony on Iles Kerguelen. Postglacial population divergence times closely match geological estimates of when these coastal breeding areas became ice free. Given the predictions regarding continued future warming in polar oceans, these responses of Antarctic fur seals to past climate variation suggest it may be worthwhile giving conservation consideration to potential future breeding locations, such as areas further south along the Antarctic Peninsula, in addition to present colony areas.

Nuclear copies of mitochondrial genes (numts) are commonplace in vertebrate genomes and have been characterized in many species. However, relatively little attention has been paid to understanding their evolutionary origins and to disentangling alternative sources of insertions. Numts containing genes with intact mitochondrial reading frames represent good candidates for this purpose. The sequences of the genes they contain can be compared with their mitochondrial homologs to characterize synonymous to nonsynonymous substitution rates, which can shed light on the selection pressures these genes have been subjected to. Here, we characterize 25 numts in the Antarctic fur seal (Arctocephalus gazella) genome. Among those containing genes with intact mitochondrial reading frames, three carry multiple substitutions in comparison to their mitochondrial homologs. Our analyses reveal that one represents a historic insertion subjected to strong purifying selection since it colonized the Otarioidea in a genomic region enriched in retrotransposons. By contrast, the other two numts appear to be more recent and their large number of substitutions can be attributed to noncanonical insertions, either the integration of heteroplasmic mtDNA or hybridization. Our study sheds new light on the evolutionary history of pinniped numts and uncovers the presence of hidden sources of mitonuclear variation. [ABSTRACT FROM AUTHOR]

The study of the population status of Arctocephalus gazella (Peters, 1875) in waters of the Argentine Islands was carried out in the period from April 2015 to March 2016 in accordance with the objectives of the State Target Scientific and Technical Research Program of Ukraine in Antarctica for 2011–2020. The aim of the ar-ticle is to study the population dynamics and distribution of the southern fur seal in waters of the Argentine Is-lands. Due to the lack of data on the specifics of the seal’s dispersal in different periods of the year and the dynamics of the species population at the southern border of the distribution range, the results of the research are relevant and of great importance. In the second half of the 20th century, some publications presented the results of monitoring of pinnipeds at the Argentine Islands and adjacent territories, but the objects of these studies usually were other seal species: Hydrurga leptonyx, Lobodon carcinophagus, Leptonychotes weddelli, and Mirounga leonina. In the early 21st century, monitoring of the fauna of the Argentine Islands was carried out by Ukrainian biologists. However, they focused on Leptonychotes weddelli and less on other species of pinnipeds. The field material was collected in waters of the Argentine Islands, which is located in the Pacific sector of Antarctica. The fur seal population census and distribution studies were conducted according to the generally accepted methods. After breeding season on the subantarctic islands, during the migration south-wards, fur seals reach the Argentine Islands, usually in the third decade of January. In the summer of 2016, the first fur seal was recorded within the archipelago on 31 January. During the study period, the largest number of animals within the archipelago was recorded in March–April and it ranged from 300 to 400 individuals. On the islands of the archipelago, the main resting places of seals were identified. The movement of animals north-wards starts in May, consequently a decrease in the number of animals in this region is observed at that time. The last individuals are recorded in the first half of August. In 2015, migration began in May and ended in ear-ly August. There are several periods that were characterized by intensive migration of the animals: late June, 5–8 July, and 29 July to 6 August. In winter, one individual was last found within the archipelago on 12 Au-gust. The migration is launched by the worsening of weather conditions, formation of a continuous ice cover, reduced availability of food, and other factors.

Much debate surrounds the importance of top-down and bottom-up effects in the Southern Ocean, where the harvesting of over two million whales in the mid twentieth century is thought to have produced a massive surplus of Antarctic krill. This excess of krill may have allowed populations of other predators, such as seals and penguins, to increase, a top-down hypothesis known as the 'krill surplus hypothesis'. However, a lack of pre-whaling population baselines has made it challenging to investigate historical changes in the abundance of the major krill predators in relation to whaling. Therefore, we used reduced representation sequencing and a coalescent-based maximum composite likelihood approach to reconstruct the recent demographic history of the Antarctic fur seal, a pinniped that was hunted to the brink of extinction by 18th and 19th century sealers. In line with the known history of this species, we found support for a demographic model that included a substantial reduction in population size around the time period of sealing. Furthermore, maximum likelihood estimates from this model suggest that the recovered, post-sealing population at South Georgia may have been around two times larger than the pre-sealing population. Our findings lend support to the krill surplus hypothesis and illustrate the potential of genomic approaches to shed light on long-standing questions in population biology. [ABSTRACT FROM AUTHOR]

