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Sensing limitations have impeded knowledge about how individual predator-prey interactions build to organized multi-species group behaviour across an ecosystem. Population densities of overlapping interacting oceanic fish predator and prey species, however, can be instantaneously distinguished and quantified from roughly the elemental individual to spatial scales spanning thousands of square kilometres by wide-area multispectral underwater-acoustic sensing, as shown here. This enables fundamental mechanisms behind large-scale ordered predator-prey interactions to be investigated. Critical population densities that transition random individual behaviour to ordered group behaviour are found to rapidly propagate to form vast adversarial prey and predator shoals of capelin and surrounding cod in the Barents Sea Arctic ecosystem for these keystone species. This leads to a sudden major shift in predator-prey balance. Only a small change in local behaviour triggers the shift due to an unstable equilibrium. Such unstable equilibria and associated balance shifts at predation hotspots are often overlooked as blind spots in present ocean ecosystem monitoring and assessment due to use of highly undersampled spatio-temporal sampling methods., (© 2024. The Author(s).)

Fish spawning location and behaviour can be challenging to detect, especially in deep water. Here we utilise two large acoustic telemetry datasets from western and mid Norway to study the vertical movement dimension of individual Atlantic cod Gadus morhua spawning behaviour in their natural habitats. The datasets comprise ~ 6 million depth detections from 644 sexed, mature cod, collected at seven different Norwegian coastal cod spawning grounds during 2017-2021. During the spawning period, females were typically found at shallower depths compared to males, while this pattern was much less pronounced or absent outside this period. Furthermore, we identify a hitherto undescribed sex-dependent vertical movement behaviour: periodic descents, where females made deep dives, putatively associated with egg release and spawning, approximately every third day. Females not showing this behaviour tended to occupy deeper positions in the water column than the "periodic descent" females and hence may approach and retreat from spawning males more horizontally. These observed sex-specific behaviours correspond well to the lek-like description of the cod mating system and with cod reproductive physiology, where females are known to mature and release batches of eggs at intervals of several days as part of a bet-hedging strategy., (© 2024. The Author(s).)

The artificial reefs in New York's waters provide structure in areas that are typically flat and sandy, creating habitat for a multitude of species as an area to spawn, forage, and reside. Passive acoustic data collected on the Fire Island and Shinnecock artificial reefs between 2018 and 2022 detected spawning-associated calls of weakfish (Cynoscion regalis) and Atlantic cod (Gadus morhua), as well as the presence of individual bottlenose dolphins (Tursiops truncatus) through their signature whistles. Weakfish and Atlantic cod were more vocally active on the Fire Island reef, where Atlantic cod grunts peaked during a new moon phase in December, and weakfish spawning experienced variable peaks between mid-July and mid-August on both reefs. Fifty-seven individual bottlenose dolphins were identified, with whistle repeats ranging from seconds to years apart. Passive acoustic monitoring allows for simultaneous collection of information on multiple species at different trophic levels as well as behavioral information that helps managers understand how these animals utilize these habitats, which can lead to improved conservation measures., (© 2024 Acoustical Society of America.)

Healthy ecosystems and species have some degree of resilience to changing conditions, however as the frequency and severity of environmental changes increase, resilience may be diminished or lost. In Sweden, one example of a species with reduced resilience is the Atlantic cod (Gadus morhua). This species has been subjected to overfishing, and with additional pressures such as habitat degradation and changing environmental conditions there has been little to no recovery, despite more than a decade of management actions. Given the historical ecological, economical, and cultural significance of cod, it is important to understand how Atlantic cod respond to global climate change to recover and sustainably manage this species in the future. A multi-stressor experiment was conducted to evaluate physiological responses of juvenile cod exposed to warming, ocean acidification, and freshening, changes expected to occur in their nursery habitat. The response to single drivers showed variable effects related to fish biometrics and increased levels of oxidative stress dependent parameters. Importantly, two separate responses were seen within a single treatment for the multi-stressor and freshening groups. These within-treatment differences were correlated to genotype, with the offshore ecotype having a heightened stress response compared to the coastal ecotype, which may be better adapted to tolerate future changes. These results demonstrate that, while Atlantic cod have some tolerance for future changes, ecotypes respond differently, and cumulative effects of multiple stressors may lead to deleterious effects for this important species., (© 2024. The Author(s).)

Increasing ocean temperature will speed up physiological rates of ectotherms. In fish, this is suggested to cause earlier spawning due to faster oocyte growth rates. Over time, this could cause spawning time to become decoupled from the timing of offspring food resources, a phenomenon referred to as trophic asynchrony. We used biological data, including body length, age, and gonad developmental stages collected from >125,000 individual Northeast Arctic cod (Gadus morhua) sampled between 59 and 73° N in 1980-2019. Combined with experimental data on oocyte growth rates, our analyses show that cod spawned progressively earlier by about a week per decade, partly due to ocean warming. It also appears that spawning time varied by more than 40 days, depending on year and spawning location. The significant plasticity in spawning time seems to be fine-tuned to the local phytoplankton spring bloom phenology. This ability to partly overcome thermal drivers and thus modulate spawning time could allow individuals to maximize fitness by closely tracking local environmental conditions important for offspring survival. Our finding highlights a new dimension for trophic match-mismatch and should be an important consideration in models used to predict phenology dynamics in a warmer climate., (© 2024 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

Marine vibrators are a new technology being developed for seismic surveys. These devices can transmit continuous instead of impulsive sound and operate over a narrower frequency band and at lower peak pressure than airguns, which is assumed to reduce their environmental impacts. We exposed spawning Atlantic cod (Gadus morhua) to sound produced by a prototype, but full-scale, marine vibrator, and monitored behavioural responses of tagged cod using acoustic telemetry. Fish were exposed to 10 × 3 h continuous sound treatments over a 4-day period using a randomised-block design. Sound exposure levels were comparable to airgun exposure experiments conducted previously with the same set-up ranging from ∼115 to 145 dB re 1 μPa 2 s during exposure. Telemetry data were used to assess 1) whether marine vibrator exposure displaced cod from the spawning ground, through estimation of residence and survival probabilities, and 2) fine-scale behavioural responses within the test site, namely swimming depth, activity levels, displacement, and home ranges. Forty-two spawning cod were tagged prior to the exposure, with 22 present during the exposure. All 22 tags were equipped with pressure sensors and ten of these additionally with accelerometers. While no premature departure from the spawning site was observed, cod reacted to the exposure by decreasing their activity levels (by up to 50%, SE = 7%) and increasing their swimming depth (by up to 2.5 m, SE = 1.0 m) within the test site during the exposure period. These behavioural responses varied by sex and time of day. Cod reactions to a marine vibrator may be more pronounced than reactions to airguns, possibly because continuous sound is more disturbing to fish than intermittent sound at the same exposure levels. However, given sample size limitations of the present study, further studies with continuous sound are necessary to fully understand its impact and biological significance., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Microplastics (MPs) have become a global issue as they are omnipresent in the ocean. Fish ingesting MPs through feed could be affected in their physiological function, e.g., disrupted enzyme production and function, reduction of feeding and reproductive failure. This study assessed the effects of feed containing naturally weathered MPs from the Oslofjord (Norway) on the reproductive physiology of Atlantic cod (Gadus morhua). Farmed cod broodstock were fed either control (C-diet) or feeds containing 1% microplastic (MP-diet) starting nine months prior to spawning, from June until May. No major differences were found between diet groups in overall biometrics or gonad histology. Sex steroid levels (testosterone, 11-ketotestosterone and 17β-estradiol) resulted in expected profiles increasing over time without any significant differences between treatments. Gene expression levels of the steroidogenic enzyme 20β-hydroxysteroid dehydrogenase (20β-hsd) and vitellogenin1 (vtg1) showed significant differences between dietary treatments with lower expression in the control group. This can be a direct effect of MPs, but endocrine disrupting effects of potentially leachable plastic additives cannot be completely ruled out. Thus, these enzymes could be indicators of exposure to contaminants that disrupt sexual maturation by affecting the production of primarily maturation-inducing steroid. Although the concentration of MPs employed in this study may not be high enough to elicit any observable short-term biological effects, the observed gene expression suggests that long-term consequences should be considered caused by an expected increase of MPs in marine environments., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Long-term changes in the age and size structure of animal populations are well documented, yet their impacts on population productivity are poorly understood. Fishery exploitation can be a major driver of changes in population age-size structure because fisheries significantly increase mortality and often selectively remove larger and older fish. Climate change is another potential driver of shifts in the demographic structure of fish populations. Northeast Arctic (NEA) cod is the largest population of Atlantic cod (Gadus morhua) and one of the world's most important commercial fish stocks. This population has experienced considerable changes in population age-size structure over the past century, largely in response to fishing. In this study, we investigate whether changes in spawner age structure have affected population productivity in NEA cod, measured as recruits per spawning stock biomass, over the past 75 years. We find evidence that shifts in age structure toward younger spawners negatively affect population productivity, implying higher recruitment success when the spawning stock is composed of older individuals. The positive effect of an older spawning stock is likely linked to maternal effects and higher reproductive output of larger females. Our results indicate a threefold difference in productivity between the youngest and oldest spawning stock that has been observed since the 1950s. Further, our results suggest a positive effect of environmental temperature and a negative effect of intraspecific cannibalism by older juveniles on population productivity, which partly masked the effect of spawner age structure unless accounted for in the model. Collectively, these findings emphasize the importance of population age structure for the productivity of fish populations and suggest that harvest-induced demographic changes can have negative feedbacks for fisheries that lead to a younger spawning stock. Incorporating demographic data into harvest strategies could thus facilitate sustainable fishery management., (© 2022 The Ecological Society of America.)

