Relative indices of abundance are key to providing science advice for the management of many fish stocks. Historical focus has been on design-based estimation, wherein mathematical formulae for aggregating data into a single index are directly informed by the underlying sampling design. Recent efforts have moved toward using index standardization models instead. However, the impacts sampling designs and allocation schemes have on these index standardization models have not been fully examined. Using a spatio-temporal multinomial index standardization model developed for survey data obtained with longline fishing gear, we develop a simulation framework to analyze the effects of five different combinations of sampling designs and allocation schemes under various conditions. These simulations expose bias in model-based indices caused by non-proportional-to-area designs, which are common in surveys that have historically utilized design-based estimation. We explore the impact of robust statistical alternatives on this bias. This effort highlights an important source of bias and the importance of periodically reassessing allocation schemes and sampling designs for scientific surveys.

Individual foraging site fidelity is a common mechanism for dealing with environmental variability across marine predator species. However, there has been little research on long-term individual repeatability to date, especially over time periods where significant environmental and ecological change has occurred. The grey seal is a long-lived pinniped species that forages on the Scotian Shelf and in the Gulf of St. Lawrence, two ecosystems which are characterized by spatio-temporal variability in oceanographic conditions and have also undergone dramatic changes to ecological structuring and functioning in recent decades. Between 1995 and 2018, 22 adult grey seals (17 females, 5 males) were repeatedly instrumented with tracking devices in two or three different years. We fitted continuous-time correlated random walk state-space models to estimate grey seal locations and move persistence along tracks. We then calculated the kernel utilization distribution overlap for home ranges (99

Growing evidence suggests that complex spatial structure occurs within the Scotian Shelf and southern Grand Banks (SSGB) Atlantic halibut stock, yet large knowledge gaps remain about migratory and spawning behaviors. Here, 71 pop-up satellite archival tags were deployed on large Atlantic halibut (FL: 87 - 166 cm) between 2012 and 2020. Migration tracks were successfully reconstructed for 43 fish using a hidden Markov geolocation model, and temperature and depth time series were available for nine fish (total n = 52). Five migratory behaviors were identified: shelf residency, slope residency, shelf-channel migration, shelf-slope migration, and dispersal. The high-resolution data for four of 20 physically recovered tags provided evidence for putative female spawning behavior in deep channels on the continental shelf and along the continental slope between January and February. Additionally, four halibut displayed previously undocumented periods of sustained, oscillatory vertical movement along the continental slope between November and February. The high migratory diversity observed in the SSGB stock supports the existence of multiple resident and migratory contingents in the stock in the apparent absence of significant genetic structure.

The recovery of many groundfish stocks throughout the Northwest Atlantic has been impeded by elevated natural (i.e., non-fishing) mortality (M) among older/larger individuals. The causes of elevated mortality are not well known, though predation by rapidly growing grey seal herds and unreported fishing are thought to be possible drivers of mortality for Atlantic Cod (Gadus morhua) on the Western Scotian Shelf and in the Bay of Fundy (known as "4X5Y cod") and in nearby ecosystems. We developed a statistical catch-at-age model for 4X5Y cod that accounted for both grey seal predation and estimated bycatch/discards to evaluate the degree to which either of these factors may influence cod mortality. The model was fit over a range of predation and discarding scenarios to account for uncertainties and a lack of data for these processes. We found that most cod M remained unaccounted for unless cod comprised a large proportion (>0.45) of the grey seal diet by weight. If the reported bycatch estimates are taken as accurate, then the magnitude of cod discards from non-directed fisheries was minor, though these estimates are highly uncertain.

Few studies have examined the impacts of externally fitted data-loggers and telemetry tags on pinnipeds. We tested for instrument effects on body mass of lactating female gray seals and their offspring and probability of pupping in the next breeding season. Known-age adult females (n = 216) were fitted with instruments in winter, spring, and fall from 1992 to 2018 at Sable Island, Nova Scotia. Of those tagged in spring and fall, 61 of 135 returning females and 59 of their offspring were weighed within 5 days postpartum and 79 pups were weighed at weaning. Instrumented females were assigned to treatments based on tag frontal area sums, tag mass, deployment duration, and acoustic tag presence compared to control females without instruments using linear mixed-effects models. None of the treatment effects were included in the preferred models predicting birth mass of offspring or probability of breeding in the following year. The small negative effect (-3% to -7%) on postpartum maternal mass and pup weaning mass (-4.7%) for females instrumented in fall may be an artifact as longer spring deployments showed no effect. Overall, we found that the instruments deployed had no detectable negative effects on the maternal and offspring variables measured.