Antarctic fur seals (AFS) are an ecologically important predator and a focal indicator species for ecosystem-based Antarctic fisheries management. This species suffered intensive anthropogenic exploitation until the early 1900s, but recolonized most of its former distribution, including the southern-most colony at Cape Shirreff, South Shetland Islands (SSI). The IUCN describes a single, global AFS population of least concern; however, extensive genetic analyses clearly identify four distinct breeding stocks, including one in the SSI. To update the population status of SSI AFS, we analyzed 20 years of field-based data including population counts, body size and condition, natality, recruitment, foraging behaviors, return rates, and pup mortality at the largest SSI colony. Our findings show a precipitous decline in AFS abundance (86% decrease since 2007), likely driven by leopard seal predation (increasing since 2001, p << 0.001) and potentially worsening summer foraging conditions. We estimated that leopard seals consumed an average of 69.3% (range: 50.3–80.9%) of all AFS pups born each year since 2010. AFS foraging-trip durations, an index of their foraging habitat quality, were consistent with decreasing krill and fish availability. Significant improvement in the age-specific over-winter body condition of AFS indicates that observed population declines are driven by processes local to the northern Antarctic Peninsula. The loss of SSI AFS would substantially reduce the genetic diversity of the species, and decrease its resilience to climate change. There is an urgent need to reevaluate the conservation status of Antarctic fur seals, particularly for the rapidly declining SSI population.

Ice is one of the most important drivers of population dynamics in polar organisms, influencing the locations, sizes, and connectivity of populations. Antarctic fur seals, Arctocephalus gazella, are particularly interesting in this regard, as they are concomitantly reliant on both ice‐associated prey and ice‐free coastal breeding areas. We reconstructed the history of this species through the Last Glacial Maximum (LGM) using genomic sequence data from seals across their range. Population size trends and divergence events were investigated using continuous‐time size estimation analysis and divergence time estimation models. The combined results indicated that a panmictic population present prior to the LGM split into two small refugial populations during peak ice extent. Following ice decline, the western refugial population founded colonies at the South Shetlands, South Georgia, and Bouvetøya, while the eastern refugial population founded the colony on Iles Kerguelen. Postglacial population divergence times closely match geological estimates of when these coastal breeding areas became ice free. Given the predictions regarding continued future warming in polar oceans, these responses of Antarctic fur seals to past climate variation suggest it may be worthwhile giving conservation consideration to potential future breeding locations, such as areas further south along the Antarctic Peninsula, in addition to present colony areas. [ABSTRACT FROM AUTHOR]

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

The ability of predators to adopt hunting tactics that minimise escape reactions from prey is crucial for efficient foraging, and depends on detection capabilities and locomotor performance of both predators and prey. Here, we investigated the efficiency of a small pinniped, the Antarctic fur seal (Arctocephalus gazella) at exploiting their small prey by describing for the first time their fine-scale predator-prey interactions. We compared these with those from another diving predator, the southern elephant seal (Mirounga leonina) that forage on the same prey type. We used data recorded by a newly developed sonar tag that combines active acoustics with ultrahigh-resolution movement sensors to study simultaneously the fine-scale behaviour of both Antarctic fur seals and prey during predator-prey interactions in more than 1200 prey capture events for eight female Antarctic fur seals. Our results showed that Antarctic fur seals and their prey detect each other at the same time, i.e. 1-2 s before the strike, forcing Antarctic fur seals to display reactive fast-moving chases to capture their prey. In contrast, southern elephant seals detect their prey up to 10 s before the strike, allowing them to approach their prey stealthily without triggering an escape reaction. The active hunting tactics used by Antarctic fur seals is probably very energy consuming compared with the stalking tactics used by southern elephant seals but might be compensated for by the consumption of faster-moving larger prey. We suggest that differences in manoeuvrability, locomotor performance and detection capacities and in pace of life between Antarctic fur seals and southern elephant seals might explain these differences in hunting styles., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Ornithogenic soils in Antarctica provide a biological archive of the occupation history and trophic ecology of penguins and other marine species over geological timescales. Hard prey remains and predator tissues, which are well preserved in ornithogenic soils, can act as paleoecological proxies of past environmental conditions. Here we examine ornithogenic soils from an active colony of Pygoscelis spp. penguins on Platter Island in the Danger Islands Archipelago along the northeastern side of the Antarctic Peninsula. We radiocarbon dated penguin tissues from excavated ornithogenic soils and parameterized an age-depth model of penguin occupation history. Hard prey remains were enumerated and recovered Pygoscelis spp. penguin and Antarctic fur seal (Arctocephalus gazella) tissues were analyzed for stable isotopes carbon (δ13C) and nitrogen (δ15N) analysis. The oldest recovered ornithogenic soils at Platter Island date to 502–653 years BP and coincide with the start of a period of increased warming and glacial discharge in the northeastern Antarctic Peninsula. Penguin tissues δ15N values increased between the oldest and youngest dated ornithogenic soils but seal tissues did not. This may indicate that the trophic level of penguins, but not seals, has increased over time, a hypothesis supported by the concurrent increase in the hard prey remains of fish and squid taxa common to penguin diets recovered from ornithogenic soils. Future studies of ornithogenic soils in the Danger Islands Archipelago are warranted to test this hypothesis and assess the potential confounding effects of varying ecosystem isotopic baselines and penguin species composition over time. [ABSTRACT FROM AUTHOR]

