The Arctic cod (Boreogadus saida) is a key species in Arctic marine ecosystems, adapted to extreme seasonality and cold environments. The overwintering survival and recruitment of age-0 Arctic cod heavily depend on achieving a sizable prewinter length (PWL) in their first year. Over the growth period, PWL is influenced by early life history traits, such as hatch date and size-at-hatch, and by environmental conditions, such as temperature and food availability. However, our knowledge of these interacting aspects of Arctic cod ecology is extremely limited. Here we coupled an individual-based transport and bioenergetic model with a sea ice-ocean model and simulated larval dispersal and growth under current environmental conditions. In addition, we tested two alternative scenarios of higher temperatures, with +2°C, and lower daily ration by 25% over the growth period. Our modeled PWL aligned well with field data on age-0 Arctic cod lengths by the end of summer. Largest PWLs resulted from winter spawns and were associated with more days with ice cover and shorter embryonic development. Under the high-temperature scenario, average PWL increased in Baffin Bay, Chukchi Sea, and Laptev Sea but declined in Svalbard, suggesting that a portion of age-0 Arctic cod are currently at their thermal tolerance limit. The recruitment success into the juvenile stage, defined as reaching a juvenile threshold length by the end of summer, was maximized in all winter spawns under the high-temperature scenario but decreased to zero in nearly all April spawns across all regions. Under the low-food scenario, reduced prey availability halved the recruitment success in all regions, indicating potentially severe consequences for future Arctic cod growth and survival. Our study illustrates how much changes in sea ice, temperature, and food availability influence the early development of Arctic cod and could impact their recruitment, highlighting the species’ increasingly uncertain future amid rapid environmental changes in the Arctic.

Body size is a key component of individual fitness and an important factor in the structure and functioning of populations and ecosystems. Disentangling the effects of environmental change, harvest and intra- and inter-specific trophic effects on body size remains challenging for populations in the wild. Herring in the Northwest Atlantic provide a strong basis for evaluating hypotheses related to these drivers given that they have experienced significant warming and harvest over the past century, while also having been exposed to a wide range of other selective constraints across their range. Using data on mean length-at-age 4 for the sixteen principal populations over a period of 53 cohorts (1962-2014), we fitted a series of empirical models for temporal and between-population variation in the response to changes in sea surface temperature. We find evidence for a unified cross-population response in the form of a parabolic function according to which populations in naturally warmer environments have responded more negatively to increasing temperature compared with those in colder locations. Temporal variation in residuals from this function was highly coherent among populations, further suggesting a common response to a large-scale environmental driver. The synchrony observed in this study system, despite strong differences in harvest and ecological histories among populations and over time, clearly indicates a dominant role of environmental change on size-at-age in wild populations, in contrast to commonly reported effects of fishing. This finding has important implications for the management of fisheries as it indicates that a key trait associated with population productivity may be under considerably less short-term management control than currently assumed. Our study, overall, illustrates the need for a comparative approach within species for inferences concerning the many possible effects on body size of natural and anthropogenic drivers in the wild.

Twenty-six years ago, in response to regionally devastating fisheries collapses in Canada, Hutchings et al. asked “Is scientific inquiry incompatible with government information control?” Now, a quarter-century later, we review how government science advice continues to be influenced by non-science interests, particularly those with a financial stake in the outcome of the advice. We use the example of salmon aquaculture in British Columbia, Canada, to demonstrate how science advice from Fisheries and Oceans Canada (DFO) can fail to be impartial, evidence-based, transparent, and independently reviewed—four widely implemented standards of robust science advice. Consequently, DFO's policies are not always supported by the best available science. These observations are particularly important in the context of DFO having struggled to sustainably manage Canada's marine resources, creating socio-economic uncertainty and putting the country's international reputation at risk as it lags behind its peers. We conclude by reiterating Hutchings et al.’s unheeded recommendation for a truly independent fisheries-science advisory body in Canada to be enshrined in the decision-making process.

Fisheries are complex social–ecological systems, meaning that the achievement of 'sustainable' fisheries demands a multifaceted approach, involving ecological, economic, social, and institutional dimensions. Addressing these diverse concerns requires the collection and synthesis of new sources of information by science-advising bodies and the engagement of multiple knowledge types from rightsholders and stakeholders. The 'modernized' (2019) Fisheries Act in Canada allows for a diverse range of considerations to form the basis of fisheries management decisions, including knowledge from community or industry groups, but it remains unclear where and when such information is available, how this information is prioritized, who contributes to information-gathering processes, and what the management consequences of information use might be. The present study uses a selection of science-advising documents and briefing notes for decision makers to explore the information and priorities informing fisheries management decisions in Atlantic Canada, with a focus on how rightsholders and stakeholders contribute to the process. These findings can inform efforts to adopt an inclusive and participatory approach to evidence-based decision making to achieve sustainable fisheries, in the broadest sense of the word.