Sustainable human exploitation of living marine resources stems from a delicate balance between yield stability and population persistence to achieve socioeconomic and conservation goals. But our imperfect knowledge of how oceanic oscillations regulate temporal variation in an exploited species can obscure the risk of missing management targets. We illustrate how applying a management policy to suppress fluctuations in fishery yield in variable environments (prey density and regional climate) can present unintended outcomes in harvested predators and the sustainability of harvesting. Using Atlantic cod (Gadus morhua, an apex predatory fish) in the Barents Sea as a case study we simulate age-structured population and harvest dynamics through time-varying, density-dependent and density-independent processes with a stochastic, process-based model informed by 27-year monitoring data. In this model, capelin (Mallotus villosus, a pelagic forage fish), a primary prey of cod, fluctuations modulate the strength of density-dependent regulation primarily through cannibalistic pressure on juvenile cod survival; sea temperature fluctuations modulate thermal regulation of cod feeding, growth, maturation, and reproduction. We first explore how capelin and temperature fluctuations filtered through cod intrinsic dynamics modify catch stability and then evaluate how management to suppress short-term variability in catch targets alters overharvest risk. Analyses revealed that suppressing year-to-year catch variability impedes management responses to adjust fishing pressure, which becomes progressively out of sync with variations in cod abundance. This asynchrony becomes amplified in fluctuating environments, magnifying the amplitudes of both fishing pressure and cod abundance and then intensifying the density-dependent regulation of juvenile survival through cannibalism. Although these transient dynamics theoretically give higher average catches, emergent, quasicyclic behaviors of the population would increase long-term yield variability and elevate overharvest risk. Management strategies that overlook the interplay of extrinsic (fishing and environment) and intrinsic (life history and demography) fluctuations thus can inadvertently destabilize fish stocks, thereby jeopardizing the sustainability of harvesting. These policy implications underscore the value of ecosystem approaches to designing management measures to sustainably harvest ecologically connected resources while achieving socioeconomic security., (© 2021 The Authors. Ecological Applications published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

According to the theory of compensatory dynamics, depleted populations should recover when the threat responsible for their decline is removed because per capita population growth is assumed to be highest when populations are at their smallest viable sizes. Yet, many seriously depleted fish populations have failed to recover despite threat mitigation. Atlantic cod ( Gadus morhua ) stocks off Newfoundland, despite 30 years of dramatically reduced fishing mortality and numerous fishery closures, have not recovered, suggesting that drivers other than fishing can regulate the growth of collapsed fish populations, inhibiting or preventing their recovery. Here, using Bayesian inference, we show strong evidence of Allee effects in a south Newfoundland cod population, based on data on recruitment and spawning stock biomass. We infer the Allee-effect threshold, below which recovery is impaired. We demonstrate the necessity of data at low population sizes to make inferences about the nature of low-abundance dynamics. Our work indicates that Allee effects are not negligible in commercially exploited fish populations, as commonly projected, and that they represent an inhibitory force that can effectively prevent recovery from overfishing. Our findings contrast with prevailing fisheries management practices that assume compensatory dynamics at low abundances with potential to seriously overestimate the recovery potential of collapsed populations.

Specific changes identified in the otolith macrostructure of Northeast Arctic cod as "spawning zones" are presumed to represent spawning events, but recent experimental studies have challenged this relationship. Because these zones are not routinely recorded outside of Norway, otoliths from multiple Atlantic cod populations with different life history and environmental traits were first examined to see if spawning zones could be identified as a general characteristic of cod. Then, a large archival collection of cod otoliths was used to investigate temporal changes in the occurrence of spawning zones and test for correlations between maturity at age derived from otolith spawning zones and gonad maturity stages. This study shows that spawning zones likely are a universal trait of Atlantic cod and not limited to certain environments or migratory behaviors as previously proposed. Maturity at age derived from spawning zone data showed trends consistent with those from gonad examinations. However, spawning zones appear to form with a one- or two-year lag with sexual maturity, which is suspected to reflect a stabilizing of energy partitioning after the first spawning events. Our results illustrate the potential for use of spawning zones, for example in species or populations with limited available maturity data, and highlights the need for addressing the physiological processes behind their formation., Competing Interests: The authors have declared that no competing interests exist.

The mode and extent of rapid evolution and genomic change in response to human harvesting are key conservation issues. Although experiments and models have shown a high potential for both genetic and phenotypic change in response to fishing, empirical examples of genetic responses in wild populations are rare. Here, we compare whole-genome sequence data of Atlantic cod ( Gadus morhua ) that were collected before (early 20th century) and after (early 21st century) periods of intensive exploitation and rapid decline in the age of maturation from two geographically distinct populations in Newfoundland, Canada, and the northeast Arctic, Norway. Our temporal, genome-wide analyses of 346,290 loci show no substantial loss of genetic diversity and high effective population sizes. Moreover, we do not find distinct signals of strong selective sweeps anywhere in the genome, although we cannot rule out the possibility of highly polygenic evolution. Our observations suggest that phenotypic change in these populations is not constrained by irreversible loss of genomic variation and thus imply that former traits could be reestablished with demographic recovery., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Anthropogenic underwater noise may negatively affect marine animals. Yet, while fishes are highly sensitive to sounds, effects of acoustic disturbances on fishes have not been extensively studied at the population level. In this study, we use a size-structured model based on energy budgets to analyse potential population-level effects of anthropogenic noise on Atlantic cod ( Gadus morhua ). Using the model framework, we assess the impact of four possible effect pathways of disturbance on the cod population growth rate. Through increased stress, changes in foraging and movement behaviour, and effects on the auditory system, anthropogenic noise can lead to (i) increased energy expenditure, (ii) reduced food intake, (iii) increased mortality, and (iv) reduced reproductive output. Our results show that population growth rates are particularly sensitive to changes in energy expenditure and food intake because they indirectly affect the age of maturation, survival and fecundity. Sub-lethal effects of sound exposure may thus affect populations of cod and fishes with similar life histories more than lethal effects of sound exposure. Moreover, anthropogenic noise may negatively affect populations when causing persistent increases of energy expenditure or decreases of food intake. Effects of specific acoustic pollutants on energy acquisition and expenditure should therefore be further investigated.

The collection and presentation of accurate reproductive data from wild fish has historically been somewhat problematic, especially for serially spawning species. Therefore, the aim of the current study was to develop a novel method of assessing female spawning status that is robust to variation in oocyte dynamics between specimens. Atlantic cod (Barents Sea stock) were used to develop the new 'ultrametric' method, that is based on the progressive depletion of the vitellogenic oocyte pool relative to the rather constant previtellogenic oocyte (PVO) pool. Fish were subsequently partitioned into one of four categories that accurately reflected changes in their oocyte size frequency distribution characteristics and gonadosomatic index throughout spawning. The ultrametric method overcomes difficulties associated with presence of bimodal oocyte distributions, oocyte tails, lack of clear hiatus region, and presence of free ova, and can be implemented at a single sampling point. Much of the workflow is fully automated, and the technique may circumvent the need for histological analysis depending on the desired outcome. The ultrametric method differs from the traditional autodiametric method in that PVOs can be separated by ultrasonication and then enumerated, and ovarian homogeneity is not a mandatory requirement per se. The method is designed for determinate spawners but might be extended to include indeterminate spawners.

The Arctic Ocean is an early warning system for indicators and effects of climate change. We use a novel combination of experimental and time-series data on effects of ocean warming and acidification on the commercially important Northeast Arctic cod (Gadus morhua) to incorporate these physiological processes into the recruitment model of the fish population. By running an ecological-economic optimization model, we investigate how the interaction of ocean warming, acidification and fishing pressure affects the sustainability of the fishery in terms of ecological, economic, social and consumer-related indicators, ranging from present day conditions up to future climate change scenarios. We find that near-term climate change will benefit the fishery, but under likely future warming and acidification this large fishery is at risk of collapse by the end of the century, even with the best adaptation effort in terms of reduced fishing pressure., Competing Interests: The authors have declared that no competing interests exist.

Physiological mechanisms determining thermal limits in fishes are debated but remain elusive. It has been hypothesised that motor function loss, observed as loss of equilibrium during acute warming, is due to direct thermal effects on brain neuronal function. To test this, we mounted cooling plates on the heads of Atlantic cod ( Gadus morhua ) and quantified whether local brain cooling increased whole-organism acute upper thermal tolerance. Brain cooling reduced brain temperature by 2-6°C below ambient water temperature and increased thermal tolerance by 0.5 and 0.6°C on average relative to instrumented and uninstrumented controls, respectively, suggesting that direct thermal effects on brain neurons may contribute to setting upper thermal limits in fish. However, the improvement in thermal tolerance with brain cooling was small relative to the difference in brain temperature, demonstrating that other mechanisms (e.g. failure of spinal and peripheral neurons, or muscle) may also contribute to controlling acute thermal tolerance., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2019. Published by The Company of Biologists Ltd.)

While many in-laboratory ecotoxicological studies have shown the adverse impact of pollutants to the fitness of an individual, direct evidence from the field on the population dynamics of wildlife animals has been lacking. Here, we provide empirical support for a negative effect of pollution on Atlantic cod (Gadus morhua) population dynamics in coastal waters of Norway by combining unique time series of juvenile cod abundance, body size, environmental concentration of toxic contaminants and a spatially structured population dynamics model. The study shows that mercury concentration might have decreased the reproductive potential of cod in the region despite the general decline in the environmental concentration of mercury, cadmium and hexachlorobenzene since the implementation of national environmental laws. However, some cod populations appeared to be more resistant to mercury pollution than others, and the strength and shape of mercury effect on cod reproductive potential was fjord-specific. Additionally, cod growth rate changed at scales smaller than fjords with a gradient related to the exposure to the open ocean and offshore cod. These spatial differences in life-history traits emphasize the importance of local adaptation in shaping the dynamics of local wildlife populations. Finally, this study highlights the possibility to mitigate pollution effects on natural populations by reducing the overall pollution level, but also reveals that pollution reduction alone is not enough to rebuild local cod populations. Cod population recovery probably requires complementary efforts on fishing regulation and habitat restoration.

A multitude of recent studies have documented the detrimental effects of crude oil exposure on early life stages of fish, including larvae and embryos. While polycyclic aromatic hydrocarbons (PAHs), particularly alkyl PAHs, are often considered the main cause of observed toxic effects, other crude oil derived organic compounds are usually overlooked. In the current study, comprehensive two-dimensional gas chromatography coupled to mass spectrometry was applied to investigate the body burden of a wide range of petrogenic compounds in Atlantic haddock (Melanogrammus aeglefinus) and cod (Gadus morhua) embryos that had been exposed to sublethal doses of dispersed crude oil. Several groups of alkylated monoaromatic compounds (e.g. alkyl tetralins, indanes and alkyl benzenes), as well as highly alkylated PAHs, were found to accumulate in the fish embryos upon crude oil exposure. To investigate the toxicity of the monoaromatic compounds, two models (1-isopropyl-4-methyltetralin and 1-isopropyl-4-methylindane) were synthesized and shown to bioaccumulate and cause delayed hatching in developing embryos. Minor developmental effects, including craniofacial and jaw deformations and pericardial edemas, were also observed at the highest studied concentrations of the alkylindane., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Atlantic cod is a species that is affected by climate change, with some populations being exposed to higher temperatures than others. The two polymorphs of its major haemoglobin type (HbI) show an inverse change in frequency along a latitudinal temperature cline in the North East Atlantic, which has been associated with differences in population performance and behavioural traits. An earlier study at the northern distribution limit of the species reported differential temperature sensitivities of red blood cell oxygen (O 2 ) affinity between the northern cold-water HbI-2 polymorph and its southern, warm-water HbI-1 counter-part, which has since widely been held as adaptive for the species across its distributional range. The present study critically re-examined this hypothesis by comparing the thermal sensitivity of O 2 binding in both purified HbI polymorphs from the southern, high-temperature distribution limit of the species under controlled conditions of allosteric modifiers of Hb function. Contrary to the prevailing view, the O 2 affinity of the major HbI polymorphs did not differ from each other under any of the tested conditions. Depending on pH and ATP concentration, the temperature-sensitive and temperature-insensitive Hb-O 2 affinity phenotypes - previously exclusively ascribed to HbI-1 and HbI-2, respectively - could be induced in both HbI polymorphs. These results are the first to establish a molecular mechanism behind a reversed temperature dependence of red blood cell O 2 affinity in a non-endotherm fish and lay the basis for future studies on alternative mechanisms behind the differences in distribution, performance and behavioural traits associated with the different HbI polymorphs of Atlantic cod., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2019. Published by The Company of Biologists Ltd.)

Exploitation and changing ocean conditions have resulted in altered species interactions and varied population dynamics within marine fish communities off northeast Newfoundland and southern Labrador, Canada. To understand contemporary species interactions, we quantified the isotopic niches, niche overlap, and ontogenetic niche change among seven dominant fish species using stable isotope analyses. Analyses used fishes from three regions differing in fish and prey diversities. Differences in fish and diet composition diversity among regions were found using Simpson's inverse diversity index. The regions of lowest diversities had higher instances of niche overlap and higher percentage of niche overlap area. The region of highest diversity had the widest spread of niches with greater distances from the community centroid. Ontogenetic shifts were observed such that larger individuals shifted towards the community centroid with the exception of Atlantic cod. Atlantic cod in particular was found to consistently be the top predator of the analyzed species. Our results reveal: (a) overlap in isotopic niches and spread within niche space was correlated with fish and diet diversity; (b) ontogenetic shifts are important when considering a species' niche and quantifying spatial variation in community niche profiles., Competing Interests: The authors have declared that no competing interests exist.

Introgressive hybridization creates networks of genetic relationships across species. Among marine fish of the Gadidae family, Pacific cod and walleye pollock are separate invasions of an Atlantic cod ancestor into the Pacific. Cods are ecological success stories, and their ecologies allow them to support the largest fisheries of the world. The enigmatic walleye pollock differs morphologically, behaviorally, and ecologically from its relatives, representing a niche shift. Here, we apply whole-genome sequencing to Pacific, Arctic, and Atlantic gadids and reveal extensive introgression among them with the ABBA-BABA test and pseudolikelihood phylogenetic network analysis. We propose that walleye pollock resulted from extensive adaptive introgression or homoploid hybrid speciation. The path of evolution of these taxa is more web than a tree. Their ability to invade and expand into new habitats and become ecologically successful may depend on genes acquired through adaptive introgression or hybrid speciation.

Collapses and regime changes are pervasive in complex systems (such as marine ecosystems) governed by multiple stressors. The demise of Atlantic cod ( Gadus morhua) stocks constitutes a text book example of the consequences of overexploiting marine living resources, yet the drivers of these nearly synchronous collapses are still debated. Moreover, it is still unclear why rebuilding of collapsed fish stocks such as cod is often slow or absent. Here, we apply the stochastic cusp model, based on catastrophe theory, and show that collapse and recovery of cod stocks are potentially driven by the specific interaction between exploitation pressure and environmental drivers. Our statistical modelling study demonstrates that for most of the cod stocks, ocean warming could induce a nonlinear discontinuous relationship between fishing pressure and stock size, which would explain hysteresis in their response to reduced exploitation pressure. Our study suggests further that a continuing increase in ocean temperatures will probably limit productivity and hence future fishing opportunities for most cod stocks of the Atlantic Ocean. Moreover, our study contributes to the ongoing discussion on the importance of climate and fishing effects on commercially exploited fish stocks, highlighting the importance of considering discontinuous dynamics in holistic ecosystem-based management approaches, particularly under climate change.

Rapid climate change in the Northeast Atlantic and Arctic poses a threat to some of the world's largest fish populations. Impacts of warming and acidification may become accessible through mechanism-based risk assessments and projections of future habitat suitability. We show that ocean acidification causes a narrowing of embryonic thermal ranges, which identifies the suitability of spawning habitats as a critical life-history bottleneck for two abundant cod species. Embryonic tolerance ranges linked to climate simulations reveal that ever-increasing CO 2 emissions [Representative Concentration Pathway (RCP) 8.5] will deteriorate suitability of present spawning habitat for both Atlantic cod ( Gadus morhua ) and Polar cod ( Boreogadus saida ) by 2100. Moderate warming (RCP4.5) may avert dangerous climate impacts on Atlantic cod but still leaves few spawning areas for the more vulnerable Polar cod, which also loses the benefits of an ice-covered ocean. Emissions following RCP2.6, however, support largely unchanged habitat suitability for both species, suggesting that risks are minimized if warming is held "below 2°C, if not 1.5°C," as pledged by the Paris Agreement.

Predicting fish stock variations on interannual to decadal time scales is one of the major issues in fisheries science and management. Although the field of marine ecological predictions is still in its infancy, it is understood that a major source of multi-year predictability resides in the ocean. Here we show the first highly skilful long-term predictions of the commercially valuable Barents Sea cod stock. The 7-year predictions are based on the propagation of ocean temperature anomalies from the subpolar North Atlantic toward the Barents Sea, and the strong co-variability between these temperature anomalies and the cod stock. Retrospective predictions for the period 1957-2017 capture well multi-year to decadal variations in cod stock biomass, with cross-validated explained variance of over 60%. For lead times longer than one year the statistical long-term predictions show more skill than operational short-term predictions used in fisheries management and lagged persistence forecasts. Our results thus demonstrate the potential for ecosystem-based fisheries management, which could enable strategic planning on longer time scales. Future predictions show a gradual decline in the cod stock towards 2024., Competing Interests: The authors have declared that no competing interests exist.

The trophic link between cod (Gadus sp.) and capelin (Mallotus sp.) is important in many panarctic ecosystems. Since the early 2000s, the Northeast Arctic cod stock (G. morhua) in the Barents Sea has increased greatly, and the sea has been exceptionally warm. Such changes have potentially large effects on species distributions and overlap, which in turn could affect the strength of species interactions. Due to its high latitude location, the Barents Sea has strong seasonal variation in physical conditions and interactions. To study drivers of variation in cod-capelin overlap, we use data from two annual surveys run in winter and in autumn of 2004-2015. We first model winter and autumn spatial distributions of mature and immature cod and capelin. We then calculate overlap from model predictions on a grid with similar spatial resolution as the survey data. Our approach allowed us to interpret changes in overlap as species-specific effects of stock size and temperature, while accounting for sampling variation due to sampling time and depth. We found that during winter both species expanded their distribution in response to increased stock sizes, but how strongly and where the expansion occurred varied. The effect of temperature on distributions varied in space, and differed for cod and capelin and for different components of the two species. The results for autumn were clearer and more consistent. Both species expanded their distribution areas as their stock sizes increased. A positive effect of temperature was found in the north-eastern Barents Sea, where temperatures were lowest at the start of the study. Overlap increased and shifted north-eastwards during the study period and remained high despite a decline in the capelin stock. The increased overlap during autumn could mainly be attributed to the shift in cod distribution with increased cod stock biomass., Competing Interests: The authors have declared that no competing interests exist.

Sustainability of commercial fisheries is best achieved when fishing gears are selective and have low impacts on bottom habitat. Pots (baited traps) are a fishing technology that typically has lower impacts than many other industrial gears. In this study we compared the efficiency of five models of pots (baited traps) designed to catch Atlantic cod (Gadus morhua) for use in Newfoundland and Labrador (NL)'s expanding cod fishery. We compared catch per unit effort (CPUE) and total lengths of cod across each pot type, as well as bycatch rates of each model. All pot types were successful at catching cod, but two models (the modified Newfoundland pot, and a four-entrance pot of our design) had highest CPUE. Specifically, we found that modifying Newfoundland pots increased their CPUE by 145% without a corresponding increase in bycatch. None of the pot types produced substantial amounts of bycatch. This study demonstrated that potting gear is an effective way to catch cod in NL, and that there is flexibility in which pot fishers can use, depending on the layout of their fishing vessel., Competing Interests: The authors have declared that no competing interests exist.

