No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals.

Despite decades of research, surprisingly little is known about the mechanism(s) by which an individual's genotype is encoded in odour. Many studies have focused on the role of the major histocompatibility complex (MHC) owing to its importance for survival and mate choice. However, the salience of MHC-mediated odours compared to chemicals influenced by the rest of the genome remains unclear, especially in wild populations where it is challenging to quantify and control for the effects of the genomic background. We addressed this issue in Antarctic fur seals by analysing skin swabs together with full-length MHC DQB II exon 2 sequences and data from 41 genome-wide distributed microsatellites. We did not find any effects of MHC relatedness on chemical similarity and there was also no relationship between MHC heterozygosity and chemical diversity. However, multilocus heterozygosity showed a significant positive association with chemical diversity, even after controlling for MHC heterozygosity. Our results appear to rule out a dominant role of the MHC in the chemical encoding of genetic information in a wild vertebrate population and highlight the need for genome-wide approaches to elucidate the mechanism(s) and specific genes underlying genotype-odour associations.

Ninety years of change, from commercial extinction to recovery, range expansion and decline for Antarctic fur seals at South Georgia.

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.

Heavy metal contamination in pristine environments: lessons from the Juan Fernandez fur seal (Arctocephalus philippii philippii).

Heavy metals, including mercury (Hg) and cadmium (Cd), occur naturally or anthropogenically and are considered toxic to the environment and human health. However, studies on heavy metal contamination focus on locations close to industrialized settlements, while isolated environments with little human activity are often ignored due to perceived low risk. This study reports heavy metal exposure in Juan Fernandez fur seals (JFFS), a marine mammal endemic to an isolated and relatively pristine archipelago off the coast of Chile. We found exceptionally high concentrations of Cd and Hg in JFFS faeces. Indeed, they are among the highest reported for any mammalian species. Following analysis of their prey, we concluded that diet is the most likely source of Cd contamination in JFFS. Furthermore, Cd appears to be absorbed and incorporated into JFFS bones. However, it was not associated with mineral changes observed in other species, suggesting Cd tolerance/adaptations in JFFS bones. The high levels of silicon found in JFFS bones may counteract the effects of Cd. These findings are relevant to biomedical research, food security and the treatment of heavy metal contamination. It also contributes to understanding the ecological role of JFFS and highlights the need for surveillance of apparently pristine environments.

Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals.

The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.

Signatures of Selection on Mitonuclear Integrated Genes Uncover Hidden Mitogenomic Variation in Fur Seals.

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.

Low heritability and high phenotypic plasticity of salivary cortisol in response to environmental heterogeneity in a wild pinniped.

Individuals are unique in how they interact with and respond to their environment. Correspondingly, unpredictable challenges or environmental stressors often produce an individualized response of the hypothalamic-pituitary-adrenal (HPA) axis and its downstream effector cortisol. We used a fully crossed, repeated measures design to investigate the factors shaping individual variation in baseline cortisol in Antarctic fur seal pups and their mothers. Saliva samples were collected from focal individuals at two breeding colonies, one with low and the other with high density, during two consecutive years of contrasting food availability. Mothers and pups were sampled concurrently at birth and shortly before weaning, while pups were additionally sampled every 20 days. We found that heritability was low for baseline cortisol, while within-individual repeatability and among-individual variability were high. A substantial proportion of the variation in baseline cortisol could be explained in pups and mothers by a combination of intrinsic and extrinsic factors including sex, weight, day, season, and colony of birth. Our findings provide detailed insights into the individualization of endocrine phenotypes and their genetic and environmental drivers in a wild pinniped. Furthermore, the strong associations between cortisol and life history traits that we report in fur seals could have important implications for understanding the population dynamics of species impacted by environmental change.

Demographic Reconstruction of Antarctic Fur Seals Supports the Krill Surplus Hypothesis.

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.

50,000 years of ice and seals: Impacts of the Last Glacial Maximum on Antarctic fur seals.

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.

Movement patterns and activity levels are shaped by the neonatal environment in Antarctic fur seal pups.

Tracking studies of juveniles are rare compared to those of adults, and consequently little is known about the influence of intrinsic and extrinsic factors on activity during this critical life stage. We used hourly GPS data, collected from 66 Antarctic fur seal pups from birth until moulting, to investigate the explanatory power of multiple individual-based and environmental variables on activity levels. Pups were sampled from two nearby breeding colonies of contrasting density during two subsequent years, and a two-state hidden Markov model was used to identify modalities in their movement behaviour, specifically 'active' and 'inactive' states. We found that movement was typified by central place exploration, with active movement away from and subsequent return to a location of inactivity. The probability of such directed exploration was unaffected by several factors known to influence marine mammal movement including sex, body condition, and temperature. Compared to pups born at the high-density colony, pups at low-density were more active, increased their activity with age, and transitioned earlier into the tussock grass, which offers protection from predators and extreme weather. Our study illustrates the importance of extrinsic factors, such as colony of birth, to early-life activity patterns and highlights the adaptive potential of movement.

