Supplementary table 2 from Empirical links between natural mortality and recovery in marine fishes

Estimates of natural mortality and maximum per capita population growth rate for marine fishes.

Workshop on ICES reference points (WKREF2)

The ICES Workshop on ICES reference points (WKREF2) was tasked review the WKREF1 report and based on the outcome develop updated guidelines for the ICES reference points system and recommendations for ACOM consideration. The WKREF1 report has suggested 5 key recommendations to simplify and harmonise the ICES reference points framework representing a major change to the current guidelines. At WKREF2, we detailed discussions and four key concerns were raised about the proposed approach. The first related to the simplification of rules to define Blim. Around two thirds of category 1 stocks would end up as WKREF1 “Blim Type 2” where Blim would be set as a fraction of B0. The Allee effect or “de…

Atlantic salmon survival at sea: temporal changes that lack regional synchrony

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 L.), 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 non-stationarity in time series data. Our results indicate that w…

Influence of dams on population persistence in Atlantic salmon (Salmo salar)

Barriers to migration can negatively affect population persistence. To explore how dams can influence the viability of a diadromous fish, we developed an empirically based stochastic model to estimate per-capita population growth rate (r) and probability of population decline (Pr(r < 0)). Our simulations incorporated life-history parameters common for many populations of Atlantic salmon (Salmo salar L., 1758), particularly in the southern part of the species range. Additionally, we explored the influence of individuals that reproduce more than once, i.e., “kelts”, on r and Pr(r < 0). For the life-history scenarios examined here, dams are forecast to negatively affect persistence, eve…

Impediments to fisheries recovery in Canada: Policy and institutional constraints on developing management practices compliant with the precautionary approach

The status of many Canadian fisheries is poor, a consequence of inadequate implementation of sustainable fishery policy within the context of the Precautionary Approach (PA). A key component of implementation lies with the provision of science advice. Scientists are responsible for advising on options likely to meet policy intent and objectives. Here, we examine PA-compliance in the role of science in Canada's fisheries management decision-making. We distinguish science-based from science-determined decisions and processes. Science-based decisions emerge from consultation processes involving stakeholders; science need not always have a clear and accountable role that can be transparently se…

Harvest‐induced evolution and effective population size

Much has been written about fishery-induced evolution (FIE) in exploited species, but relatively little attention has been paid to the consequences for one of the most important parameters in evolutionary biology-effective population size (N-e). We use a combination of simulations of Atlantic cod populations experiencing harvest, artificial manipulation of cod life tables, and analytical methods to explore how adding harvest to natural mortality affects N-e, census size (N), and the ratio N-e/N. We show that harvest-mediated reductions in N-e are due entirely to reductions in recruitment, because increasing adult mortality actually increases the N-e/N ratio. This means that proportional red…

Incorporating intra-annual variability in fisheries abundance data to better capture population dynamics

Abstract 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…

Increasing temperatures accentuate negative fitness consequences of a marine parasite

AbstractInfectious diseases are key drivers of wildlife populations and agriculture production, but whether and how climate change will influence disease impacts remains controversial. One of the critical knowledge gaps that prevents resolution of this controversy is a lack of high-quality experimental data, especially in marine systems of significant ecological and economic consequence. Here, we performed a manipulative experiment in which we tested the temperature-dependent effects on Atlantic salmon (Salmo salar) of sea lice (Lepeophtheirus salmonis)—a parasite that can depress the productivity of wild-salmon populations and the profits of the salmon-farming industry. We explored sea-lou…

Explicit incorporation of spatial variability in a biomass dynamics assessment model

Abstract The sustainable management of fisheries has largely relied on stock assessment models that assume stocks are homogeneous throughout their domain. However, ignoring complex underlying spatial patterns can lead to increased risk of failures in management. Utilizing geostatistical approaches in conjunction with a traditional fishery biomass dynamics model, we develop a spatially-explicit modelling framework that treats the underlying population dynamics as spatial processes. Simulation experiments demonstrate that this approach reliably estimates variance parameters and accurately captures true patterns of population change. We further demonstrate the utility of our modelling framewor…

