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The highly dynamic nature of the marine environment can have a substantial influence on the foraging behaviour and spatial distribution of marine predators, particularly in pelagic marine systems. However, knowledge of the susceptibility of benthic marine predators to environmental variability is limited. This study investigated the influence of local-scale environmental conditions and large-scale climate indices on the spatial distribution and habitat use in the benthic foraging Australian fur seal ( Arctocephalus pusillus doriferus ; AUFS). Female AUFS provisioning pups were instrumented with GPS or ARGOS platform terminal transmitter tags during the austral winters of 2001–2019 at Kanowna Island, south-eastern Australia. Individuals were most susceptible to changes in the Southern Oscillation Index that measures the strength of the El Niño Southern Oscillation, with larger foraging ranges, greater distances travelled and more dispersed movement associated with 1-yr lagged La Niña-like conditions. Additionally, the total distance travelled was negatively correlated with the current year sea surface temperature and 1-yr lagged Indian Ocean Dipole, and positively correlated with 1-yr lagged chlorophyll- a concentration. These results suggest that environmental variation may influence the spatial distribution and availability of prey, even within benthic marine systems.

Knowledge of the factors shaping the foraging behaviour of species is central to understanding their ecosystem role and predicting their response to environmental variability. To maximise survival and reproduction, foraging strategies must balance the costs and benefits related to energy needed to pursue, manipulate, and consume prey with the nutritional reward obtained. While such information is vital for understanding how changes in prey assemblages may affect predators, determining these components is inherently difficult in cryptic predators. The present study used animal-borne video data loggers to investigate the costs and benefits related to different prey types for female Australian fur seals (Arctocephalus pusillus doriferus), a primarily benthic foraging species in the low productivity Bass Strait, south-eastern Australia. A total of 1,263 prey captures, resulting from 2,027 prey detections, were observed in 84.5 h of video recordings from 23 individuals. Substantial differences in prey pursuit and handling times, gross energy gain and total energy expenditure were observed between prey types. Importantly, the profitability of prey was not significantly different between prey types, with the exception of elasmobranchs. This study highlights the benefit of animal-borne video data loggers for understanding the factors that influence foraging decisions in predators. Further studies incorporating search times for different prey types would further elucidate how profitability differs with prey type.

Age structure is a fundamental aspect of animal population biology. Age is strongly related to individual physiological condition, reproductive potential and mortality rate. Currently, there are no robust molecular methods for age estimation in birds. Instead, individuals must be ringed as chicks to establish known-age populations, which is a labour-intensive and expensive process. The estimation of chronological age using DNA methylation (DNAm) is emerging as a robust approach in mammals including humans, mice and some non-model species. Here, we quantified DNAm in whole blood samples from a total of 71 known-age Short-tailed shearwaters (Ardenna tenuirostris) using digital restriction enzyme analysis of methylation (DREAM). The DREAM method measures DNAm levels at thousands of CpG dinucleotides throughout the genome. We identified seven CpG sites with DNAm levels that correlated with age. A model based on these relationships estimated age with a mean difference of 2.8 years to known age, based on validation estimates from models created by repeated sampling of training and validation data subsets. Longitudinal observation of individuals re-sampled over 1 or 2 years generally showed an increase in estimated age (6/7 cases). For the first time, we have shown that epigenetic changes with age can be detected in a wild bird. This approach should be of broad interest to researchers studying age biomarkers in non-model species and will allow identification of markers that can be assessed using targeted techniques for accurate age estimation in large population studies.

DNA methylation (DNAm) is a key mechanism for regulating gene expression in animals and levels are known to change with age. Recent studies have used DNAm changes as a biomarker to estimate chronological age in humans and these techniques are now also being applied to domestic and wild animals. Animal age is widely used to track ongoing changes in ecosystems, however chronological age information is often unavailable for wild animals. An ability to estimate age would lead to improved monitoring of (i) population trends and status and (ii) demographic properties such as age structure and reproductive performance. Recent studies have revealed new examples of DNAm age association in several new species increasing the potential for developing DNAm age biomarkers for a broad range of wild animals. Emerging technologies for measuring DNAm will also enhance our ability to study age-related DNAm changes and to develop new molecular age biomarkers.