Evidence for an Allee effect in a declining fur seal population.

Allee effects play an important role in the dynamics of many populations and can increase the risk of local extinction. However, some authors have questioned the weight of evidence for Allee effects in wild populations. We therefore exploited a natural experiment provided by two adjacent breeding colonies of contrasting density to investigate the potential for Allee effects in an Antarctic fur seal (Arctocephalus gazella) population that is declining in response to climate change-induced reductions in food availability. Biometric time-series data were collected from 25 pups per colony during two consecutive breeding seasons, the first of which was among the worst on record in terms of breeding female numbers, pup birth weights and foraging trip durations. In previous decades when population densities were higher, pup mortality was consistently negatively density dependent, with rates of trauma and starvation scaling positively with density. However, we found the opposite, with higher pup mortality at low density and the majority of deaths attributable to predation. In parallel, body condition was depressed at low density, particularly in the poor-quality season. Our findings shed light on Allee effects in wild populations and highlight a potential emerging role of predators in the ongoing decline of a pinniped species.

Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible.

Replication studies are essential for evaluating the validity of previous research findings. However, it has proven challenging to reproduce the results of ecological and evolutionary studies, partly because of the complexity and lability of many of the phenomena being investigated, but also due to small sample sizes, low statistical power and publication bias. Additionally, replication is often considered too difficult in field settings where many factors are beyond the investigator's control and where spatial and temporal dependencies may be strong. We investigated the feasibility of reproducing original research findings in the field of chemical ecology by performing an exact replication of a previous study of Antarctic fur seals (Arctocephalus gazella). In the original study, skin swabs from 41 mother-offspring pairs from two adjacent breeding colonies on Bird Island, South Georgia, were analyzed using gas chromatography-mass spectrometry. Seals from the two colonies differed significantly in their chemical fingerprints, suggesting that colony membership may be chemically encoded, and mothers were also chemically similar to their pups, hinting at the possible involvement of phenotype matching in mother-offspring recognition. In the current study, we generated and analyzed chemical data from a non-overlapping sample of 50 mother-offspring pairs from the same two colonies 5 years later. The original results were corroborated in both hypothesis testing and estimation contexts, with p-values remaining highly significant and effect sizes, standardized between studies by bootstrapping the chemical data over individuals, being of comparable magnitude. However, exact replication studies are only capable of showing whether a given effect can be replicated in a specific setting. We therefore investigated whether chemical signatures are colony-specific in general by expanding the geographic coverage of our study to include pups from a total of six colonies around Bird Island. We detected significant chemical differences in all but a handful of pairwise comparisons between colonies. This finding adds weight to our original conclusion that colony membership is chemically encoded, and suggests that chemical patterns of colony membership not only persist over time but can also be generalized over space. Our study systematically confirms and extends our previous findings, while also implying more broadly that spatial and temporal heterogeneity need not necessarily negate the reproduction and generalization of ecological research findings.

Determinants of genetic variation across eco-evolutionary scales in pinnipeds.

The effective size of a population (Ne), which determines its level of neutral variability, is a key evolutionary parameter. Ne can substantially depart from census sizes of present-day breeding populations (NC) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent Ne for 17 pinniped species represented by 36 population samples (total n = 458 individuals). Ne estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with NC ([Formula: see text] = 0.59; P = 0.0002). Ne/NC ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species' ecological and life-history variables such as breeding habitat. Residual variation in Ne/NC, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary NC than would be expected from their long-term Ne. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention.

Risk exposure trade-offs in the ontogeny of sexual segregation in Antarctic fur seal pups.

Sexual segregation has important ecological implications, but its initial development in early life stages is poorly understood. We investigated the roles of size dimorphism, social behavior, and predation risk on the ontogeny of sexual segregation in Antarctic fur seal, Arctocephalus gazella, pups at South Georgia. Beaches and water provide opportunities for pup social interaction and learning (through play and swimming) but increased risk of injury and death (from other seals, predatory birds, and harsh weather), whereas tussock grass provides shelter from these risks but less developmental opportunities. One hundred pups were sexed and weighed, 50 on the beach and 50 in tussock grass, in January, February, and March annually from 1989 to 2018. Additionally, 19 male and 16 female pups were GPS-tracked during lactation from December 2012. Analysis of pup counts and habitat use of GPS-tracked pups suggested that females had a slightly higher association with tussock grass habitats and males with beach habitats. GPS-tracked pups traveled progressively further at sea as they developed, and males traveled further than females toward the end of lactation. These sex differences may reflect contrasting drivers of pup behavior: males being more risk prone to gain social skills and lean muscle mass and females being more risk averse to improve chances of survival, ultimately driven by their different reproductive roles. We conclude that sex differences in habitat use can develop in a highly polygynous species prior to the onset of major sexual size dimorphism, which hints that these sex differences will increasingly diverge in later life.

