Intraspecific diversity in life histories and movement behaviour can buffer population dynamics of animals against environmental change and potentially improve the reliability of ecosystem services such as fisheries yields. We used a combination of acoustic telemetry and genetics to study the movement behaviour of 2 sympatric ecotypes of Atlantic cod Gadus morhua across a wide range of body sizes (N = 389, body lengths = 35-101 cm), during their foraging season (July-December) within 3 subarctic fjords in northern Norway. As expected, most tagged fish belonged to a coastal ecotype (93%). In addition, a migratory Northeast Arctic ecotype was also seen in all 3 fjords during the foraging season (7%). On average, individuals belonging to the Northeast Arctic ecotype used deeper locations in the fjords compared to the coastal ecotype. The 2 ecotypes behaved similarly in terms of horizontal and vertical movements. Larger individuals were typically detected at more locations (i.e. a higher horizontal movement activity) and greater depths, while smaller individuals on average had more extensive vertical movements. Females (N = 200) and males (N = 189) showed similar movement behaviours. Our findings imply that conservation measures, such as marine protected areas, should connect shallow and deep fjord habitats to effectively preserve Atlantic cod. Similarly, the biodiversity impact of anthropogenic pressures such as fishing and aquaculture will likely depend on their specific location within fjords.

The largest remaining cod stock in the Atlantic, the Northeast Arctic cod (NEAC), is facing climate change and poor recruitment. It is currently assumed to represent a single biological population. In coastal waters, both in Northern Norway and down to mid-Norway during the spawning season, NEAC overlaps with another cod ecotype, the conspecific coastal cod (CC), which is managed as a separate stock. Here, we analysed otoliths and conducted genotyping of 3900 cod to investigate population structure and potential ecotype mixtures in the Barents Sea. The annual surveys cover both the spawning and feeding areas of the NEAC stock with the purpose of collecting data for the annual stock assessment. While classification of individual cod to population-of-origin with the genetic markers currently available remains challenging, we-for the first time-infer the presence of CC and potential NEAC × CC hybrids also far offshore in the Barents Sea. Moreover, the CC were not homogenously distributed in the Barents Sea, but were higher in the west (including Svalbard) and in the far east, as well as near the Norwegian coast. Most of these putatively identified CC fish carried NEAC-type otoliths. Thus, cod otolith type seems a poor indicator of genetic ancestry and instead reflects environmental conditions. Many questions remain on the temporal stability of the NEAC and CC mixing in the Barents Sea, and not least, the management implications of such stock mixing. More generally, further studies are needed on the connection between within-species genetic differences and the implications of such differences for stock dynamics in a management context.

The stock delineation of European hake, Merluccius merluccius has long been debated due to the persistent discrepancies between biologically defined populations and management units, despite the species' significant economic importance. This study investigated population genetic structure within the northern European hake stock using 44 SNP markers following linkage disequilibrium-pruning. Whereas two of the loci were identified as consensus candidate outliers for positive selection, no balancing selection was detected. We found further evidence to challenge the current stock delineation by identifying a genetically distinct subunit in the Skagerrak. Likewise, and beyond the management delineation of the northern stock, European hake in a coastal/fjordic area of the Norwegian Sea was found to be significantly different. Our findings suggest that fine-scale genetic population structure should be explored in combination with life history traits to align biologically meaningful units with stock boundaries and facilitate sound resource management. Additionally, this study also contributes to the growing body of literature documenting marine species with populations in the Skagerrak that are genetically or ecologically distinct from those in adjacent seas; a differentiation that is partially driven by the strong salinity gradients resulting from the mixing of saline Atlantic and brackish Baltic waters.

ABSTRACT The blue ling, a deep‐water fish widespread in the Northeast Atlantic, has suffered major population declines from intensive fishing since the 1970s. Individuals sampled from four Norwegian fjords and offshore locations, including the Norwegian shelf, Faroe Islands, Rockall, Iceland and Greenland, were genotyped at 61 SNP loci. Results revealed weak but significant overall differentiation (FST = 0.005***) and no evidence of isolation by distance. While fjord and offshore groups showed no broad genetic separation, Yrkefjord displayed a distinct pattern relative to most other locations, warranting further investigation. Moreover, linkage disequilibrium analysis of SNPs produced a PCA pattern consistent with the characteristic three‐band structure associated with chromosomal inversions.

