Greenland halibut (Reinhardtius hippoglossoides) is a commercially important species in the North Atlantic whose spatial population structure has not yet been fully determined across its entire range. We genotyped individuals from across the North Atlantic using a subset of informative single nucleotide polymorphic (SNP) markers to assess their usability as a SNP panel. We assessed whether these purportedly structured SNPs had any association with sex. We found several of these loci to be in sex-determining chromosomes and that their inclusion generated genetic structure mainly in males. The population structure without the sex-associated SNPs was weak and followed an isolation-by-distance pattern, likely with a large regional population on each side of the North Atlantic. We discuss how different sex ratios in the samples and/or an evolving sex-determination system in this species likely caused the inclusion of sex-associated loci in the panel. We found suggestive evidence of polymorphisms at sex-determining chromosomes differentiating males on east and west locations, indicating evolution of the sex-determination system. These results highlight the importance of documenting sex-based differences in genetic studies and call for a better understanding of genomic architecture to understand sex-determination systems across the whole distribution of sexually dimorphic species.

Understanding spatiotemporal movements of targeted species is fundamental to fisheries management. In the Arctic, Greenland halibut ( Reinhardtius hippoglossoides) fisheries are managed as separate stocks, and potential future fisheries growth requires improved understanding of broadscale movements and migration phenologies. We tagged Greenland halibut in the community fishery of Pond Inlet, Nunavut, Canada with acoustic transmitters to assess inshore and offshore movements over 4 years. Fish tagged in summer showed longer residency in Pond Inlet (54 ± 27 days) compared to offshore (2 ± 3 days) southern Baffin Bay/northern Davis Strait. Winter-tagged fish also showed high residency in Pond Inlet (92 ± 47 days) and minimal overlap with summer-tagged fish (December–April vs. June–November). Offshore migrations were detected in the majority of summer-tagged (70%) and winter-tagged fish (83%). Few summer-tagged fish returned to Pond Inlet in subsequent years, while most winter-tagged fish returned to Pond Inlet. These complex movements indicate Greenland halibut as a highly migratory species, which should be considered when developing management policies for both offshore and inshore fisheries.

The Greenland halibut (Reinhardtius hippoglossoides) is an ecologically and economically important marine fish species in the Northern Hemisphere. In the North Atlantic, the current spatial management units comprise four large offshore stocks and eight additional inshore stocks. However, the underlying biological basis for stock separation is uncertain. This may risk misrepresenting key population characteristics and reference points for sustainable management. To identify population structuring and boundaries for Greenland halibut, we here apply a spatial statistical approach using an extensive collection of scientific bottom trawl-surveys. Our analysis demonstrates two overall clusters separating the Northwest and Northeast Atlantic. Our findings are broadly consistent with recent studies on population structuring based on available tagging data and population genetics. However, it is still challenging to establish whether the results of clustering accurately reflect the true population boundaries, especially at a finer spatial scale. Therefore, we call for a broader synthesis of knowledge on population structuring of Greenland halibut utilizing all available sources of information to facilitate the designation of ecologically relevant management units and boundaries.

Assessing maturity status of fish and invertebrate species is important for understanding population dynamics with results (e.g., estimates of reproductive potential) often used to inform fisheries management strategies (e.g., the setting of minimum legal size requirements for fishing). Maturity rates may vary substantially across a population's range, as well as between years. In addition, maturity data are typically obtained from fisheries-independent surveys that may be incomplete (or missing) from year to year. Here we propose a spatial generalized linear mixed model (GLMM) framework for maturity data that includes spatially correlated random effects to address variations in space, and a sliding window approach to deal with unbalanced maturity data in both space and time. We demonstrate, with both real data and a simulation study, that this combined approach results in unbiased estimates of important growth parameters. Results of using our spatial GLMM framework with Greenland halibut (Rheinhardtius hippoglossoides) mature-at-length data from surveys of the eastern Canadian Arctic show that females mature at a much larger size than do males. The length at which 50% of the stock is mature (L50$$ {L}_{50} $$) is found to be higher in Baffin Bay compared to Davis Strait, and a declining trend in the L50$$ {L}_{50} $$ in recent years is revealed for both sexes. Our proposed methodology extends far beyond our current application in being useful for analyzing unbalanced spatiotemporal data from an array of diverse scientific fields.

