Ontogeny of movement patterns in naïve grey seal pups inhabiting a complex continental shelf ecosystem.

Most vertebrate offspring must transition from the relative security of parental care (nutrition and protection) to independent foraging. Offspring face many challenges during this critical period, particularly in species where parental care ends at weaning, such as the grey seal (Halichoerus grypus). We studied the development of movement behaviour in naïve grey seal pups from their first trips to sea to about five months of age. Twenty-five (12 males and 13 females) newly-weaned pups were fitted with satellite-linked GPS tags on Sable Island, Nova Scotia, Canada in January 2016. The influence of fixed effects (pup size, sex, week) and the random effect of pup identity on trip characteristics were examined. Movement behaviour was analyzed using a move persistence mixed-effects model. Habitat use was highly variable among individuals and covered much of the geographic distribution of the population. Unlike older juveniles, subadults, and adults in this population, most naïve pups used multiple haulout sites to begin and end trips. There was little evidence of area-restricted search behaviour during trips, suggesting that naïve pups were using an opportunistic foraging tactic that may result in more variable foraging success than that of older, experienced animals. Naïve pups made longer trips with longer haulout durations between them than observed for older greys seals. Males and females differed in some trip characteristics, but sex effects were small over the first few months of life. Offspring size at weaning was not a useful predictor of trip characteristics. Move persistence of grey seal pups was initially high and then decreased over time as individuals gained experience. Both intrinsic and extrinsic factors were influential on the movements of grey seal pups. Greater body length at weaning, longer duration spent on shore after weaning, shallower water column depth, and farther distance from shore were all associated with lower move persistence. Female grey seal pups had lower move persistence than males. Overall, the movements of naïve grey seal pups during the first few months of life were characterized by extensive exploration, but move persistence decreased over time suggesting they may be using an exploration-refinement foraging tactic.

Individual Quality Drives Life History Variation in a Long-Lived Marine Predator.

AbstractIndividual quality and environmental conditions may mask or interact with energetic trade-offs in life history evolution. Deconstructing these sources of variation is especially difficult in long-lived species that are rarely observed on timescales long enough to disentangle these effects. Here, we investigated relative support for variation in female quality and costs of reproduction as factors shaping differences in life history trajectories using a 32-year dataset of repeated reproductive measurements from 273 marked, known-age female gray seals (Halichoerus grypus). We defined individual reproductive investment using two traits, reproductive frequency (a female's probability of breeding) and provisioning performance (offspring weaning mass). Fitted hierarchical Bayesian models identified individual investment relative to conspecifics (over a female's entire life and in three age classes) and subsequently estimated how these investment metrics and the Atlantic Multidecadal Oscillation are associated with longevity. Individual differences (i.e., quality) contributed a large portion of the variance in reproductive traits. Females that consistently invest well in their offspring relative to other females survive longer. The best-supported model estimated survival as a function of age class-specific provisioning performance, where late-life performance was particularly variable and had the greatest impact on survival, possibly indicating individual variation in senescence. There was no evidence to support a trade-off in reproductive performance and survival at the individual level. Overall, these results suggest that in gray seals, individual quality is a stronger driver in life history variation than individual strategies resulting from energetic trade-offs.

Large offspring have enhanced lifetime reproductive success: Long-term carry-over effects of weaning size in gray seals (Halichoerus grypus).

An individual's size in early stages of life may be an important source of individual variation in lifetime reproductive performance, as size effects on ontogenetic development can have cascading physiological and behavioral consequences throughout life. Here, we explored how size-at-young influences subsequent reproductive performance in gray seals (Halichoerus grypus) using repeated encounter and reproductive data on a marked sample of 363 females that were measured for length after weaning, at ~4 weeks of age, and eventually recruited to the Sable Island breeding colony. Two reproductive traits were considered: provisioning performance (mass of weaned offspring), modeled using linear mixed effects models; and reproductive frequency (rate at which a female returns to breed), modeled using mixed effects multistate mark-recapture models. Mothers with the longest weaning lengths produced pups 8 kg heavier and were 20% more likely to breed in a given year than mothers with the shortest lengths. Correlation in body lengths between weaning and adult life stages, however, is weak: Longer pups do not grow to be longer than average adults. Thus, covariation between weaning length and future reproductive performance appears to be a carry-over effect, where the size advantages afforded in early juvenile stages may allow enhanced long-term performance in adulthood.

Cryogenic and hermetically sealed packaging of photonic chips for optomechanics.