Warming temperatures and ectoparasitic sea lice impair internal organs in juvenile Atlantic salmon

As a consequence of climate change and open net-pen salmon farming, wild Atlantic salmon Salmo salar are increasingly likely to encounter elevated temperatures and parasite abundances during their early marine migration. Such stressors can compromise fitness by diminishing liver energy stores and impairing cardiac muscle. To assess whether temperature and infestation by salmon lice Lepeophtheirus salmonis are important correlates of liver energy stores and cardiac muscle performance in juvenile salmon, we experimentally infested fish at 3 abundances of louse infestation (zero, low, and high) and 5 temperatures (10, 13, 16, 19, and 22°C). At the end of the experiment (i.e. when sea lice reac…

Small-scale life history variability suggests potential for spatial mismatches in Atlantic cod management units

Lobster reserves as a management tool in coastal waters: Two decades of experience in Norway

9 pages, 4 figures.-- Under a Creative Commons license

Genomic reaction norms inform predictions of plastic and adaptive responses to climate change

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 popu…

Fine-Scale Population Differences in Atlantic Cod Reproductive Success: A Potential Mechanism for Ecological Speciation in a Marine Fish

Abstract Successful resource‐management and conservation outcomes ideally depend on matching the spatial scales of population demography, local adaptation, and threat mitigation. For marine fish with high dispersal capabilities, this remains a fundamental challenge. Based on daily parentage assignments of more than 4,000 offspring, we document fine‐scaled temporal differences in individual reproductive success for two spatially adjacent (<10 km) populations of a broadcast‐spawning marine fish. Distinguished by differences in genetics and life history, Atlantic cod (Gadus morhua) from inner‐ and outer‐fjord populations were allowed to compete for mating and reproductive opportunities. After …

Pervasive declines in monkfish (Lophius americanus) size structure throughout the northwest Atlantic

Abstract Shifts in size structure have been documented for many commercially exploited marine fish stocks, thought to be attributed to size-selective harvesting practices coupled with changing oceanic conditions. Northwest Atlantic monkfish (Lophius americanus) is a commercially valued species in the United States that is commonly caught as bycatch in Canadian scallop and groundfish fisheries. This uniquely positioned stock is bisected by the Canadian–American jurisdictional boundary, with considerable differences in exploitation and management across its range. The status of this species was assessed two decades ago (2000) in the Maritimes region of Canada and more recently (2016) in the U…

Combining population genomics with demographic analyses highlights habitat patchiness and larval dispersal as determinants of connectivity in coastal fish species

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…

Transcriptomic responses to environmental change in fishes: Insights from RNA sequencing

The need to better understand how plasticity and evolution affect organismal responses to environmental variability is paramount in the face of global climate change. The potential for using RNA sequencing (RNA-seq) to study complex responses by non-model organisms to the environment is evident in a rapidly growing body of literature. This is particularly true of fishes for which research has been motivated by their ecological importance, socioeconomic value, and increased use as model species for medical and genetic research. Here, we review studies that have used RNA-seq to study transcriptomic responses to continuous abiotic variables to which fishes have likely evolved a response and th…

A Brief History of Fisheries in Canada

Throwing down a genomic gauntlet on fisheries-induced evolution

Beginning with studies on crypsis and camouflage, the hypothesis that predators can generate evolutionary change in their prey has a long and rich history (1). Few predators, however, rival humans in their potential to generate selection responses and concomitant phenotypic change on contemporary timescales. In the 1930s, J. B. S. Haldane (2) mused that fishing would be an ideal candidate for such “observable evolution” within a human lifetime, proceeding “with extreme and abnormal speed.” However, it was not until the late 1970s that research on fisheries-induced evolution (FIE) gained a substantive scientific foothold, beginning with thought-provoking work on Canadian whitefish ( Coregonu…