Modelling life history trait variation at appropriate spatial and temporal scales is crucial for understanding population dynamics and developing effective fisheries management strategies. However, most efforts to model life history traits ignore spatial correlations and make a priori assumptions about the spatial structuring of populations, potentially clouding the ability to recognize true spatial structure. Here we develop spatiotemporal maturation models for Greenland halibut (Reinhardtius hippoglossoides) in the Northwest Atlantic, a species with large-scale movement patterns that can lead to uncertainty regarding effective stock boundaries. Our analysis using data from three Fisheries and Oceans Canada survey regions, Baffin Bay and Davis Strait in the eastern Canadian Arctic, Newfoundland and Labrador (NL), and the northern Gulf of St. Lawrence (GSL), is the first at such a large spatial scale. We also extend the traditional binary maturity status to a multinomial one that accounts for seasonal changes in maturation. Results show a decreasing temporal trend in size at maturity across the entire area. Spatial results regarding size at maturity provide new insight linking Greenland halibut south of Newfoundland (Northwest Atlantic Fisheries Organization Subdivision 3Ps) to the GSL stock rather than the NL stock. Results also highlight parts of the Davis Strait area, where size at maturity is smaller than in waters both north and south. Multinomial model results identify areas in GSL and Davis Strait that may be important for reproductive development in the summer and fall. Our analyses also reveal constraints on size at maturity that correspond with the well-known positive association between fish length and bottom depth. Broad-scale analyses of high resolution spatial patterns in life history traits, such as those performed here for Greenland halibut maturation, may identify recurrent patterns of association with environmental or habitat characteristics that might not otherwise be evident on a stock- or survey-specific basis.

Understanding the genetic differentiation among populations of most marine fish requires investigating the differences among spawning grounds. However, this can be challenging as spawning grounds for some species are not well known, or spawning fish are difficult to collect. An alternative is to collect juvenile fish in nursery habitats closely associated with potential spawning grounds. Greenland halibut is a deep-dwelling, commercially important species with at least two identified major offshore spawning grounds in the North Atlantic and weak genetic differentiation across the Atlantic. In this study, we sampled juveniles from three sites representing the Davis Strait spawning area in the northwest Atlantic and one site in the northeast Atlantic representing the primary spawning area along the western slope of the Barents Sea. We applied genotype by sequencing and discovered 90 genetic markers that could be used to assess genetic differentiation among the four sites. The northeast and northwest Atlantic showed major genetic differentiation, supporting the existence of the two primary spawning clusters. Additionally, we found genetic differentiation between the three northwest Atlantic samples implying the existence of more than one spawning area in the northwest.

Marine fisheries are often allocated to stocks that reflect pragmatic considerations and may not represent the species' spatial population structure, increasing the risk of mismanagement and unsustainable harvesting. Here we compile mark-recapture data collected across the North Atlantic to gain insight into the spatial population structure of Greenland halibut (Reinhardtius hippoglossoides), an issue that has been unresolved for decades. The dataset contains 168130 fish tagged from 1952 to 2021, with 5466 (3.3%) recaptured individuals. Our results indicate that fish tagged at <50 cm body length migrate at higher rates, suggesting that mark-recapture studies on adult individuals underestimate population-level migration rates. We find evidence for migrations across management units in the North Atlantic indicating two regional offshore populations: one in the Northeast Atlantic, where the West Nordic and Northeast Arctic stocks, currently managed separately, likely belong to a single population that spans from the Kara Sea to Southeast Greenland; and one in the Northwest Atlantic where migration was observed between the Newfoundland and Labrador stock and the Northwest Arctic stock in Davis Strait and Baffin Bay. Our findings indicate complex population structure with implications for international and domestic fisheries management of this long-lived species.

Excess bycatch of marine species during commercial fishing trips is a challenging problem in fishery management worldwide. The aims of this paper are twofold: to introduce methods and provide a practical guide for spatiotemporal modelling of bycatch data, as well as to apply these methods and present a thorough examination of Greenland shark (Somniosus microcephalus) bycatch weight in a Canadian Arctic fishery. We introduce the spatially explicit two-part model and offer a step by step guide for applying the model to any form of bycatch data, from data cleaning, exploratory data analysis, variable and model selection, model checking, to results interpretation. We address various problems encountered in decision making and suggest that researchers proceed cautiously and always keep in mind the aims of the analysis when fitting a spatiotemporal model. Results identified spatiotemporal hotspots and indicated month and gear type were key drivers of high bycatch. The importance of onboard observers in providing robust bycatch data was also evident. These findings will help to inform conservation strategies and management decisions, such as limiting access to spatial hotspots, seasonal closures and gear restrictions.