Most seabirds do not have any outward identifiers of their chronological age, so estimation of seabird population age structure generally requires expensive, long-term banding studies. We investigated the potential to use a molecular age biomarker to estimate age in short-tailed shearwaters (Ardenna tenuirostris). We quantified DNA methylation in several A. tenuirostris genes that have shown age-related methylation changes in mammals. In birds ranging from chicks to 21 years of age, bisulphite treated blood and feather DNA was sequenced and methylation levels analysed in 67 CpG sites in 13 target gene regions. From blood samples, five of the top relationships with age were identified in KCNC3 loci (CpG66: R2 = 0.325, p = 0.019). In feather samples ELOVL2 (CpG42: R2 = 0.285, p = 0.00048) and EDARADD (CpG46: R2 = 0.168, p = 0.0067) were also weakly correlated with age. However, the majority of markers had no clear association with age (of 131 comparisons only 12 had a p-value < 0.05) and statistical analysis using a penalised lasso approach did not produce an accurate ageing model. Our data indicate that some age-related signatures identified in orthologous mammalian genes are not conserved in the long-lived short tailed shearwater. Alternative molecular approaches will be required to identify a reliable biomarker of chronological age in these seabirds.

BACKGROUND: Determining the relative contribution of intrinsic and extrinsic factors to fluctuations in population size, trends and demographic composition is analytically complex. It is often only possible to examine the combined effects of these factors through measurements made over long periods, spanning an array of population densities or levels of food availability. Using age-structured mark-recapture models and datasets spanning five decades (1950-1999), and two periods of differing relative population density, we estimated age-specific probabilities of survival and examined the combined effects of population density and environmental conditions on juvenile survival of southern elephant seals at Macquarie Island. RESULTS: First-year survival decreased with density during the period of highest population size, and survival increased during years when the Southern Oscillation Index (SOI) anomaly (deviation from a 50-year mean) during the mother's previous foraging trip to sea was positive (i.e., El Niño). However, when environmental stochasticity and density were considered together, the effect of density on first-year survival effectively disappeared. Ignoring density effects also leads to models placing too much emphasis on the environmental conditions prevailing during the naïve pup's first year at sea. CONCLUSION: Our analyses revealed that both the state of the environment and population density combine to modify juvenile survival, but that the degree to which these processes contributed to the variation observed was interactive and complex. This underlines the importance of evaluating the relative contribution of both the intrinsic and extrinsic factors that regulate animal populations because false conclusions regarding the importance of population regulation may be reached if they are examined in isolation.

Fatty acid signature analysis of blubber has been used to study the foraging ecology of some marine mammals. However, species-specific information on fatty acid (FA) deposition, distribution and mobilization is required to develop further the application of FA as trophic markers within the marine environment. Blubber samples were collected from adult female Weddell seals post-parturition and end of lactation, and were divided into inner and outer half sections. We determined the degree to which there was vertical stratification in FA composition, and how this changed over the lactation period. Inner and outer layers of postparturition blubber cores separated into two distinct groups. Sixty-two per cent of the dissimilarity between the two layers was accounted for by a higher abundance of monounsaturated fatty acids (18:1ω9c and 16:1ω7c) in the outer blubber layer, and more saturated fatty acids (16:0 and 14:0) in the inner layer. By end of lactation, the FA composition of the inner layer was different to post-parturition samples, and 20:5ω3 had the highest fractional mobilization of all FA. In contrast, the proportion of FA in the outer layer did not change, and there was more variability in the fractional mobilization of FA indicating mobilization was not uniform across the blubber layer. Dietary predictions changed considerably when highly mobilized FA were removed from analyses, and predictions were more consistent with previous dietary studies. The lack of uniformity in FA mobilization adds problems to the future use of FASA in dietary predictions, highlighting the need for more detailed information on FA mobilization.