Understanding the effects of human exploitation on the genetic composition of wild populations is important for predicting species persistence and adaptive potential. We therefore investigated the genetic legacy of large-scale commercial harvesting by reconstructing, on a global scale, the recent demographic history of the Antarctic fur seal (Arctocephalus gazella), a species that was hunted to the brink of extinction by 18th and 19th century sealers. Molecular genetic data from over 2,000 individuals sampled from all eight major breeding locations across the species' circumpolar geographic distribution, show that at least four relict populations around Antarctica survived commercial hunting. Coalescent simulations suggest that all of these populations experienced severe bottlenecks down to effective population sizes of around 150–200. Nevertheless, comparably high levels of neutral genetic variability were retained as these declines are unlikely to have been strong enough to deplete allelic richness by more than around 15%. These findings suggest that even dramatic short-term declines need not necessarily result in major losses of diversity, and explain the apparent contradiction between the high genetic diversity of this species and its extreme exploitation history. [ABSTRACT FROM AUTHOR]

Competition for resources within a population can lead to niche partitioning between sexes, throughout ontogeny and among individuals, allowing con-specifics to co-exist. We aimed to quantify such partitioning in Antarctic fur seals, Arctocephalus gazella, breeding at South Georgia, which hosts ~95% of the world's population. Whiskers were collected from 20 adult males and 20 adult females and stable isotope ratios were quantified every 5 mm along the length of each whisker. Nitrogen isotope ratios (δ15N) were used as proxies for trophic position and carbon isotope ratios (δ13C) indicated foraging habitat. Sexual segregation was evident: δ13C values were significantly lower in males than females, indicating males spent more time foraging south of the Polar Front in maritime Antarctica. In males δ13C values declined with age, suggesting males spent more time foraging south throughout ontogeny. In females δ13C values revealed two main foraging strategies: 70% of females spent most time foraging south of the Polar Front and had similar δ15N values to males, while 30% of females spent most time foraging north of the Polar Front and had significantly higher δ15N values. This niche partitioning may relax competition and ultimately elevate population carrying capacity with implications for ecology, evolution and conservation. [ABSTRACT FROM AUTHOR]

Despite an increasing appreciation of the importance of host–microbe interactions in ecological and evolutionary processes, the factors shaping microbial communities in wild populations remain poorly understood. We therefore exploited a natural experiment provided by two adjacent Antarctic fur seal (Arctocephalus gazella) colonies of high and low social density and combined 16S rRNA metabarcoding with microsatellite profiling of mother–offspring pairs to investigate environmental and genetic influences on skin microbial communities. Seal‐associated bacterial communities differed profoundly between the two colonies, despite the host populations themselves being genetically undifferentiated. Consistent with the hypothesis that social stress depresses bacterial diversity, we found that microbial alpha diversity was significantly lower in the high‐density colony. Seals from one of the colonies that contained a stream also carried a subset of freshwater‐associated bacteria, indicative of an influence of the physical environment. Furthermore, mothers and their offspring shared similar microbial communities, in support of the notion that microbes may facilitate mother–offspring recognition. Finally, a significant negative association was found between bacterial diversity and heterozygosity, a measure of host genetic quality. Our study thus reveals a complex interplay between environmental and host genetic effects, while also providing empirical support for the leash model of host control, which posits that bacterial communities are driven not only by bottom‐up species interactions, but also by top‐down host regulation. Taken together, our findings have broad implications for understanding host–microbe interactions as well as prokaryotic diversity in general. [ABSTRACT FROM AUTHOR]