An 85K SNP Array Uncovers Inbreeding and Cryptic Relatedness in an Antarctic Fur Seal Breeding Colony.

High density single nucleotide polymorphism (SNP) arrays allow large numbers of individuals to be rapidly and cost-effectively genotyped at large numbers of genetic markers. However, despite being widely used in studies of humans and domesticated plants and animals, SNP arrays are lacking for most wild organisms. We developed a custom 85K Affymetrix Axiom array for an intensively studied pinniped, the Antarctic fur seal (Arctocephalus gazella). SNPs were discovered from a combination of genomic and transcriptomic resources and filtered according to strict criteria. Out of a total of 85,359 SNPs tiled on the array, 75,601 (88.6%) successfully converted and were polymorphic in 270 animals from a breeding colony at Bird Island in South Georgia. Evidence was found for inbreeding, with three genomic inbreeding coefficients being strongly intercorrelated and the proportion of the genome in runs of homozygosity being non-zero in all individuals. Furthermore, analysis of genomic relatedness coefficients identified previously unknown first-degree relatives and multiple second-degree relatives among a sample of ostensibly unrelated individuals. Such "cryptic relatedness" within fur seal breeding colonies may increase the likelihood of consanguineous matings and could therefore have implications for understanding fitness variation and mate choice. Finally, we demonstrate the cross-amplification potential of the array in three related pinniped species. Overall, our SNP array will facilitate future studies of Antarctic fur seals and has the potential to serve as a more general resource for the wider pinniped research community.

Publisher Correction: The genetic legacy of extreme exploitation in a polar vertebrate.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The genetic legacy of extreme exploitation in a polar vertebrate.

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.

Intra-specific Niche Partitioning in Antarctic Fur Seals, Arctocephalus gazella.

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.

Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals.

Numerous studies have reported correlations between the heterozygosity of genetic markers and fitness. These heterozygosity-fitness correlations (HFCs) play a central role in evolutionary and conservation biology, yet their mechanistic basis remains open to debate. For example, fitness associations have been widely reported at both neutral and functional loci, yet few studies have directly compared the two, making it difficult to gauge the relative contributions of genome-wide inbreeding and specific functional genes to fitness. Here, we compared the effects of neutral and immune gene heterozygosity on death from bacterial infection in Antarctic fur seal (Arctocephalus gazella) pups. We specifically developed a panel of 13 microsatellites from expressed immune genes and genotyped these together with 48 neutral loci in 234 individuals, comprising 39 pups that were classified at necropsy as having most likely died of bacterial infection together with a five times larger matched sample of healthy surviving pups. Identity disequilibrium quantified from the neutral markers was positive and significant, indicative of variance in inbreeding within the study population. However, multilocus heterozygosity did not differ significantly between healthy and infected pups at either class of marker, and little evidence was found for fitness associations at individual loci. These results support a previous study of Antarctic fur seals that found no effects of heterozygosity at nine neutral microsatellites on neonatal survival and thereby help to refine our understanding of how HFCs vary across the life cycle. Given that nonsignificant HFCs are underreported in the literature, we also hope that our study will contribute toward a more balanced understanding of the wider importance of this phenomenon.

Sex-specific effects of fisheries and climate on the demography of sexually dimorphic seabirds.

Many animal taxa exhibit sex-specific variation in ecological traits, such as foraging and distribution. These differences could result in sex-specific responses to change, but such demographic effects are poorly understood. Here, we test for sex-specific differences in the demography of northern (NGP, Macronectes halli) and southern (SGP, M. giganteus) giant petrels - strongly sexually size-dimorphic birds that breed sympatrically at South Georgia, South Atlantic Ocean. Both species feed at sea or on carrion on land, but larger males (30% heavier) are more reliant on terrestrial foraging than the more pelagic females. Using multi-event mark-recapture models, we examine the impacts of long-term changes in environmental conditions and commercial fishing on annual adult survival and use two-sex matrix population models to forecast future trends. As expected, survival of male NGP was positively affected by carrion availability, but negatively affected by zonal winds. Female survival was positively affected by meridional winds and El Niño-Southern Oscillation (ENSO), and negatively affected by sea ice concentration and pelagic longline effort. Survival of SGPs did not differ between sexes; however, survival of males only was positively correlated with the Southern Annular Mode (SAM). Two-sex population projections indicate that future environmental conditions are likely to benefit giant petrels. However, any potential increase in pelagic longline fisheries could reduce female survival and population growth. Our study reveals that sex-specific ecological differences can lead to divergent responses to environmental drivers (i.e. climate and fisheries). Moreover, because such effects may not be apparent when all individuals are considered together, ignoring sex differences could underestimate the relative influence of a changing environment on demography.