Fatty acid signature analysis of blubber has been used to study the foraging ecology of some marine mammals. However, species-specific information on fatty acid (FA) deposition, distribution and mobilization is required to develop further the application of FA as trophic markers within the marine environment. Blubber samples were collected from adult female Weddell seals post-parturition and end of lactation, and were divided into inner and outer half sections. We determined the degree to which there was vertical stratification in FA composition, and how this changed over the lactation period. Inner and outer layers of postparturition blubber cores separated into two distinct groups. Sixty-two per cent of the dissimilarity between the two layers was accounted for by a higher abundance of monounsaturated fatty acids (18:1ω9c and 16:1ω7c) in the outer blubber layer, and more saturated fatty acids (16:0 and 14:0) in the inner layer. By end of lactation, the FA composition of the inner layer was different to post-parturition samples, and 20:5ω3 had the highest fractional mobilization of all FA. In contrast, the proportion of FA in the outer layer did not change, and there was more variability in the fractional mobilization of FA indicating mobilization was not uniform across the blubber layer. Dietary predictions changed considerably when highly mobilized FA were removed from analyses, and predictions were more consistent with previous dietary studies. The lack of uniformity in FA mobilization adds problems to the future use of FASA in dietary predictions, highlighting the need for more detailed information on FA mobilization.

New Zealand fur seals (Arctocephalus forsteri) are common in the Australian-New Zealand region, but vital demographic data are lacking. Accurate determination of the age of individuals is critical to the study of agespecific life-history parameters. A cross-sectional sample of female and male New Zealand fur seals was caught and animals were individually marked on Kangaroo Island, South Australia, between 2000 and 2003. Seals were aged through examination of a postcanine tooth, which was removed from each animal. Annual formation of cementum layers was confirmed and accuracy in age estimation was determined by examination of teeth removed from individuals of known age. Indirect methods of assessing reproductive maturity based on characteristics of mammary teats indicated that females 1st gave birth between 4 and 8 years of age, with an average age at reproductive maturity (ARM) of 5 years. No females were observed to breed beyond 22 years. Age of 1st territory tenure in males ranged from 8 to 10 years. Variation in ARM between individuals appears to be related in part to body size and condition. Classification of mammary teat status in combination with techniques for aging live animals provided a means of assessing ARM in the absence of extensive longitudinal data.

Determination of seabird diet usually relies on the analysis of stomach-content remains obtained through stomach flushing; this technique is both invasive and logistically difficult. We evaluate the usefulness of DNA-based faecal analysis in a dietary study on chick-rearing macaroni penguins (Eudyptes chrysolophus) at Heard Island. Conventional stomach-content data was also collected, allowing comparison of the approaches. Methodology/Principal Findings. Preyspecific PCR tests were used to detect dietary DNA in faecal samples and amplified prey DNA was cloned and sequenced. Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in the early (guard) stage of chick-rearing, and detection of DNA from the myctophid fish Krefftichthys anderssoni and amphipods became more common in samples collected in the later (cre`che) stage. These trends followed those observed in the penguins’ stomach contents. In euphausiid-specific clone libraries the proportion of sequences from the two dominant euphausiid prey species (Euphausia vallentini and Thysanoessa macrura) changed over the sampling period; again, this reflected the trend in the stomach content data. Analysis of prey sequences in universal clone libraries revealed a higher diversity of fish prey than identified in the stomachs, but non-fish prey were not well represented. Conclusions/Significance. The present study is one of the first to examine the full breadth of a predator’s diet using DNA based faecal analysis. We discuss methodological difficulties encountered and suggest possible refinements. Overall, the ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds.

The diet of free-living pinnipeds is most frequently estimated through identification of otoliths, squid mouth-parts and exoskeletons of prey in scats. This is because, although important prey types may not always be detected, sample collection is non-invasive and analysis is easy. Identification of prey DNA in scats is a nascent approach to determining the diet of marine vertebrates that may overcome some of the limitations of hard part analysis. This is the first study to experimentally compare the utility of genetic scatology for identifying consumption of prey types by seals with the occurrence of morphological remains of prey in scats. The occurrences of DNA and hard part remains of one squid and two fish taxa in scats of captive Arctocephalus seals fed mixed prey diets were compared. Both methods detected ingestion of these taxa 7.5–39.5 h prior to defaecation. Although all test prey had robust hard parts, detecting consumption during this period was 1.4 to 5.8 times more likely using genetic analysis than morphological analysis of scats. Based on frequency of occurrence calculations, neither method provided quantitative descriptions of the known diet. Identification of prey using DNA was not compromised by complexity of the diet; each test taxon was unambiguously detected against a background of a multi-species diet. Our results suggest that where diagnostic hard remains of prey are not well represented in scats, or the sample size is small, genetic scatology provides a valuable addition to morphological scat analysis for identifying the recent diet of free-living seals.