Abstract Colonies of mammals and sea birds are known hotspots for biogeochemical cycles with potentially large element stocks and fast turnover in the soil. Although penguin and seal colonies are sites with potentially extremely fast biogeochemical turnover, these sites as potential sources of GHG have largely been neglected. This study aims to quantify magnitudes and environmental drivers of GHG fluxes effected by the activity of Antarctic fur seal (Arctocephalus gazella) and King penguin (Aptenodytes patagonicus) in South Georgia, sub-Antarctica. In-situ CO 2 and CH 4 gas flux measurements were combined with laboratory incubations of intact soil cores collected from sites along two transects away from a seal and a penguin colony. Variations in laboratory incubations were consistent with the in-situ fluxes measured in February 2017, and showed high ecosystem respiration rates at colonies (mean 44.3 μg CO 2 cm−3 h−1 for seal colony, and 52.9–159 μg CO 2 cm−3 h−1 for penguin colony) and a marked decrease away from these hotspots. Moderate methane production rates were found within the colonies (mean 0.1 ng CH 4 cm−3 h−1 for seal colony, 44–145.5 ng CH 4 cm−3 h−1 for penguin colony), while relatively high consumption rates (mean −1.8 ng CH 4 cm−3 h−1) occurred outside the colonies. Incubations also included N 2 O production rates, which were highly variable within the colonies (1.1–293 ng N 2 O cm−3 h−1 for seal colony, 0.8–594.7 ng N 2 O cm−3 h−1 for penguin colony) and decreased markedly to near zero away from the colonies. Bacterial and pmoA communities and drivers of GHG turnover and microbe community along both transects varied according to the sea animal activity intensity gradient. This is the first study at these latitudes to quantify the overall capacity of in-situ soil methane uptake at hot spots linked to sea animal colonies versus ambient conditions. All colony sites in this study were net sources of N 2 O, while sites beyond colonies, which dominate the ice-free areas in South Georgia, were sinks of methane. Highlights • High CH 4 uptake rates are observed in bare soil areas but decreased towarsds seal and penguin colonies. • Colonies were hotspots for CO 2 , CH 4 and N 2 O emissions due to large excreta deposits. • Spatial trends in gas rates were correlated to microbial community distribution. • Dominate methanotrophs differed between sites. [ABSTRACT FROM AUTHOR]

The Antarctic fur seal (Arctocephalus gazella) is a key marine predator in the Southern Ocean, a region that has recently started to show changes as a result of global climate change. Here, carbon (δ13C) and nitrogen (δ15N) stable isotope analyses on whole blood and plasma samples were used to examine the isotopic niche of lactating female Antarctic fur seals. Using recently developed Bayesian approaches to determine changes in isotopic niche, a significant increase in δ13C and δ15N was found between 1997 and 2015; this change occurred at an average rate of 0.067‰ (δ13C) and 0.072‰ (δ15N) per year over this period. This suggests that a marked isotopic niche shift has occurred over this period, which very likely corresponds to a shift in diet towards prey at a higher trophic level, such as fish (replacing krill). Although our sampling design prevented us from exploring a seasonal trend in a conclusive manner, our data suggest that concurrent increases in δ13C and δ15N might occur as the breeding season progresses. At a seasonal scale, an average decrease of −0.7‰ per month (95% confidence interval=[−0.9; −0.6]) in δ13C might have occurred, concurrently with an average increase of 1.1‰ per month in δ15N. The results of this study constitute the first isotopic assessment for female Antarctic fur seals from Bouvetøya and provide a baseline for the use of this predator species as a sentinel of the marine trophic system in one of the least studied areas within this species’ distributional range.