We demonstrate a hermetically sealed packaging system for integrated photonic devices at cryogenic temperatures with plug-and-play functionality. This approach provides the ability to encapsulate a controlled amount of gas into the optical package allowing helium to be used as a heat-exchange gas to thermalize photonic devices, or condensed into a superfluid covering the device. This packaging system was tested using a silicon-on-insulator slot waveguide resonator which fills with superfluid 4He below the transition temperature. To optimize the fiber-to-chip optical integration 690 tests were performed by thermally cycling optical fibers bonded to various common photonic chip substrates (silicon, silicon oxide and HSQ) with a range of glues (NOA 61, NOA 68, NOA 88, NOA 86H and superglue). This showed that NOA 86H (a UV curing optical adhesive with a latent heat catalyst) provided the best performance under cryogenic conditions for all the substrates tested. The technique is relevant to superfluid optomechanics experiments, as well as quantum photonics and quantum optomechanics applications.

Measuring repeatability of compositional diet estimates: An example using quantitative fatty acid signature analysis.

By measuring the temporal consistency, or repeatability, in the diets of predators, we can gain a better understanding of the degree of individual specialization in resource utilization and implications for predator-prey interactions, population dynamics, and food web structure. To measure repeatability, we require repeated diet estimates of individuals over time, such as those derived from quantitative fatty acid signature analysis (QFASA), a popular diet estimation technique. However, diet estimates are often lengthy compositional vectors with many zeros, as some prey will not be consumed by all individuals, precluding the use of previously proposed measures of repeatability. In this paper, we propose a novel approach for inferring repeatability for multivariate data and, in particular, compositional diet estimates. We extend the commonly used measure of repeatability for univariate data to the multivariate compositional setting by utilizing the mean squares obtained from a nonparametric multivariate analysis of variance, and an appropriate choice of statistical distance. Our measure and its extension are compatible with both balanced and unbalanced data sets. Associated confidence intervals via nonparametric bootstrapping are also developed for the case of QFASA diet estimates that incorporate both sampling error and measurement error, where the latter error arises because the diets of predators are estimated. Simulation study results suggest that for practical levels of repeatability, our methods yield confidence intervals with the desired coverage probability even when the sample size relative to the dimension of the data (i.e., number of prey species eaten) is small. We tested our methods using QFASA diet estimates for free-ranging Northwest Atlantic grey seals. Given the importance of understanding how predator diets vary over time and space, our method may find broad application to other compositional diet estimates, including those derived from the stomach or fecal contents, and stable isotope analyses.

Key questions in marine mammal bioenergetics.

Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as 'key' questions because they received votes from at least 50% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations.

Sequence Diversity and Differences at the Highly Duplicated MHC-I Gene Reflect Viral Susceptibility in Sympatric Pinniped Species.

Differences in disease susceptibility among species can result from rapid host-pathogen coevolution and differences in host species ecology that affect the strength and direction of natural selection. Among 2 sympatric pinniped species that differ in sociality and putative disease exposure, we investigate observed differences in susceptibility through an analysis of a highly variable, duplicated gene family involved in the vertebrate immune response. Using high-throughput amplicon sequencing, we characterize diversity at the 2 exons that encode the peptide binding region of the major histocompatibility complex class I (MHC-I) gene in harbor (N = 60) and gray (N = 90) seal populations from the Northwest Atlantic. Across species, we identified 106 full-length exon 2 and 103 exon 3 sequence variants and a minimum of 11 duplicated MHC-I loci. The sequence variants clustered in 15 supertypes defined by the physiochemical properties of the peptide binding region, including a putatively novel Northwest Atlantic MHC-I diversity sublineage. Trans-species polymorphisms, dN/dS ratios, and evidence of gene conversion among supertypes are consistent with balancing selection acting on this gene. High functional redundancy suggests particularly strong selection among gray seals at the novel Northwest Atlantic MHC-I diversity sublineage. At exon 2, harbor seals had a significantly greater number of variants per individual than gray seals, but fewer supertypes. Supertype richness and private supertypes are hypothesized to contribute to observed differences in disease resistance between species, as consistently, across the North Atlantic and many disease outbreaks, gray seals appear to be more resistant to respiratory viruses than harbor seals.

Genetic association with boldness and maternal performance in a free-ranging population of grey seals (Halichoerus grypus).

