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Intraperitoneal (i.p.) injection vaccination is considered effective to protect European sea bass (Dicentrarchus labrax) from economically important diseases. Water-based as well as oil-adjuvanted vaccine formulations are being widely used. The oil adjuvants used to potentiate antigen effects lead to higher and more prolonged immune response but also to chronic peritoneal inflammatory reactions, regarded as adverse or side-effects. During a three-year field study conducted throughout Greek mariculture, the intra-abdominal lesions were assessed on fish sampled prior to, and at different times post i.p. injection with different oil-adjuvanted vaccine formulations. The scope was to create a macroscopic side-effect intensity scale for sea bass in line with those applicable to salmonids (Salmo salar, Oncorhynchus mykiss) and cod (Gadus morhua). The diversity of lesions observed ranged from none (presumably non-injected; score 0) to widespread, strong adhesions with granuloma, pigmented or not (score 6). The occurrence of small nodules apparently containing vaccine remains, encapsulated by layers of connective tissue is described. The proposed scoring system is described and illustrated, intended to guide farm staff to evaluate the intensity of post-injection vaccination side-effects by necropsy on site.

Photo-enhanced toxicity of crude oil is produced by exposure to ultraviolet (UV) radiation. Atlantic cod (Gadus morhua) embryos were exposed to crude oil with and without UV radiation (290–400 nm) from 3 days post fertilization (dpf) until 6 dpf. Embryos from the co-exposure experiment were continually exposed to UV radiation until hatching at 11 dpf. Differences in body burden levels and cyp1a expression in cod embryos were observed between the exposure regimes. High doses of crude oil produced increased mortality in cod co-exposed embryos, as well as craniofacial malformations and heart deformities in larvae from both experiments. A higher number of differentially expressed genes (DEGs) and pathways were revealed in the co-exposure experiment, indicating a photo-enhanced effect of crude oil toxicity. Our results provide mechanistic insights into crude oil and photo-enhanced crude oil toxicity, suggesting that UV radiation increases the toxicity of crude oil in early life stages of Atlantic cod. publishedVersion

Background Pacific cod (Gadus macrocephalus) is an ecologically important species that supports a valuable commercial fishery throughout Alaska waters. Although its life history includes seasonal movement for spawning and feeding, little is known about its movement ecology. Here, we present results from the first study to use pop-up satellite archival tags (PSATs) to track the within-year movements of Pacific cod to understand their potential seasonal movement patterns within the Aleutian Islands. This study was part of a cooperative research project; tagging was conducted onboard commercial vessels during the winter fishing season while Pacific cod were aggregated to spawn in the central Aleutian Islands. Results Of the 36 PSATs deployed, we were able to obtain movement data from 13 Pacific cod that were at liberty between 60 and 360 days. We determined that three tagged Pacific cod were predated on by marine mammals and three were recaptured by the commercial fishery. Geolocation models were produced for four migrating individuals. Eight Pacific cod moved to a productive foraging ground near Seguam Island located 64 to 344 km from their release site and presumed spawning ground within a few weeks of their release. These movements indicate that some Pacific cod in the Aleutian Islands undergo seasonal migration. Three Pacific cod remained near their release locations (within 50 km) for more than 75 days suggesting the existence of partial migration in the population. Two Pacific cod undertook larger movements (378 and 394 km) during which they swam over deep passes and crossed several management boundaries highlighting the potential connectedness of Pacific cod throughout the Aleutian Islands. Conclusions This study provided important initial insights into the seasonal movement patterns of Pacific cod in the Aleutian Islands. Most tracked Pacific cod (77%) undertook migrations in the middle of March (64–394 km) from their winter spawning areas to summer foraging areas, but a few individuals remained in their capture location suggesting a partial migration strategy. Their ability to cross deep passes that were previously seen as potential barriers to movement has expanded our understanding of population connectivity.

Measuring fish population responses to climate change requires timely ecological information, warranting innovative approaches to data collection in fisheries research and management. Fourier transform near-infrared (FT-NIR) spectroscopy is a promising tool to efficiently and cost-effectively obtain multiple types of fisheries data including fish physiological health and energetics that can provide indicators of stock status and environmental change. We tested the applicability of FT-NIR spectroscopy to determine fish physiological state and condition by developing calibration models for morphometric indices of body condition [Fulton’s K and hepatosomatic index (HSI)], biochemical measurements of tissue composition (lipid content and energy density), and a nucleic acid-based index of recent growth (RNA:DNA) of juvenile Pacific cod (Gadus macrocephalus). Calibration models had the best predictive ability for lipid content followed by HSI and energy density, whereas spectral data had weak relationships with Fulton’s K and RNA:DNA. For lipid content, energy density, and HSI, informative spectral regions were primarily associated with carbon-hydrogen bonds in lipid molecules. Additionally, FT-NIR spectroscopy calibration models better predicted lipid content than morphometric measurements that are often used as proxies for measuring energy reserves, indicating that FT-NIR spectroscopy might serve as a more informative index of body condition and energy stores than other rapid methods. Efficient sample analysis by FT-NIR spectroscopy can supplement traditional metrics of body condition and be especially useful for ensuring the availability of monitoring data in support of fisheries research and management.

Atlantic cod, Gadus morhua, is a highly appreciated fish in European seafood markets and is one of the most substituted fish species in the world. Fraud have been detected in European markets in the last decade, finding different substitute species sold as G. morhua or Atlantic cod on the label. In this study, we analyzed 252 samples of fresh and frozen cod fillets sold in Germany, the Netherlands, and France using DNA barcoding. Different trends were found in different countries: while the level of mislabeling found in Germany and the Netherlands remained at zero in the last years, a significant increase was found in the French markets comparing the current results with previous studies on fillets in France. On the one hand, this mislabeling proves the need to encourage European efforts to control seafood authenticity, on the other, zero mislabeling in two countries shows the success of current European regulations.

Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation. Copyright © 2021 Martínez-García, Ferrari, Oosting, Ballantyne, van der Jagt, Ystgaard, Harland, Nicholson, Hamilton-Dyer, Baalsrud, Brieuc, Atmore, Burns, Schmölcke, Jakobsen, Jentoft, Orton, Hufthammer, Barrett and Star. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

Until recently, polar night constituted truly a “mare incognitum” of our times. Yet, the first records from this very little-explored period showcased a surprisingly rich and active ecosystem. This investigation aims to reveal the level of scavenger activity during both Arctic polar night and day. It compares the shallow-water scavenging fauna observed during two contrasting seasons (winter vs. summer) in a high Arctic fjord (Kongsfjorden, 79° N, Spitsbergen, Svalbard Archipelago). In each of January and July 2015, two different bait types – Atlantic cod (Gadus morhua) and a bird carcass (chicken meat) were deployed at a depth of 12 m. Fauna were monitored remotely using time-lapse cameras equipped with bait traps, with photographs taken every 15 min over a period of 4 days. Thirty taxa were recorded at baits, dominated by lysianassid amphipods (Onisimus sp. 88%, Anonyx sp. 2%, but only during winter), and buccinid gastropods (B. undatum 5%, B. glaciale 1%, Buccinum sp. 3%, in both seasons). In most cases, buccinids were the first animals to appear at bait. The total number of recorded taxa, mean species richness per sampling unit, total abundance and associations among taxa were higher, on average, in winter than in summer deployments, while Pielou’s evenness index showed the opposite pattern. Scavenger assemblages differed significantly between the two seasons and also in response to the two different bait types, with seasonal effects being strongest. Contrary to expectations, bait consumption rates differed very little between the two seasons, being slow in general and only slightly faster in summer (0.05 g of cod bait consumed in 1 min) compared to winter (0.04 g min–1), yielding novel insights into ecological interactions and functions in shallow marine ecosystems during Arctic polar nights.

Quantifying the spatial and temporal footprint of multiple environmental stressors on marine fisheries is imperative to understanding the effects of changing ocean conditions on living marine resources. Pacific Cod (Gadus macrocephalus), an important marine species in the Gulf of Alaska ecosystem, has declined dramatically in recent years, likely in response to extreme environmental variability in the Gulf of Alaska related to anomalous marine heatwave conditions in 2014–2016 and 2019. Here, we evaluate the effects of two potential environmental stressors, temperature variability and ocean acidification, on the growth of juvenile Pacific Cod in the Gulf of Alaska using a novel machine-learning framework called “stress-scapes,” which applies the fundamentals of dynamic seascape classification to both environmental and biological data. Stress-scapes apply a probabilistic self-organizing map (prSOM) machine learning algorithm and Hierarchical Agglomerative Clustering (HAC) analysis to produce distinct, dynamic patches of the ocean that share similar environmental variability and Pacific Cod growth characteristics, preserve the topology of the underlying data, and are robust to non-linear biological patterns. We then compare stress-scape output classes to Pacific Cod growth rates in the field using otolith increment analysis. Our work successfully resolved five dynamic stress-scapes in the coastal Gulf of Alaska ecosystem from 2010 to 2016. We utilized stress-scapes to compare conditions during the 2014–2016 marine heatwave to cooler years immediately prior and found that the stress-scapes captured distinct heatwave and non-heatwave classes, which highlighted high juvenile Pacific Cod growth and anomalous environmental conditions during heatwave conditions. Dominant stress-scapes underestimated juvenile Pacific Cod growth across all study years when compared to otolith-derived field growth rates, highlighting the potential for selective mortality or biological parameters currently missing in the stress-scape model as well as differences in potential growth predicted by the stress-scape and realized growth observed in the field. A sensitivity analysis of the stress-scape classification result shows that including growth rate data in stress-scape classification adjusts the training of the prSOM, enabling it to distinguish between regions where elevated sea surface temperature is negatively impacting growth rates. Classifications that rely solely on environmental data fail to distinguish these regions. With their incorporation of environmental and non-linear physiological variables across a wide spatio-temporal scale, stress-scapes show promise as an emerging methodology for evaluating the response of marine fisheries to changing ocean conditions in any dynamic marine system where sufficient data are available.

How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.

peer-reviewed Irish Journal of Agricultural and Food Research | Volume 58: Issue 1 Sensory and ATP derivative-based indicators for assessing the freshness of Atlantic salmon (Salmo salar) and cod (Gadus morhua) Colin Fogarty , Conor Smyth , Paul Whyte , Nigel Brunton and Declan Boltonemail DOI: https://doi.org/10.2478/ijafr-2019-0008 | Published online: 31 Oct 2019 PDF       Abstract Article PDF References Recommendations Abstract To estimate the shelf life of fresh fish, the processor must know the period of time between catch/harvest and arrival at the processing plant. This information is not always available, necessitating the provision of methods to estimate the time since catch or harvest. The objectives of this study were therefore to develop and/or validate sensory and ATP derivative-based methods for rapidly assessing the freshness of fish. A quality index method (QIM; raw fish) and a quantitative descriptive analysis (QDA; cooked fish) were developed and validated (against bacterial count [total viable count (TVC)] and time) for salmon (Salmo salar) and cod (Gadus morhua). The production of inosine monophosphate (IMP), inosine and hypoxanthine (Hx) and associated ratios (IMP/Hx, K1-value or H-value) were also investigated for use as freshness markers. There was a linear relationship between QIM and TVC (R2 = 0.93 for salmon and R2 = 0.89 for cod), QIM and time (R2 = 0.96 for salmon and R2 = 0.98 for cod), QDA and TVC (R2 = 0.93 for salmon and R2 = 0.77 for cod) and QDA and time (R2 = 0.94 for salmon and R2 = 0.87 for cod), suggesting that the QIM and QDA schemes developed could be used to monitor/assess freshness. The H-value also increased linearly with TVC (R2 = 0.88 for salmon and R2 = 0.89 for cod) and time (R2 = 0.93 for salmon and R2 = 0.84 for cod). It was therefore concluded that both the QIM/QDA approach and monitoring ATP degradation, specifically expressed as the H-value, could be used as rapid methods to assess the freshness of salmon and cod arriving at the processing plant

Eomesodermin (Eomes) is a member of T-box transcription factor family and plays an important role in the regulation of a wide variety of developmental processes and immune response in animals. Here we report cloning and characterization of the full-length cDNA of Atlantic cod Eomes (GmEomes), which possesses a TBOX_3 domain similar to its counterpart in mammals. The regulated expression was observed in head kidney and spleen in response to live Vibrio anguillarum infection in vivo, and spleen leukocytes in vitro after PMA and poly I:C stimulation. Furthermore, we determined a 694 bp sequence, upstream of the transcriptional start site (TSS), to contain a number of sequence motifs that matched known transcription factor-binding sites. Activities of the presumptive regulatory gene were assessed by transfecting different 5′-deletion constructs in CHSE-214 cells. The results showed that the basal promoters and positive transcriptional regulator activities of GmEomes were dependent by sequences located from −694 to −376 bp upstream of TSS. Furthermore, we found that some Eomes binding sites were present in the 5′-flanking regions of the cod IFNγ gene predicted by bioinformatics. However, Co-transfection of eomesodermin overexpression plasmids with INFγ reporter vector into CHSE-214 cells determined that Atlantic cod eomesodermin played a minor role in activation of the INFγ promoter.