Viral diversity associated with Antarctic wildlife remains poorly studied. Nonetheless, over the past 5 years, there has been a concerted effort using viral metagenomics approaches to identify and characterize viruses associated with Antarctic pinniped and avian species. Here we used a viral metagenomics approach to identify circular DNA viruses in buccal swab samples from Antarctic fur seals (Arctocephalus gazella) breeding on Livingston Island, Antarctica during the 2016/2017 field season. We identified two new lineages of anelloviruses, torque teno Arctocephalus gazella virus (TTAgV)-1 (2083 nts) and -2 (2127-2143 nts), which are most closely related to and cluster with a previously identified anellovirus associated with California sea lions (Zalophus californianus) sharing ~ 60% genome-wide pairwise identity. The ORF1 of TTAgVs share 26-41% amino acid similarity to the ORF1 of other previously identified pinniped-associated anelloviruses. [ABSTRACT FROM AUTHOR]

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 by around 400 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 organization. [ABSTRACT FROM AUTHOR]

Fur chromatic disorders, which include albinism, leucism and melanism, are rare in mammals. Worldwide these atypical cases are naturally infrequent and poorly reported in the literature, particularly in pinnipeds. The knowledge available about colouration in mammals comes from studies in mice and other domestic mammals. Generally this information is homologous to most mammals. However, adaptive interpretation of atypical colouration patterns in pinnipeds and its biological relevance are uncertain. Hence, this report is indirect evidence of a source of misunderstood genetic variability for this group of carnivores. Here, we present an opportunistic observation of leucism in an Antarctic Fur Seal, Arctocephalus gazella, from Peninsula Coppermine, in Robert Island, South Shetland Islands, Antarctica. A young male with a leucistic dilute phenotype was recorded on February 5th, 2013. This is the first confirmed record of a leucistic fur seal on this island. Additionally, we provide some general comments on the nomenclature used for colour morphs. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Time and energy are the two most important currencies in animal bioenergetics. How much time animals spend engaged in different activities with specific energetic costs ultimately defines their likelihood of surviving and successfully reproducing. However, it is extremely difficult to determine the energetic costs of independent activities for free-ranging animals. In this study, we developed a new method to calculate activity-specific metabolic rates, and applied it to female fur seals. We attached biologgers (that recorded GPS locations, depth profiles, and triaxial acceleration) to 12 northern ( Callorhinus ursinus) and 13 Antarctic fur seals ( Arctocephalus gazella), and used a hierarchical decision tree algorithm to determine time allocation between diving, transiting, resting, and performing slow movements at the surface (grooming, etc.). We concomitantly measured the total energy expenditure using the doubly-labelled water method. We used a general least-square model to establish the relationship between time-activity budgets and the total energy spent by each individual during their foraging trip to predict activity-specific metabolic rates. Results show that both species allocated similar time to diving (~29%), transiting to and from their foraging grounds (~26-30%), and resting (~8-11%). However, Antarctic fur seals spent significantly more time grooming and moving slowly at the surface than northern fur seals (36% vs. 29%). Diving was the most expensive activity (~30 MJ/day if done non-stop for 24 hr), followed by transiting at the surface (~21 MJ/day). Interestingly, metabolic rates were similar between species while on land or while slowly moving at the surface (~13 MJ/day). Overall, the average field metabolic rate was ~20 MJ/day (for all activities combined). The method we developed to calculate activity-specific metabolic rates can be applied to terrestrial and marine species to determine the energetic costs of daily activities, as well as to predict the energetic consequences for animals forced to change their time allocations in response to environmental shifts. [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]

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]

Assessing the trophic ecology of fur seals is essential for defining their roles as a top predator in Antarctic marine ecosystems. To this end, we examined the diet of Antarctic fur seals, Arctocephalus gazella, in the South Shetlands. While previous studies have considered the diet of this species at this location in summer, to the best of our knowledge, this is the first study to report on the diet of this population in winter, thus adding essential information on the extent of seasonal variation. A total of 224 scats were collected in the winter 2004 ( n = 118) and summer 2004/2005 ( n = 106) on the coasts of Stranger Point, Isla 25 de Mayo/King George. For the total study period krill ( Euphausia superba) was the main prey taxon, followed by fish, cephalopods and penguins. During winter Pleuragramma antarcticum was dominant, while myctophids were almost absent. Conversely, in summer Electrona antarctica and Gymnoscopelus nicholsi, followed by P. antarcticum, dominated the fish diet. It is concluded that fur seals centred their foraging activity on a krill community and fish associated with krill aggregations. [ABSTRACT FROM AUTHOR]