Large bodied species are known to live longer than small bodied species. However, it is less clear whether the positive correlation varies across taxa. In this short communication, we combine data entries from literature and databases on body mass and maximum life span for 3722 species covering taxonomic Classes Chondrichthyes, Teleostei, Amphibia, Reptilia, Aves, and Mammalia. We then analyse the log(maximum life span) – log(body mass) relationship using generalized linear model with nested random intercepts and slopes for Class/Order/Family. Our analyses generally demonstrate the positive longevity – body mass relationship but also reveal that slopes and intercepts differ slightly among all Classes except Reptilia and Amphibia. Highest slopes can be found in Classes Aves and Chondrichthyes. Differences between the smallest and largest Family-level slopes was more than threefold. While these preliminary analyses provide a brief overview of body size – longevity relationships across taxa, the dataset collated in the present study could serve as a start point for in-depth phylogenetic analyses to uncover complex pathways through which body size and its correlates might have evolved.

In nature, organisms are exposed to variable environmental conditions that impact their performance and fitness. Despite the ubiquity of environmental variability, substantial knowledge gaps in our understanding of organismal responses to nonconstant thermal regimes remain. In the present study, using zebrafish (Danio rerio) as a model organism, we applied geometric morphometric methods to examine how challenging but ecologically realistic diel thermal fluctuations experienced during different life stages influence adult body shape, size, and condition. Zebrafish were exposed to either thermal fluctuations (22-32°C) or a static optimal temperature (27°C) sharing the same thermal mean during an early period spanning embryonic and larval ontogeny (days 0-30), a later period spanning juvenile and adult ontogeny (days 31-210), or a combination of both. We found that body shape, size, and condition were affected by thermal variability, but these plasticity-mediated changes were dependent on the timing of ontogenetic exposure. Notably, after experiencing fluctuating temperatures during early ontogeny, females displayed a deeper abdomen while males displayed an elongated caudal peduncle region. Moreover, males displayed beneficial acclimation of body condition under lifelong fluctuating temperature exposure, whereas females did not. The present study, using ecologically realistic thermal regimes, provides insight into the timing of environmental experiences that generate phenotypic variation in zebrafish.

Understanding larval growth, mediated by the interaction of early life traits and environmental conditions, is crucial to elucidate population dynamics. We used a bioenergetic model as an integrative tool to simulate the growth of Arctic cod (Boreogadus saida) larvae and to test the sensitivity of modeled growth to temperature and food quantity and quality. The growth was computed as the energy gained through food consumption minus the energy lost through respiration and other metabolic processes. We extended a previously published bioenergetic model to cover the full range of larval length and used a simplified feeding module. This simplification allowed us to build a predictive tool that can be applied to larval Arctic cod at a large spatial scale. Our model suggested that with subzero temperatures in the High Arctic, larvae need to increase food consumption in order to reach the observed length-at-age in late summer. The modeled growth agreed well with the field observations in the High Arctic but was 2–3 times higher than the laboratory-derived growth rate, probably due to differences in food type and selective mortality. Our study reveals important knowledge gaps in our understanding of larval cod growth in the High Arctic, including the lack of empirical estimations of daily ration and respiration for larvae under the natural habitat temperatures.

Spatial and temporal synchrony in abundance or survival trends can be indicative of whether populations are affected by common environmental drivers. In Atlantic salmon ( Salmo salar), return rates to natal rivers have generally been assumed to be affected primarily by shared oceanic conditions, leading to spatially synchronous trends in mortality. Here, we investigated the existence of parallel trends in salmon sea survival, using data on migrating smolts and returning adults from seven Canadian populations presumed to share feeding grounds. We analysed sea survival, using a Bayesian change-point model capable of detecting nonstationarity in time series data. Our results indicate that while salmon have experienced broadly comparable patterns in survival, finer-scale temporal shifts are not synchronous among populations. Our findings are not consistent with the hypothesis that salmon populations consistently share the same mortality-related stressors in the marine environment. Although populations may have shared greater synchrony in survival patterns in the past, this synchrony may be breaking down. It may be prudent to direct greater attention to smaller-scale regional and population-level correlates of survival.

Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common-garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common-garden-gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco-evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high-dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco-evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common-garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible.