Many Atlantic salmon (Salmo salar) populations have experienced significant declines for decades throughout North America and Europe. Mortality due to marine mammal predation during their early marine life could be an important factor contributing to these declines and limiting their population recoveries. However, quantifying predation events, and particularly the extent of marine mammal predation on Atlantic salmon, remains a challenge. In this study, we estimated the contribution of mesothermic and endothermic species predation to the mortality of Atlantic salmon post-smolts during their early marine life using acoustic telemetry. Predation events were inferred from changes in temperatures and depths experienced by acoustically tagged hatchery-reared Atlantic salmon smolts. No salmon were consumed by mesothermic predators, with most endothermic predation events being classified as marine mammals. Post-smolt mortality during the study period was low overall in both years (13.1%-16.7%), with endothermic predation accounting for 33.1%-42.9% of all marine mortality events (5.2%-5.6% mortality). Our results suggest that the current low return of adult Atlantic salmon observed in this area in recent years was not heavily influenced by endothermic predation on post-smolts in the first weeks at sea.

The ability to identify sex is necessary in population biology for a proper understanding of the dynamics of a population. In Atlantic halibut, phenotypic sex identification is not possible due to the lack of significant external morphological differences. We developed an Illumina SNP panel for Atlantic halibut with 4000 SNPs spread evenly throughout the genome with a minor allele frequency MAF ≥ 0.4, except for N = 249 SNPs located in a sex-determining region on chromosome 12, N = 176 of these SNPs were selected to genetically identify male and female individuals using a DAPC analysis. The genomic identification of sex allows for non-lethal sex determination and validation of sex identification in the field. The SNP panel is a new genomic resource for Atlantic halibut that will make it possible to generate the genotypic data for the large number of individuals needed to estimate population abundance using genomics and the Close Kin Mark Recapture (CKMR) approach, an emerging component of fisheries management and stock monitoring.

Individual 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.

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 similar to 4weeks 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 8kg 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.

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.

Interactions between spatial dynamics and stock structure in marine fishes have largely focused on stocks in decline; stock structure is rarely re-visited for expanding species. Here, the spatial ecology of Atlantic halibut (Hippoglossus hippoglossus L.), managed as four stocks in the Northwest Atlantic, is reviewed. Halibut collapsed under high exploitation in the mid-19th century, but the Canadian fisheries value has increased seven-fold since the early 2000s. Atlantic halibut's thermal habitat has increased due to warming, possibly contributing to its expansion. Genomic evidence differentiates two populations in the four management units, whereas there is non-genetic spatial structure within each of the stock boundaries. There are different core juvenile areas and a diversity of spawning migration patterns influenced by timing, fish size, maturity state, and distance between summer-feeding and over-wintering habitats. From tagging studies, multiple estimates of median distance at recapture (similar to 3-90 km) are much less than the spatial domain of each stock. Growth rates are faster in the warmer south, as predicted by growing degree day. The current perspective of Atlantic halibut spatial structure is that there are two distinct populations, and within each, there are subpopulations composed of multiple migratory contingents. The level of mixing on common spawning grounds both among and within subpopulations is only partly understood.

Atlantic halibut (Hippoglossus hippoglossus) support an economically important fishery on the eastern coast of Canada. Like other species that are not well sampled by trawl surveys, halibut in this area are monitored using longline surveys. These surveys present challenges that can make obtaining indices of abundance difficult. Issues include gear saturation, which can result in a non-linear relationship between catch per unit effort and local abundance. The current approach to obtain a relative index consists of fitting a multinomial exponential model to a subset of hooks from each survey station. While this approach accounts for hook competition, it does not account for the presence of spatial patterns. We therefore extend the multinomial exponential model to include spatial random fields for both Atlantic halibut and non-target species, set-specific soak time, and data from the hooks. Furthermore, we propose a method for aggregating the resulting spatially varying indices to obtain an annual index for the entirety of the modelled area. This novel approach identifies Atlantic halibut hotspots in multiple years, while simultaneously providing relative abundance indices for 2017 through 2020. These outcomes demonstrate the widespread applicability of our methods for improving the scientific advice upon which fisheries management decisions are based.