Portable clinical analysers are gradually being involved in on-site assessment of haematic parameters in fish. The purpose of this study was to evaluate the i-STAT portable clinical analyser (i-STAT PCA) for accuracy and reliability of measuring blood pH, partial pressure of oxygen (pO2), haematocrit, haemoglobin, sodium, potassium and calcium in Atlantic cod (Gadus morhua). Haematological parameters detected with the i-STAT PCA were compared with conventional laboratory techniques (CLTs). Two types of disposable cartridges were used (CHEM8+ and CG4+) with the i-STAT PCA, and experiments were performed at two different temperature regimes (5 °C and 15 °C) and four different carbon dioxide (CO2) levels (0%, 0.1%, 0.5% and 1%). All blood parameters measured with the i-STAT PCA showed heterogeneous inaccuracy under the tested conditions, but the highest discrepancies were registered in blood pO2. The i-STAT PCA systematically overestimated the pO2 measurements. Our research suggests that i-STAT PCA is not an appropriate tool for pO2 measurements especially in coldwater fish species. The i-STAT PCA consistently underestimated the pH and haematocrit values especially at a lower temperature, although those parameters indicate significant high correlation at 15 °C. Furthermore, the analysed ions showed overestimation of sodium and underestimation of potassium and calcium.

How predators select their prey largely defines ecosystem trophic structure, function and dynamics. In aquatic systems, organism body size is an important trait explaining predator− prey interactions. Here, we used a unique Atlantic cod Gadus morhua stomach content dataset with diet information from over 100 000 individuals collected from the Baltic Sea in 1963−2014, to explore prey size distribution and predator−prey mass ratios in the diet of Eastern Baltic cod. Maximum and average prey sizes increased with predator size, as for cod in other systems. However, the prey size spectra found in Eastern Baltic cod stomachs reflect the low species diversity in the Baltic Sea. In general, Eastern Baltic cod feed on smaller prey in relation to their body size than other cod populations. Due to the truncated prey size distribution in the Baltic Sea, cod cannibalism functions as a compensatory mechanism that allows Baltic cod to reach their prey size potential. On the other hand, small- and intermediate-sized cod prey mainly on a few invertebrate prey species, potentially making them vulnerable to changes in these prey populations. Our results encourage further studies disentangling the relative effects of prey preference and prey availability on cod trophodynamics in species-poor systems such as the Baltic Sea.

Polar cod (Boreogadus saida) is the most abundant and ubiquitous fish species throughout the Arctic Ocean. As such, they serve an important ecosystem role linking upper and lower trophic levels and transferring energy between the benthic and pelagic realms. Our objective is to explore what limits the southern distribution of polar cod in Pacific and Atlantic sectors by examining time series of survey and oceanographic data. We quantify the variability in the southern extent of the polar cod distribution in the Bering and Labrador Seas, and determine mechanisms (bottom temperature and potential predators: Pacific cod Gadus macrocephalus, Atlantic cod Gadus morhua, and Greenland halibut Reinhardtius hippoglossoides and competitors: capelin Mallotus villosus and walleye pollock Gadus chalcogrammus) driving the variability. When temperatures were lower, polar cod occupied larger areas and had higher abundances in both regions, suggesting that as temperatures increase with climate warming the range of polar cod is likely to contract. Temperature had a much larger impact on polar cod abundance than competitor abundance and predator abundance, especially in the eastern Bering Sea. However, when we included data from northern and eastern Bering Sea in 2010 and 2017, polar cod were less likely to occur in warmer waters when either Pacific cod or walleye pollock were present. Northward range expansions of subarctic Pacific cod and walleye pollock may further restrict polar cod distributions.

Atlantic cod (Gadus morhua) represents a unique immune system among teleost fish, making it a species of interest for immunological studies, and especially for investigating the evolutionary history of immune gene families. The interferon regulatory factor (IRF) gene family encodes transcription factors which function in the interferon pathway, but also in areas including leukocyte differentiation, cell growth, autoimmunity, and development. We previously characterized several IRF family members in Atlantic cod (Irf4a, Irf4b, Irf7, Irf8, and two Irf10 splice variants) at the cDNA and putative amino acid levels, and in the current study we took advantage of the new and improved Atlantic cod genome assembly in combination with rapid amplification of cDNA ends (RACE) to characterize the remaining family members (i.e. Irf3, Irf5, Irf6, Irf9, and two Irf2 splice variants). Real-time quantitative PCR (QPCR) was used to investigate constitutive expression of all IRF transcripts during embryonic development, suggesting several putative maternal transcripts, and potential stage-specific roles. QPCR studies also showed 11 of 13 transcripts were responsive to stimulation with poly(I:C), while 6 of 13 transcripts were responsive to lipopolysaccharide (LPS) in Atlantic cod head kidney macrophages, indicating roles for cod IRF family members in both antiviral and antibacterial responses. This study is the first to investigate expression of the complete IRF family in Atlantic cod, and suggests potential novel roles for several of these transcription factors within immunity as well as in early development of this species.

This study supports the hypothesis that well-fed cod (Gadus morhua) seek higher temperatures to increase growth rate, and poorly fed cod select lower temperatures to save metabolic energy. Depth and temperature of free-ranging adult cod (44–79 cm) were studied with data storage tags as part of a ranching project in an Icelandic fjord. Forage fish were regularly provided at four feeding stations where cod formed distinct “herds” (herd cod) that did not mingle much with the rest of the unconditioned cod in the fjord (wild cod). Several parameters (stomach fullness, liver index (fat reserves), condition factor, and growth rate) indicated that food intake was much greater in herd cod than in wild cod. In August, when the thermocline was well established, the herd cod remained in shallow (15–35 m) and warm water (8–10 °C), whereas the wild cod stayed in deep (80–90 m) and cold water (3–4 °C), but occasionally both groups explored depths and temperatures outside their preferred range. After vertical mixing in autumn when thermoregulation was not possible, the depth difference between the two groups decreased significantly.