Whether gill area constrains fish metabolism through oxygen limitation is a debated topic. Here, the authors provide insights into this question by analysing mass-specific metabolic rates across 44 teleost fishes extracted from FishBase. They explore whether species deviations from metabolic rates predicted by body mass can be explained by species gill area. They show that the gill area explains c. 26%-28% of species-level deviations from mass-specific metabolic rates. Their findings suggest that gill area might indeed be one of the factors limiting metabolic rate in fishes.

Can the advantage of risk-managing life-history strategies become a disadvantage under human-induced evolution? Organisms have adapted to the variability and uncertainty of environmental conditions with a vast diversity of life-history strategies. One such evolved strategy is multiple-batch spawning, a spawning strategy common to long-lived fishes that ‘hedge their bets' by distributing the risk to their offspring on a temporal and spatial scale. The fitness benefits of this spawning strategy increase with female body size, the very trait that size-selective fishing targets. By applying an empirically and theoretically motivated eco-evolutionary mechanistic model that was parameterized for Atlantic cod (Gadus morhua), we explored how fishing intensity may alter the life-history traits and fitness of fishes that are multiple-batch spawners. Our main findings are twofold; first, the risk-spreading strategy of multiple-batch spawning is not effective against fisheries selection, because the fisheries selection favours smaller fish with a lower risk-spreading effect; and second, the ecological recovery in population size does not secure evolutionary recovery in the population size structure. The beneficial risk-spreading mechanism of the batch spawning strategy highlights the importance of recovery in the size structure of overfished stocks, from which a full recovery in the population size can follow.

To reduce the risk of overexploitation and the ensuing conservation and socio-economic consequences, fisheries management relies on receiving accurate scientific advice from stock assessments. Biomass dynamics models used in stock assessment tend to rely primarily on indices of abundance and commercial landings data. Standard practice for calculating the indices used in these models typically involves taking averages of survey tow data over large, diverse spatial domains. There is a lot of variability in the choice of methodologies used to propagate index uncertainty into the assessment model, many of which require specifying it through expert knowledge or prior distributions. Here we propose an alternative approach that treats each individual survey tow as an independent estimate of the true underlying biomass in the stock assessment model itself. This reduces information loss and propagates uncertainties into the model directly. A simulation study demonstrates that this approach accurately captures underlying population dynamics and reliably estimates variance parameters. We further demonstrate its utility with data from the Inshore Scallop Fishery of south-west Nova Scotia. Results show significant improvements in parameter estimation over previous models while providing similar predictions of biomass with less uncertainty. This reduced uncertainty can improve the resulting scientific advice and lead to improved decision-making by fisheries managers.

Objective As sequencing technologies become more accessible and bioinformatic tools improve, genomic resources are increasingly available for non-model species. Using a draft genome to guide transcriptome assembly from RNA sequencing data, rather than performing assembly de novo , affects downstream analyses. Yet, direct comparisons of these approaches are rare. Here, we compare the results of the standard de novo assembly pipeline (‘Trinity’) and two reference genome-based pipelines (‘Tuxedo’ and the ‘new Tuxedo’) for differential expression and gene ontology enrichment analysis of a companion study on Atlantic cod ( Gadus morhua ). Results The new Tuxedo pipeline produced a higher quality assembly than the Tuxedo suite. However, greater enrichment of Trinity-identified differentially expressed genes suggests that a higher proportion of them represent biologically meaningful differences in transcription, as opposed to transcriptional noise or false positives. Coupled with the ability to annotate novel loci, the increased sensitivity of the Trinity pipeline might make it preferable over the reference genome-based approaches for studies aimed at broadly characterizing variation in the magnitude of expression differences and biological processes. However, the ‘new Tuxedo’ pipeline might be appropriate when a more conservative approach is warranted, such as for the identification of candidate genes.

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.

Human-driven increases in global mean temperatures are associated with concomitant increases in thermal variability. Yet, few studies have explored the impacts of thermal variability on fitness-related traits, limiting our ability to predict how organisms will respond to dynamic thermal changes. Among the myriad organismal responses to thermal variability, one of the most proximate to fitness-and, thus, a population's ability to persist-is reproduction. Here, we examine how a model freshwater fish (Danio rerio) responds to diel thermal fluctuations that span the species's viable developmental range of temperatures. We specifically investigate reproductive performance metrics including spawning success, fecundity, egg provisioning and sperm concentration. Notably, we apply thermal variability treatments during two ontogenetic timepoints to disentangle the relative effects of developmental plasticity and reversible acclimation. We found evidence of direct, negative effects of thermal variability during later ontogenetic stages on reproductive performance metrics. We also found complex interactive effects of early and late-life exposure to thermal variability, with evidence of beneficial acclimation of spawning success and modification of the relationship between fecundity and egg provisioning. Our findings illuminate the plastic life-history modifications that fish may undergo as their thermal environments become increasingly variable.