Selection of birth-site habitat can have important effects on the reproductive success of females and the survival of offspring. We studied birth-site habitat selection by gray seals (Halichoerus grypus) on Sable Island, Nova Scotia, and the associated effect on offspring body mass at weaning. We identified a mosaic of eight habitats using orthorectified imagery from a photographic aerial survey conducted in January 2016. The distribution of birth sites of 814 females in 2014-2016 compared to the available habitat in 2016 provided evidence for positive selection of habitats that were not subject to tidal influence or flooding. The habitat selected for parturition varied with both female age and parity. Younger and inexperienced females were more likely to pup in beach habitat, while older and more experienced females were more commonly found inland and on vegetated dunes. Longitudinal data from 540 females observed between 2006 and 2016 revealed moderate repeatability of birth-site habitat selection (r = 0.269, 95% CI [0.236-0.326]). Pups born in inland sand habitat that did not flood averaged 1.5 kg heavier (similar to 2%) at weaning than those born on tidally influenced beach habitat. Overall, birth-site habitat selection was associated with small effects on offspring body mass at weaning.

Selection of birth-site habitat can have important effects on the reproductive success of females and the survival of offspring. We studied birth-site habitat selection by gray seals ( ) on Sable Island, Nova Scotia, and the associated effect on offspring body mass at weaning. We identified a mosaic of eight habitats using orthorectified imagery from a photographic aerial survey conducted in January 2016. The distribution of birth sites of 814 females in 2014–2016 compared to the available habitat in 2016 provided evidence for positive selection of habitats that were not subject to tidal influence or flooding. The habitat selected for parturition varied with both female age and parity. Younger and inexperienced females were more likely to pup in beach habitat, while older and more experienced females were more commonly found inland and on vegetated dunes. Longitudinal data from 540 females observed between 2006 and 2016 revealed moderate repeatability of birth-site habitat selection (  = 0.269, 95% CI [0.236–0.326]). Pups born in inland sand habitat that did not flood averaged 1.5 kg heavier (~2%) at weaning than those born on tidally influenced beach habitat. Overall, birth-site habitat selection was associated with small effects on offspring body mass at weaning.

An individual’s size when young may be an important source 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 natal size influences subsequent reproductive performance in grey seals ( Halichoerus grypus ) using mark-recapture and repeated measures reproductive data on a marked sample of 363 females that were measured for standard length at roughly 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 (the rate at which a female returns to breed), modeled using mixed-effects multistate mark-recapture models. After accounting for female age, experience, and offspring sex, we found a positive association between natal length and our measures of reproductive performance. Mothers with the longest natal lengths produced pups nearly 8 kg heavier and were 20% more likely to breed in a given year than mothers with the shortest natal lengths. Because correlation in individual body length between natal and adult life stages is weak (animals that were longer than average as pups do not always grow to be longer than average adults), the covariation between natal length and future reproductive performance reported here may act more as a carry-over effect from the size advantages afforded in the juvenile stage that allow for greater adult performance, rather than a physical trait that is maintained throughout life. ### Competing Interest Statement The authors have declared no competing interest.

Life history variation is thought to be mainly a result of energetic trade-offs among fitness components; however, detecting these trade-offs in natural populations has yielded mixed results. Individual quality and environmental variation may mask expected relationships among fitness components because some higher quality individuals may be able to acquire more resources and invest more in all functions. Thus, life history variation may be more affected by variation in individual quality than varying strategies to resolve energetic trade-offs, e.g. costs of reproduction. Here, we investigated whether variation in female quality or costs of reproduction is a larger factor in shaping differences in life history trajectories by assessing the relationship between survival and individual reproductive performance using a 32-year longitudinal data set of repeated reproductive measurements from 273 individually marked, known-aged female grey seals ( Halichoerus grypus ) from the Sable Island breeding colony. We defined individual reproductive performance using two traits: reproductive frequency (a female’s probability of breeding) and provisioning performance (provisions given to young measured by offspring mass), computed using mixed effects models separately for (1) all reproductive events, and (2) an age-class specific reproductive investment. Individual differences contributed a large portion of the variance in reproductive traits, with individuals displaying a range in individual reproductive frequencies from 0.45 to 0.94, and a range of average pup weaning masses from 34.9 kg to 61.8 kg across their lifetime. We used a Cormack-Jolly-Seber open-population model to estimate the effect of these reproductive performance traits on adult survival probability. Our approach estimated a positive relationship between reproductive performance and survival, where individuals that consistently invest well in their offspring survive longer. The best supported model estimated survival as a function of age-class specific provisioning performance, where late-life performance was quite 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. These results suggest that in grey seals, individual quality is a stronger driver in life history variation than varying strategies to mitigate trade-offs among fitness components. ### Competing Interest Statement The authors have declared no competing interest.

The northwest Atlantic subspecies of gray seal (Halicheorus grypus grypus) has been increasing for more than a half century and has reestablished breeding colonies in Canadian and US waters. In 2016, visual, oblique, and vertical large-format digital photographic surveys were conducted at all known breeding colonies in the northwest Atlantic. Total pup production in the northwest Atlantic was estimated to be 109,000 (SE = 17,500) pups. At 87,500 (SE = 15,100) pups, Sable Island accounts for 80% of total pup production. Regional differences in pup production trends are evident. Pup production in the Gulf of St. Lawrence and along the eastern shore of Nova Scotia has been relatively stable. Since 2004, the rate of increase in pup production at Sable Island has slowed to about 5%-7% per year, while the newer colonies in southwest Nova Scotia and the northeastern United States are increasing rapidly. In 2016, the Muskeget Island (MA) breeding colony produced 3,900 (SE = 200) pups, making it the third largest breeding colony in the northwest Atlantic. This southward shift in production may reflect climate-mediated changes in population growth as well as reestablishment of colonies throughout the former range associated with increased protection.

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.

The recovery of marine mammal populations has led to increased predation on commercially valuable prey species, creating conflicts with fisheries and calls for predator control. Grey seals are important predators of Atlantic Cod and Winter Skate in the southern Gulf of St. Lawrence (sGSL), and both species are likely to be extirpated unless grey seal presence in that ecosystem is strongly reduced. We aimed to identify harvest strategies that reduced grey seal presence in the sGSL to levels that favour fish recovery while maintaining grey seal conservation goals. We fit an integrated population model to grey seal abundance, reproductive and mark-recapture data, and projected future presence in the sGSL while varying the magnitude and age-composition of the annual commercial quota. We found that both removal and conservation targets could be met with annual quotas of 6000 seals if 50% of hunted seals were young of the year (YOY), though small amounts of overhunting reduced seal abundance below limit reference levels. Harvest strategies that targeted higher proportions of YOY were less likely to trigger conservation concerns, though these strategies required much larger quotas to achieve removal targets.

Characterizing the nature of genetic differentiation among individuals and populations and its distribution across the genome is increasingly important to inform both conservation and management of exploited species. Atlantic Halibut (Hippoglossus hippoglossus) is an ecologically and commercially important fish species, yet knowledge of population structure and genomic diversity in this species remains lacking. Here, we use restriction-site associated DNA sequencing and a chromosome-level genome assembly to identify over 86 000 single nucleotide polymorphisms mapped to 24 chromosome-sized scaffolds, genotyped in 734 individuals across the Northwest Atlantic. We describe subtle but significant genome-wide regional structuring between the Gulf of St. Lawrence and adjacent Atlantic continental shelf. However, the majority of genetic divergence is associated with a large putative chromosomal rearrangement (5.74 megabases) displaying high differentiation and linkage disequilibrium, but no evidence of geographic variation. Demographic reconstructions suggest periods of expansion coinciding with glacial retreat, and more recent declines in N-e. This work highlights the utility of genomic data to identify multiple sources of genetic structure and genomic diversity in commercially exploited marine species.