Comparative analysis of abundance–occupancy relationships for species at risk at both broad taxonomic and spatial scales

The abundance–occupancy relationship is one of the most well-examined relationships in ecology. At the species level, a positive association has been widely documented. However, until recently, research on the nature of this relationship at broad taxonomic and spatial scales has been limited. Here, we perform a comparative analysis of 12 taxonomic groups across a large spatial scale (Canada), using data on Canadian species at risk: amphibians, arthropods, birds, freshwater fishes, lichens, marine fishes, marine mammals, molluscs, mosses, reptiles, terrestrial mammals, and vascular plants. We find a significantly positive relationship in all taxonomic groups with the exception of freshwater…

Multiple‐batch spawning as a bet‐hedging strategy in highly stochastic environments: An exploratory analysis of Atlantic cod

Stochastic environments shape life‐history traits and can promote selection for risk‐spreading strategies, such as bet‐hedging. Although the strategy has often been hypothesised to exist for various species, empirical tests providing firm evidence have been rare, mainly due to the challenge in tracking fitness across generations. Here, we take a ‘proof of principle’ approach to explore whether the reproductive strategy of multiple‐batch spawning constitutes a bet‐hedging. We used Atlantic cod (Gadus morhua) as the study species and parameterised an eco‐evolutionary model, using empirical data on size‐related reproductive and survival traits. To evaluate the fitness benefits of multiple‐batc…

Empirical links between natural mortality and recovery in marine fishes

Probability of species recovery is thought to be correlated with specific aspects of organismal life history, such as age at maturity and longevity, and how these affect rates of natural mortality ( M ) and maximum per capita population growth ( r max ). Despite strong theoretical underpinnings, these correlates have been based on predicted rather than realized population trajectories following threat mitigation. Here, we examine the level of empirical support for postulated links between a suite of life-history traits (related to maturity, age, size and growth) and recovery in marine fishes. Following threat mitigation (medium time since cessation of overfishing = 20 years), 71% of 55 tem…

Variation in spawning time promotes genetic variability in population responses to environmental change in a marine fish.

Common-garden experiments suggest that the response of Atlantic cod larvae to temperature differs among populations that spawn at different times of year. Populations appear to be adapted to the temperatures experienced during the larval stage at a small spatial scale, despite a lack of physical barriers to gene flow.

Temporal variability in offspring quality and individual reproductive output in a broadcast-spawning marine fish

Abstract The protracted spawning period of broadcast-spawning marine fishes has potential to generate considerable variability in metrics of individual reproductive output. We undertook a temporally detailed genetic study of larvae produced by Atlantic cod (Gadus morhua) from two spatially proximate populations spawning under controlled semi-natural conditions over 94 days. Based on daily samples of larvae (n = 4489 in total), we document fine-scaled temporal changes in, and correlates of, offspring phenotype and reproductive output (egg batches produced or fertilized). Larval length and standardized yolk-sac volume declined 11 and 49% over the spawning period, respectively. The adaptive si…

Cyclical and stochastic thermal variability affects survival and growth in brook trout

Directional changes in temperature have well-documented effects on ectotherms, yet few studies have explored how increased thermal variability (a concomitant of climate change) might affect individual fitness. Using a common-garden experimental protocol, we investigated how bidirectional temperature change can affect survival and growth of brook trout (Salvelinus fontinalis) and whether the survival and growth responses differ between two populations, using four thermal-variability treatments (mean: 10 °C; range: 7–13 °C): (i) constancy; (ii) cyclical fluctuations every two days; (iii) low stochasticity (random changes every 2 days); (iv) high stochasticity (random changes daily). Recently …

Five centuries of cod catches in Eastern Canada

Abstract 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 researc…

Disentangling conditional effects of multiple regime shifts on Atlantic cod productivity