Deep-sea marine fishes support important fisheries but estimates of their distributions are often incomplete as the data behind them may reflect fishing practices, access rights, or political boundaries, rather than actual geographic distributions. We use a simple suitable habitat model based on bottom depth, temperature, and salinity to estimate the potential distribution of Greenland halibut (Reinhardtius hippoglossoides). A large presence-only dataset is examined using multivariate kernel densities to define environmental envelopes, which we link to spatial distribution using a pan-Arctic oceanographic model. Occurrences generally fit the model well, although there were gaps in the predicted circum-Arctic distribution likely due to limited survey activity in many of the ice-covered seas around the Arctic Ocean. Bottom temperature and depth were major factors defining model fit to observations, but other factors, such as ecosystem interactions and larval drift could also influence distribution. Model predictions can be tested by increasing sampling effort in poorly explored regions and by studying the connectivity of putative populations. While abundances of Greenland halibut in the High Arctic are currently low, some areas are predicted to be suitable habitat for this species, suggesting that on-going sea-ice melt may lead to fisheries expansion into new areas.

Despite the commercial importance of Greenland Halibut (Reinhardtius hippoglossoides), important gaps still persist in our knowledge of this species, including its reproductive biology and sex determination mechanism. Here, we combined single-molecule sequencing of long reads (Pacific Sciences) with chromatin conformation capture sequencing (Hi-C) data to assemble the first chromosome-level reference genome for this species. The high-quality assembly encompassed more than 598 Megabases (Mb) assigned to 1594 scaffolds (scaffold N50 = 25Mb) with 96% of its total length distributed among 24 chromosomes. Investigation of the syntenic relationship with other economically important flatfish species revealed a high conservation of synteny blocks among members of this phylogenetic clade. Sex determination analysis revealed that similar to other teleost fishes, flatfishes also exhibit a high level of plasticity and turnover in sex determination mechanisms. A low-coverage whole-genome sequence analysis of 198 individuals revealed that Greenland Halibut possesses a male heterogametic XY system and several putative candidate genes implied in the sex determination of this species. Our study also suggests for the first time in flatfishes that a putative Y-autosomal fusion could be associated with a reduction of recombination typical of the early steps of sex chromosome evolution.

The deep sea plays a critical role in global climate regulation through uptake and storage of heat and carbon dioxide. However, this regulating service causes warming, acidification and deoxygenation of deep waters, leading to decreased food availability at the seafloor. These changes and their projections are likely to affect productivity, biodiversity and distributions of deep‐sea fauna, thereby compromising key ecosystem services. Understanding how climate change can lead to shifts in deep‐sea species distributions is critically important in developing management measures. We used environmental niche modelling along with the best available species occurrence data and environmental parameters to model habitat suitability for key cold‐water coral and commercially important deep‐sea fish species under present‐day (1951–2000) environmental conditions and to project changes under severe, high emissions future (2081–2100) climate projections (RCP8.5 scenario) for the North Atlantic Ocean. Our models projected a decrease of 28%–100% in suitable habitat for cold‐water corals and a shift in suitable habitat for deep‐sea fishes of 2.0°–9.9° towards higher latitudes. The largest reductions in suitable habitat were projected for the scleractinian coral Lophelia pertusa and the octocoral Paragorgia arborea, with declines of at least 79% and 99% respectively. We projected the expansion of suitable habitat by 2100 only for the fishes Helicolenus dactylopterus and Sebastes mentella (20%–30%), mostly through northern latitudinal range expansion. Our results projected limited climate refugia locations in the North Atlantic by 2100 for scleractinian corals (30%–42% of present‐day suitable habitat), even smaller refugia locations for the octocorals Acanella arbuscula and Acanthogorgia armata (6%–14%), and almost no refugia for P. arborea. Our results emphasize the need to understand how anticipated climate change will affect the distribution of deep‐sea species including commercially important fishes and foundation species, and highlight the importance of identifying and preserving climate refugia for a range of area‐based planning and management tools.

Aim Climate change is altering marine ecosystems worldwide and is most pronounced in the Arctic. Economic development is increasing leading to more disturbances and pressures on Arctic wildlife. Identifying areas that support higher levels of predator abundance and biodiversity is important for the implementation of targeted conservation measures across the Arctic. Location Primarily Canadian Arctic marine waters but also parts of the United States, Greenland and Russia. Methods We compiled the largest data set of existing telemetry data for marine predators in the North American Arctic consisting of 1,283 individuals from 21 species. Data were arranged into four species groups: (a) cetaceans and pinnipeds, (b) polar bears Ursus maritimus (c) seabirds, and (d) fishes to address the following objectives: (a) to identify abundance hotspots for each species group in the summer-autumn and winter-spring; (b) to identify species diversity hotspots across all species groups and extent of overlap with exclusive economic zones; and (c) to perform a gap analysis that assesses amount of overlap between species diversity hotspots with existing protected areas. Results Abundance and species diversity hotpots during summer-autumn and winter-spring were identified in Baffin Bay, Davis Strait, Hudson Bay, Hudson Strait, Amundsen Gulf, and the Beaufort, Chukchi and Bering seas both within and across species groups. Abundance and species diversity hotpots occurred within the continental slope in summer-autumn and offshore in areas of moving pack ice in winter-spring. Gap analysis revealed that the current level of conservation protection that overlaps species diversity hotspots is low covering only 5% (77,498 km(2)) in summer-autumn and 7% (83,202 km(2)) in winter-spring. Main conclusions We identified several areas of potential importance for Arctic marine predators that could provide policymakers with a starting point for conservation measures given the multitude of threats facing the Arctic. These results are relevant to multilevel and multinational governance to protect this vulnerable ecosystem in our rapidly changing world.

Pan-Arctic fisheries are highly diverse in their purpose, species biology, productivity, economic and strategic importance as well as in how they are prosecuted. They range from full industrial fisheries to community-based artisanal, sport and subsistence fisheries. The nature of Arctic ecosystems in the region varies from extremely productive to relatively barren in terms of fisheries production. Gear types vary, but offshore trawl fisheries and inshore and freshwater gillnet fisheries are the most common. Rights-based fisheries (e.g., for indigenous inhabitants) are more prominent in the Canadian and American Arctic than in European jurisdictions. The principal harvested species in freshwater environments tend to be from few taxa mainly Salvelinus spp. and from the family Coregonidae, while the marine taxa are more diverse. Compared to north temperate fisheries, Arctic fisheries have impressive variation across longitudes; some jurisdictions support only small-scale subsistence fisheries, whereas others contain some of the largest yields among industrial fisheries. Approaches to scientific assessment are also highly diverse with a range from catch-based indicators to sophisticated fully age-structured population models.

Management boundaries that define populations or stocks of fish form the basis of fisheries planning. In the Arctic, decreasing sea ice extent is driving increasing fisheries development, highlighting the need for ecological data to inform management. In Cumberland Sound, southwest Baffin Island, an indigenous community fishery was established in 1987 targeting Greenland halibut (Reinhardtius hippoglossoides) through the ice. Following its development, the Cumberland Sound Management Boundary (CSMB) was designated and a total allowable catch (TAC) assigned to the fishery. The CSMB was based on a sink population of Greenland halibut resident in the northern section of the Sound. Recent fishing activities south of the CSMB, however, raised concerns over fish residency, the effectiveness of the CSMB and the sustainability of the community-based winter fishery. Through acoustic telemetry monitoring at depths between 400 and 1200 m, and environmental and fisheries data, this study examined the movement patterns of Greenland halibut relative to the CSMB, the biotic and abiotic factors driving fish movement and the dynamics of the winter fishery. Greenland halibut undertook clear seasonal movements between the southern and northern regions of the Sound driven by temperature, dissolved oxygen, and sea ice cover with most fish crossing the CSMB on an annual basis. Over the lifespan of the fishery, landfast ice cover initially declined and then became variable, limiting accessibility to favored fisher locations. Concomitantly, catch per unit effort declined, reflecting the effect of changing ice conditions on the location and effort of the fishery. Ultimately, these telemetry data revealed that fishers now target less productive sites outside of their favored areas and, with continued decreases in ice, the winter fishery might cease to exist. In addition, these novel telemetry data revealed that the CSMB is ineffective and led to its relocation to the entrance of the Sound in 2014. The community fishery can now develop an open-water fishery in addition to the winter fishery to exploit the TAC, which will ensure the longevity of the fishery under projected climate-change scenarios. Telemetry shows great promise as a tool for understanding deep-water species and for directly informing fisheries management of these ecosystems that are inherently complex to study.

1. Globally, small-scale inshore fisheries are being recognized as highly beneficial for underdeveloped coastal communities since they directly contribute to local economies. Community coastal fisheries, however, may target species that are simultaneously harvested by large commercial vessels in adjacent offshore waters, creating uncertainty over stock units and connectivity that complicate management. 2. Greenland halibut Reinhardtius hippoglossoides, a commercially important flatfish species in the Arctic, were tagged in Scott Inlet, coastal Baffin Island, Canada, with acoustic transmitters and tracked for a 1-year period. Our aim was to measure fish movement and connectivity between inshore habitats, where Inuit fisheries are developing, and offshore waters, where an established commercial fishery operates. Four movement metrics were established, and cluster analysis and a mixed effects model were used to define movement types and identify environmental covariates of the presence/absence within the coastal environment respectively. 3. Two distinct movement patterns were characterized for Greenland halibut; the majority were transients that were no longer detected inshore by the end of November (n = 47, 72%), and a smaller group of intermittently resident fish that moved into the offshore at the same time as transient fish, but returned to the coastal environment in the winter (n = 8, 12%), with the remainder being undefined. The presence of Greenland halibut in the inshore was negatively correlated with ice cover, indicating that fish moved offshore as sea ice formed. 4. Synthesis and applications. Greenland halibut were previously thought to be highly resident within the coastal environment of Baffin Bay; however, our data demonstrates that this is not true for all areas. In Scott Inlet and adjacent coastal regions, Greenland halibut exhibit complex inshore-offshore connectivity, suggesting inshore and offshore fisheries require a shared quota. We recommend that in the face of developing global small-scale coastal fisheries, improved understanding of stock connectivity between environments is required to sustainably manage commercial fish species.

Pan-Arctic fisheries are highly diverse in their purpose, species biology, productivity, economic and strategic importance as well as in how they are prosecuted. They range from full industrial fisheries to community-based artisanal, sport and subsistence fisheries. The nature of Arctic ecosystems in the region varies from extremely productive to relatively barren in terms of fisheries production. Gear types vary, but offshore trawl fisheries and inshore and freshwater gillnet fisheries are the most common. Rights-based fisheries (e.g., for indigenous inhabitants) are more prominent in the Canadian and American Arctic than in European jurisdictions. The principal harvested species in freshwater environments tend to be from few taxa mainly Salvelinus spp. and from the family Coregonidae, while the marine taxa are more diverse. Compared to north temperate fisheries, Arctic fisheries have impressive variation across longitudes; some jurisdictions support only small-scale subsistence fisheries, whereas others contain some of the largest yields among industrial fisheries. Approaches to scientific assessment are also highly diverse with a range from catch-based indicators to sophisticated fully age-structured population models.

Greenland Halibut (Reinhardtius hippoglossoides) is a large circumpolar, right-eyed flounder that supports several international fisheries. Age estimates for this stock have customarily been obtained by counting annuli on the surface of whole otoliths but a matched pair comparison indicated that ages estimated from whole and thin-sectioned otoliths were the same up until age 9 (∼60 cm), after which whole otoliths underestimated the true age of the fish by up to 60% and 18 years. Bomb radiocarbon analyses on otolith cores from thin sections were similar to expectations based on the Greenland Halibut reference chronology, indicating that on average, thin sections gave an accurate age for fish in the 57–108 cm TL range. Growth curves estimated using thin-sectioned otoliths indicated that Greenland Halibut in this region are slower growing and longer lived than was previously thought. A comparison of growth parameters with other populations of Greenland Halibut showed that although the Pacific and Arctic are faster-growing, the stock off the East Coast of Canada is longer lived. This study represents the first age validation study for this stock in the Northwest Atlantic. Since the fishable portion of the population is largely <60 cm, it is possible that these results may not change the current perception of stock status. However, the increased longevity and reduced growth rates will undoubtedly affect other biological parameters and further work should be done to incorporate the new ageing knowledge into the Management Strategy Evaluation for this stock.