The positive effects of reduced fishing pressure in marine protected areas (MPAs) are now well documented globally. Yet, evidence of MPA benefits from long-term replicated before-after control-impact (BACI) studies and their usefulness in protecting target species are still rare, especially in northern temperate areas. Scientific rigor in the monitoring of MPAs is considered important for obtaining trust and compliance and can increase interest and enthusiasm for the benefits of marine conservation. Off the coast of southern Norway, a MPA implementation process started up in 2002. Based on comprehensive consultations with local fishers and managers, four experimental lobster reserves were appointed in 2004. Two years later (2006), the reserves came into effect as the Norwegian Directorate of Fisheries implemented regulations as a by-law of the Saltwater Fisheries Act that effectively banned all fixed gear. Long-term monitoring of the MPAs and adjacent control areas has enabled a rigorous scientific evaluation of the effects of these MPAs on lobster populations, including effects on density, growth, demography, behavior, and phenotypic diversity. As protection effects started to manifest, the lobster reserves attracted high public attention and were soon considered a credible supplement to traditional fisheries management. In the period from 2002 to 2021, more than 50 lobster reserves have been implemented in Norway. Here, we review the experiences since the lobster reserves were designated, implemented, and embraced by local communities in Norway, and over two decades have become an important tool for fishery management. Thoughts on the future of MPAs along the coast of Norway are discussed.

Parasitic salmon lice (Lepeophtheirus salmonis) threaten the economic and ecological sustainability of salmon farming, and their evolved resistance to treatment with emamectin benzoate (EMB) has been a major problem for salmon farming in the Atlantic Ocean. In contrast, the Pacific Ocean, where wild salmon are far more abundant, has not seen widespread evolution of EMB-resistant lice. Here, we use EMB bioassays and counts of lice on farms from the Broughton Archipelago, Canada-a core region of salmon farming in the Pacific-to show that EMB sensitivity has dramatically decreased since 2010, concurrent with marked decrease in the field efficacy of EMB treatments. Notably, these bioassay data were not made available through public reporting by industry or by the federal regulator, but rather through Indigenous-led agreements that created a legal obligation for salmon-farming companies to provide data to First Nations. Our results suggest that salmon lice in the Pacific Ocean have recently evolved substantial resistance to EMB, and that salmon-louse outbreaks on Pacific farms will therefore be more difficult to control in the coming years.

Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with nonmigratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats is expected to influence the distribution of biological populations and their connectivity patterns. We used whole genome sequencing to study demographic history and reduced representation (double-digest restriction associated DNA) sequencing data to analyse spatial genetic structure in broadnosed pipefish (Syngnathus typhle). Its main habitat is eelgrass beds, which are patchily distributed along the study area in southern Norway. Demographic connectivity among populations was inferred from long-term (~30-year) population counts that uncovered a rapid decline in spatial correlations in abundance with distance as short as ~2 km. These findings were contrasted with data for two other fish species that have a pelagic larval stage (corkwing wrasse, Symphodus melops; black goby, Gobius niger). For these latter species, we found wider spatial scales of connectivity and weaker genetic isolation-by-distance patterns, except where both species experienced a strong barrier to gene flow, seemingly due to lack of suitable habitat. Our findings verify expectations that a fragmented habitat and absence of a pelagic larval stage promote genetic structure, while presence of a pelagic larvae stage increases demographic connectivity and gene flow, except perhaps over extensive habitat gaps.

Synopsis 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.

In our original contribution, we used a new simple method (CMSY, Froese et al., 2017) and the time series of catches of Hutchings and Myers (1995) to analyse five centuries of cod catches in eastern Canada (Schijns et al., 2021). Holm et al. (2022) point out that there was actually an improved historical time series that we had overlooked. As we note in our paper, it is important to use the best available data, including all withdrawals in the case of catches, in order to realize the full potential of an exploited resource. Thus, we are in agreement with the points raised by Holm et al. (2022), and acknowledge that the more complete and accurate data they point out will improve the reliability of the assessment results. We welcome this opportunity to bring together interdisciplinary thinkers, such as fisheries scientists and historians. Therefore, we have agreed to collaborate on a joint paper where we will perform CMSY modelling on revised historical catch estimates to investigate what the consequences of these new catch levels are for stock and fisheries sustainability. In this effort, catches will be updated from 1500 to 1790 based on Holm et al. (2021), from 1815 to 1934 based on the Government of Newfoundland data (HistStats, 1970, Table K-7; Alexander, 1976), and will include new reconstructed estimates based on domestic consumption and the French exports from part of the area.