AbstractRegime shifts are increasingly prevalent in the ecological literature. However, definitions vary, and many detection methods are subjective. Here, we employ an operationally objective means of identifying regime shifts, using a Bayesian online change-point detection algorithm able to simultaneously identify shifts in the mean and(or) variance of time series data. We detected multiple regime shifts in long-term (59-154 years) patterns of coastal Norwegian Atlantic cod (&gt;70% decline) and putative drivers of cod productivity: North Atlantic Oscillation (NAO); sea-surface temperature; zooplankton abundance; fishing mortality (F). The consequences of an environmental or climate-relate…

Life-history variability and conservation status of landlocked Atlantic salmon: an overview

Nonanadromous Atlantic salmon (Salmo salar) exhibit a combination of variation in life history, habitat, and species co-existence matched by few vertebrates. Distributed in eastern North America and northern Europe, habitat ranges from hundreds of metres of river to Europe’s largest lakes. As juveniles, those with access to a lake usually migrate to feed and grow prior to reproduction. Prey such as smelt (Osmerus mordax, Osmerus eperlanus) and vendace (Coregonus albula) facilitate large body size (50–85 cm at maturity) and persistence in high-diversity (&gt;20 fish species) environments; small-bodied salmon (10–30 cm at maturity), relying on insects as prey, coexist with few (fewer than fi…

Cryptic microgeographic variation in responses of larval Atlantic cod to warmer temperatures

AbstractAlthough temperature is known to drive species dynamics and distributions, our understanding of the extent to which thermal plasticity varies within species is poor. Differences in plasticity can arise through local adaptation to heterogeneous environments, hybridization, and the release of cryptic genetic variation in novel environments. Here, wild Atlantic cod (Gadus morhua) from contrasting environments inside and outside of a fjord system in southern Norway spawned freely in a semi-natural laboratory environment, generating pure crosses and reciprocal hybrids. A common-garden rearing experiment of the larvae at 6°C, 9.5°C, and 13°C revealed cryptic genetic variation in thermal r…

Supplementary Material For 'Differential reproductive plasticity under thermal variability in a freshwater fish (Danio rerio)'

Includes supplemental methods and visual model checks.

Supplementary table 1 from Empirical links between natural mortality and recovery in marine fishes

Life-history trait data for recovered and non-recovered temperate marine fish populations.

Supplementary table 1 from Empirical links between natural mortality and recovery in marine fishes

Life-history trait data for recovered and non-recovered temperate marine fish populations.

Sustaining Canadian marine biodiversity: Policy and statutory progress

A 2012 Expert Panel Report on marine biodiversity by the Royal Society of Canada (RSC) concluded that Canada faced significant challenges in achieving sustainable fisheries, regulating aquaculture, and accounting for climate change. Relative to many countries, progress by Canada in fulfilling international obligations to sustain biodiversity was deemed poor. To track progress by Canada since 2012, the RSC struck a committee to track policy and statutory developments on matters pertaining to marine biodiversity and to identify policy challenges, and leading options for implementation that lie ahead. The report by the Policy Briefing Committee is presented here. It concluded that Canada has …

Implications of fisheries‐induced evolution for population recovery: Refocusing the science and refining its communication

The argument that sufficiently high fishing mortality (selective or not) can effect genetic change in fished populations has gained considerable traction since the late 1970s. The intervening decades have provided compelling experimental and model‐based evidence that fisheries‐induced evolution (FIE) can cause genetic changes in life history, behaviour and body shape, given sufficiently high trait heritability, selection intensity and time. Fisheries‐induced evolution research has also identified or inferred negative implications to population recovery and sustainable yield, prompting calls for evolutionarily enlightened management to reduce the probability of FIE and mitigate its risks. Su…

Differential reproductive plasticity under thermal variability in a freshwater fish (Danio rerio)

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 sp…

Thermal variability during ectotherm egg incubation: A synthesis and framework.