Evolved patterns of resource expenditure for reproduction have resulted in a life history continuum across species. A strictly capital-breeding strategy relies extensively on stored energy for reproduction, whereas income breeding uses energy acquired throughout the reproductive period. However, facultative income breeding has been shown in some classically capital-breeding animals, and was originally thought to provide a nutritional refuge for smaller females incapable of securing sufficient reserves during pre-partum foraging. We examined milk composition and milk output for the Weddell seal to determine to what degree lactation was aided by food intake, and what factors contributed to its manifestation. Milk composition was independent of maternal post-partum mass and condition, but did change over lactation. Changes were most likely in response to energetic and nutritional demands of the pup at different stages of development. During early lactation, females fasted and devoted 54.9% of total energy loss to milk production. Later in lactation 30.5% more energy was devoted to milk production and evidence suggested that larger females fed more during lactation than smaller females. It appears that Weddell seals may exhibit a flexible strategy to adjust reproductive investment to local resource levels by taking advantage of periods when prey are occasionally abundant, although it is restricted to larger females possessing the physiological capacity to dive for longer and exploit different resources during lactation. This supports the assumption that although body mass and phylogenetic history explain most of the variation in lactation patterns (20–69%), the remaining variation has likely resulted from physiological adaptations to local environmental conditions. Our study confirms that Weddell seals use a mixed capital–income breeding strategy, and that considerable intraspecific variation exists. Questions remain as to the amount of energy gain derived from the inco

For polygynous mammals with no paternal care, the number of offspring sired is often the sole measure of male reproductive success. The potential for polygyny is highest when resources or other environmental factors such as restricted breeding sites force females to aggregate. In these circumstances, males compete intensely for females and mating success may vary greatly among males, further intensifying selection for those traits that confer an advantage in reproduction. Hence, determinants of male success in competition for females are likely to be under strong sexual selection. Paternity analysis was used in conjunction with measures of age, site fidelity, and behavior during the breeding season to assess variance in male breeding success in Weddell seals (Leptonychotes weddellii) breeding at Turtle Rock, McMurdo Sound (77.727S, 166.85E) between 1997 and 2000. Paternity could be assigned to 177 pups at relaxed or 80% confidence level or 111 pups at strict or 95% confidence levels. Weddell seals at Turtle Rock show a modest degree of polygyny with the greatest number of pups sired by any individual male in a single season equalling 5 or ∼10% of the pups born. Over four consecutive years, most (89.2%) males sired at least one pup. In a generalized linear model (GLM), age and the age first seen at the study site as an adult were unrelated to mating success, but adult experience, either site-specific or elsewhere in McMurdo Sound, over the reproductive life span of males explained nearly 40% of variance in total mating success with 80% confidence and 24% of variance at 95% confidence. While learning where females are likely to be may enhance male reproductive success, aquatic mating reduces the ability of males to monopolize females, and thereby increases equity in mating success.

Determination of seabird diet usually relies on the analysis of stomach-content remains obtained through stomach flushing; this technique is both invasive and logistically difficult. We evaluate the usefulness of DNA-based faecal analysis in a dietary study on chick-rearing macaroni penguins (Eudyptes chrysolophus) at Heard Island. Conventional stomach-content data was also collected, allowing comparison of the approaches. Methodology/Principal Findings. Preyspecific PCR tests were used to detect dietary DNA in faecal samples and amplified prey DNA was cloned and sequenced. Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in the early (guard) stage of chick-rearing, and detection of DNA from the myctophid fish Krefftichthys anderssoni and amphipods became more common in samples collected in the later (cre`che) stage. These trends followed those observed in the penguins’ stomach contents. In euphausiid-specific clone libraries the proportion of sequences from the two dominant euphausiid prey species (Euphausia vallentini and Thysanoessa macrura) changed over the sampling period; again, this reflected the trend in the stomach content data. Analysis of prey sequences in universal clone libraries revealed a higher diversity of fish prey than identified in the stomachs, but non-fish prey were not well represented. Conclusions/Significance. The present study is one of the first to examine the full breadth of a predator’s diet using DNA based faecal analysis. We discuss methodological difficulties encountered and suggest possible refinements. Overall, the ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds.