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The recovery of many groundfish stocks in the Northwest Atlantic has been impeded by elevated mortality among older/larger individuals. The sources of groundfish mortality are generally uncertain, though predation by growing grey seal herds and unreported fishing are thought to be drivers of mortality for Atlantic cod (Gadus morhua) on the Western Scotian Shelf and Bay of Fundy (4X5Y), as well as in nearby ecosystems. We developed a statistical catch-at-age model for 4X5Y cod that accounted for grey seal predation and bycatch/discards and tested the model across a broad range of consumption and discard scenarios. We found that most cod mortality was unexplained by seal predation and fishing when cod comprised a small to moderate portion of the grey seal diet. Predation and fishing accounted for slightly more than half of recent cod mortality when cod was highly prevalent in the seal diet (45% by weight) but explained little historical mortality. Bycatch was a minor source of mortality prior to 2019 and accounted for 0.%1–8.1% of recent mortality. Increased sampling of seal diets and monitoring of emerging seal colonies is necessary for reducing uncertainties around seal predation effects in the Northwest Atlantic. [ABSTRACT FROM AUTHOR]

With a biomass of ∼4 million tonnes, and annual catches of 900 000 tonnes, the northeast Atlantic (NEA) cod stock in the Barents Sea is the world's largest. Scientists have been trying to explain the variability in recruitment of this stock for over 100 years, in particular connecting it to spawning stock biomass and environmental factors such as temperature. It has been suggested that the combination of ocean acidification and global warming will lead to a significant decrease in the spawning stock biomass and an eventual (end of this century) collapse of the NEA cod stock in the Barents Sea. We show that a temperature- and OA-driven decline in recruits will likely lead to a smaller cod stock, but not to a collapse. Instead, the level of fishing pressure and, not least, the choice of the recruitment function applied in simulations and how it relates to temperature, is extremely important when making such forecasts. Applying a non-linear relationship between temperature and spawning stock biomass—as has been done in studies that predict a collapse of the NEA cod stock—does not improve accuracy and, in addition, adds a large decrease in number of recruits that is not biologically supported. [ABSTRACT FROM AUTHOR]

The International Union for Conservation of Nature (IUCN) Red List identifies threatened and endangered species and is a key instrument in global biodiversity conservation efforts. Our understanding of the structure and value of genetic biodiversity below the species level is rapidly increasing. Nonetheless, the IUCN assessment criteria overlook genetic variation within species. Here, we address this blind spot and discuss the principles of species conservation status classification relative to intraspecific biodiversity. We focus on coastal species, which thrive in heterogeneous environments known to drive genetic differentiation. The focal example species, Atlantic cod and sugar kelp, have contrasting life histories, are ecologically and economically important constituents of the coastal ecosystem, and are currently not classified as threatened in Norway and Canada. We expose important variation in population structure, the presence of ecotypes and genetic-environment covariation, as well as loss of ecotypes that threatens the conservation of these species. Because the genetic makeup of species directly influences their resilience, omitting this information from conservation status assessments can result in loss of adaptive capacity to future stressors, such as climate change. Consequently, recognizing and preserving intraspecific variation emerges as vital for species' abilities to adapt to and survive in future ocean conditions. [ABSTRACT FROM AUTHOR]

Although early embryonic protein production relies exclusively on maternal molecules such as messenger RNAs (mRNAs) incorporated into ovarian follicles, knowledge about any thermally induced, intergenerational effects is scarce in ectotherms. Here, we investigated how elevated temperatures (9°–12°C vs. 6°C) during oogenesis influenced the next generation by targeting maternal mRNAs in Atlantic cod (Gadus morhua) embryos, in view of up- and down-regulated genes in ovarian follicles of pre-spawning adults. Overall, the spawning female liver showed significantly higher levels of free amino acids and N-metabolites at 9°C than at 6°C. Higher-than-optimal temperatures induced adjustments in embryo transcriptome proportional to the temperature increase relative to the control group. The adjustments included alterations in maternal-effect genes, which are developmentally conserved among vertebrates. The transcriptomic differences for a selection of genes in embryos were reflected in ovarian follicles (containing multiple cell types) several months ahead of the spawning season, implying that environmental conditions of the adults are key for adjusting the genetic instructions for offspring development. This programming of fundamental traits from mother to offspring appears part of a sophisticated process to adapt the offspring to a changing ocean, though within life stage-specific, physiological thermal tolerance windows. [ABSTRACT FROM AUTHOR]

Climate change and harvesting result in temporal and spatial changes and variability in spawning, and thus in offspring ambient drift conditions. As a result, variable survival of offspring and thereby in recruitment are expected. This is especially true for species with long reproduction migration as is the case for some Atlantic cod stocks. We utilize biophysical model simulations to analyze survival from spawning until age 1 resulting from different scenarios of spatial and temporal changes in spawning. We find that survival is 1.5–2 times higher when spawning is shifted southwards as compared to northerly shifts. In general, survival is more sensitive to shifts in spawning location than in spawning time. Early spawning is only favourable if spawning is concurrently shifted farther north. A future spawning scenario with a northward shift in spawning grounds beyond what has been observed historically suggests reduced offspring survival and increased sensitivity to the timing of spawning. [ABSTRACT FROM AUTHOR]

Methods for jointly estimating both the size-specific relative retention and absolute retention (retention probability) of two experimental trawl gears are considered. One approach would be to undertake comparative fishing of both gears, from which their comparative catchability can be estimated directly. If comparative catchability can be corrected for differing sampling effort and fishing efficiency of the two gears, then relative retention can be estimated. Furthermore, if a suitable functional form of the absolute retention curve is assumed, then estimates of absolute retention can potentially be obtained. However, these estimated retention curves are seen to have extremely large statistical variability and will not be useful in practice. On the other hand, if the gears are each fished with a non-selective control, then absolute retention can be directly estimated, from which estimates of relative retention can immediately be obtained. However, these estimates of relative retention have greater variability than would be obtained by comparative fishing with the same level of sampling effort. It is shown that a hybrid selectivity design that includes both comparative fishing of the experimental trawls and fishing with a non-selective control provides a more balanced approach. An extensive simulation study is conducted using scenarios based on recently published work on selectivity experiments targeting cod (Gadus Morhua) and hoki/blue grenadier (Macruronus novaezelandiae). [ABSTRACT FROM AUTHOR]

To better understand spawning vocalizations of Norwegian coastal cod (Gadus morhua), a prototype eight-element coherent hydrophone array was deployed in stationary vertical and towed horizontal modes to monitor cod sounds during an experiment in spring 2019. Depth distribution of cod aggregations was monitored concurrently with an ultrasonic echosounder. Cod vocalizations recorded on the hydrophone array are analysed to provide time–frequency characteristics, and source level distribution after correcting for one-way transmission losses from cod locations to the hydrophone array. The recorded cod vocalization frequencies range from ∼20 to 600 Hz with a peak power frequency of ∼60 Hz, average duration of 300 ms, and mean source level of 163.5 ± 7.9 dB re 1 μPa at 1 m. Spatial dependence of received cod vocalization rates is estimated using hydrophone array measurements as the array is towed horizontally from deeper surrounding waters to shallow water inlet areas of the experimental site. The bathymetric-dependent probability of detection regions for cod vocalizations are quantified and are found to be significantly reduced in shallow-water areas of the inlet. We show that the towable hydrophone array deployed from a moving vessel is invaluable because it can survey cod vocalization activity at multiple locations, providing continuous spatial coverage that is complementary to fixed sensor systems that provide continuous temporal coverage at a given location. [ABSTRACT FROM AUTHOR]

Predicting recruitment in a reliable fashion is a great challenge within operational fisheries advice. Here, we consulted the unique but undercommunicated IMR Cod Larva Project (1975–1990), its spin-offs, placed in an international era of advancements over the last 50 years to glance into the future. Few initiatives of this kind have applied such extensive research approaches, spanning from laboratory, mesocosm, tank, and field studies to process modelling. The "critical period" concept appeared misleading, covering months rather than days of the early life history stages (ELHS) of Northeast Arctic cod. Larval feeding success was strongly modified by improved encounter rates from wind-induced turbulence. In addition, the following maternal effect studies evidenced that the dynamics of stock demography prior to spawning should be upheld to promote recruitment success. Although we now have lower-trophic level models as well as ELHS individual-based models, such models are still insufficiently reflecting the needed spatiotemporal resolution. The same problem applies to climate/circulation models. Nevertheless, this long-lasting research has significantly improved the mechanistic understanding of ELHS dynamics but also of the more predictable adult reproductive parameters. Based on a "to-list list," we suggest research avenues that should be pursued to further improve our ability predicting recruitment strength in marine fish stocks. [ABSTRACT FROM AUTHOR]

An ecosystem's ability to maintain key functions during environmental change is largely determined by its biodiversity. We compared fish species composition, richness, diversity, catch per unit effort (CPUE), and fish size between a 1.5 km2 no-take marine protected area (MPA) and a nearby fished area on the southern Norwegian coast annually for one decade (2011–2021), including before-protection status. In total, >26 thousand fish representing 31 species were sampled using a beach seine. No significant effect of protection was detected on either species richness, diversity, or evenness. For selected species of small-bodied intermediate predators, there was a significant decline in mean body size in the MPA area compared to the fished area, indicative of a response to protection involving trophic interactions. No significant effect of the MPA was detected on either CPUE or body size of Atlantic cod (Gadus morhua), a top predator mainly captured at the juvenile stage by our sampling. The limited responses seen in this study may be linked to the small size of the MPA compared to the dispersal and movement capabilities of species such as the cod. [ABSTRACT FROM AUTHOR]

To improve the ecological and economic sustainability in the Dutch beam trawl fishery, tickler chains were replaced by electrical pulse stimulation to drive common sole (Solea solea) out of the seabed. Because electrical stimulation may cause internal injuries, we quantified this risk by sampling fish species from commercial beam trawlers and recording spinal injuries and haemorrhages from X-radiographs and autopsy. To distinguish mechanically-induced and electrical-pulse-induced injuries, we compared injuries in ten species sampled from pulse (PUL) and tickler-chain (TCK) trawlers and four species sampled from PUL trawlers with the stimulus switched on or off. Co-occurrence of a major spinal injury and major haemorrhage at the same location was only observed in PUL samples, and were frequently (40%) observed in Atlantic cod (Gadus morhua) and in low numbers (0–2%) in whiting (Merlangius merlangus), grey gurnard (Eutrigla gurnardus), and greater sandeel (Hyperoplus lanceolatus), but not in flatfishes and other species. In cod, injury occurrence correlated with fish length, with lower probabilities for small fish. Major spinal injury or major haemorrhage occurrence in PUL (range: <1–16%) was lower than in TCK (range: <1–42%) in eight of the ten species studied. Population level consequences of pulse-induced injuries are considered negligible. [ABSTRACT FROM AUTHOR]

An organism's body condition describes its mass given its length and is often positively associated with fitness. The condition of Atlantic cod (Gadus morhua) in the Baltic Sea has declined dramatically since the early 1990s, possibly due to increased competition for food and hypoxia. However, the effects of biotic and abiotic variables on body condition have not been evaluated at local scales, which is important given spatial heterogeneity. We evaluate changes in distribution, experienced environmental conditions, and individual-level condition of cod in relation to covariates at different spatial scales using geostatistical models with spatial and spatiotemporal random effects. Sprat, Saduria entomon , temperature and oxygen were positively associated with condition, and depth was negatively associated. However, the effects of explanatory variables were small—spatial and spatiotemporal latent variables explained 5.7 times more variation than all covariates together (year excluded). Weighting environmental oxygen with local biomass densities revealed steeper declining trends compared to the unweighted oxygen in the environment, while the effect of weighting was less clear for condition. Understanding the drivers of spatiotemporal variation in body condition is critical for predicting responses to environmental change and to effective fishery management; yet low explanatory power of covariates on individual condition constitutes a major challenge. [ABSTRACT FROM AUTHOR]

Wild fish attracted to salmon farms feed on waste feed that presently contain high levels of fatty acids of terrestrial origin. This study examines whether mature Atlantic cod (Gadus morhua) caught at spawning grounds has eaten salmon waste feed. Cod were caught at four spawning grounds around Smøla (Norway), an area with multiple salmon farms, during the spawning season in 2018 (n = 327) and 2019 (n = 488). The fatty acid (FA) profile of their livers, gonads (ovary and testis), and muscles (2019) were determined. Multivariate k-mean cluster analysis of liver FA profiles revealed three main clusters, which could be allocated to trophic niches using known fatty acid trophic markers (FATMs). Of the sampled cod in 2018 and 2019, 13 % and 20 % respectively had high liver concentrations of terrestrial FATMs (18:1n-9, 18:2n-6, and 18:3n-3), indicating waste feed feeding. The remaining cod could be assigned to either the pelagic or benthic food chain. The cod identified as feeding on waste feed had large, fatty livers. The terrestrial FAs were also transferred to the muscle and gonad lipids. It is postulated that the latter may result in gametes with sub-optimal lipid composition, potentially impacting fitness, which warrants further investigation. [ABSTRACT FROM AUTHOR]

Seismic airgun surveys to map petroleum deposits in the seabed may impact behaviour of marine animals over large distances. Understanding whether fish spawning behaviour is affected by this anthropogenic noise source is important because reproductive success may be impacted. The fine-scale behavioural responses of Atlantic cod to airgun exposure over an extended period were investigated using an acoustic telemetry positioning system on a spawning ground in Norway. During 2019 to 2021, 135 spawning cod were equipped with telemetry sensor tags and were exposed to airgun shooting during the spawning periods of 2020 and 2021, with varying received sound levels comparable to a full-scale survey at distances of 5 to >40 km. Cod demonstrated only weak responses to the disturbance from repeated 3-h treatment periods over 5-d, swimming on average slightly deeper during seismic exposure compared to silent control periods. This response varied between individuals. Longer-term effects of seismic exposure on swimming depth were not detected. No changes in swimming acceleration, displacement, or area use occurred. These results suggest that relatively distant seismic surveys do not substantially alter cod behaviour during the spawning period at received sound exposure levels varying between 115 and 145 dB re 1 µPa2s over a 5-d period. [ABSTRACT FROM AUTHOR]

Cryptic population structure in exploited fishes poses a major challenge for fisheries management. In Atlantic cod, sympatric ecotypes are well-known, for instance off the coast of northern Norway. Recently, two sympatric cod ecotypes have also been documented in the Skagerrak and Kattegat, where adult cod has declined dramatically. One ecotype has an apparent offshore origin and displays a more migratory lifestyle than the other, which is generally resident at the coast throughout its life. To investigate their relative abundances along the Swedish west coast, juvenile cod were collected at high spatial resolution along the coast and genetically assigned to ecotypes. The results reveal large proportions of the coastal ecotype in the southern Kattegat, Öresund, and inshore Swedish Skagerrak, whereas the offshore ecotype dominates in offshore areas. A regression model comparison suggests that differences in bottom depth, rather than distance from the open sea, explain the heterogeneous spatial distribution of the two ecotypes. In addition, the two ecotypes display genetic differences suggesting adaptation to different environments. The results underline that successful fisheries management requires identification and consideration of locally adapted sympatric ecotypes. [ABSTRACT FROM AUTHOR]

Marine recreational fishing is popular in Norway, but current estimates of the catches by resident and tourist anglers are lacking due to several challenges, in particular Norway's long and intricate coastline with no defined access points and the large tourist fishery. To test methods for long-term monitoring of boat-based marine recreational anglers, estimate their catches, and characterize the fishery, we conducted a roving creel survey based on a novel spatial sampling frame and a survey of tourist fishing businesses in Troms and Hordaland County. These surveys showed that cod (Gadus morhua) and saithe (Pollachius virens) dominated the catches in Troms, while mackerel (Scomber scombrus) and saithe dominated the catches in Hordaland. The estimated total annual harvest of cod by all marine recreational anglers was 2 160 tonnes (relative standard error, or RSE 44%) in Troms and 73 tonnes (RSE 29%) in Hordaland, of which ∼40% (in weight) were landed in registered tourist fishing businesses, based on data from the tourist fishing survey. The results indicate that recreational anglers in Hordaland harvest more cod in coastal waters than commercial fishers. This study provides information for developing marine recreational fisheries monitoring in challenging survey situations to support science-based fisheries management. [ABSTRACT FROM AUTHOR]

Fishermen make repeated choices with respect to when, where, and how to catch their target species. While these targeting tactics—and the factors shaping them—are known to fishers and some experts, knowledge about them is largely informal and not well utilized for management purposes. To formalize information on targeting tactics, we propose a set of methods combining model-based classification of target species with generalized linear models. We apply these methods to Norwegian coastal fishing vessels that caught Atlantic cod (Gadus morhua) as a part of their catch portfolio in 2019. The data contains nearly 32000 fishing trips by 761 vessels. Gaussian mixture models identify eight latent targeting tactics. Cod contributes significantly to three of the tactics. The Herfindahl–Hirschman Index, a measure of vessel-level diversity of tactics, shows that one quarter of the vessels had a specialized strategy (targeting cod plus at most one additional tactic). While cod is often studied as a single-species fishery, we show that cod-catching vessels can be engaged in relatively pure fisheries during some fishing trips but switch to different, often more mixed targets during other trips. We term this as "sequential mixed fisheries". This is both a challenge and an opportunity for the fisheries management. [ABSTRACT FROM AUTHOR]

Seismic airgun surveys may disturb and displace fish at large ranges. If such displacement causes fish to abandon spawning grounds, reproductive success could be impacted. To investigate whether airgun sound causes cod (Gadus morhua L.) to leave their spawning grounds, acoustic telemetry arrays were deployed on two cod spawning grounds: a test and a reference site. From 2019 to 2021, 136 mature cod from the test site and 45 from the reference site were tagged with acoustic transmitters. Intermittent seismic shooting of two 40 in.3 airguns for 1 week during the spawning periods of 2020–2021 resulted in fluctuating sound exposure levels (SEL) at the test site, comparable to a full-scale industrial survey 5–>40 km away. Residency and survival of tagged cod were analysed with capture–mark–recapture models fitted to the detection and recapture data. Departure rate of the mature cod varied between spawning seasons but was similar between the test and reference sites. Neither survival nor departure significantly differed between seismic exposure and baseline periods. The results indicated that exposure to airguns at received SEL of up to ∼145 dB re 1 µPa2 s, comparable to a seismic survey occurring several kilometres away, did not displace tagged cod from spawning grounds. [ABSTRACT FROM AUTHOR]

We compared stock origin, size- and age-distributions, and length growth rates derived from Atlantic cod otoliths from archaeological excavations at two sites in northern Norway: Vágar in Lofoten (68°12′N, ad 1156–1285) and the Værbukta site (70°57′N, ad 1450–1680). For comparison, modern otoliths were sampled during 1993–2001 from areas situated close to Vágar and Værbukta. Length-at-age from pre-20th century samples was back-calculated from otolith growth increments. The pre-20th century cod from Vágar was dominated by northeast Arctic cod (NEAC) of age 9–16 years and were much older and larger than the pre-20th century cod from Værbukta, which were dominated by coastal cod of age 2–6 years. Cod from Vágar had smaller increments and a shorter back-calculated length-at-age than modern cod from Lofoten. In contrast, the predominantly coastal cod from Værbukta had similar increments width and length-at-age as in modern samples. Age-distributions and mortality rates of the pre-20th century Vágar cod and NEAC from Lofoten in the 1930s were similar, indicating that both age at maturity and longevity were similar for these time periods. This contrasts with truncated and young age-distributions of spawning NEAC in the 1980s and 1990s following the strong increase in fishing and total mortality rate in the period 1955–2000. [ABSTRACT FROM AUTHOR]

Temperature profoundly affects ectotherm physiology. Although differential thermal responses influence fitness, thus driving population dynamics and species distributions, our understanding of the molecular architecture underlying these responses is limited, especially during the critical larval stage. Here, using RNA-sequencing of laboratory-reared Atlantic cod (Gadus morhua) larvae of wild origin, we find changes in gene expression in thousands of transcripts consistent with a severe cellular stress response at both ambient and projected (+2°C and +4°C) temperatures. In addition, specific responses to stress, heat, and hypoxia were commonly identified in gene ontology enrichment analyses and 33 of the 44 genes comprising the minimum stress proteome of all organisms were upregulated. Earlier onset of the stress response was evident at higher temperatures; concomitant increased growth and mortality suggests a reduction in fitness. Temporal differences in gene expression levels do not correspond to differences in growing degree days, suggesting negative physiological consequences of warming beyond accelerated development. Because gene expression is costly, we infer that the upregulation of thousands of transcripts in response to warming in larval cod might act as an energetic drain. We hypothesize that the energetically costly stress response, coupled with increased growth rate at warmer temperatures, leads to faster depletion of energy reserves and increased risk of mortality in larval cod. As sea surface temperatures continue to rise over the next century, reduced fitness of Atlantic cod larvae might lead to population declines in this ecologically and socioeconomically important species. Further, our findings expand our understanding of transcriptomic responses to temperature by ectothermic vertebrate larvae beyond the critical first-feeding stage, a time when organisms begin balancing the energetic demands of growth, foraging, development, and maintenance. Linking the molecular basis of a thermal response to key fitness-related traits is fundamentally important to predicting how global warming will affect ectotherms. [ABSTRACT FROM AUTHOR]

Knowledge of recruitment and its variability in marine fish populations contributes to sustainable fisheries but a full understanding remains elusive. An earlier study showed that haddock (Melanogrammus aeglefinus) stocks exhibited consistently higher variability and lower reproductive rates compared to cod (Gadus morhua) stocks in the geographic regions where they co-occurred. Thus, cod may have a higher resilience to overexploitation, whereas haddock stocks may be more likely to be rescued by chance strong recruitments events. Since that initial study, the ecosystems and stocks have experienced large structural and functional changes, as well as changes in management practice and ocean warming. Here, we updated the previous earlier analysis with new data and found that despite large changes in the ecosystems explored, the patterns of recruitment variability have persisted. Recruitment variability remains higher in haddock than in cod, and the maximum annual reproduction rate at low spawning stock biomass (SSB) remains higher in cod than in haddock, although the latter difference is now less pronounced. Despite the economic and ecological importance of cod and haddock, and their long history of scientific scrutiny, the persistent difference in their reproductive biology remains unexplained. [ABSTRACT FROM AUTHOR]

Two decades of use of the compulsory selectivity gear configuration in the Northeast Atlantic bottom trawl fishery, which consists of a rigid sorting grid followed by a diamond mesh codend, have revealed problems with performance and efficiency. Size selectivity gear alternatives to this configuration are being pursued, and recent studies of codends with shortened lastridges have reported promising results. In this study, we compared the size selectivity and catch efficiency for cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) caught using a sorting grid with 55 mm bar spacing followed by a 130 mm knotted diamond mesh codend (i.e. the compulsory gear) that same configuration but considering only the catch in the 130 mm diamond mesh codend (regular codend), and an alternative knotless codend with shortened lastridge ropes and a thinner twine. We also addressed the question of whether size-selective gear is even needed to avoid exceeding the bycatch limits of the fishery. Our results demonstrated that the alternative codend improved size selectivity by reducing the loss of fish above minimum legal size (MLS), with a minor increase in the retention of fish below MLS , compared to the compulsory combined grid and codend configuration. The regular codend also reduced the loss of fish above MLS , but the retention of haddock below MLS approached the legal limit of 15% by number. Our results also showed that the abundance of cod below MLS in the fishing area during the trials was low. They also suggested that spatial and seasonal closures in combination with a flexible choice of selection device and modern monitoring tools could be an alternative to rigid enforcement of the use of selective fishing gear. [ABSTRACT FROM AUTHOR]

To supplement catch and effort regulations with the purpose to rebuild the cod (Gadus morhua) stock in Kattegat, Sweden and Denmark established a large (426 km2) year-round no-take zone (NTZ) surrounded by partially protected areas (PPAs) in 2009. The purpose of these spatial regulations was to prohibit cod fishing on the spawning grounds and to displace fisheries bycatch of cod from areas where mature cod aggregate in the Kattegat. The aim of this study is to evaluate the effects of the established NTZ and PPAs on the local fish assemblage, including cod. Based on a spatially high-resolution bottom trawl survey in the Kattegat (covering 2008–2021), multivariate analyses revealed significant shifts in the fish assemblage. A closer analysis indicated that six to seven fish species, including cod increased in the NTZ relative to control areas depending on if abundance or biomass was used as dependent variable. Univariate analysis showed that two flatfish species dab (Limanda limanda) and lemon sole (Microstomus kitt), and Norway lobster (Nephrops norvegicus) significantly increased in biomass in the NTZ, and turbot (Scophthalmus maximus) in the PPA relative to the control areas. These results suggest that the NTZ protected even relatively mobile species in an open sea system, such as the Kattegat. However, neither cod abundance nor biomass showed a significant increase as an effect of the NTZ and PPA despite two relatively strong year classes in 2012 and 2013, which possibly would have helped the recovery of the cod stock. As assessed by the International Council for the Exploration of the Sea in 2022, Kattegat cod continuously suffer from being severely overfished with low recruitment, and high discard rates in the mixed N. norvegicus fishery, is considered the major driver behind the reinforced depletion of the stock. [ABSTRACT FROM AUTHOR]

Discarding can be an unknown source of biases and uncertainties in stock assessments. Discarding patterns and quantities vary so a routine methodology for estimating discards is important to give a better picture of total catches, and potentially mortality, in fisheries. Using data from the Norwegian Reference Fleet between 2012 and 2018, this study presents a revised methodology for estimating discards of cod (Gadus morhua) in the Norwegian coastal gillnet fisheries, which accounts for variations in discarding between vessels and uncertainties in the conversion of numbers to weight discarded. The estimated average discard rate of cod (weight of cod discarded as percentage of total weight caught) is 0.55% (95% confidence interval: 0.45–0.70%), although discard rates in southern areas were an order of magnitude higher than in northern areas. We also present an exploratory analysis of the drivers behind discarding using a random forest regression model. Spatial variations and fishing intensity were identified as the most important drivers of discarding. Results from this study suggest ways in which self-sampled data can be used to estimate discards in Norwegian coastal fisheries, and where the accuracy of future estimates can be improved when a higher resolution data collection programme is established. [ABSTRACT FROM AUTHOR]

Mixed-stock fisheries pose a challenge for fisheries management recommendations and management, as mixed stocks can lead to unintentional over- or under-exploitation of stocks, with both short- and long-term biological and economic consequences. This study demonstrates practical application and implementation of year-round high-resolution genetic stock monitoring in management of mixed Atlantic cod (Gadus morhua) stocks in western Greenland. Using a panel of 96 high resolution gene-associated SNPs, we identified the stock of origin for four cod stocks in the two major inshore mixed-stock fisheries. Contribution of individual stocks was quantified to identify if fjord sections, times of year, and fish size, would allow a "clean fishery" with a minimal contribution of the depleted West Greenland Offshore (WGO) population. High level of mixing was identified with 50% of inshore catches originating from the inshore stock, 20% from the East Greenland/Iceland offshore stock, and 30% from the WGO stock. Although some spatiotemporal variation of stock proportions was identified, a practice allowing exclusively fishing a specific stock was not possible. Accordingly, we demonstrate the need to allocate catches at the biological stock level and show that application of high-resolution genetics is a reliable and necessary tool. [ABSTRACT FROM AUTHOR]

Natural mortality (M) is difficult to measure directly in exploited fish stocks. Therefore, in stock assessments, M has usually been assumed to be constant for age classes of fishable size. However, M is likely to vary annually due to temporal changes in food availability, predation, fish size at age, and other biological and environmental factors. We suggest that M of fish at age and year is the sum of length-related mortality and condition-related mortality (M = ML + MC). We propose that MC is directly proportional to PKH, the percentage of fish in the stock with condition factor (K) and liver condition (H) below critical values. This relationship is used to demonstrate likely patterns in annual variation in MC for ages 2–9+ in Icelandic cod (Gadus morhua) based on fish measurements in groundfish surveys in spring and autumn. There were annual fluctuations and temporal trends observed in MC for different age classes attributable to variation in food availability. The described method is suitable for age-structured stock assessments of cod and other fish stocks. Our results indicate that basic stock assessments may be improved by including estimates of variable MC. [ABSTRACT FROM AUTHOR]

In subarctic Newfoundland, age-0 juvenile Atlantic cod (Gadus morhua) settle into coastal habitats in several summer and fall pulses, yielding a broad length-frequency distribution prior to their first winter. The first winter is often associated with physiological and metabolic stress and has been considered a critical survival period determining cohort strength. We evaluated size-structured overwinter mortality and movement using mark–recapture and condition metrics by marking 226 cod in two batches one week apart, in October 2016. We estimated fall and overwinter mortality, and documented movement of fish recaptured in May 2017 using Cormack–Jolly–Seber models. We recaptured 30 marked juveniles. High fall mortality characterized late settling cohorts relative to earlier settling cohorts (16.6%∙d−1 vs. 4.5–7.7% ∙d−1). Overwinter mortality was unexpectedly low (0.0052 and 0.0022% ∙d−1). Individual condition (Fulton's K) of juvenile cod remained high throughout winter across all size groups. We expected higher mortality of juvenile cod and broad dispersal of juveniles over winter (32 weeks). In contrast, our results indicated low mortality and high site-fidelity in their first winter. This study indicates the period leading up to winter is important for survival, suggesting winter is not a survival bottleneck and may even provide a refuge compared to the rest of the year. [ABSTRACT FROM AUTHOR]

Effects of offshore wind farm (OSW) development in the US on fishery resources have been predicted based on European experience. A seven-year study of the first US OSW documented the response of demersal fish and invertebrates to construction and operation. Local fishermen and scientists designed a monthly demersal trawl survey using a Before-After-Control-Impact (BACI) design to assess potential effects of Block Island Wind Farm (BIWF), a pilot scale 30 MW project completed in 2016. Common species did not exhibit statistically significant (α = 0.10) BACI interactions in catch per unit effort (CPUE) due to BIWF operation. CPUE of structure-oriented species, such as black sea bass (Centropristis striata) and Atlantic cod (Gadus morhua), increased at BIWF following turbine installation. Fall and spring biomass varied synchronously between BIWF and a regional survey for several species including longfin squid (Loligo pealeii) and winter flounder (Pseudopleuronectes americanus). Spatial-temporal interaction between reference areas provided an estimate of the minimum effect sizes (approximately 40% to 63% among the fish evaluated) that may be considered ecologically significant when assessing potential OSW impacts. Results from this first North American OSW fisheries monitoring study provide valuable information for future OSW development on the northeastern US coastline. [ABSTRACT FROM AUTHOR]

Hypoxia is presently seen as the principal driver behind the decline of the former dominating Eastern Baltic cod stock (EBC ; Gadus morhua). It has been proposed that both worsening conditions for reproduction and lower individual growth, condition, and survival are linked to hypoxia. Here, we elucidate the ecological envelope of EBC in terms of salinity stratification, oxygen content, and benthic animal biomasses, and how it has affected EBC productivity over time. The spawning conditions started deteriorating in the Gotland Deep in the 1950s due to oxygen depletion. In contrast, in the Bornholm Basin, hydrographic conditions have remained unchanged over the last 60 years. Indeed, the current extent of both well-oxygenated areas and the frequency of hypoxia events do not differ substantially from periods with high EBC productivity in the 1970s–1980s. Furthermore, oxygenated and therefore potentially suitable feeding areas are abundant in all parts of the Baltic Sea, and our novel analysis provides no evidence of a reduction in benthic food sources for EBC over the last 30 years. We find that while reproduction failure is intricately linked to hydrographic dynamics, a relationship between the spread of hypoxia and the decline in EBC productivity during the last decades cannot be substantiated. [ABSTRACT FROM AUTHOR]

Providing science-based advice can be challenging. Personal in its reflections, the story that follows asks throughout: What constitutes an appropriate model for the communication of science-based advice that best serves society? The first "front line," in 1992, involved tenuous hypotheses on the collapse and recovery of Newfoundland's Northern cod (Gadus morhua), raising troubling questions about political influence on science-based advice and on its integrity. These questions subsequently motivated a critique written with two colleagues on the communication of science to decision-makers, provoking a telling invective from a government department in defence of the status quo. The story transitions to my 2000–2012 tenure as a member and then as chair of Canada's national body advising which species should be on the legally binding national at-risk register, illustrating how politically sensitive science-based advice can be objectively, effectively, and independently communicated, unfiltered by vested interests. Since 2009, I have served as independent science advisor on the sourcing of sustainable seafood to Canada's largest food retailer, providing a meaningful, impactful opportunity to advise their decision-makers. Science-based advice, free from political and advocacy-driven vested interests, is a requisite return for tax-supported investments in science. If provision of such advice is a "moral imperative," as argued more than 60 years ago by C.P. Snow, then scientists are obliged to be the best advisors that we can be. [ABSTRACT FROM AUTHOR]

Gillnets are used world-wide for harvesting groundfish and pelagic species at sea and in freshwater. Little consideration has been given to how fish are caught in gillnets, even though the capture mode provides valuable information for understanding gear catchability. This paper describes a new method of estimating the length-dependent fish capture modes in gillnets. Using this method, we investigated the length-dependent capture modes for cod (Gadus morhua) in commercial monofilament nylon gillnets. Cod is a target species for several fisheries in the Northern Atlantic. This is the first time the capture mode was formally related to fish size with a direct representation of the experimental observations. The results demonstrated that gillnets are clearly designed for gilling. However, capture modes were size dependent, with small fish being caught by the mouth and larger fish by the maxillary. The application of the method is relevant when used by gear technologists to evaluate different gear characteristics to improve size or species selectivity. Changing the hanging ratio, for instance, or replacing nylon twine by thicker biodegradable material may considerably change the capture modes and their effect on gear efficiency. [ABSTRACT FROM AUTHOR]

The fishery for Northern Atlantic cod (Gadus morhua) off Newfoundland and Labrador, Eastern Canada, presents the most spectacular case of an exploited stock crashed in a few decades by an industrial bottom trawl fishery under a seemingly sophisticated management regime after half a millennium of sustainable fishing. The fishery, which had generated annual catches of 100000 to 200000 tonnes from the beginning of the 16th century to the 1950s,  peaked in 1968 at 810000 tonnes, followed by a devastating collapse and closure 24 years later. Since then, stock recovery may have been hindered by premature openings, with vessels targeting the remains of the cod population. Previous research paid little attention towards using multicentury time series to inform sustainable catches and recovery plans. Here, we show that a simple stock assessment model can be used to model the cod population trajectory for the entire period from 1508 to 2019 for which catch estimates are available. The model suggests that if fishing effort and mortality had been stabilized in the 1980s,  precautionary annual yields of about 200000 tonnes could have been sustained. Our analysis demonstrates the value of incorporating prior knowledge to counteract shifting baseline effects on reference points and contemporary perceptions of historical stock status. [ABSTRACT FROM AUTHOR]

While the importance of early life survival and growth variations for population dynamics is well documented, there is still a relatively limited understanding of how survival and growth is affected by the species' spatial distribution. Using Barents Sea spatial bottom survey data (1994–2018), we study the spatiotemporal variability of the juvenile Atlantic cod (Gadus morhua) growth and survival. We used indices of the spatial distribution of juvenile cod at age-1 to study the role of distribution for the change in abundance and mean body size through their second winter of life (from age-1 to age-2). Over the 24 years analysed, we found that the location where the age-1 cod are in the Barents Sea matters for their growth and survival. We found that year-classes growing up in the western Barents Sea have higher mortality but faster growth than year-classes distributed farther east. Our results indicate that the biotic and abiotic conditions encountered at the settlement location may influence the spatial survival and growth of age-1 cod and subsequently the population dynamics. Our results underscore the importance of distribution for survival and growth early in life and by providing this essential information has implications for stock assessment and spatial fisheries management. [ABSTRACT FROM AUTHOR]

Populations are shaped by their history. It is crucial to interpret population structure in an evolutionary context. Pairwise FST measures population structure, whereas population-specific FST measures deviation from the ancestral population. To understand the current population structure and a population’s history of range expansion, we propose a representation method that overlays population-specific FST estimates on a sampling location map, and on an unrooted neighbor-joining tree and a multi-dimensional scaling plot inferred from a pairwise FST distance matrix. We examined the usefulness of our procedure using simulations that mimicked population colonization from an ancestral population and by analyzing published human, Atlantic cod, and wild poplar data. Our results demonstrated that population-specific FST values identify the source population and trace the evolutionary history of its derived populations. Conversely, pairwise FST values represent the current population structure. By integrating the results of both estimators, we obtained a new picture of the population structure that incorporates evolutionary history. The generalized least squares estimate of genome-wide population-specific FST indicated that the wild poplar population expanded its distribution to the north, where daylight hours are long in summer, to coastal areas with abundant rainfall, and to the south where summers are dry. Genomic data highlight the power of the bias-corrected moment estimators of FST, whether global, pairwise, or population-specific, that provide unbiased estimates of FST. All FST moment estimators described in this paper have reasonable processing times and are useful in population genomics studies. [ABSTRACT FROM AUTHOR]

Stock-recruitment relationships (SRRs) may differ substantially among environmental regimes. We developed a methodology including a Hidden Markov Stock-recruitment Model (HMSM), the maximum likelihood approach and a model selection procedure to identify abrupt changes of stock-recruitment (SR) dynamics. This method allows us to objectively identify the unobserved regimes, estimate regime-specific parameters, and predict the transition probabilities among regimes. First, we used simulation to verify that our method could identify the correct number of regimes and estimate the model parameters well. Then, we applied the models to an Atlantic cod stock on the southern Grand Bank off Newfoundland, Canada. Results indicated that the HMSM assuming 2 regimes performed the best, and the cod stock shifted to a regime characterized with lower productivity and higher density dependence in late 1980s. Additionally, the estimated probability to return to the previous high-productivity regime was very low, suggesting the cod stock may remain at the low-productivity regime for a prolonged period. Overall, we consider the methodology proposed in this paper as a useful tool to model regime shifts of SRRs in fisheries stock assessment. [ABSTRACT FROM AUTHOR]

The iconic Atlantic cod (Gadus morhua Linnaeus, 1758) has inspired a substantial body of fishing-gear research across its geographical range, with recent efforts predominately to reduce catches of this species in fisheries where their populations are fragile. Despite their iconic status and long history of study compared to other species, our understanding of cod behaviour during the capture process in a bottom trawl remains frustratingly limited. Much of our understanding is derived indirectly through catch results, supported to a limited extent by direct observations of cod in situ or held in laboratories. In this paper, we describe four research challenges and directions that we consider critical to advance our knowledge of cod behaviour, and ultimately, to improve the selectivity of bottom trawls to reduce catches of cod. These include the resurrection of behavioural research to directly observe and measure their reaction and sensory capabilities, and improved interpretation of their behaviour in response to a bottom trawl. It is also our view that progress in limiting catches of cod should emphasize stimulating avoidance in advance or at the mouth of an approaching bottom trawl, rather than retrospectively attempting to do so after they have entered the trawl mouth. [ABSTRACT FROM AUTHOR]

Schijns et al. use a historical time series to inform a stock assessment model for the northern Atlantic cod (Gadus morhua) fishery from 1508 to 2019. They find that catches from the sixteenth century to the 1950s did not exceed 200000 t per annum and could have been sustained today "if fishing effort and mortality had been stabilized in the 1980s". Had Schijns et al. used a more complete and representative time series (as identified below), they would have found that catches were substantially higher during much of the time period, possibly affecting their conclusions regarding the timing and onset of unsustainable exploitation. In an earlier paper, based on original archival documentation, we have argued that total landings in the Newfoundland fishery averaged 400000 t in the eighteenth century and peaked at 600000 t in 1788. We contend that pre-industrial technology was sufficient to have a significant impact on marine life. [ABSTRACT FROM AUTHOR]

Stock–recruitment relationships (SRRs) may vary over time due to ecological and anthropogenic impacts, challenging traditional approaches of calculating maximum sustainable yield (MSY)-based reference points that assume constant population traits. We compare seven methods to calculate MSY, F MSY and B MSY by modelling constant, stochastic (uncorrelated), and autocorrelated SRRs using simulations and two case studies [Atlantic cod (Gadus morhua) and American plaice (Hippoglossoides platessoides) on the Grand Bank off Newfoundland, Canada]. Results indicated that the method used to model SRRs strongly affected the temporal pattern of recruitment projection, and the variations generated by autocorrelated SRRs were more similar to observed patterns. When the population productivity had low-frequency and large-magnitude variations, stochastic SRRs generated greater MSY and F MSY estimates than constant or autocorrelated SRRs, while no consistent pattern of B MSY was detected. In the case studies, stochastic and autocorrelated SRRs produced asymmetric relationships between fishing mortality and yield, with higher risk of overfishing by going beyond F MSY. Overall, our results suggest that caution should be taken when calculating MSY-based reference points in highly dynamic ecosystems, and correctly accounting for non-stationary population dynamics could, therefore, lead to more sustainable fisheries. [ABSTRACT FROM AUTHOR]

Atlantic cod (Gadus morhua) is one of the most commercially important fish species in the North Atlantic. Environmental factors, such as water temperatures, influence growth of individuals over time, thus forming population-specific growth patterns across climatic regions. Here we develop an integrative approach to investigate the role of temperature in shaping geographic differences of cod growth in the Celtic Sea, North Sea, Iceland, and Barents Sea. We combine a physiology-based growth model and 50-years observational temperature data of 0.5 × 0.5° spatial resolution to simulate continuous growth of cod. The model generated weight-at-age data for the period 1959–2007 which we compared to observational data from fishery-independent scientific surveys. In the Celtic and the northern North Sea, simulated growth matches well observational data. We also show that relatively warm temperatures in the Celtic Sea facilitate maximum growth rates; future warming is likely to have a negative impact on growth of these cod stocks. Growth simulations in Icelandic waters and the Barents Sea are less consistent with local observational data. More complex growth patterns in these regions are probably shaped by ontogenetic shifts in temperature regimes, feeding conditions and physiological adaptations. These findings should stimulate further research on critical processes to be considered in population-specific projections of growth of cod and productivity. [ABSTRACT FROM AUTHOR]

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

The snow crab (Chionoecetes opilio) is a newly established species in the Barents Sea, increasing in both distribution and abundance in recent years. We explore the potential importance of North-east Arctic cod (Gadus morhua) predation in structuring the snow crab population expansion in the Barents Sea, through an analysis of cod stomach content data from 2003 to 2018. Spatio-temporal patterns of snow crab within cod diet are assessed across years, between seasons, as well as ontogenetic trends, including predator–prey size relationships. Snow crab represents a new prey item for cod and in recent years the most dominant demersal crustacean species in cod diet. The proportion of snow crab within cod diet increases over time. Primarily 60–110 cm cod prey upon snow crab, mainly during the summer/autumn season. Our results support the idea that the snow crab is still expanding, shifting distribution north and westwards. Cod has the potential to regulate the snow crab population but is unlikely to be in direct competition with the fishery in the Barents Sea. This work suggests that cod can be used as biological sampling tools together with other monitoring programmes to elucidate how new species may affect predator–prey and food-web dynamics within an ecosystem context. [ABSTRACT FROM AUTHOR]

Fish pots have lower catch efficiency than gillnets and trawls and, therefore, are rarely used for catching Atlantic cod (Gadus morhua) and similar species. Fish-retention devices (FRDs), non-return devices that permit fish to enter the pot while impeding exit, reduce the pot exit rate and therefore can increase catches. Conventional FRDs, however, also reduce entry rate and may not improve catches. To increase pot-catch efficiency, we developed and tested a new trigger-type FRD, made of transparent acrylic glass, which we named acrylic fingers (AFs). AFs are almost invisible underwater and offer little resistance to entering cod. We compared AFs with Neptune fingers (NFs), a conventional trigger-type FRD with a distinct visual outline, by observing cod entry and exit rates through both trigger types rigged to a pot in a net pen. Both trigger types significantly reduced exit rates compared with a funnel without triggers; however, NFs also reduced entry rates by visually deterring cod. Specifically, AFs have higher entry-to-exit ratios and therefore improve catch efficiency. Combining AFs with funnels further increased catch efficiency. Thus, transparent acrylic triggers present a promising new approach to increasing pot-catch efficiency and may increase the uptake of the cod pot, an environmentally low-impact gear. [ABSTRACT FROM AUTHOR]

Fish fraud is a problematic issue for the industry. For it to be properly addressed will require the use of accurate, rapid, and cost-effective tools. In this work, near infrared reflectance spectroscopy (NIRS) was used to predict nutritional values (protein, lipids, and moisture) as well as to discriminate between sources (farmed vs. wild fish) and conditions (fresh or defrosted fish). Samples of five whitefish species—Alaskan pollock (Gadus chalcogrammu), Atlantic cod (G. morhua), European plaice (Pleuronectes platessa), common sole (Solea solea), and turbot (Psetta maxima)—including farmed, wild, fresh, and frozen ones, were scanned by a low-cost handheld near infrared reflectance spectrometer with a spectral range between 900 and 1700nm. Several machine learning algorithms were explored for both regression and classification tasks, achieving precisions and coefficients of determination higher than 88% and 0.78, respectively. Principal component analysis (PCA) was used to cluster samples according to classes where good linear discriminations were denoted. Loadings from PCA revealed bands at 1150, 1200, and 1400nm as the most discriminative spectral regions regarding classification of both source and condition, suggesting the absorbance of OH, CH, CH2, and CH3 groups as the most important ones. This study shows the use of NIRS and both linear and non-linear learners as a suitable strategy to address fish fraud and fish QC. [ABSTRACT FROM AUTHOR]

Harbour porpoise (Phocoena phocoena) bycatch for Norwegian commercial gillnet fisheries from 2006 to 2018 was estimated using a traditional ratio estimator and generalized additive linear mixed models, with weight of fish landed and number of gillnet hauls as proxies for fishing effort. Estimates were derived from data collected with a contracted reference fleet of small coastal vessels and scaled up to the whole fleet using data from landing statistics. Bycatch estimates exhibited large yearly variations, ranging from 1151 to 6144 porpoises per year. Bycatch estimates in 4 of the last 5 years were significantly less than in the preceding 2 years. The best ratio-based and model-based yearly bycatch estimates were 1580 porpoises [coefficient of variation, (C.V.) 0.10, 95% confidence interval (CI) 1302–1902] and 1642 porpoises (C.V. 0.15, 95% CI 1165–2142), respectively. About 75% of bycaught porpoises were taken in the cod (Gadus morhua) and monkfish (Lophius piscatorius) fisheries, while the rest were taken in a variety of different gillnet fisheries. Our results suggest that bycatch of harbour porpoise in Norwegian gillnet fisheries has been unsustainable for several of the last 13 years but are currently within international bycatch limits due to a recent reduction in monkfish fishing effort. [ABSTRACT FROM AUTHOR]

This article describes a method for the quantitative analysis of fish behaviour relative to selection devices in trawl gears. Based on video observations, the method estimates probabilities for a given event to happen and establishes behavioural tree diagrams representing and quantifying behavioural patterns in relation to the selection device under assessment. Double bootstrapping is used to account for the uncertainty originating from a limited number of fish observations and the natural variation in fish behaviour. The method is used here to supplement standard analysis of catch data for the performance assessment of a flatfish excluder (FLEX). The Baltic Sea trawl fishery targeting cod (Gadus morhua) provides the pilot case. Results obtained by comparing catches with and without FLEX installed revealed that >75% of bycaught flatfish individuals escaped through the device, while no evidence was found that catches of cod in the targeted sizes were reduced. The behavioural analysis produced values of escape efficiency comparable to those obtained in the catch analysis. Furthermore, it revealed that ∼80% of the flatfish went calmly into the excluder, while most of the roundfish displayed avoidance swimming reactions. The method provides quantitative information of fish behaviour that can be relevant for developing and optimizing selection devices. [ABSTRACT FROM AUTHOR]

Fisheries enforcement relies on visual catch identification and quantification at sea or when landed. Silage (fish dissolved in acid) and fish blocks (block frozen fish) are promising methods for on-board processing and storage of low-value catches. We examined the use of non-destructive sampling and two DNA-based methods, quantitative PCR (qPCR) and metabarcoding, to assess species composition and relative abundance in industrial grade experimental silage and fish blocks. We demonstrate the ability to identify and quantify DNA from fish species in both products. qPCR analysis of small silage samples collected over 21 days detected all target control species. DNA from one species (Atlantic wolffish) was consistently overrepresented while, for three species of gadoids (Atlantic cod, haddock and whiting), the DNA content matched input tissue proportions with high accuracy. qPCR and metabarcoding of fish blocks, sampled as run-off water and exterior swabs, provided consistent species detection, with the highest variance observed in quantification from swab samples. Our analysis shows that DNA-based methods have significant potential as a tool for species identification and quantification of complex on-board-processed seafood products and are readily applicable to taxonomically and morphologically similar fish. There is, however, a need for establishing DNA/weight calibration factors for primary fisheries species. [ABSTRACT FROM AUTHOR]

Practical and applied knowledge of local fishers can help to improve our understanding of target species ecology and fisheries management decisions. In the Western Baltic Sea (WBS), the spatio-temporal distribution of cod is still largely unknown despite decades of research. We studied changes in cod distribution by obtaining information on temporal depth and habitat use of cod from commercial gillnet fishers using semi-directed interviews supplemented by at-sea observer data. Linear and non-linear regression analyses revealed significant relationships between depth use of cod and sea surface temperature (SST) as well as thermal stratification. Moreover, habitat use was related to SST and residence depth of cod. Areas deeper than 15 m were favoured from late December until March during low SST and a mixed water column (spawning) and also from July until August during high SST and strong thermal stratification (summer aestivation). Shallower areas were favoured during the rest of the year. The depth and habitat use displayed distinct seasonal up- and downslope movements of cod. This study highlights the importance of shallow-water and structured habitats for cod in the WBS and the value of local knowledge held by fishers for a better understanding of the distributional dynamics of important marine resource populations. [ABSTRACT FROM AUTHOR]

Currently available genome assemblies for Atlantic cod (Gadus morhua) have been constructed from fish belonging to the Northeast Arctic Cod (NEAC) population; a migratory population feeding in the Barents Sea. These assemblies have been crucial for the development of genetic markers which have been used to study population differentiation and adaptive evolution in Atlantic cod, pinpointing four discrete islands of genomic divergence located on linkage groups 1, 2, 7 and 12. In this paper, we present a high-quality reference genome from a male Atlantic cod representing a southern population inhabiting the Celtic sea. The genome assembly (gadMor_Celtic) was produced from long-read nanopore data and has a combined contig length of 686 Mb with an N50 of 10 Mb. Integrating contigs with genetic linkage mapping information enabled us to construct 23 chromosome sequences which mapped with high confidence to the latest NEAC population assembly (gadMor3) and allowed us to characterize, to an extent not previously reported large chromosomal inversions on linkage groups 1, 2, 7 and 12. In most cases, inversion breakpoints could be located within single nanopore contigs. Our results suggest the presence of inversions in Celtic cod on linkage groups 6, 11 and 21, although these remain to be confirmed. Further, we identified a specific repetitive element that is relatively enriched at predicted centromeric regions. Our gadMor_Celtic assembly provides a resource representing a ‘southern’ cod population which is complementary to the existing ‘northern’ population based genome assemblies and represents the first step towards developing pan-genomic resources for Atlantic cod. [ABSTRACT FROM AUTHOR]

Many studies demonstrate the importance of the commensal microbiomes to animal health and development. However, the initial community assembly process is poorly understood. It is unclear to what extent the hosts select for their commensal microbiota, whether stochastic processes contribute, and how environmental conditions affect the community assembly. We investigated community assembly in Atlantic cod larvae exposed to distinct microbial metacommunities. We aimed to quantify ecological processes influencing community assembly in cod larvae and to elucidate the complex relationship between the bacteria of the environment and the fish. Selection within the fish was the major determinant for community assembly, but drift resulted in inter-individual variation. The environmental bacterial communities were highly dissimilar from those associated with the fish. Still, differences in the environmental bacterial communities strongly influenced the fish communities. The most striking difference was an excessive dominance of a single OTU (Arcobacter) for larvae reared in two of the three systems. These larvae were exposed to environments with higher fractions of opportunistic bacteria, and we hypothesise that detrimental host–microbe interactions might have made the fish susceptible to Arcobacter colonisation. Despite strong selection within the host, this points to a possibility to steer the metacommunity towards mutualistic host–microbe interactions and improved fish health and survival. [ABSTRACT FROM AUTHOR]

The stock–recruitment relationship is the basis of any stock prediction and thus fundamental for fishery management. Traditional parametric stock–recruitment models often poorly fit empirical data, nevertheless they are still the rule in fish stock assessment procedures. We here apply a multi-model approach to predict recruitment of 20 Atlantic cod (Gadus morhua) stocks as a function of adult biomass and environmental variables. We compare the traditional Ricker model with two non-parametric approaches: (i) the stochastic cusp model from catastrophe theory and (ii) multivariate simplex projections , based on attractor state-space reconstruction. We show that the performance of each model is contingent on the historical dynamics of individual stocks, and that stocks which experienced abrupt and state-dependent dynamics are best modelled using non-parametric approaches. These dynamics are pervasive in Western stocks highlighting a geographical distinction between cod stocks, which have implications for their recovery potential. Furthermore, the addition of environmental variables always improved the models' predictive power indicating that they should be considered in stock assessment and management routines. Using our multi-model approach, we demonstrate that we should be more flexible when modelling recruitment and tailor our approaches to the dynamical properties of each individual stock. [ABSTRACT FROM AUTHOR]