Atlantic cod Gadus morhua is a keystone species in the North Atlantic and Barents Sea ecosystems. Coastal Atlantic cod stocks have declined in recent decades, raising concerns about their recovery. Knowledge about cod behaviour, ecology and habitat use is vital to a management that ensures better costal cod population resilience and recovery. In this study, we aimed to quantify seascape use by Atlantic cod, using 3-dimensional acoustic telemetry to track 82 coastal cod (35-118 cm) from April through September in a 20 km(2) subarctic Norwegian fjord. We calculated continuous swimming trajectories in individual Atlantic cod with high precision (similar to 15 m) and combined this with high-resolution bottom substrate classification and bathymetric maps with derivatives such as terrain slope and bathymetric position index. Bedrock and mixed gravel/stone substrates were among the least available habitats in the fjord, yet small cod (<55 cm) spent the most time in these habitats and avoided substrates containing mud and/or sand. Large cod (>55 cm) spent the most time in association with mud and sandy substrate. Large cod used deeper fjord parts than small cod, with only 24% overlap between the average depth distributions of the 2 size groups. Small cod were associated with steeper terrain slopes. The combination of the precise tracking method, detailed bathymetry and high-resolution habitat mapping provided new understanding of the size-dependent habitat use by Atlantic cod, and may serve as an important tool for marine research as well as coastal planning and management.

Most of the previously large cod stocks in the North Atlantic are depleted to very low levels. A notable exception has been the Northeast Arctic cod inhabiting the Barents Sea. This cod stock reached a record high level around 2013, but since then has declined sharply, with older fish being fished out and few new recruits entering the stock. More specifically, since 2006 the average recruitment at age 3 per unit spawning stock biomass has dropped to a very low level. Here we review recent literature and data to evaluate potential causes of poor recruitment. We find that in most years the large spawning stock was successful in producing offspring up to the 0-group stage, but the survival thereafter was reduced-leading to few recruits into the fishable stock. Evidence points to consequences of northwards shifts of spawning locations, reduced inflow of Calanus and density dependent factors influencing pre-recruit survival at times when the spawning stock was at a record high level. However, large uncertainties in the causes of recruitment failure remain at a time when the Barents Sea ecosystem is experiencing unprecedented warming. A precautionary measure to avoid further decline and potential stock collapse in the current situation is to lower fishing pressure and improve management by setting reference points based on the recent period with low productivity. Including demographic characteristics like age diversity as explicit management targets to ensure spatial and temporal spread in spawning should be a goal for future method development.

The redfishes (genus Sebastes) are long-lived, commercial species in the North Atlantic. Excessive harvest through decades has led to a decline in the mature population of golden redfish (Sebastes norvegicus) in Norwegian waters, which is currently considered severely depleted. Accumulating genetic evidence suggests a more complex structure within this genus in the North Atlantic, which has recently inspired the hypotheses of cryptic species within S. norvegicus. Despite apparent genetic divergence between two types, they have yet to be verified morphologically. The morphology of genetically assigned fishes from Norwegian and Greenland waters was investigated using traditional morphometric methods, applying Linear Discriminant Analysis and Random Forest classification procedures to identify and evaluate the performance of descriptive characters. Combined with non-parametric meristic analysis, the results show that features such as beak length and eye diameter provide sufficient discrimination between the proposed cryptic species as well as separating them from the sympatric species S. mentella and S. viviparus. These findings support the presence of an additional redfish species in the North Atlantic, distinguishable both by morphological and genetic characters. This needs to be taken into consideration in future monitoring and management strategies for North Atlantic redfish.

ABSTRACTThe genus Sebastes in the North Atlantic comprises of long lived deep‐waters species that have been extensively fished upon, and many stocks are severely depleted across the Atlantic. This is particularly evident for the species Sebastes norvegicus. In recent papers, cryptic species have been indicated within this genus and molecular markers are therefore needed to provide identification for the Sebastes species, including the cryptic species as a basis for advice regarding management and rebuilding of the stocks. A suite of 2800 Single Nucleotide Polymorphism (SNP) markers were identified from ddRAD sequencing data, of which 56 SNPs were organized in two multiplex reactions and tested on 191 Sebastes spp. from different sampling locations from Norway and Greenland. Good‐quality amplification products were successfully obtained from 49 SNP markers for Sebastes species ID, and 3 TaqMan probes were designed to successfully assign S. mentella, S. viviparus, and the two cryptic species S. norvegicus types A and B. A total 47 SNPs were biallelic, with averaged HE per locus ranging between 0.053 and 0.50. This SNP‐based method establishes a foundation for genetically identifying the Northeast Atlantic Sebastes species. The findings presented should be followed by an effort to look for morphological characters to recognize the S. norvegicus cryptic species on site. In general, the SNP markers are a proper tool for monitoring the distribution of the species from a management perspective.

Sustainable fisheries require reliable specimen identification and understanding of underlying genetic hierarchies within target species. Three Sebastes species are commonly found in the northeastern Atlantic: Sebastes mentella (beaked redfish), S. norvegicus (golden redfish), and S. viviparus (Norway redfish). These species are morphologically similar and have largely overlapping distribution ranges. Furthermore, three cryptic species for S. norvegicus and three depth-defined ecotypes for S. mentella have been suggested. Genetic knowledge and methods are needed to identify and monitor these species and to survey their geographic distribution. Here, a total of 99 specimens of S. mentella, S. viviparus, and cryptic S. norvegicus type A and B were used for pooled sequencing and aligned against a reference genome from a sister species, S. fasciatus (Acadian redfish). The measured divergence between all pairs, including the cryptic species pair S. norvegicus A and B, was high (mean FST = 0.33-0.61) and encompassing throughout genomes. Several shared megabase-scale regions of elevated divergence were observed, likely representing regions of reduced recombination. Moreover, 2914 fish collected across the northeastern Atlantic and analysed with a discriminatory single nucleotide polymorphism (SNP) panel of high resolution (mean FST = 0.60-0.91), revealed few possible hybrids, and supported further substructuring within S. mentella and S. norvegicus B. The latter was split into two groups, one of which was the previously recognized 'giant' morph, confirmed here for the first time in Norway. In S. mentella, two to three genetic groups were found, likely representing previously identified depth-related ecotypes. Our study shows high genetic distinctiveness between acknowledged northeast-Atlantic Sebastes species, and between the cryptic species S. norvegicus A and B. Previously identified, fast-growing 'giant' morphs seem closely related to S. norvegicus B. Only few SNP markers are necessary for accurate species determination, facilitating further studies and widely applicable monitoring.

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.

As global fishery resources face increasing pressure, robust data are essential for implementing sustainable management practices. Key insights into migration patterns, connectivity, and mortality rates, both natural and fisheries-induced, are essential for effective management strategies. This study presents a unique tagging and recapture dataset of Atlantic cod. Within this dataset, we focussed on mortality rates and displacement distances of Norwegian coastal cod (NCC), including 23 231 cod released between 1954 and 1983 across four specific release zones north of 62 degrees N, along with 7010 recaptures. Specific subsets of these data were chosen for targeted statistical analyses. Our findings indicate that mean instantaneous total annual mortality (Z) of NCC was >1.0, and possibly even higher in the southern area. NCC tagged during the feeding season (June-October) displayed median displacement distances of 33-115 km, with 5%-35% of individuals dispersing >200 km, and 2%-15% dispersing >500 km. Displacement distances increased with time between tagging and recapture, size at tagging, and was highest for fish recaptured during the spawning season and in the northern zones (Finnmark). These results suggest stronger connectivity between fjords and coastal areas in northern Norway than further south. The size of the release zones used in this study (ranging from 8000 to 29 000 km(2)) align with NCC's generally limited dispersal in the southern zones, highlighting their potential as management units, while further analyses are needed for the northern zones.

Rapid expansion in coastal salmon farming has coincided with declines in coastal Atlantic cod Gadus morhua populations in Norway, raising suspicions over a causal relationship. One established effects pathway concerns the discharge of exogenous waste feed; however, food-web-related pathways remain poorly understood. Here we present a study conducted in 3 neighbouring fjords that are also important cod spawning areas, one of which has several active salmon farms. The study combines spatially explicit information on benthic ecology, cod stomach contents (via eDNA), dietary groups (via fatty acid profiling) and cod source-stock and demographics. Results confirmed that in addition to an anticipated fish diet, wild cod fed on a diverse array of benthic invertebrates, including shrimps, echinoderms, crabs, benthic worms and other infauna. Cod diets differed strongly with proximity to fish farms. Most (69%) cod caught adjacent to a farm had fatty acid trophic markers in their stomachs and/or livers consistent with a salmon pellet diet, and their stomachs contained benthic fauna that proliferate with organic enrichment. This trend was very localised, indicating a degree of residency and feeding specialisation or adaptability. When feeding off the bottom, cod are also likely to ingest contaminated sediments, which can (1) be toxic to marine life, (2) have a strongly altered microbiome and (3) contain known fish pathogens. We conclude that cod are influenced by farm-induced changes to food-web pathways, both in terms of the type and availability of suitable prey species and the composition of their tissues.

Arctic cod Boreogadus saida represents the most widespread and abundant fish in the Arctic Ocean and is a key trophic link in Arctic marine ecosystems. As the Arctic undergoes further rapid warming, understanding the ecological dynamics of this species is critical for developing effective Arctic marine conservation efforts. In this study, we assessed the relationship between ontogenetic shifts in gill raker density and diet composition of Arctic cod in the Canadian Beaufort Sea-Amundsen Gulf, using diet analyses and dietary tracers. Our results support the hypothesis that ontogenetic changes in gill raker density are associated with age-specific dietary shifts, leading to changes in the species' habitat preferences, from surface to deeper waters in the Canadian Beaufort Sea-Amundsen Gulf. As Arctic cod mature, their gill raker density decreases, making them less efficient at foraging on small prey found near the surface. Older fish, with sparser gill rakers, likely relocate to deeper areas to forage on larger prey, as reflected in their diet item sizes, proportions, and dietary tracers. These insights improve our understanding of how gill raker density, along with factors such as predation and thermoregulation, likely drive diet and habitat shifts in Arctic cod, contributing to our knowledge of their ecological role in Arctic marine systems.

When haemoglobin genotyping was implemented in the early 1960s to investigate population genetic structure in Atlantic cod (Gadus morhua), it became one of the first molecular genetic markers deployed in fisheries research worldwide. However, its suitability was questioned due to its potential for selection. While the issue of neutrality concerned the first population geneticists, markers under selection are now routinely used to study population genetic structure. Here, we revisited haemoglobin genotyping half a decade later to analyse >6000 mature Atlantic cod from 73 spawning locations throughout Norway’s approximately 2500 km coastline. A latitudinal gradient in allele frequencies, with a decrease in the HbI-2 allele towards the south, was observed. Our observed HbI-2 frequencies were consistently slightly lower than data from the 1960s, potentially reflecting adaptive changes to increasing sea temperatures. However, despite this difference, the observed north–south pattern in allele frequencies observed here and in the historical studies overlapped, aligning with current knowledge of population genetic structure in this species. We therefore conclude that this once questioned marker, which provided the first molecular genetic insights into genetic structure in Atlantic cod, provides knowledge consistent with the isolation by distance pattern revealed through decades of research in this species in this region.

Information on connectivity and genetic structure of marine organisms remains sparse in frontier ecosystems such as the Arctic Ocean. Filling these knowledge gaps becomes increasingly urgent, as the Arctic is undergoing rapid physical, ecological and socio-economic changes. The abundant and widely distributed polar cod (Boreogadus saida) is highly adapted to Arctic waters, and its larvae and juveniles live in close association with sea ice. Through a reduced-representation sequencing approach, this study explored the spatial genetic structure of polar cod at a circum-Arctic scale. Genomic variation was partitioned into neutral and adaptive components to respectively investigate genetic connectivity and local adaptation. Based on 922 high-quality single nucleotide polymorphism (SNP) markers genotyped in 611 polar cod, broad-scale differentiation was detected among three groups: (i) Beaufort -Chukchi seas, (ii) all regions connected by the Transpolar Drift, ranging from the Laptev Sea to Iceland, including the European Arctic and (iii) West Greenland. Patterns of neutral genetic structure suggested broadscale oceanographic and sea ice drift features (i.e., Beaufort Gyre and Transpolar Drift) as important drivers of connectivity. Genomic variation at 35 outlier loci indicated adaptive divergence of the West Greenland and the Beaufort-Chukchi Seas populations, possibly driven by environmental conditions. Sea ice decline and changing ocean currents can alter or disrupt connectivity between polar cod from the three genetic groups, potentially undermining their resilience to climate change, even in putative refugia, such as the Central Arctic Ocean and the Arctic Archipelago.

The present study investigated the impact of salmon aquaculture on the fatty acid composition in the liver of Atlantic cod Gadus morhua L. in northern Norway, comparing Northeast Arctic cod (NEAC) and Norwegian coastal cod (NCC) ecotypes. Cod were sampled seasonally near salmon farms at 1 impact location (<5 km) and 3 control sites farther from farms (>10 km) from October 2019 to October 2020. Fatty acid profiles were analyzed after lipid extraction of liver samples and gas chromatography. Generalized linear mixed models and multivariate analyses were used to assess differences between treatments, ecotypes, and other biological factors. Results showed that cod caught near farms had distinct fatty acid compositions with higher concentrations of aquafeed-derived fatty acids (e.g. oleic, linoleic, α-linolenic acid), indicating direct and/or indirect consumption (e.g. prey fish, benthic invertebrates) of unconsumed aquafeed. These effects were independent of ecotype, age, and sex. No significant seasonal changes or accumulation of fatty acids over time were detected. Both NEAC and NCC exhibited similar fatty acid profiles, suggesting comparable residency rates around salmon cages. A measurement of energetic reserves, the hepatosomatic index, significantly influenced fatty acid concentrations, highlighting the importance of liver fat storage. While cod near farms maintained relatively high concentrations of marine-based essential fatty acids (e.g. docosahexaenoic acid), the potential long-term physiological impacts (e.g. growth, reproduction, recruitment) warrant further investigation. This study emphasizes the need for a precautionary approach in spatial planning of salmon aquaculture, considering its potential effects on wild cod populations and recovery.

Managing natural resources in a sustainable manner requires understanding the complexity of ecosystems and the species that are associated with the different parts of the ecosystem. Much of this knowledge is derived from traditional sampling methods (e.g., different types of trawls). The analysis of environmental DNA (eDNA) can provide increased knowledge, complementary to the traditional methods. In the present pilot study, we sampled eDNA from two geographical areas, north and west of Svalbard (NWS) and in the southwestern Barents Sea (SWBS). The combination of trawling, visual identification of mammals and eDNA collection facilitated a robust analysis of fish and marine mammal diversity and species composition. Through 12S MiFish metabarcoding of the eDNA samples, we found that incorporating eDNA data provided an additional level of information on both the diversity of fish and marine mammals in the study areas. By adding eDNA data to the trawl data, we found that richness increased from 32 to 49 fish taxa. Significant differences in diversity and composition of the fish communities were detected by eDNA between the two study areas. Considering degradation and dilution factors it is postulated that the results represent resident species to the Barents Sea and that long -transported DNA from other areas are less likely.

Understanding the dietary habits and trophic niches of species is crucial for the conservation and management of species and ecosystems. Science-based fisheries management requires large-scale data of prey and parasites of fish species that enables the analysis of multitrophic interactions in an ecosystem. Using one of the commercially exploited beaked redfish (Sebastes mentella) from the Barents Sea, our study aims to understand its diet composition and parasites. We used 12S and COI markers to analyze the stomach and intestine contents of uncleaned, water-cleaned, and bleach-cleaned fish samples to also trace how external contamination affects diet analysis of fishes. We detected 19 potential prey taxa each of vertebrates and invertebrates from the guts of beaked redfish. While invertebrates were the major food source of redfish, our analysis indicated only two taxa of vertebrates that significantly contributed to the diet composition. In addition, we also detected two jellyfish species which were among the dominant prey taxa. Several parasites that have been frequently reported from redfish by visual examination were also detected by metabarcoding of gut contents. As in metabarcoding studies in general, it is important to build the reference libraries of fish parasites to fully harness the power of molecular approaches in achieving multi-trophic interactions. We underscore that metabarcoding captures both the common prey as well as delicate taxa which may not be available for visual examinations such as jellyfishes or other cryptic taxa. Our study showcases the importance of gut metabarcoding in terms of simultaneous detection of diets and parasites.

Coastal aquaculture and local fisheries interact in shared marine environments, influencing each other synergistically and/or antagonistically. Salmon farming, notably with open-net sea cages along the Norwegian coast, attracts wild fish due to increased food availability from uneaten feed, but it also exposes wild fish to farm emissions like waste and toxic chemicals (de-lice treatments, antifouling and medical agents). The attraction behaviour of wild fish can impact fatty acid composition in fish tissues, influenced by the high terrestrial fat content in salmon aquafeed. We study how the Atlantic cod, aggregating around salmon farms in a subarctic fjord in Northern Norway, can be affected, potentially altering their natural diet and fatty acid profiles. Our study compares the muscle-tissue fatty acid compositions of cod caught near aquaculture facilities (impact) versus fish caught in neighbouring fjords (control), and we hypothesise decreased omega-3 fatty acids near farms. The analysis revealed no significant differences in the fatty acid concentrations or categories between the impacted and control fish, challenging our initial expectations. However, differences were found for C18:1(n9)t (elaidic acid), with a higher value in the impacted fish. These findings suggest that salmon farming’s influence on cod’s fatty acid profiles in the flesh (i.e., relevant for the nutritional quality of the fillets that consumers eat) may be limited or minimal despite their aggregative behaviours around farms. The threshold levels of salmon feed consumed by wild cod before it affects the quality and survival of, e.g., sperm or other life stages, are not known and require new investigations. This study underscores the complexity of interactions between aquaculture and wild fisheries, impacting both ecological dynamics and consumer perspectives on seafood quality and health benefits.

Abstract Environmental DNA (eDNA) has gained popularity as a tool for ecosystem biomonitoring and biodiversity assessment. Although much progress has been made regarding laboratory and fieldwork protocols, the issue of sampling efficiency requires further investigation, particularly in three‐dimensional marine systems. This study focuses on fish community composition in marine ecosystems and aims to analyze the efficiency of sampling design given the sampling effort for distinguishing between different communities. We sampled three fjords in Northern Norway, taking samples along fjord transects and at three different depths, and amplified a fragment of the mitochondrial 12S rRNA gene of bony fishes using the MiFish primers. We evaluated the effect of (i) the number of sampling stations, (ii) samples' spatial distribution, and (iii) the data treatment approach (presence/absence versus semiquantitative) for maximizing the efficiency of eDNA metabarcoding sampling when inferring differences of fish community compositions between fjords. We found that the manner of data treatment strongly affected the minimum number of sampling stations required to detect differences among communities; because the semiquantitative approach retained some information about abundance of the underlying reads, it was the most efficient. Furthermore, we found little‐to‐no difference of fish communities in samples from intermediate depths when comparing vertical fish communities. Lastly, we found that the differences between fish communities at the surface were the highest across the horizontal distance and overall, samples ~30 km apart showed the highest variation in the horizontal distribution. Boosting sampling efficiency (reducing sampling effort without compromising ecological inferences) can significantly contribute to enhanced biodiversity management and efficient biomonitoring plans.