Natural populations of ectothermic oviparous vertebrates typically experience thermal variability in their incubation environment. Yet an overwhelming number of laboratory studies incubate animals under constant thermal conditions that cannot capture natural thermal variability. Here, we systematically searched for studies that incubated eggs of ectothermic vertebrates, including both fishes and herpetofauna, under thermally variable regimes. We ultimately developed a compendium of 66 studies that used thermally variable conditions for egg incubation. In this review, we qualitatively discuss key findings from literature in the compendium, including the phenotypic effects resulting from diff…

Multiple-batch spawning: a risk-spreading strategy disarmed by highly intensive size-selective fishing rate

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 …

Salmon lice in the Pacific Ocean show evidence of evolved resistance to parasiticide treatment

AbstractParasitic 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 bioass…

Gill area explains deviations from body size–metabolic rate relationship in teleost fishes

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.

Genetic variation in plasticity of life-history traits between Atlantic cod (Gadus morhua) populations exposed to contrasting thermal regimes

We employed common-garden experiments to test for genetic variation in responses of larval life-history traits to temperature between two populations of Atlantic cod (Gadus morhua L., 1758) that naturally experience contrasting thermal environments during early life due to spatial and temporal differences in spawning. Southern Gulf of St. Lawrence cod larvae experienced faster growth in warmer water and low, uniform survival across all experimental temperatures (3, 7, 11 °C), consistent with previous studies on this spring-spawning population. In contrast, larvae from fall-spawning Southwestern Scotian Shelf cod collected near Sambro, Nova Scotia, lacked plasticity for growth but experienc…

Spatial reference points for groundfish

Abstract According to density-dependent habitat selection theory, areas of high density can be indicative of high population productivity and have positive individual fitness consequences. Here, we explore six groundfish populations on the Scotian Shelf, Canada, where a decline in areas of high density beyond a certain threshold is associated with disproportionately large declines in Spawning Stock Biomass (SSB). This is evidenced by empirical, concave, positive relationships between high-density areas (HDAs) and SSB. We introduce a methodology to estimate the threshold below which SSB declines increasingly faster per unit of HDA decline. The spatial threshold among these six stocks was rem…

Thresholds for impaired species recovery

Studies on small and declining populations dominate research in conservation biology. This emphasis reflects two overarching frameworks: the small-population paradigm focuses on correlates of increased extinction probability; the declining-population paradigm directs attention to the causes and consequences of depletion. Neither, however, particularly informs research on the determinants, rate or uncertainty of population increase. By contrast, Allee effects (positive associations between population size and realized per capita population growth rate, r realized , a metric of average individual fitness) offer a theoretical and empirical basis for identifying numerical and temporal threshol…

Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and nonmigratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the >100 000-year-old trans-Atlantic separation of Atlantic cod. The long…

Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

Abstract Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analysed genetic origin of 6,483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two gene…

Consequences of single-locus and tightly linked genomic architectures for evolutionary responses to environmental change

AbstractGenetic and genomic architectures of traits under selection are key factors influencing evolutionary responses. Yet, knowledge of their impacts has been limited by a widespread assumption that most traits are controlled by unlinked polygenic architectures. Recent advances in genome sequencing and eco-evolutionary modelling are unlocking the potential for integrating genomic information into predictions of population responses to environmental change. Using eco-evolutionary simulations, we demonstrate that hypothetical single-locus control of a life history trait produces highly variable and unpredictable harvesting-induced evolution relative to the classically applied multi-locus mo…

Supplementary table 2 from Empirical links between natural mortality and recovery in marine fishes

Estimates of natural mortality and maximum per capita population growth rate for marine fishes.

Corrigendum to: When phenotypes fail to illuminate underlying genetic processes in fish and fisheries science

Correlation between body size and longevity : New analysis and data covering six taxonomic classes of vertebrates

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 a…

Communication of Science Advice to Government

There are various ways to construct good processes for soliciting and understanding science. Our critique of advisory models finds that a well-supported chief science advisor (CSA) best ensures the provision of deliberative, informal, and emergency advice to government. Alternatively, bias, increasingly manifest as science-based advocacy, can hinder communication, diminish credibility, and distort scientific evidence.

