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…

Correction: Size does matter—the eco-evolutionary effects of changing body size in fish

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…

Exploring individual and population eco-evolutionary feedbacks under the coupled effects of fishing and predation

Intensive fishing that selects for large and old individuals can have pervasive effects on traits directly associated with the fecundity and survival of the target species. The observed reduction in fish body size can result in earlier sexual maturity at a smaller body size, leading to a lower individual reproductive output and population productivity in the long term. In addition, increased predation can induce similar responses in age and size at maturity due to the release of intraspecific competition and the lower population density. Thus, the combined impact of fisheries and predation is more difficult to predict due to their competition for fish, ultimately limiting and directing the …

Potential for managing life history diversity in a commercially exploited intermediate predator, the goldsinny wrasse (Ctenolabrus rupestris)

Abstract Small-bodied wrasse species are important for structuring coastal marine ecosystems but are also increasingly harvested as parasite cleaners on farmed salmon. Identifying management regulations that will support long-term sustainability of wrasse fisheries is challenging, because there is still limited knowledge about the impacts of fisheries on the demography of these intermediate predators in their natural environments. To this end, we studied individual growth histories of goldsinny wrasse (Ctenolabrus rupestris) at a fine spatial scale across replicated marine protected areas (MPAs) and areas open to commercial harvesting on the Norwegian coast. The MPAs were established 1–7 ye…

Competition between marine mammals and fisheries in contemporary harvested marine ecosystems

Competitive interactions between marine mammals and fisheries represent some of the most complex challenges in marine resource management worldwide. The development of commercial fisheries and recovering marine mammal populations have contributed to a decrease in fish availability. Whilst ecosystem-based fisheries management (EBFM) can counteract this decrease, achieving the EBFM objectives faces certain major obstacles including insufficient or unreliable data, inapplicable assessment models, as well as inadequate management decisions that do not account for fisheries-induced morphological alterations (FIMA) and marine mammal management. Despite a body of evidence addressing various aspect…

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…

Effects of temporal abiotic drivers on the dynamics of an allometric trophic network model

Current ecological research and ecosystem management call for improved understanding of the abiotic drivers of community dynamics, including temperature effects on species interactions and biomass accumulation. Allometric trophic network (ATN) models, which simulate material (carbon) transfer in trophic networks from producers to consumers based on mass-specific metabolic rates, provide an attractive framework to study consumer–resource interactions from organisms to ecosystems. However, the developed ATN models rarely consider temporal changes in some key abiotic drivers that affect, for example, consumer metabolism and producer growth. Here, we evaluate how temporal changes in carrying ca…

The effect of fish life-history structures on the topologies of aquatic food webs

Biological organisms can vastly change their ecological functionality due to changes in body size and diet across their life. Consequently, it has been increasingly recognized that to attain sufficient biological realism, food webs may need to include life-history structures. The objective of the work is to study theoretically whether and how the inclusion of life-history structures affects the food web topology. Topological research was done by applying network theory metrics for three different food web types with two different sizes that were generated by using the niche-model. The dynamical modeling was performed by using an allometric trophic network modeling approach. The different ty…

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…

Size does matter — the eco-evolutionary effects of changing body size in fish

Body size acts as a proxy for many fitness-related traits. Body size is also subject to directional selection from various anthropogenic stressors such as increasing water temperature, decreasing dissolved oxygen, fisheries, as well as natural predators. Changes in individual body size correlate with changes in fecundity, behaviour, and survival and can propagate through populations and ecosystems by truncating age and size structures and changing predator–prey dynamics. In this review, we will explore the causes and consequences of changing body size in fish in the light of recent literature and relevant theories. We will investigate the central role of body size in ecology by first discu…

Species’ ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Fish stocking is used worldwide in conservation and management, but its effects on food-web dynamics and ecosystem stability are poorly known. To better understand these effects and predict the outcomes of stocking, we used an empirically validated network model of a well-studied lake ecosystem. We simulate two stocking scenarios with two native fish species valuable for fishing. In the first scenario, we stock planktivorous fish (whitefish) larvae in the ecosystem. This leads to a 1% increase in adult whitefish biomasses and decreases the biomasses of the top predator (perch). In the second scenario, we also stock perch larvae in the ecosystem. This decreases the planktivorous whitefish an…