Individual variation in quantitative traits clearly influence many ecological and evolutionary processes. Moderate to high heritability estimates of personality and life-history traits suggest some level of genetic control over these traits. Yet, we know very little of the underlying genetic architecture of phenotypic variation in the wild. In this study, we used a candidate gene approach to investigate the association of genetic variants with repeated measures of boldness and maternal performance traits (weaning mass and lactation duration) collected over an 11- and 28-year period, respectively, in a free-ranging population of grey seals on Sable Island National Park Reserve, Canada. We isolated and re-sequenced five genes: dopamine receptor D4 (DRD4), serotonin transporter (SERT), oxytocin receptor (OXTR), and melanocortin receptors 1 (MC1R) and 5 (MC5R). We discovered single nucleotide polymorphisms (SNPs) in each gene; and, after accounting for loci in linkage disequilibrium and filtering due to missing data, we were able to test for genotype-phenotype relationships at seven loci in three genes (DRD4, SERT, and MC1R). We tested for association between these loci and traits of 180 females having extreme shy-bold phenotypes using mixed-effects models. One locus within SERT was significantly associated with boldness (effect size = 0.189) and a second locus within DRD4 with weaning mass (effect size = 0.232). Altogether, genotypes explained 6.52-13.66% of total trait variation. Our study substantiates SERT and DRD4 as important determinants of behaviour, and provides unique insight into the molecular mechanisms underlying maternal performance variation in a marine predator.

Foraging behaviour of a continental shelf marine predator, the grey seal (Halichoerus grypus), is associated with in situ, subsurface oceanographic conditions.

BACKGROUND: The heterogeneous oceanographic conditions of continental shelf ecosystems result in a three-dimensionally patchy distribution of prey available to upper-trophic level predators. The association of bio-physical conditions with movement patterns of large marine predators has been demonstrated in diverse taxa. However, obtaining subsurface data that are spatio-temporally relevant to the decisions made by benthically-foraging species can be challenging. METHODS: Between 2009 and 2015, grey seals were captured on Sable Island, Nova Scotia, Canada during summer and fall and instrumented with high-resolution archival GPS tags. These tags recorded location data as well as depth (m), temperature (°C), and light level measurements during dives, until animals returned to the haulout site to breed. Hidden Markov models were used to predict apparent foraging along movement tracks for 79 individuals (59 females, 20 males) every 3 h. In situ measurements were used to estimate chlorophyll-a concentration (mg m- 3) and temperature within the upper-water column (50 m) and temperature and depth at the bottom of dives. As chlorophyll-a could only be estimated from 10:00 to 14:00 AST for dive depths ≥50 m, we formulated two generalized linear mixed-effects models to test the association of predicted grey seal behavioural states with oceanographic conditions and phytoplankton biomass: the first representing conditions of the upper-water column likely to influence primary productivity, and a second model including environmental conditions encountered by grey seals at the bottom of dives, when seals were more likely to be foraging. RESULTS: Predicted grey seal behavioural states were associated with fine-scale chlorophyll-a concentrations and other environmental conditions they encountered across the continental shelf. In the Water Column Model, season had no influence on the probability of observing apparent foraging, but chlorophyll-a, upper-water column temperature, and sex did, with females having a greater probability of foraging than males. In the Bottom Conditions Model, again season had no influence on the probability of apparent foraging, but females were over twice as likely as males to be foraging. CONCLUSIONS: The results of this study highlight the value of in situ measurements of oceanographic properties that can be collected at high temporal resolution by animal-borne data loggers. These data provide insight into how inferred behavioural decisions made by large marine predators, such as the grey seal, may be influenced by fine-scale oceanographic conditions.

Sex-differences in fine-scale home-range use in an upper-trophic level marine predator.

BACKGROUND: The distribution of prey in the ocean is spatially and temporally patchy. How predators respond to this prey patchiness may have consequences on their foraging success, and thus physical condition. The recent ability to record fine-scale movements of marine animals combined with novel home-range analyses that incorporate the dimension of time should permit a better understanding of how individuals utilise different regions of space and the consequences on their foraging success. METHODS: Over a six-year study, we used T-LoCoH (Time-Local Convex Hull) home-range software to model archival GPS (Global Positioning System) data from 81 grey seals to investigate the fine-scale spatio-temporal use of space and the distribution of apparent foraging effort. Regions of home-ranges were classified according to the frequency of return visits (site fidelity) and duration of visits (intensity of use). Generalized linear mixed -effects models were used to test hypotheses on seasonal changes in foraging distribution and behaviour and the role of space-use and state on determining foraging success. RESULTS: Male grey seals had larger home-ranges and core areas than females, and both sexes showed a contraction in home-range and core area in fall leading up to the breeding season compared with summer. Heavier individuals had smaller core areas than lighter ones, suggesting access to higher quality habitat might be limited to those individuals with greater foraging experience and competitive ability. The size of the home-range or core area was not an important predictor of the rate of mass gain. A fine-scale spatio-temporal analysis of habitat use within the home-range provided evidence of intra-annual site fidelity at presumed foraging locations, suggesting predictably in prey distribution. Neither sex nor season were useful predictors for classifying behaviour. Rather, individual identity explained much of the variation in fine-scale behaviour. CONCLUSIONS: Understanding how upper-trophic level marine predators use space provides opportunities to explore the consequences of variation in foraging tactics and their success on fitness. Having knowledge of the drivers that shape this intraspecific variation can contribute toward predicting how these predators may respond to both natural and man-made environmental forcing.