Cod (Gadus morhua), an important fish species in the Baltic Sea, is the paratenic host for many parasite species, including the zoonotic nematodes, Anisakis sp. and Contracaecum osculatum. We aimed to identify which invertebrate species (found in situ in the fish stomach) are responsible for infection of cod with zoonotic nematodes. We found that Crangon crangon and Gammarus sp., both invertebrate prey species of cod, were infected with Anisakis simplex and C. osculatum, respectively. These host–parasite systems are reported here for the first time, implicating C. crangon and Gammarus sp. as sources of infection of Baltic cod with zoonotic nematodes.

To counteract water losses from processing fish and fish products, many water-binding food additives such as condensed phosphates, citrate, citric acid or carbonates may be used, which results in an increased weight of the products. 240 fillets of cod (Gadus morhua) were treated with water-binding food additive solutions in different treatment periods and temperatures. Tested parameters were the sensory aspects and texture, water content, protein, fat, salt, phosphate, carbonate, citrate, and pH. This study provides authentic and systematically determined information about the effects of water-binding food additives on the properties of cod fillets. The treatment with hydrogencarbonate or with triphosphate increased the water content up to 87.5% and 87.0%, respectively. Except for citric acid, where the least effect on the water content was observed, the treatment temperature at 25 °C achieved a greater uptake of water than at 0 °C. The determination of pH showed a shift to the alkaline side of up to 8.4 when hydrogencarbonate was used. The treatment with citric acid resulted in an acidic pH value of 4. Additionally, this study provides reference data of the mentioned parameters of untreated fillets originating from whole, uneviscerated cod. The results provide a potential tolerance limit for the water to protein ratio for untreated cod fillets of 4.7. In summary, the results facilitate the assessment of added water in fishery products to protect the consumer from food fraud.

Background Archival tags have been used on fish for a number of years to measure temperature, pressure and salinity, among other parameters. Measurements of heart rate in fish can be used in a wide variety of biological and ecological studies, e.g., for evaluating short- and long-term effects of stressful conditions involved with fishing and farming practices, or events that are non-related to human activity, such as predator–prey interactions. Furthermore, if a relationship between temperature, heart rate and metabolic rate has been established there are potentials to establish long-term bioenergy models that include seasonal effects on feeding, locomotion, spawning and migration. However, heart-rate measurements in fish have been difficult to conduct in the wild due to lack of commercial availability, large size of the recording systems, difficulties with proper placement of external electrodes and restriction in setup with external systems. This work presents a validation of a commercial ECG (Electrocardiogram)-derived heart rate data logger on farmed Atlantic cod. This validation focuses on assessing the logger’s signal processing algorithm and recording quality. Results The eight fish studied showed both individual periodical variation, as well as individual baseline variation of the heart rate during the experimental period. Mean heart rate ranged from 29.9 ± 6.3 to 48.3 ± 4.9 bpm, at 10.2 ± 0.1 °C. This is comparable with previous research on Atlantic cod. The loggers were set up to record heart rate and temperature every 5 min and to store the ECG records used to calculate the heart rate every 30 min. The quality index (QI), which is an algorithmic assigned value of the quality of the ECG, was used to filter the data set eliminating a total of 21,643 measurements (19% of the recorded heart rate data). It was possible to manually calculate 18,490 out of 19,042 ECG records (97%). Conclusions This study presented a validation of using a commercial implantable data logging device in Atlantic cod that records ECG, and can calculate both heart rate, and a novel quality index for the ECG record with an on-board algorithm.

A suite of statistical catch-at-age models with time-varying natural mortality (M), selectivity and catchability were fitted to data for eastern Georges Bank Atlantic Cod (Gadus morhua) and Georges Bank Yellowtail Flounder (Limanda ferruginea) to address hypotheses regarding nonstationarities in these systems. Model averaging and ensemble methods were used to combine the results of converged models for each species. Model averaging was based on both predictive (i.e., cross-validation, AIC) and retrospective performance metrics. Models allowing large shifts in M provided the best fit to observed data for both species and were also regarded as the most plausible. For Atlantic Cod, variance in biomass estimates among the individual models was very high and multimodel estimates were sensitive to the relative weight given to competing models. In contrast, converged Yellowtail Flounder models produced broadly similar output and multimodel estimates were more robust to model weights. Our results suggest that the plausibility of competing models should be scrutinized, particularly when structural uncertainty is high.

Following stock collapse and over twenty years of moratoria, the state of Canada’s Northern Atlantic cod (Gadus morhua) remains precarious. To test if recent stock growth was of endogenous or exogenous origin, we performed a whole genome scan (ddRAD) on 135 adults captured in 2015 at three offshore spawning locations spanning the range of the offshore stock along the northeastern Newfoundland and Labrador shelf (Hawke Channel, Notre Dame Channel and Bonavista Corridor), with an additional 105 adults from three more southern locations (St. Anns Bank, Browns Bank and Bay of Fundy). Population structure analysis using 5,077 single nucleotide polymorphisms (SNPs) detected a distinct genetic break off the coast of Nova Scotia near 45 °N. Gene flow between groups north and south of this divide appears to be limited despite the presence of several northern-type and admixed individuals present in the southern area. North of the genetic divide, allele frequencies of neutral loci were indicative of a panmictic population. Several outlier SNPs were found to be associated with ecologically relevant physical characteristics (visual pigments, fin development, response to hypoxia, and various metabolic processes), which may be indicative of different ecological niches.

Napping combined with ultra-flash profile (UFP) is a rapid descriptive sensory method which allows discriminating between the samples. Several researches have used napping-UFP as an alternative to other conventional techniques due to the reduction in cost and time. The objective of this work was to study the applicability of napping-UFP to evaluate the influence of cooking methods and conditions on sensory characteristics of pork loin and cod (Gadus morhua). Moreover, quantitative descriptive analysis (QDA) was carried out, and comparison between these techniques was presented and discussed. Pork loin samples were oven-cooked at 150 and 180 °C for 45, 60 and 75 min; and confited during 120, 180 and 240 min. Cod samples were oven-cooked at 150 and 180 °C during 10, 15 and 20 min and boiled for 5, 10 and 15 min. Compared to QDA, napping-UFP provided additional information related to the acceptability of samples since participants spontaneously described the similarities and dissimilarities between cod and pork samples. Comparison of napping and QDA revealed that both techniques allowed obtaining a good discrimination among tested samples particularly in relation to the temperature effect, resulting in acceptable Escoufier’s coefficient values between both techniques.

We present the results of a study of the connectivity between Pacific cod spawning and nursery areas, and settlement of Pacific cod in the Gulf of Alaska. This work was conducted to address the hypothesis that spatial and temporal patterns of recruitment are related to variability in connectivity between spawning and nursery areas. To examine this hypothesis, we developed a Lagrangian, biophysical, individual-based model of Pacific cod early life history and dispersal using the Dispersal Model for Early Life Stages (DisMELS) framework. This model is driven by currents and scalars such as temperature from a version of the Regional Oceanographic Model System (ROMS) developed for the Gulf of Alaska. Results of our study show connectivity patterns predicted by the model that agree with our understanding (based on genetic analyses) that there is a high degree of localized retention in Pacific cod. The results indicate that the Shumagin Islands and Prince William Sound regions may serve as important collectors of Pacific cod recruits from upstream spawning areas. We also find correlations between individual-based model outputs and several large-scale climate indicators that appear to show settlement in several important nursery areas, and recruitment overall, are positively affected by slower gyre circulation in the Gulf of Alaska. We hypothesize that this is due to enhancement of retention, settlement in the Shumagin Island region, and reduction of transport of young cod out of the Gulf of Alaska to the southwest.

Given climate change projections, the limited ability of fish reared in sea-cages to behaviourally thermoregulate, and that thermal tolerance may be heritable, studies that examine family-related differences in upper thermal tolerance are quite relevant to the aquaculture industry. Thus, we investigated the upper thermal tolerance of 15 Atlantic cod (Gadus morhua L.) families by challenging them with acute (2 °C h-1) and incremental (1 °C every 4 days) temperature increases (CTmax and ITmax tests, respectively) under normoxia (~ 100% air saturation) and mild hypoxia (~ 75% air sat.). The cod's CTmax was 22.5 ± 0.1 °C (mean ± S.E.) during normoxia and 21.8 ± 0.1 °C during hypoxia (P < 0.001); and these two CTmax values were significantly correlated across families. In both the normoxic and hypoxic ITmax tests, feed intake fell by ~50% between 17 and 18 °C, and stopped entirely by 21 °C. No mortalities were observed under 20 °C in the normoxic and hypoxic ITmax tests, and the ITmax value was ~21.7 °C in both groups. Differences in the upper thermal tolerance between families were only observed in the CTmax experiment. No correlation was found between the specific growth rate and the CTmax of the families. Further, no correlation existed between CTmax and ITmax. This study is the first to compare the thermal tolerance of fish families to both CTmax and ITmax challenges, and the data: 1) suggest that the Atlantic cod is quite tolerant of acute (i.e., hours) or short-term (i.e., weeks) exposure to high water temperatures (i.e., up to 20 °C); 2) indicate that it might be difficult to select fish with higher ITmax values; and 3) question the relevance of CTmax for selecting fish that are destined for sea-cages where temperatures slowly warm over the summer.

The Gulf of Alaska Integrated Ecosystem Research Program is a multi-disciplinary study examining interactions between physical and biological oceanography to understand how the environment influences the survival and recruitment of early life stages of select commercially and ecologically important groundfish species. Biological and oceanographic surveys in the eastern and western Gulf of Alaska were conducted during spring and summer of 2011 and 2013; we present a synthesis of ichthyoplankton data. The results describe seasonal (spring vs. summer), regional (eastern vs. western Gulf of Alaska), and interannual (2011 vs. 2013) variation in distribution, abundance, and larval sizes of the focal species. In spring, Pacific Cod (Gadus macrocephalus) larvae were more abundant in 2013 than 2011 and occurred primarily in the western Gulf of Alaska near Kodiak Island, over the shelf, and over the continental slope. Walleye Pollock (Gadus chalcogrammus) larvae were also more abundant in the western Gulf of Alaska, with substantially higher abundance in 2013. Larval rockfish (predominantly Pacific Ocean Perch; Sebastes alutus) were collected in deep water or were associated with the slope, troughs and canyons intersecting the slope, and the outer shelf. Rockfish larvae were collected throughout the study region in spring, with no significant differences in abundance between regions or years. In summer, rockfish (predominantly species other than Pacific Ocean Perch) were more widely distributed over the shelf and were more abundant in the eastern Gulf of Alaska both within and across years, indicating species-specific spawning events. Sablefish (Anoplopoma fimbria) larvae, however, were more abundant in the eastern Gulf of Alaska and in 2011 and were predominantly collected near areas of deep water such as Yakutat Canyon. In 2011, Arrowtooth Flounder (Atheresthes stomias) abundances of larvae were higher in the western Gulf of Alaska, whereas in 2013 abundances were higher in the eastern Gulf of Alaska. Arrowtooth Flounder larvae were collected primarily along the slope and near canyons and troughs. The results from individual years presented here can be used in individual-based model validation of connectivity matrices, delineating transport patterns to suitable nursery habitat, and evaluating recruitment bottlenecks for these focal species in the Gulf of Alaska. Future research will examine patterns of community structure and assemblage diversity using the comprehensive ichthyoplankton dataset. The observed ecological patterns provide insight into how environmental forcing may influence early life history aspects of recruitment.

Management strategy evaluation (MSE) is an effective tool to evaluate the performance of harvest control rules (HCRs) and alternative management strategies. However, a comprehensive MSE framework advising management is still absent for the severely depleted Gulf of Maine (GoM) cod (Gadus morhua). In the present study, we developed a conceptual MSE framework and conditioned on this stock utilizing stock-specific parameterization. We highlighted the simulation of a few key processes with semi-independent sub-models and accounted for uncertainties from multiple sources. The simulated population dynamics was calibrated and validated against the historical trend in hindcasting. Forecasting simulations were also conducted and validated to examine the effectiveness in the context of uncertainty. Hindcasting results suggested that the calibrated MSE framework could capture the stock dynamics assuming different recruitment dynamics indicated by residuals lower than 5%. Forecasting stochastic runs demonstrated a minor disparity between management effects of fishing-mortality-based and catch-based HCRs when the segregated stock recruitment relationship was adopted with a difference in simulated spawning stock biomass lower than 10%. Additionally, the results were comparable to assessment and projections made in the stock assessment, indicating the robustness of the framework. The framework can potentially help disentangle complex issues related to the mixed fishery, decision-making, and performance evaluation of a monitoring system.

Six groups have been identified in the species' population structure based on the analysis of microsatellite markers' polymorphism in Pacific cod Gadus macrocephalus samples within the entire western part of the North Pacific, including waters of the Pacific coast of Canada. The first group includes cod from waters of the Yellow Sea; the second group consists of cod from the Sea of Japan (eastern coast of Korea and Peter the Great Bay); the third group combines cod from Tatar Strait and the South Kuril Islands (both Sea of Okhotsk and Pacific Ocean sides); the fourth group is formed by cod from the northwestern Sea of Okhotsk and Taui Bay; the fifth-largest group includes cod from waters off western Kamchatka, the North Kuril Islands (Sea of Okhotsk and Pacific Ocean sides), Karaginsky Bay, Navarinsky area in the Bering Sea, and Anadyr Bay; the sixth group is formed by cod from coastal waters of Canada.

A comparative analysis of the variability of morphobiological and genetic characteristics in samples from the largest stocks of Atlantic cod in waters of the Northeast and Northwest Atlantic was conducted. Using the results of pairwise assessment of genetic differentiation for the studied microsatellite loci, it was established that the dataset from waters of the New England shelf differed significantly from Iceland–Greenland and Lofoten–Barents Sea cod stocks. It was noted that samples of cod from the waters of East and West Greenland and cod from the waters of the Norwegian and Barents seas, despite significant geographical separation, showed a high level of identity. Special features of application of the model for isolation by distance to studying the formation mechanisms of the population structure were reviewed.

Shallow coastal waters of the Gulf of Alaska (GOA) serve as nursery habitats for young-of-year Pacific cod ( Gadus macrocephalus ). However, little is known regarding the relative contribution of these areas to the adult offshore stock. Trace elements incorporated into the otolith matrix can reflect the environmental conditions to which a fish has been exposed during its lifetime. When analyzed together, a suite of elements can serve as a natural marker, characteristic of a particular environment. We evaluated the potential of otolith elemental signatures to identify nursery habitats of age-0 Pacific cod, focusing on spatial patterns within and across the eastern and western GOA. Fish were collected from shallow nearshore areas within five large embayments in summer and fall, and element:calcium ratios were measured from two different time stanzas within the otolith. Elemental ratios were found to change over short (2 month) time periods and were related to seasonal changes in temperature and salinity. Fish were classified to nursery habitats using quadratic discriminant analysis based on their otolith elemental signatures; classification accuracy to individual bays ranged from 30% to 95%, with an overall success rate of 59%. Classification accuracy improved to 78% at greater spatial scales (eastern versus western GOA). Our results point out the limitations of this application to Gulf of Alaska Pacific cod and other widely distributed species residing in coastal embayments. While some nursery habitats impart unique chemical signatures to otoliths, it may not be possible to distinguish among specific areas without considering additional factors. However, our work demonstrates that otolith microchemistry may be a useful tool for understanding source contributions to the Pacific cod population at larger regional scales within the GOA.

Identifying and quantifying the major ecosystem processes that regulate recruitment strength of commercially and ecologically important fish species is a central goal of fisheries management research. In the Gulf of Alaska (GOA) five groundfish species are of particular interest: sablefish (Anoplopoma fimbria), Pacific cod (Gadus macrocephalus), walleye pollock (Gadus chalcogrammus), arrowtooth flounder (Atheresthes stomias), and Pacific ocean perch (Sebastes alutus). Habitat suitability models (HSM) were developed for the demersal early juvenile stage to inform survival to recruitment for these species, using catch data and seafloor habitat metrics with presence-only models. Regional-scale maps were produced that predict the probability of suitable habitat available in the GOA from settlement through residency in nursery areas. For example, the HSM for sablefish (150–399 mm) described suitable habitat as bathymetrically low-lying areas with low rocky structure within 25–300 m depth. In contrast, the HSM for Pacific ocean perch (50–200 mm) described suitable habitat as bathymetry rises with rocky structure present on north-south facing slopes within 85–270 m depth. These habitat covariates are useful to refine population estimates for North Pacific groundfish species and to inform life stage-specific definitions of Essential Fish Habitat. This application of MaxEnt models should be applicable for species with low occurrence of spatial data in other marine ecosystems globally.

This study assesses spatiotemporal and sex-specific growth of Atlantic cod Gadus morhua in Icelandic waters. We use a Bayesian approach which lends itself to fitting and comparing nested models such as these. We then compare fitted parameters of these models to potential explanatory variables using a redundancy analysis (RDA) to look for drivers of growth in G. morhua. Results indicate that models that incorporate differences in growth among time, space and sex are the best-fitting models according to deviance information criterion (DIC). Results from RDA indicate that capelin Mallotus villosus recruitment and biomass is highly correlated with deviations in the von Bertalannfy growth parameter k and that L∞ is correlated with G. morhua landings in the model that uses year to account for time-varying growth and estimated G. morhua recruitment in the model that uses cohort to account for time-varying growth.

In Norway, mine tailings waste can be deposited by coastal submarine dispersal. Mine tailings slurry includes fine particles, Exposure to mine tailings particles increases mortality in Atlantic cod larvae and results in increased expression of genes involved in epigenetic regulation.

Infectious diseases are one of the main factors having a negative influence on the Atlantic cod aquaculture. Fish epidermis is a barrier which provides primary interaction between the host and pathogenic organisms. The study of the epidermis of the Atlantic cod Gadus morhua L. has been carried out on the experimental base of the Nord University of Bodo (Norway). Ultrathin sectioning of cod epidermis has been carried out with the help of the Department of Electronic Microscopy of the University of Tromso (Norway). Embryos, pre-larvae from the moment of hatching and larvae up to 3 weeks after hatching, as well as juvenile cod at the age of 5 months, 1 year and 1.5 years have been selected for light-optical and electronic microscope examination. The material for optical studies is fixed with 10 % neutral formalin. The fixation of the material for electronic microscope studies has been made with 25 % glutaraldehyde (sodium cacodylate, pH 7.2). Saccular cells have been found in the cod epidermis of all investigated age groups. The cells have a round or predominantly oval shape and also vacuoles. Vacuoles are filled with an electron-transparent material, but most cells do not have secretory content. It has been found out that secretory material in most cases was absent in the vacuoles of opened cells, where vesicles and tubules, however, remained. During the research, morphological and functional features of these cells are first identified on the basis of studying their distribution, quantity and chemical composition depending on the age of the fish. New data on the spatial distribution of Atlantic cod saccular cells at different stages of ontogenesis have been presented. The results indicate the secretory, bactericidal and protective functions of the saccular cells in the epidermis of Atlantic cod and reflect the ecological features of cod as an epibenthic-pelagic species.

The consumption of raw or inadequately cooked marine fish can lead to several disorders caused by the ingestion of viable anisakid nematodes. Although anisakid larvae can be killed by subzero temperatures, making freezing an important control measure for this potential health hazard, these parasites can survive freezing under some conditions. Therefore, the aim of the present study was to experimentally evaluate the time-temperature conditions needed to kill Anisakis simplex and Pseudoterranova spp. The effectiveness of freezing was tested on two species of fish: cod, Gadus morhua from the North Atlantic, and herring, Clupea harengus membras from the southern Baltic Sea. Samples, which comprised skinless fillets of cod (n = 40) with visible parasites and whole herring (n = 240), were separately frozen at − 15, − 18, or − 20 °C for 24 h, or at − 20 °C for 48 h in the single-compressor freezer and at − 20, − 25, or − 35 °C for 24 h in the double-compressor freezer. After thawing, parasites were stained with malachite green and examined under the microscope for viability. All A. simplex and Pseudoterranova spp. larvae in cod fillets died at a temperature of − 15 °C or lower. However, freezing did not kill all the A. simplex larvae in whole herring: spontaneous movement of these parasites was observed in samples stored in the single-compressor freezer at − 15, − 18, and − 20 °C over 24 h. Our results demonstrate that the freezing procedure must consider both the capability of the freezing device and the nature of the fish product to ensure consumer safety.

Prey modify their behaviour to avoid predation, but dilemmas arise when predators vary in hunting style. Behaviours that successfully evade one predator sometimes facilitate exposure to another predator, forcing the prey to choose the lesser of two evils. In such cases, we need to quantify behavioural strategies in a mix of predators. We model optimal behaviour of Atlantic cod Gadus morhua larvae in a water column, and find the minimal vulnerability from three common predator groups with different hunting modes; 1) ambush predators that sit‐and‐wait for approaching fish larvae; 2) cruising invertebrates that eat larvae in their path; and 3) fish which are visually hunting predators. We use a state‐dependent model to find optimal behaviours (vertical position and swimming speed over a diel light cycle) under any given exposure to the three distinct modes of predation. We then vary abundance of each predator and quantify direct and indirect effects of predation. The nature and strength of direct and indirect effects varied with predator type and abundance. Larvae escaped about half the mortality from fish by swimming deeper to avoid light, but their activity level and cumulative predation from ambush predators increased. When ambush invertebrates dominated, it was optimal to be less active but in more lit habitats, and predation from fish increased. Against cruising predators, there was no remedy. In all cases, the shift in behaviour allowed growth to remain almost the same, while total predation were cut by one third. In early life stages with high and size‐dependent mortality rates, growth rate can be a poor measure of the importance of behavioural strategies. publishedVersion

We performed a population genetic analysis of 22 Pacific cod sample sets (n = 986) based on the mtDNA control region (599 bp) polymorphism, which made it possible to specify four distinguished groups of this species: (1) within the seaward parts of the Bering Sea and Sea of Okhotsk and northern part of the Pacific Ocean, affected by the Pacific Ocean gyres; (2) coastal areas of the East/Japan Sea; (3) northern part of the Sea of Okhotsk, more similar to the second group from the East/Japan Sea by haplotype sets than to the seaward groups, despite limited reproductive contacts, special hydrological conditions, and the history of formation of the sea areas; (4) fundamentally different Pacific cod from the Yellow Sea adapted to the conditions of the shallow water area in the subtropical region.

Liver samples of two gadoid species, Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus), sampled in the southern Barents Sea in the period 1992–2015, were studied for the levels of six types of persistent organic pollutants (POPs): polychlorinated biphenyls (PCBs), chlorinated organic pesticides (DDTs, hexachlorocyclohexanes (HCHs), hexachlorobenzene (HCB), trans-nonachlor (TNC)), and polybrominated diphenyl ethers (PBDEs). Higher average levels were found in cod than in haddock. Sampling approximately every third year allowed studies of temporal trends for all the compound groups except PBDEs. Time series are reported for 1992–2015 for Atlantic cod and for 1998–2015 for haddock. Decreasing temporal trends have been modeled in cod for the analyzed POPs for this time period. The decrease seems to be slowing down in the later years. HCB levels showed least decrease with time among all the contaminants, with the poorest fit to the proposed model. Similar time trends were found in haddock, but the decrease is less apparent due to shorter time series. The observed time trends of legacy POPs document the effectiveness of efforts during the 1990s to reduce the levels of these contaminants in the marine environment but question the possibility to eliminate them altogether from the marine environment in the foreseeable future.

High-latitude seas, which support a number of commercially important fisheries, are predicted to be most immediately impacted by ongoing ocean acidification (OA). Elevated CO2 levels have been shown to induce a range of impacts on the physiology and behavior of marine fish larvae. However, these responses have yet to be characterized for most fishery species, including Pacific cod (Gadus macrocephalus). Based on laboratory experiments, we present a multi-faceted analysis of the sensitivity of Pacific cod larvae to elevated CO2. Fish behavior in a horizontal light gradient was used to evaluate the sensitivity of behavioral phototaxis in 4–5 week old cod larvae. Fish at elevated CO2 levels (∼1500 and 2250 μatm) exhibited a stronger phototaxis (moved more quickly to regions of higher light levels) than fish at ambient CO2 levels (∼600 μatm). In an independent experiment, we examined the effects of elevated CO2 levels on growth of larval Pacific cod over the first 5 weeks of life under two different feeding treatments. Fish exposed to elevated CO2 levels (∼1700 μatm) were smaller and had lower lipid levels at 2 weeks of age than fish at low (ambient) CO2 levels (∼500 μatm). However, by 5 weeks of age, this effect had reversed: fish reared at elevated CO2 levels were slightly (but not significantly) larger and had higher total lipid levels and storage lipids than fish reared at low CO2. Fatty acid composition differed significantly between fish reared at high and low CO2 levels (p

Factors that influence the survival rate of northeastern Arctic haddock Melanogrammus aeglefinus at different stages of the formation of the year-class abundance are considered. It is shown that the patterns of the formation of the year-class abundance of haddock have changed due to warming in the Barents Sea. Since the late 1990s, an enhancement of the relationship is recorded between the year-class numbers at the 0-group stage and at age 3 years. The mortality of this fry during the first two wintering periods has lost its dominant value for the emergence of strong year-classes. Under these conditions, the predation role of cod Gadus morhua as a regulator of the abundance of haddock demersal juveniles increased. This is due to the fact that the increase in water temperature in the Barents Sea provides favorable conditions for the abundance growth not only for haddock but also for its main predator, i.e., cod.