The mechanistic basis of demographic Allee effects: The search for mates

In Focus: Berec, L., Kremer, A.M., Bernhauverova, V., & Drake, J.M. (2017). Density-dependent selection on mate-finding Allee effects. Journal of Animal Ecology, 87, 24-35. https://doi.org/10.1111/1365-2656.12662 In Focus: Shaw, A.K., Kokko, H., & Neubert, M.G. (2017). Details of mate finding drive dynamics of sex structured invasions. Journal of Animal Ecology, 87, 36-46. https://doi.org/10.1111/1365-2656.12658 Lowered population growth ability at low abundances is called the demographic Allee effect. The difficulty of finding mates in a sparse population is the best documented pathway through which a demographic Allee effect might arise. The articles in focus here aim to establish the mec…

Toward a mechanistic understanding of vulnerability to hook-and-line fishing: Boldness as the basic target of angling-induced selection

In passively operated fishing gear, boldness-related behaviors should fundamentally affect the vulnerability of individual fish and thus be under fisheries selection. To test this hypothesis, we used juvenile common-garden reared carp (Cyprinus carpio) within a narrow size-range to investigate the mechanistic basis of behavioral selection caused by angling. We focused on one key personality trait (i.e., boldness), measured in groups within ponds, two morphological traits (body-shape and head-shape), and one life-history trait (juvenile growth capacity) and studied mean standardized selection gradients caused by angling. Carp behavior was highly repeatable within ponds. In the short-term, ov…

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…

Marine food web perspective to fisheries‐induced evolution

Abstract Fisheries exploitation can cause genetic changes in heritable traits of targeted stocks. The direction of selective pressure forced by harvest acts typically in reverse to natural selection and selects for explicit life histories, usually for younger and smaller spawners with deprived spawning potential. While the consequences that such selection might have on the population dynamics of a single species are well emphasized, we are just beginning to perceive the variety and severity of its propagating effects within the entire marine food webs and ecosystems. Here, we highlight the potential pathways in which fisheries‐induced evolution, driven by size‐selective fishing, might reson…

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

Figure S4 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult whitefish and perch biomasses in response to increased whitefish (Wht300; black) and perch stocking (Wht300+Per50; red) compared to the whitefish baseline (Wht200; gray) under Fmax = 0.4 (10% lower fishing pressure than in the main text), Fmax = 0.5 (fishing pressure in the main text), and under Fmax = 0.6 (10% higher fishing pressure than in the main text). Dashed lines indicate the time point when fishing was introduced to the simulations.

A modified niche model for generating food webs with stage‐structured consumers: The stabilizing effects of life‐history stages on complex food webs

Abstract Almost all organisms grow in size during their lifetime and switch diets, trophic positions, and interacting partners as they grow. Such ontogenetic development introduces life‐history stages and flows of biomass between the stages through growth and reproduction. However, current research on complex food webs rarely considers life‐history stages. The few previously proposed methods do not take full advantage of the existing food web structural models that can produce realistic food web topologies.We extended the niche model developed by Williams and Martinez (Nature, 2000, 404, 180–183) to generate food webs that included trophic species with a life‐history stage structure. Our me…

Environmentally‐induced noise dampens and reddens with increasing trophic level in a complex food web

Stochastic variability of key abiotic factors including temperature, precipitation and the availability of light and nutrients greatly influences species’ ecological function and evolutionary fate. Despite such influence, ecologists have typically ignored the effect of abiotic stochasticity on the structure and dynamics of ecological networks. Here we help to fill that gap by advancing the theory of how abiotic stochasticity, in the form of environmental noise, affects the population dynamics of species within food webs. We do this by analysing an allometric trophic network model of Lake Constance subjected to positive (red), negative (blue), and non‐autocorrelated (white) abiotic temporal …

Detection of Allee effects in marine fishes: analytical biases generated by data availability and model selection

The demographic Allee effect, or depensation, implies positive association between per capita population growth rate and population size at low abundances, thereby lowering growth ability of sparse populations. This can have far-reaching consequences on population recovery ability and colonization success. In the context of marine fishes, there is a widespread perception that Allee effects are rare or non-existent. However, studies that have failed to detect Allee effects in marine fishes have suffered from several fundamental methodological and data limitations. In the present study, we challenge the prevailing perception about the rarity of Allee effects by analysing nine populations of …

Figure S1 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult whitefish and perch catches (as biomass densities) in response to increased whitefish (Wht300; black) and perch stocking (Wht300+Per50; red) compared to the whitefish baseline (Wht200; gray) during the 100 year fishing period.