Variation in individual reproductive performance amplified with population size in a long-lived carnivore.

Individual variation in reproductive ability is a key component of natural selection within populations, driving the evolution of life histories and population responses to changing environmental conditions. Evidence that population density affects individual-level fitness in wild populations is limited, particularly for long-lived animals, which are difficult to observe on a biologically relevant scale. We tested for individual heterogeneity in reproductive performance in female grey seals (Halichoerus grypus) using 35 yr of mark-resighting data at Sable Island, Canada (43.93° N 59.91° W). We used Bayesian generalized linear mixed-effect models and multistate open robust design mark-resight models to investigate whether population size negatively influences individual reproductive performance. We measured reproductive performance in two ways: reproductive frequency (the probability of returning to the island to breed) and annual provisioning performance (the probability of successfully weaning a pup given a female bred). Sighting histories of 1,655 known-aged females with a total of 22,961 pupping events were used for analysis. After accounting for effects of female age, parity, and random year effects, we found that both provisioning performance and reproductive frequency demonstrated a strong, positive correlation with population size. Among-individual variance in reproductive traits and responses to population size indicated considerable heterogeneity in overall reproductive performance. As population size grew, "robust" females increased their reproductive performance more than their more "frail" conspecifics in both reproductive traits, resulting in an amplification of differences among individuals. Consequently, simulations from posterior distributions revealed a large fitness consequence of heterogeneity in this population, with "frail" individuals having 47.1% fewer successful pups than more "robust" females (mean reproductive output ± SD: 9.12 ± 3.77 pups for frail individuals, 16.97 ± 2.94 for robust individuals). Repeatability of overall reproductive performance across environments indicates individual quality may be more influential to lifetime reproductive success than costs associated with reproductive investment. This quantification of relative fitness and its dynamics is crucial to understanding broad evolutionary processes in natural populations.

Translating Marine Animal Tracking Data into Conservation Policy and Management.

There have been efforts around the globe to track individuals of many marine species and assess their movements and distribution, with the putative goal of supporting their conservation and management. Determining whether, and how, tracking data have been successfully applied to address real-world conservation issues is, however, difficult. Here, we compile a broad range of case studies from diverse marine taxa to show how tracking data have helped inform conservation policy and management, including reductions in fisheries bycatch and vessel strikes, and the design and administration of marine protected areas and important habitats. Using these examples, we highlight pathways through which the past and future investment in collecting animal tracking data might be better used to achieve tangible conservation benefits.

Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds.

Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site-associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half-century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well-described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.

Characterization of enamel caries lesions in rat molars using synchrotron X-ray microtomography.

Dental caries is a ubiquitous infectious disease with a nearly 100% lifetime prevalence. Rodent caries models are widely used to investigate the etiology, progression and potential prevention or treatment of the disease. To explore the suitability of these models for deeper investigations of intact surface zones during enamel caries, the structures of early-stage carious lesions in rats were characterized and compared with previous reports on white spot enamel lesions in humans. Synchrotron X-ray microcomputed tomography non-destructively mapped demineralization in carious rat molar specimens across a range of caries severity, identifying 52 lesions across the 30 teeth imaged. Of these lesions, 13 were shown to have intact surface zones. Depth profiles of fractional mineral density were qualitatively similar to lesions in human teeth. However, the thickness of the surface zone in the rat model ranges from 10 to 58 µm, and is therefore significantly thinner than in human enamel. These results indicate that a fraction of lesions in rat caries possess an intact surface zone and are qualitatively similar to human lesions at the micrometer scale. This suggests that rat caries models may be a suitable analog through which to investigate the structure of surface zone enamel and its role during dental caries.

Ethical issues and best practice in clinically based genomic research: Exeter Stakeholders Meeting Report.

Current guidelines on consenting individuals to participate in genomic research are diverse. This creates problems for participants and also for researchers, particularly for clinicians who provide both clinical care and research to their patients. A group of 14 stakeholders met on 7 October 2015 in Exeter to discuss the ethical issues and the best practice arising in clinically based genomic research, with particular emphasis on the issue of returning results to study participants/patients in light of research findings affecting research and clinical practices. The group was deliberately multidisciplinary to ensure that a diversity of views was represented. This report outlines the main ethical issues, areas of best practice and principles underlying ethical clinically based genomic research discussed during the meeting. The main point emerging from the discussion is that ethical principles, rather than being formulaic, should guide researchers/clinicians to identify who the main stakeholders are to consult with for a specific project and to incorporate their voices/views strategically throughout the lifecycle of each project. We believe that the mix of principles and practical guidelines outlined in this report can contribute to current debates on how to conduct ethical clinically based genomic research.