Ocean acidification (OA), the dissolution of excess anthropogenic carbon dioxide in ocean waters, is a potential stressor to many marine fish species. Whether species have the potential to acclimate and adapt to changes in the seawater carbonate chemistry is still largely unanswered. Simulation experiments across several generations are challenging for large commercially exploited species because of their long generation times. For Atlantic cod (Gadus morhua), we present first data on the effects of parental acclimation to elevated aquatic CO 2 on larval survival, a fundamental parameter determining population recruitment. The parental generation in this study was exposed to either ambient or elevated aquatic CO 2 levels simulating end-of-century OA levels (~1100 µatm CO 2 ) for six weeks prior to spawning. Upon fully reciprocal exposure of the F1 generation, we quantified larval survival, combined with two larval feeding regimes in order to investigate the potential effect of energy limitation. We found a significant reduction in larval survival at elevated CO 2 that was partly compensated by parental acclimation to the same CO 2 exposure. Such compensation was only observed in the treatment with high food availability. This complex 3-way interaction indicates that surplus metabolic resources need to be available to allow a transgenerational alleviation response to ocean acidification.

The semi-enclosed nature and estuarine characteristics, together with its strongly alternating bathymetry, make the Baltic Sea prone to much stronger interannual variations in the abiotic environment, than other spawning habitats of Atlantic cod (Gadus morhua). Processes determining salinity and oxygen conditions in the basins are influenced both by long term gradual climate change, e.g. global warming, but also by short-term meteorological variations and events. Specifically one main factor influencing cod spawning conditions, the advection of highly saline and well-oxygenated water masses from the North Sea, is observed in irregular frequencies and causes strong interannual variations in stock productivity. This study investigates the possibility to use the available hydrographic process knowledge to predict the annual spawning conditions for Eastern Baltic cod in its most important spawning ground, the Bornholm Basin, only by salinity measurements from a specific location in the western Baltic. Such a prediction could serve as an environmental early warning indicator to inform stock assessment and management. Here we used a hydrodynamic model to hindcast hydrographic property fields for the last 40+ years. High and significant correlations were found for months early in the year between the 33m salinity level in the Arkona Basin and the oxygen-dependent cod spawning environment in the Bornholm Basin. Direct prediction of the Eastern Baltic cod egg survival in the Bornholm Basin based on salinity values in the Arkona Basin at the 33 m depth level is shown to be possible for eggs spawned by mid-age and young females, which currently predominate the stock structure. We recommend to routinely perform short-term predictions of the Eastern Baltic cod spawning environment, in order to generate environmental information highly relevant for stock dynamics. Our statistical approach offers the opportunity to make best use of permanently existing infrastructure in the western Baltic to timely provide scientific knowledge on the spawning conditions of Eastern Baltic cod. Furthermore it could be a tool to assist ecosystem-based fisheries management with a cost-effective implementation by including the short term predictions as a simple indicator in the annual assessments.

Most fishes and crustaceans respond to light, and artificial light sources may therefore be an efficient stimulus to manipulate behaviours in aquatic animals. It has been hypothesised that the catch efficiency of pots could be increased if prey, for example krill, can be attracted into the pots providing a visual stimulus and a source of live bait. To find which light characteristics are most attractive to krill, we tested the effects of light intensity and wavelength composition on Northern krill's (Meganyctiphanes norvegica) behavioural response to an artificial light source. The most attractive individual wavelength was 530 nm (green light), while broadband (425-750 nm) white light was an equally attractive light source. The intensity of the emitted light did not appear to have a direct effect on attraction to the light source, however it did significantly increase swimming activity among the observed krill. The most promising light stimuli for krill were tested to determine whether they would have a repulsive or attractive effect on cod (Gadus morhua); These light stimuli appeared to have a slightly repulsive, but non-significant, effect on cod. However, we suggest that a swarm of krill attracted to an artificial light source may produce a more effective visual stimulus to foraging cod.

The visual system is for many fishes essential in guiding behaviors, such as foraging, predator avoidance and mate choice. The marine environment is characterized by large spatio-temporal fluctuations in light intensity and spectral composition. However, visual capabilities are restricted by both space limitations set by eye size and by the genomic content of light-absorbing opsin genes. The rich array of visual opsins in teleosts may be used differentially to tune vision towards specific needs during ontogeny and to changing light. Yet, to what extent visual plasticity is a pre-programmed developmental event, or is triggered by photic environment, is unclear. Our previous studies on Atlantic cod revealed an evolutionary genomic loss of UV-sensitive sws1 and red-sensitive lws opsin families, while blue-sensitive sws2 and green-sensitive rh2 opsins had duplicated. The current study has taken an opsin expression approach to characterize visual plasticity in cod towards different spectral light during the larval stage, to maturation and extreme seasonal changes in the Barents Sea. Our data suggest that opsin plasticity in cod larvae is controlled by developmental programme rather than immediate light environment. The lack of expressional changes during maturation suggests a less important role for visual modulation related to mate choice. Although no seasonal effects on visual opsins were detected in migratory Northeast Arctic cod, the expressed opsin subset differed from the more stationary Norwegian coastal cod described in previous studies. Interestingly, these data provide the first indications of a population difference in actively used visual opsins associated with cod ecotypes., Competing Interests: Competing interestsThe authors declare no competing or financial interests., (© 2018. Published by The Company of Biologists Ltd.)

Stellwagen Bank National Marine Sanctuary is located in Massachusetts Bay off the densely populated northeast coast of the United States; subsequently, the marine inhabitants of the area are exposed to elevated levels of anthropogenic underwater sound, particularly due to commercial shipping. The current study investigated the alteration of estimated effective communication spaces at three spawning locations for populations of the commercially and ecologically important fishes, Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus). Both the ambient sound pressure levels and the estimated effective vocalization radii, estimated through spherical spreading models, fluctuated dramatically during the three-month recording periods. Increases in sound pressure level appeared to be largely driven by large vessel activity, and accordingly exhibited a significant positive correlation with the number of Automatic Identification System tracked vessels at the two of the three sites. The near constant high levels of low frequency sound and consequential reduction in the communication space observed at these recording sites during times of high vocalization activity raises significant concerns that communication between conspecifics may be compromised during critical biological periods. This study takes the first steps in evaluating these animals' communication spaces and alteration of these spaces due to anthropogenic underwater sound.

Commercial fishing generally removes large and old individuals from fish stocks, reducing mean age and age diversity among spawners. It is feared that these demographic changes lead to lower and more variable recruitment to the stocks. A key proposed pathway is that juvenation and reduced size distribution causes reduced ranges in spawning period, spawning location, and egg buoyancy; this is proposed to lead to reduced spatial distribution of fish eggs and larvae, more homogeneous ambient environmental conditions within each year-class, and reduced buffering against negative environmental influences. However, few, if any, studies have confirmed a causal link from spawning stock demographic structure through egg and larval distribution to year class strength at recruitment. We here show that high mean age and size in the spawning stock of Barents Sea cod (Gadus morhua) is positively associated with high abundance and wide spatiotemporal distribution of cod eggs. We find, however, no support for the hypothesis that a wide egg distribution leads to higher recruitment or a weaker recruitment-temperature correlation. These results are based on statistical analyses of a spatially resolved data set on cod eggs covering a period (1959-1993) with large changes in biomass and demographic structure of spawners. The analyses also account for significant effects of spawning stock biomass and a liver condition index on egg abundance and distribution. Our results suggest that the buffering effect of a geographically wide distribution of eggs and larvae on fish recruitment may be insignificant compared with other impacts., Competing Interests: The authors declare no conflict of interest.

Atlantic cod are a commercially important species believed to be threatened by warming seas near their southern, equatorward upper thermal edge of distribution. Limitations to circulatory O 2 transport, in particular cardiac output, and the geographic distribution of functionally different haemoglobin (Hb) genotypes have separately been suggested to play a role in setting thermal tolerance in this species. The present study assessed the thermal sensitivity of O 2 binding in Atlantic cod red blood cells with different Hb genotypes near their upper thermal distribution limit and modelled its consequences for the arterio-venous O 2 saturation difference, Sa-v O 2 , another major determinant of circulatory O 2 supply rate. The results showed statistically indistinguishable red blood cell O 2 binding between the three HbI genotypes in wild-caught Atlantic cod from the Irish Sea (53° N). Red blood cells had an unusually low O 2 affinity, with reduced or even reversed thermal sensitivity between pH 7.4 and 7.9, and 5.0 and 20.0°C. This was paired with strongly pH-dependent affinity and cooperativity of red blood cell O 2 binding (Bohr and Root effects). Modelling of Sa-v O 2  at physiological pH, temperature and O 2 partial pressures revealed a substantial capacity for increases in Sa-v O 2  to meet rising tissue O 2 demands at 5.0 and 12.5°C, but not at 20°C. Furthermore, there was no evidence for an increase of maximal Sa-v O 2  with temperature. It is suggested that Atlantic cod at such high temperatures may solely depend on increases in cardiac output and blood O 2 capacity, or thermal acclimatisation of metabolic rate, for matching circulatory O 2 supply to tissue demand., (© 2017. Published by The Company of Biologists Ltd.)

We conducted a literature review of reported temperature, salinity, pH, depth and oxygen preferences and thresholds of important marine species found in the Gulf of St. Lawrence and Scotian Shelf region. We classified 54 identified fishes and macroinvertebrates as important either because they support a commercial fishery, have threatened or at risk status, or meet one of the following criteria: bycatch, baitfish, invasive, vagrant, important for ecosystem energy transfer, or predators or prey of the above species. The compiled data allow an assessment of species-level impacts including physiological stress and mortality given predictions of future ocean physical and biogeochemical conditions. If an observed, multi-decadal oxygen trend on the central Scotian Shelf continues, a number of species will lose favorable oxygen conditions, experience oxygen-stress, or disappear due to insufficient oxygen in the coming half-century. Projected regional trends and natural variability are both large, and natural variability will act to alternately amplify and dampen anthropogenic changes. When estimates of variability are included with the trend, species encounter unfavourable oxygen conditions decades sooner. Finally, temperature and oxygen thresholds of adult Atlantic wolffish (Anarhichas lupus) and adult Atlantic cod (Gadus morhua) are assessed in the context of a potential future scenario derived from high-resolution ocean models for the central Scotian Shelf., Competing Interests: The authors have declared that no competing interests exist.

How fisheries will be impacted by climate change is far from understood. While some fish populations may be able to escape global warming via range shifts, they cannot escape ocean acidification (OA), an inevitable consequence of the dissolution of anthropogenic carbon dioxide (CO2) emissions in marine waters. How ocean acidification affects population dynamics of commercially important fish species is critical for adapting management practices of exploited fish populations. Ocean acidification has been shown to impair fish larvae's sensory abilities, affect the morphology of otoliths, cause tissue damage and cause behavioural changes. Here, we obtain first experimental mortality estimates for Atlantic cod larvae under OA and incorporate these effects into recruitment models. End-of-century levels of ocean acidification (~1100 μatm according to the IPCC RCP 8.5) resulted in a doubling of daily mortality rates compared to present-day CO2 concentrations during the first 25 days post hatching (dph), a critical phase for population recruitment. These results were consistent under different feeding regimes, stocking densities and in two cod populations (Western Baltic and Barents Sea stock). When mortality data were included into Ricker-type stock-recruitment models, recruitment was reduced to an average of 8 and 24% of current recruitment for the two populations, respectively. Our results highlight the importance of including vulnerable early life stages when addressing effects of climate change on fish stocks., Competing Interests: The authors have declared that no competing interests exist.

Aquaculture production of cod has decreased from over 20,000 tonnes in 2009 to less than 2,000 tonnes in 2014 and the industry faces many challenges, one of which is high and unpredictably variable mortality rates in the early life stages. Hence, full-cycle farming with hatchery produced juveniles is still considered unprofitable compared to fisheries and on-growing of wild cod. In the present study, potential batch differences in progeny survival of wild-caught, hatchery-spawned Faroe Bank cod (Gadus morhua L.) were investigated at two defined periods during early life history; i) the embryo stage (60 day degrees post fertilisation) and ii) the fry stage (110 days post hatch), post metamorphosis. The fry stage experiment was conducted in three replicates (N = 300 per replicate), and a panel of three polymorphic microsatellite markers was used for parental analysis. Mean survival rate at the embryo stage was 69% (± 20% SD). Survival was positively associated with egg diameter (P < 0.01), explaining 90% of the variation in egg survival rates. The data were too scarce to conclude either way concerning a possible correlation between survival rates between the two periods (P < 0.10). Offspring from three batches (from a total of eight) dominated in the fry stage, contributing over 90% of the progeny, and results were consistent over all three replicate tanks. The skewed batch representation observed may be of relevance to the effective management of selective breeding programmes for cod.

Northwest Atlantic cod (Gadus morhua) have been heavily overfished in recent years and have not yet recovered. Passive acoustic technology offers a new approach to identify the spatial location of spawning fish, as well as their seasonal and long term persistence in an area. To date, the lack of a species-specific detector has made searching for Atlantic cod grunts in large amounts of passive acoustic data cumbersome. To address this problem, an automatic grunt detection and recognition algorithm that processes yearlong passive acoustic data recordings was designed. The proposed technique is a two-stage hypothesis testing algorithm that includes detecting and recognizing all grunt-like sounds. Test results demonstrated that the algorithm provided a detection probability of 0.93 for grunts with a signal-to-noise ratio (SNR) higher than 10 dB, and a detection probability of 0.8 for grunts with the SNR ranging from 3 to 10 dB. This detector is being used to identify cod in current and historical data from U.S. waters. Its use has significantly reduced the time required to find and validate the presence of cod grunts.

Fish exhibit a wide range of species-specific blood glucose levels. How this relates to glucose utilization is yet to be fully realized. Here, we assessed glucose transport and metabolism in myocytes isolated from Atlantic cod (Gadus morhua) and short-horned sculpin (Myoxocephalus scorpius), species with blood glucose levels of 3.7 and 0.57 mmol l(-1), respectively. Glucose metabolism was assessed by the production of (3)H2O from [2-(3)H]glucose. Glucose metabolism was 3.5- to 6-fold higher by myocytes from Atlantic cod than by those from short-horned sculpin at the same level of extracellular glucose. In Atlantic cod myocytes, glucose metabolism displayed what appears to be a saturable component with respect to extracellular glucose, and cytochalasin B inhibited glucose metabolism. These features revealed a facilitated glucose diffusion mechanism that accounts for between 30% and 55% of glucose entry at physiological levels of extracellular glucose. Facilitated glucose diffusion appears to be minimal in myocytes for short-horned sculpin. Glucose entry by simple diffusion occurs in both cell types with the same linear relationship between glucose metabolism and extracellular glucose concentration, presumably due to similarities in membrane composition. Oxygen consumption by myocytes incubated in medium containing physiological levels of extracellular glucose (Atlantic cod 5 mmol l(-1), short-horned sculpin 0.5 mmol l(-1)) was similar in the two species and was not decreased by cytochalasin B, suggesting that these cells have the capability of oxidizing alternative on-board metabolic fuels. Cells produced lactate at low rates but glycogen levels did not change during the incubation period. In cells from both species, glucose utilization assessed by both simple chemical analysis of glucose disappearance from the medium and (3)H2O production was half the rate of lactate production and as such extracellular glucose was not available for oxidative metabolism. Overall, extracellular glucose makes only a minor contribution to ATP production but a sustained glycolysis may be necessary to support Ca(2+) transport mechanisms at either the sarcoplasmic reticulum or the sarcolemmal membrane., (© 2016. Published by The Company of Biologists Ltd.)

Similar to many marine teleost species, Atlantic cod undergo remarkable physiological changes during the early life stages with concurrent and profound changes in feeding biology and ecology. In contrast to the digestive system, very little is known about the ontogeny and the localization of the centers that control appetite and feed ingestion in the developing brain of fish. We examined the expression patterns of three appetite regulating factors (orexigenic: neuropeptide Y, NPY; prepro-orexin, pOX and anorexigenic: cocaine- and amphetamine-regulated transcript, CART) in discrete brain regions of developing Atlantic cod using chromogenic and double fluorescent in situ hybridization. Differential temporal and spatial expression patterns for each appetite regulator were found from first feeding (4 days post hatch; dph) to juvenile stage (76 dph). Neurons expressing NPY mRNA were detected in the telencephalon (highest expression), diencephalon, and optic tectum from 4 dph onward. CART mRNA expression had a wider distribution along the anterior-posterior brain axis, including both telencephalon and diencephalon from 4 dph. From 46 dph, CART transcripts were also detected in the olfactory bulb, region of the nucleus of medial longitudinal fascicle, optic tectum and midbrain tegmentum. At 4 and 20 dph, pOX mRNA expression was exclusively found in the preoptic region, but extended to the hypothalamus at 46 and 76 dph. Co-expression of both CART and pOX genes were also observed in several hypothalamic neurons throughout larval development. Our results show that both orexigenic and anorexigenic factors are present in the telencephalon, diencephalon and mesencephalon in cod larvae. The telencephalon mostly contains key factors of hunger control (NPY), while the diencephalon, and particularly the hypothalamus may have a more complex role in modulating the multifunctional control of appetite in this species. As the larvae develop, the overall progression in temporal and spatial complexity of NPY, CART and pOX mRNAs expression might be correlated to the maturation of appetite control regulation. These observations suggest that teleost larvae continue to develop the regulatory networks underlying appetite control after onset of exogenous feeding.

To our knowledge, there is no report on microRNA (miRNA) expression and their target analysis in relation to the type of the first feed and its effect on the further growth of fish. Atlantic cod (Gadus morhua) larvae have better growth and development performance when fed natural zooplankton as a start-feed, as compared with those fed typical aquaculture start-feeds. In our experiment, two groups of Atlantic cod larvae were fed reference feed (zooplankton, mostly copepods, filtered from a seawater pond) v. aquaculture feeds: enriched rotifers (Brachionus sp.) and later brine shrimp (Artemia salina). We examined the miRNA expressions of six defined developmental stages as determined and standardised by body length from first feeding for both diet groups. We found eight miRNA (miR-9, miR-19a, miR-130b, miR-146, miR-181a, miR-192, miR-206 and miR-11240) differentially expressed between the two feeding groups in at least one developmental stage. We verified the next-generation sequencing data using real-time RT-PCR. We found 397 putative targets (mRNA) to the differentially expressed miRNA; eighteen of these mRNA showed differential expression in at least one stage. The patterns of differentially expressed miRNA and their putative target mRNA were mostly inverse, but sometimes also concurrent. The predicted miRNA targets were involved in different pathways, including metabolic, phototransduction and signalling pathways. The results of this study provide new nutrigenomic information on the potential role of miRNA in mediating nutritional effects on growth during the start-feeding period in fish larvae.

In several species genetic differentiation across environmental gradients or between geographically separate populations has been reported to center at "genomic islands of divergence," resulting in heterogeneous differentiation patterns across genomes. Here, genomic regions of elevated divergence were observed on three chromosomes of the highly mobile fish Atlantic cod (Gadus morhua) within geographically fine-scaled coastal areas. The "genomic islands" extended at least 5, 9.5, and 13 megabases on linkage groups 2, 7, and 12, respectively, and coincided with large blocks of linkage disequilibrium. For each of these three chromosomes, pairs of segregating, highly divergent alleles were identified, with little or no gene exchange between them. These patterns of recombination and divergence mirror genomic signatures previously described for large polymorphic inversions, which have been shown to repress recombination across extensive chromosomal segments. The lack of genetic exchange permits divergence between noninverted and inverted chromosomes in spite of gene flow. For the rearrangements on linkage groups 2 and 12, allelic frequency shifts between coastal and oceanic environments suggest a role in ecological adaptation, in agreement with recently reported associations between molecular variation within these genomic regions and temperature, oxygen, and salinity levels. Elevated genetic differentiation in these genomic regions has previously been described on both sides of the Atlantic Ocean, and we therefore suggest that these polymorphisms are involved in adaptive divergence across the species distributional range., (© The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Marine recreational fishing is a popular outdoor activity. However, knowledge about the magnitude of recreational catches relative to commercial catches in coastal fisheries is generally sparse. Coastal Atlantic cod (Gadus morhua) is a target species for recreational fishers in the North Atlantic. In Norway, recreational fishers are allowed to use a variety of traps and nets as well as long-line and rod and line when fishing for cod. From 2005 to 2013, 9729 cod (mean size: 40 cm, range: 15-93 cm) were tagged and released in coastal Skagerrak, southeast Norway. Both high-reward (NOK 500) and low-reward tags (NOK 50) were used in this study. Because some harvested fish (even those posting high-reward tags) may go unreported by fishers, reporting rates were estimated from mark-recovery models that incorporate detection parameters in their structure, in addition to survival and mortality estimates. During 2005 to 2013, a total of 1707 tagged cod were recovered and reported by fishers. We estimate the overall annual survival to be 33% (SE 1.5). Recreational rod and line fishing were responsible for 33.7% (SE 2.4) of total mortality, followed by commercial fisheries (15.1% SE 0.8) and recreational fixed gear (6.8% SE 0.4). Natural mortality was 44.4% (SE 2.5) of total mortality. Our findings suggest that recreational fishing-rod and line fishing in particular-is responsible for a substantial part of fishing mortality exerted on coastal cod in southern Norway.

Animal-borne data loggers allow movement, associated behaviours and energy expenditure in fish to be quantified without direct observations. As with any tagging, tags that are attached externally may adversely affect fish behaviour, swimming efficiency and survival. We report on free-swimming wild Atlantic cod (Gadus morhua) held in a large mesocosm that exhibited distinctly aberrant rotational swimming (scouring) when externally tagged with accelerometer data loggers. To quantify the phenomenon, the cod were tagged with two sizes of loggers (18 and 6 g; <2% body mass) that measured tri-axial acceleration at 50 Hz. An automated algorithm, based on body angular rotation, was designed to extract the scouring movements from the acceleration signal (98% accuracy). The algorithm also identified the frequency pattern and associated energy expenditure of scouring in relation to tag load (% body weight). The average per cent time spent scouring (5%) was independent of tag load. The vector of the dynamic body acceleration (VeDBA), used as a proxy for energy expenditure, increased with tag load (r(2)=0.51), and suggests that fish with large tags spent more energy when scouring than fish with small tags. The information allowed us to determine potential detrimental effects of an external tag on fish behaviour and how these effects may be mitigated by tag size. The algorithm can potentially identify similar rotational movements associated with spawning, courtship, feeding and parasite-load shedding in the wild. The results infer a more careful interpretation of data derived from external tags and the careful consideration of tag type, drag, buoyancy and placement, as well as animal buoyancy and species., (© 2016. Published by The Company of Biologists Ltd.)

Background: In marine fish species, where pelagic egg and larvae drift with ocean currents, population structure has been suggested to be maintained by larval retention due to hydrographic structuring and by homing of adult fish to natal areas. Whilst natal homing of adults has been demonstrated for anadromous and coral reef fishes, there are few documented examples of philopatric migration in temperate marine fish species., Results: Here, we demonstrate temporally stable genetic differentiation among spawning populations of Atlantic cod (Gadus morhua L.), and present genetic and behavioural evidence for larval drift and philopatric migration in the eastern North Sea-Skagerrak-Kattegat area. We show that juvenile cod collected in the eastern Skagerrak and central Kattegat are genetically similar to cod from offshore spawning areas in the eastern North Sea. Genetic assignment of individual 2-5 year old fish indicates that cod residing at, or migrating towards, spawning areas in Kattegat and the North Sea display philopatric behaviours., Conclusions: Together these findings suggest a loop between spawning, larval drift and adult return-migrations to spawning areas and underlines that both oceanographic processes and migratory behaviour in the adult phase may be important for stock separation and integrity in marine temperate fishes such as Atlantic cod.

Anthropogenic noise impacts behaviour and physiology in many species, but responses could change with repeat exposures. As repeat exposures can vary in regularity, identifying regimes with less impact is important for regulation. We use a 16-day split-brood experiment to compare effects of regular and random acoustic noise (playbacks of recordings of ships), relative to ambient-noise controls, on behaviour, growth and development of larval Atlantic cod (Gadus morhua). Short-term noise caused startle responses in newly hatched fish, irrespective of rearing noise. Two days of both regular and random noise regimes reduced growth, while regular noise led to faster yolk sac use. After 16 days, growth in all three sound treatments converged, although fish exposed to regular noise had lower body width-length ratios. Larvae with lower body width-length ratios were easier to catch in a predator-avoidance experiment. Our results demonstrate that the timing of acoustic disturbances can impact survival-related measures during development. Much current work focuses on sound levels, but future studies should consider the role of noise regularity and its importance for noise management and mitigation measures., (© 2015 The Authors.)

Gadus morhua (Atlantic cod) stocks in the Barents Sea are currently at levels not seen since the 1950s. Causes for the population increase last century, and understanding of whether such large numbers will be maintained in the future, are unclear. To explore this, we digitised and interrogated historical cod catch and diet datasets from the Barents Sea. Seventeen years of catch data and 12 years of prey data spanning 1930-1959 cover unexplored spatial and temporal ranges, and importantly capture the end of a previous warm period, when temperatures were similar to those currently being experienced. This study aimed to evaluate cod catch per unit effort and prey frequency in relation to spatial, temporal and environmental variables. There was substantial spatio-temporal heterogeneity in catches through the time series. The highest catches were generally in the 1930s and 1940s, although at some localities more cod were recorded late in the 1950s. Generalized Additive Models showed that environmental, spatial and temporal variables are all valuable descriptors of cod catches, with the highest occurring from 15-45°E longitude and 73-77°N latitude, at bottom temperatures between 2 and 4°C and at depths between 150 and 250 m. Cod diets were highly variable during the study period, with frequent changes in the relative frequencies of different prey species, particularly Mallotus villosus (capelin). Environmental variables were particularly good at describing the importance of capelin and Clupea harengus (herring) in the diet. These new analyses support existing knowledge about how the ecology of the region is controlled by climatic variability. When viewed in combination with more recent data, these historical relationships will be valuable in forecasting the future of Barents Sea fisheries, and in understanding how environments and ecosystems may respond.

Diagnosing the processes that threaten species persistence is critical for recovery planning and risk forecasting. Dominant threats are typically inferred by experts on the basis of a patchwork of informal methods. Transparent, quantitative diagnostic tools would contribute much-needed consistency, objectivity, and rigor to the process of diagnosing anthropogenic threats. Long-term census records, available for an increasingly large and diverse set of taxa, may exhibit characteristic signatures of specific threatening processes and thereby provide information for threat diagnosis. We developed a flexible Bayesian framework for diagnosing threats on the basis of long-term census records and diverse ancillary sources of information. We tested this framework with simulated data from artificial populations subjected to varying degrees of exploitation and habitat loss and several real-world abundance time series for which threatening processes are relatively well understood: bluefin tuna (Thunnus maccoyii) and Atlantic cod (Gadus morhua) (exploitation) and Red Grouse (Lagopus lagopus scotica) and Eurasian Skylark (Alauda arvensis) (habitat loss). Our method correctly identified the process driving population decline for over 90% of time series simulated under moderate to severe threat scenarios. Successful identification of threats approached 100% for severe exploitation and habitat loss scenarios. Our method identified threats less successfully when threatening processes were weak and when populations were simultaneously affected by multiple threats. Our method selected the presumed true threat model for all real-world case studies, although results were somewhat ambiguous in the case of the Eurasian Skylark. In the latter case, incorporation of an ancillary source of information (records of land-use change) increased the weight assigned to the presumed true model from 70% to 92%, illustrating the value of the proposed framework in bringing diverse sources of information into a common rigorous framework. Ultimately, our framework may greatly assist conservation organizations in documenting threatening processes and planning species recovery., (© 2014 Society for Conservation Biology.)

The difference between maximum metabolic rate and standard metabolic rate is referred to as aerobic scope, and because it constrains performance it is suggested to constitute a key limiting process prescribing how fish may cope with or adapt to climate warming. We use an evolutionary bioenergetics model for Atlantic cod (Gadus morhua) to predict optimal life histories and behaviours at different temperatures. The model assumes common trade-offs and predicts that optimal temperatures for growth and fitness lie below that for aerobic scope; aerobic scope is thus a poor predictor of fitness at high temperatures. Initially, warming expands aerobic scope, allowing for faster growth and increased reproduction. Beyond the optimal temperature for fitness, increased metabolic requirements intensify foraging and reduce survival; oxygen budgeting conflicts thus constrain successful completion of the life cycle. The model illustrates how physiological adaptations are part of a suite of traits that have coevolved., (© 2015 The Author(s) Published by the Royal Society. All rights reserved.)

Teleosts show a great variety in visual opsin complement, due to both gene duplication and gene loss. The repertoire ranges from one subfamily of visual opsins (scotopic vision) including rod opsin only retinas seen in many deep-sea species to multiple subfamilies of visual opsins in some pelagic species. We have investigated the opsin repertoire of Atlantic cod (Gadus morhua) using information in the recently sequenced cod genome and found that despite cod not being a deep sea species it lacks visual subfamilies sensitive towards the most extreme parts of the light spectra representing UV and red light. Furthermore, we find that Atlantic cod has duplicated paralogs of both blue-sensitive SWS2 and green-sensitive RH2 subfamilies, with members belonging to each subfamily linked in tandem within the genome (two SWS2-, and three RH2A genes, respectively). The presence of multiple cone opsin genes indicates that there have been duplication events in the cod ancestor SWS2 and RH2 opsins producing paralogs that have been retained in Atlantic. Our results are supported by expressional analysis of cone opsins, which further revealed an ontogenetic change in the array of cone opsins expressed. These findings suggest life stage specific programs for opsin regulation which could be linked to habitat changes and available light as the larvae is transformed into an early juvenile. Altogether we provide the first molecular evidence for color vision driven by only two families of cone opsins due to gene loss in a teleost.