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…

Are there plenty of fish in the sea? How life history traits affect the eco-evolutionary consequences of population oscillations

Understanding fish population oscillations is important for both fundamental population biology and for fisheries science. Much research has focused on the causes of population oscillations, but the eco-evolutionary consequences of population oscillations are unclear. Here, we used an empirically parametrised individual-based simulation model to explore the consequences of oscillations with different amplitudes and wavelengths. We show that oscillations with a wavelength shorter than the maximum lifespan of the fish produce marked differences in the evolutionary trajectories of asymptotic length. Wavelengths longer than the maximum lifespan of the fish, in turn, mainly manifest as ecologica…

ESM - Material and Methods from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Fish stocking is used worldwide in conservation and management, but its effects on food-web dynamics and ecosystem stability are poorly known. To better understand these effects and predict the outcomes of stocking, we used an empirically validated network model of a well-studied lake ecosystem. We simulate two stocking scenarios with two native fish species valuable for fishing. In the first scenario, we stock planktivorous fish (whitefish) larvae in the ecosystem. This leads to a 1% increase in adult whitefish biomasses and decreases the biomasses of the top predator (perch). In the second scenario, we also stock perch larvae in the ecosystem. This decreases the planktivorous whitefish an…

Return of the Apex Predator : How Brown Trout (Salmo trutta) Re-Establishment Shapes an Ecosystem

Re-establishment of a declined apex predator fish species in a lake ecosystem may have dramatic effects on other fish and plankton community already inhabiting the ecosystem. We studied mechanistically potential impacts of re-establishment of the brown trout (Salmo trutta) in the west-central European Lake Constance focusing on two commercially important fish species: whitefish and Eurasian perch. We compared simulation model outputs from two versions of an allometric trophic network model for Lake Constance, one with and one without the trout as the apex predator. The re-establishment of the declined brown trout reduced the perch population directly by predation and indirectly by increased…

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 …

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.

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…

Building up an ecologically sustainable and socially desirable post-COVID-19 future

AbstractCOVID-19 crisis has emphasized how poorly prepared humanity is to cope with global disasters. However, this crisis also offers a unique opportunity to move towards a more sustainable and equitable future. Here, we identify the underlying environmental, social, and economic chronic causes of the COVID-19 crisis. We argue in favour of a holistic view to initiate a socio-economic transition to improve the prospects for global sustainability and human well-being. Alternative approaches to “Business-As-Usual” for guiding the transition are already available for implementation. Yet, to ensure a successful and just transition, we need to change our priorities towards environmental integrit…

Figure S4 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult whitefish and perch biomasses in response to increased whitefish (Wht300; black) and perch stocking (Wht300+Per50; red) compared to the whitefish baseline (Wht200; gray) under Fmax = 0.4 (10% lower fishing pressure than in the main text), Fmax = 0.5 (fishing pressure in the main text), and under Fmax = 0.6 (10% higher fishing pressure than in the main text). Dashed lines indicate the time point when fishing was introduced to the simulations.

Figure S3 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult perch biomasses in response to perch stocking (Wht300+Per50 [red]; Wht300+Per25 [pink]; Wht300+Per75 [orange]) compared to the increased whitefish stocking (Wht300 [black]). Dashed lines indicate the time point when fishing was introduced to the simulations.

Figure S1 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult whitefish and perch catches (as biomass densities) in response to increased whitefish (Wht300; black) and perch stocking (Wht300+Per50; red) compared to the whitefish baseline (Wht200; gray) during the 100 year fishing period.

Figure S2 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult whitefish biomasses in response to increased whitefish stocking (Wht250 [light blue]; Wht300 [black]; Wht350 [dark blue]) compared to the whitefish baseline (Wht200 [light gray]). Dashed lines indicate the time point when fishing was introduced to the simulations.

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…

Figure S2 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult whitefish biomasses in response to increased whitefish stocking (Wht250 [light blue]; Wht300 [black]; Wht350 [dark blue]) compared to the whitefish baseline (Wht200 [light gray]). Dashed lines indicate the time point when fishing was introduced to the simulations.