Scat analysis and stable isotope analysis (δ13C Archipelago, trophic variation, stable isotopes, and δ15N) were used to perform a trophic com- scat analysis parison between two existing Guadalupe fur seal (Arctocephalus philippii townsendi) colonies Introduction on Guadalupe Island (GI) and the San Benito Archipelago (SBA) during the 2013 breeding The Guadalupe fur seal (Arctocephalus philipseason. The stable isotope analysis included 67 pii townsendi) (GFS) is recognized as an endansamples from GI and 36 from the SBA, indicat- gered species under Mexican law (NOM-059- ing that this otariid is a teuthophagous specialist. SEMARNAT-2010). The only well-established The two colonies showed different trophic levels: breeding colony of the species is located on (1) 4.5 for GI, for which the most dominant prey Guadalupe Island (GI), where an estimate of was the jumbo squid, and (2) 4.0 for the SBA, for ~17,000 GFSs are found (International Union for which the main item was the opalescent squid. The Conservation of Nature [IUCN], 2015); meanstable isotope analysis included 15 fur samples while, the San Benito Archipelago (SBA), 268 km from each site. Both analyses were complemen- southeast, has a colony of up to 3,700 to 4,500 tary, identifying prey species from an oceanic individuals that is undergoing a process of recolohabitat, with fur seal δ13C values that are typically nization since the late 1990s (Maravilla-Chávez & associated to that environment. Although assigned Lowry, 1999; Sierra, 2015) and is mainly composed a higher trophic level (scat analysis), GI had lower of juveniles and subadults. Additionally, vagrant δ15N and δ13C values, suggesting latitudinal segre- GFSs on the islands off California have become gation. These differences between colonies may be more frequent since the 1980s (IUCN, 2015). related to their distinct age proportions or a strategy Female GFSs make foraging trips that vary to avoid intrapopulation competition. Our contribu- from 222 to 589 km and around 14 d in duration tion regarding trophic variation is based on a snap- (Gallo-Reynoso et al., 2008). Foraging variation shot regarding scat analysis and a time window may exist between individuals within a given pinof ~16 wks prior to collection reflected by stable niped population because of physiological limitaisotope analysis in fur. Additionally, this species is tions associated with age (Kuhn et al., 2006) or sex currently experiencing population growth, which (Weise & Costa, 2007), and may even occur when increases the possibility of overlap for resources phenotypes and dispersion capabilities are similar between both colonies. Therefore, it is important to (Van Valen, 1965; Bolnick et al., 2003; Estes et al., establish baselines and continue these comparative 2003) as evidenced via telemetry in Antarctic fur analyses over time to determine their significance seals (Arctocephalus gazella; Staniland & Boyd, within its recovery. [ABSTRACT FROM AUTHOR]

Optimal foraging models applied to breath-holding divers predict that diving predators should optimize the time spent foraging at the bottom of dives depending on prey encounter rate, distance to prey patch (depth) and physiological constraints., We tested this hypothesis on a free-ranging diving marine predator, the Antarctic fur seal Arctocephalus gazella, equipped with accelerometers or Hall sensors ( n = 11) that recorded mouth-opening events, a proxy for prey capture attempts and thus feeding events. Over the 5896 dives analysed (>15 m depth), the mean number of mouth-opening events per dive was 1·21 ± 1·69 (mean ± SD). Overall, 82% of mouth-openings occurred at the bottom of dives., As predicted, fur seals increased their inferred foraging time at the bottom of dives with increasing patch distance (depth), irrespective of the number of mouth-openings., For dives shallower than 55 m, the mean bottom duration of dives without mouth-openings was shorter than for dives with mouth-opening events. However, this difference was only due to the occurrence of V-shaped dives with short bottom durations (0 or 1 s). When removing those V-shaped dives, bottom duration was not related to the presence of mouth-openings anymore. Thus, the decision to abandon foraging is likely related to other information about prey availability than prey capture attempts (i.e. sensory cues) that seals collect during the descent phase. We did not observe V-shaped dives for dives deeper than 55 m, threshold beyond which the mean dive duration exceeded the apparent aerobic dive limit. For dives deeper than 55 m, seals kept on foraging at bottom irrespective of the number of mouth-openings performed., Most dives occurred at shallower depths (30-55 m) than the 60 m depth of highest foraging efficiency (i.e. of greatest number of mouth-opening events per dive). This is likely related to physiological constraints during deeper dives., We suggest that foraging decisions are more complex than predicted by current theory and highlight the importance of the information collected by the predator during the descent as well as its physiological constraints. Ultimately, this will help establishing reliable predictive foraging models for marine predators based on diving patterns only., A is available for this article. [ABSTRACT FROM AUTHOR]

Background: Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of 'putative' SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Results: Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Conclusions: Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms. [ABSTRACT FROM AUTHOR]