Despite the possible increase in use of anionic polyacrylamide (APAM) in enhanced oil recovery operations, very little relevant information regarding ecotoxicity exists. The current study assessed acute and sub-lethal toxicity in sensitive early life stages (ELS) of Atlantic cod (Gadus morhua) exposed to 200 kDa APAM under controlled laboratory conditions. Two experiments (screening and long-term study) were conducted covering ecologically relevant endpoints (survival, hatching, growth, deformations, respiration and heart rate) in fish developing through embryogenesis, hatching, yolk-sac larvae stage and the first feeding period. The screening experiment was an 8-day exposure of embryos, whereas in the long-term experiments embryos and developing larvae were exposed continuously for 23 days. In the screening experiment, a significant reduction in embryonic heart rate was observed during exposure to 150 and 1500 mg APAM/L. However, we observed no effects on fitness-related endpoints (survival, hatching and growth) at concentrations up to 1500 mg L−1 APAM. Also, for the long-term exposure from late embryo to first feeding larvae stage, we observed reduced heart rate at 125 mg L−1. No consistent responses on survival, growth or respiration were observed except for the highest concentration tested (6000 mg L−1). Dispersion modelling based on expected and relevant discharged polymer concentrations and durations showed that predicted environmental concentrations were orders of magnitude lower than the concentrations tested in our experiments, indicating that 200 kDa APAM will have a limited probability of causing fitness-related effects on Atlantic cod ELS.

This study investigated the amino acid composition and in vitro antioxidant, antihypertensive, and anti-inflammatory activities of protein from steamed, baked, and high hydrostatic pressure (HHP) treated cod (Gadus morhua). Steaming and baking decreased the estimated protein efficiency ratio and total amino acid content (p

This paper presents a comparative analysis of the variability of genetic characteristics in samples from the largest stocks of the Atlantic cod Gadus morhua Linnaeus, 1758 in the Northeast Atlantic (NEA) and the Northwest Atlantic (NWA) waters. The results of a pairwise estimation of the genetic differentiation, performed using allozyme and microsatellite markers, detected a significant difference between the cod sample from the New England Shelf (NWA) and the cod of the Icelandic–Greenlandic and Norwegian–Barents Sea stocks. At the same time, cod samples from areas of East and West Greenland and samples from the Barents Sea, despite considerable geographic differences, demonstrated a high level of identity according to molecular genetic markers. The peculiarities of the formation of the cod population structure in the Quaternary period are considered in connection with the dynamics of global climatic and oceanological processes.

Most stocks of Atlantic cod (Gadus morhua) in the Northwest Atlantic collapsed in the early 1990s, with little sign of recovery since then. In the southern Gulf of St. Lawrence (sGSL), the failed recovery is due to severe increases in the natural mortality of adult Atlantic cod. We examined the role of predation by grey seals (Halichoerus grypus) in this failed recovery by directly incorporating grey seal predation in the population model for Atlantic cod via a functional response. Estimated predation mortality of adult Atlantic cod increased sharply during the cod collapse and has continued to increase, comprising the majority of mortality since the late 1990s. While predation by grey seals appeared to play a minor role in the collapse of Atlantic cod, we found it to be the main factor preventing recovery. Our results are consistent with the hypothesis that failed recovery is due to predation-driven Allee effects, a demographic effect due to the decline in cod abundance and an emergent effect resulting from increasing grey seal abundance. Under current conditions, extirpation of sGSL Atlantic cod appears likely unless there is a large decline in the abundance of grey seals.

Demersal and benthivorous fish depend on prey availability in benthic habitats for their diet. Prey availability may in turn be affected by bottom trawling. Our study attempted to link the prey consumed by fish directly to those available in the benthic environment. We test the hypothesis that bottom trawling significantly affected the trait composition of fish diets with a strong link to benthic habitats. Stomach content data were analysed for seven demersal and benthivorous fish species in the southern and central North Sea and were related to habitat fauna collected by grab and epi-benthic trawl data across the same spatial extent. Biological trait analysis was used to avoid taxonomic bias in large-scale comparisons across habitats and to quantify the effect of bottom trawling, which tends to shift prey diversity in favour of small, opportunistic and short-lived species and traits. The diets of two demersal omnivores (whiting, Merlangius merlangus and Atlantic cod, Gadus morhua) and two opportunistic benthivores (haddock, Melanogrammus aeglefinus and long-rough dab, Hippoglossoides platessoides) did not appear to reflect either infaunal or epifaunal traits that were abundant in the benthic environment. The diets of European plaice (Pleuronectes platessa) and Dover sole (Solea solea), however, showed strong links with infaunal prey trait composition in shallow sand to muddy sand habitats located in the eastern North Sea and the Dogger Bank. Such strong links were also observed for the diets of Common dab (Limanda limanda) and plaice in similar habitats in deeper waters. Plaice targeted small to medium sized infaunal burrowers and deeper dwelling infaunal species. Its diet was significantly affected by bottom trawling, which caused a reduction in prey biomass in their stomachs rather than a shift in trait composition. Our study showed that the diets of benthivorous fish across large spatial scales are strongly linked with the prey trait availability in their benthic habitats and that bottom trawling significantly affected the diet of plaice, a species with strong habitat-diet associations.

Interleukin 1b (IL-1b) is a member of the cytokine family that serves as major mediators for early pro-inflammatory responses. During artificial breeding of Pacific cod ( Gadus macrocephalus ), outbreaks of NNV in the early development stages could lead to high mortality. Recent research reported that IL-1b participated in the host-virus interaction against NNV infection, however, no IL-1b gene has been identified from Pacific cod so far. In this study, we described the identification and characterization of a IL-1b from Pacific cod transcriptome at both transcript and protein level. Sequence alignment and phylogenetic analysis were conducted to determine and confirm their evolutionary relationship. Expression analysis revealed that IL-1b was expressed in all tested tissues and the western blot analysis confirmed the same expression profiles using purified recombinant IL-1b protein. In addition, significant up-regulation was detected in IL-1b transcripts during early development stages at 30dph and 50dph. After challenged with poly I:C, IL-1b was significantly induced after 24 h. Taken together, these results strongly suggested that IL-1b might play an essential role in innate defense mechanism of Pacific cod.