Allee effects and the Allee-effect zone in northwest Atlantic cod

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 str…

When phenotypes fail to illuminate underlying genetic processes in fish and fisheries science

Abstract Advances in genetic and genomic technologies have become widely available and have potential to provide novel insights into fish biology and fisheries science. In the present overview, we explore cases for which genomic analyses have proven instrumental in the rejection of hypotheses that have been well-motivated based on phenotypic and ecological properties of individuals and populations. We focus on study systems for which information derived using genomic tools contradicts conclusions drawn from traditional fisheries science methodologies and assumptions. We further illustrate the non-intuitive interplay of genomics and ecology in Atlantic salmon (Salmo salar L.) owing to the re…

The role of fish life histories in allometrically scaled food‐web dynamics

Body size determines key ecological and evolutionary processes of organisms. Therefore, organisms undergo extensive shifts in resources, competitors, and predators as they grow in body size. While empirical and theoretical evidence show that these size‐dependent ontogenetic shifts vastly influence the structure and dynamics of populations, theory on how those ontogenetic shifts affect the structure and dynamics of ecological networks is still virtually absent. Here, we expand the Allometric Trophic Network (ATN) theory in the context of aquatic food webs to incorporate size‐structure in the population dynamics of fish species. We do this by modifying a food web generating algorithm, the nic…

Trends in marine survival of Atlantic salmon populations in eastern Canada

Abstract Declines in wild Atlantic salmon (Salmo salar) abundance throughout the north Atlantic are primarily attributed to decreases in survival at sea. However, comparing trends in marine survival among populations is challenging as data on both migrating smolts and returning adults are sparse and models are difficult to parameterize due to their varied life histories. We fit a hierarchical Bayesian maturity schedule model to data from seven populations in eastern Canada to estimate numbers of out-migrating smolts, survival in the first and second year at sea, and the proportion returning after 1 year. Trends in survival at sea were not consistent among populations; we observe positive, n…

Data from: Fine-scale population differences in Atlantic cod reproductive success: a potential mechanism for ecological speciation in a marine fish

Successful resource-management and conservation outcomes ideally depend on matching the spatial scales of population demography, local adaptation, and threat mitigation. For marine fish with high dispersal capabilities, this remains a fundamental challenge. Based on daily parentage assignments of more than 4000 offspring, we document fine-scaled temporal differences in individual reproductive success for two spatially adjacent (&lt;10km) populations of a broadcast-spawning marine fish. Distinguished by differences in genetics and life history, Atlantic cod (Gadus morhua) from inner- and outer-fjord populations were allowed to compete for mating and reproductive opportunities. After accounti…

Data from: Stable coexistence of genetically divergent Atlantic cod ecotypes at multiple spatial scales

Coexistence in the same habitat of closely related yet genetically different populations is a phenomenon that challenges our understanding of local population structure and adaptation. Identifying the underlying mechanisms for such coexistence can yield new insight into adaptive evolution, diversification, and the potential for organisms to adapt and persist in response to a changing environment. Recent studies have documented cryptic, sympatric populations of Atlantic cod (Gadus morhua) in coastal areas. We analyzed genetic origin of 6483 individual cod sampled annually over 14 years from 125 locations along the Norwegian Skagerrak coast and document stable coexistence of two genetically d…

Data from: Trans-oceanic genomic divergence of Atlantic cod ecotypes is associated with large inversions

Chromosomal rearrangements such as inversions can play a crucial role in maintaining polymorphism underlying complex traits and contribute to the process of speciation. In Atlantic cod (Gadus morhua), inversions of several megabases have been identified that dominate genomic differentiation between migratory and non-migratory ecotypes in the Northeast Atlantic. Here, we show that the same genomic regions display elevated divergence and contribute to ecotype divergence in the Northwest Atlantic as well. The occurrence of these inversions on both sides of the Atlantic Ocean reveals a common evolutionary origin, predating the more than 100,000 years old trans-Atlantic separation of Atlantic co…