Nonlinear optomechanical measurement of mechanical motion.

Precision measurement of nonlinear observables is an important goal in all facets of quantum optics. This allows measurement-based non-classical state preparation, which has been applied to great success in various physical systems, and provides a route for quantum information processing with otherwise linear interactions. In cavity optomechanics much progress has been made using linear interactions and measurement, but observation of nonlinear mechanical degrees-of-freedom remains outstanding. Here we report the observation of displacement-squared thermal motion of a micro-mechanical resonator by exploiting the intrinsic nonlinearity of the radiation-pressure interaction. Using this measurement we generate bimodal mechanical states of motion with separations and feature sizes well below 100 pm. Future improvements to this approach will allow the preparation of quantum superposition states, which can be used to experimentally explore collapse models of the wavefunction and the potential for mechanical-resonator-based quantum information and metrology applications.

Key Questions in Marine Megafauna Movement Ecology.

It is a golden age for animal movement studies and so an opportune time to assess priorities for future work. We assembled 40 experts to identify key questions in this field, focussing on marine megafauna, which include a broad range of birds, mammals, reptiles, and fish. Research on these taxa has both underpinned many of the recent technical developments and led to fundamental discoveries in the field. We show that the questions have broad applicability to other taxa, including terrestrial animals, flying insects, and swimming invertebrates, and, as such, this exercise provides a useful roadmap for targeted deployments and data syntheses that should advance the field of movement ecology.

Dental caries - not just holes in teeth! A perspective.

Cavitation in teeth results from a pathogenic process termed dental caries that has occurred on the tooth surface for weeks or even years. Accumulation of dental plaque (biofilm) on the tooth is usually the first manifestation of the disease. Although acid production is the immediate and proximal cause of dissolution of teeth; it is the milieu within which the acid is formed that should be of primary concern. Focusing on the 'critical pH' has detracted attention from the more biological aspects (biofilm formation) of dental caries. Dental caries is unique; it is a biological process occurring on essentially an inert surface. Investigation of the multitude of interactions occurring in plaque ranging from enamel interfaces to surfaces of bacteria and matrices poses challenges worthy of the best scientific minds. The mouth clearly offers unique opportunities to investigate the multi facets of biofilm formation in vivo, generating data that have relevance way beyond the mouth. Prevention of this ubiquitous disease, dental caries, continues to present serious challenges. The public health benefits of fluoride delivered in its various formats are well recognized. Nevertheless, additional preventive approaches are required. Overcoming the rapid clearance of agents from the mouth is particularly challenging. Building on the polymerizing capacity of glucosyltransferases it may be possible to incorporate a therapeutic agent into the matrix plaque, thereby delivering therapeutic agents precisely to where they are needed.

A novel approach to quantifying the spatiotemporal behavior of instrumented grey seals used to sample the environment.

BACKGROUND: Paired with satellite location telemetry, animal-borne instruments can collect spatiotemporal data describing the animal's movement and environment at a scale relevant to its behavior. Ecologists have developed methods for identifying the area(s) used by an animal (e.g., home range) and those used most intensely (utilization distribution) based on location data. However, few have extended these models beyond their traditional roles as descriptive 2D summaries of point data. Here we demonstrate how the home range method, T-LoCoH, can be expanded to quantify collective sampling coverage by multiple instrumented animals using grey seals (Halichoerus grypus) equipped with GPS tags and acoustic transceivers on the Scotian Shelf (Atlantic Canada) as a case study. At the individual level, we illustrate how time and space-use metrics quantifying individual sampling coverage may be used to determine the rate of acoustic transmissions received. RESULTS: Grey seals collectively sampled an area of 11,308 km (2) and intensely sampled an area of 31 km (2) from June-December. The largest area sampled was in July (2094.56 km (2)) and the smallest area sampled occurred in August (1259.80 km (2)), with changes in sampling coverage observed through time. CONCLUSIONS: T-LoCoH provides an effective means to quantify changes in collective sampling effort by multiple instrumented animals and to compare these changes across time. We also illustrate how time and space-use metrics of individual instrumented seal movement calculated using T-LoCoH can be used to account for differences in the amount of time a bioprobe (biological sampling platform) spends in an area.