Limited effects of size-selective harvesting and harvesting-induced life-history changes on the temporal variability of biomass dynamics in complex food webs

Harvesting has been implicated in destabilizing the abundances of exploited populations. Because selective harvesting often targets large individuals, some studies have proposed that exploited populations often experience demographic shifts toward younger, smaller individuals and become more sensitive to environmental fluctuations. The theory of consumer–resource dynamics has been applied to address the impacts of harvesting in simple modular food webs, but harvested populations are embedded in a complex food web in nature. In addition, exploited populations have been shown to undergo trait evolution or phenotypic changes toward early maturation at smaller sizes. Using an empirically derive…

Marine food web perspective to fisheries-induced evolution

Fisheries exploitation can cause genetic changes in heritable traits of targeted stocks. The direction of selective pressure forced by harvest acts typically in reverse to natural selection and selects for explicit life-histories, usually for younger and smaller spawners with deprived spawning potential. While the consequences that such selection might have on the populational dynamics of a single species are well emphasised, we are just beginning to perceive the variety and severity of its propagating effects within the entire marine food webs and ecosystems. Here, we highlight the potential pathways in which fishing-induced evolution, driven by size-selective fishing, might resonate throu…

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.

Bridging Ecology and Evolution

Already by the early dawn of evolutionary biology, it was appreciated that ecological differences among species’ habitats, resources, and environments were key drivers of evolution and speciation. Thus, research on interactions between ecology and evolution is not a novel endeavor. It has, however, become increasingly popular to provide these interactions with ‘a new wrapping’, that is, the study of eco-evolutionary dynamics [1]. Consequently, eco-evolutionary dynamics is not a newly developed theory but rather a novel framework within which to study the interplay of ecology and evolution.

Temporary Allee effects among non‐stationary recruitment dynamics in depleted gadid and flatfish populations

Many considerably declined fish populations have not fully recovered despite reductions in fishing pressure. One of the possible causes of impaired recovery is the (demographic) Allee effect. To investigate whether low-abundance recruitment dynamics can switch between compensation and depensation, the latter implying the presence of the Allee effect, we analysed the stock–recruitment time series of 17 depleted cod-type and flatfish populations using a Bayesian change point model. The recruitment dynamics were represented with the sigmoidal Beverton–Holt and the Saila–Lorda stock–recruitment models, allowing the parameters of the models to shift at a priori unknown change points. Our synthes…

Fishing triggers trophic cascade in terms of variation, not abundance, in an allometric trophic network model

Trophic cascade studies often rely on linear food chains instead of complex food webs and are typically measured as biomass averages, not as biomass variation. We study trophic cascades propagating across a complex food web including a measure of biomass variation in addition to biomass average. We examined whether different fishing strategies induce trophic cascades and whether the cascades differ from each other. We utilized an allometric trophic network (ATN) model to mechanistically study fishing-induced changes in food web dynamics. Different fishing strategies did not trigger traditional, reciprocal trophic cascades, as measured in biomass averages. Instead, fishing triggered a varia…

Eco‐evolutionary dynamics driven by fishing : from single species models to dynamic evolution within complex food webs

Evidence of contemporary evolution across ecological time scales stimulated research on the eco‐evolutionary dynamics of natural populations. Aquatic systems provide a good setting to study eco‐evolutionary dynamics owing to a wealth of long‐term monitoring data and the detected trends in fish life‐history traits across intensively harvested marine and freshwater systems. In the present study, we focus on modelling approaches to simulate eco‐evolutionary dynamics of fishes and their ecosystems. Firstly, we review the development of modelling from single‐species to multispecies approaches. Secondly, we advance the current state‐of‐the‐art methodology by implementing evolution of life‐history…

Age is not just a number—Mathematical model suggests senescence affects how fish populations respond to different fishing regimes

Abstract Senescence is often described as an age‐dependent increase in natural mortality (known as actuarial senescence) and an age‐dependent decrease in fecundity (known as reproductive senescence), and its role in nature is still poorly understood. Based on empirical estimates of reproductive and actuarial senescence, we used mathematical simulations to explore how senescence affects the population dynamics of Coregonus albula, a small, schooling salmonid fish. Using an empirically based eco‐evolutionary model, we investigated how the presence or absence of senescence affects the eco‐evolutionary dynamics of a fish population during pristine, intensive harvest, and recovery phases. Our si…

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…

Age is not just a number : Mathematical model suggests senescence affects how fish populations respond to different fishing regimes

Senescence is often described as an age-dependent increase in natural mortality (known as actuarial senescence) and an age-dependent decrease in fecundity (known as reproductive senescence), and its role in nature is still poorly understood. Based on empirical estimates of reproductive and actuarial senescence, we used mathematical simulations to explore how senescence affects the population dynamics of Coregonus albula, a small, schooling salmonid fish. Using an empirically based eco-evolutionary model, we investigated how the presence or absence of senescence affects the eco-evolutionary dynamics of a fish population during pristine, intensive harvest, and recovery phases. Our simulation …

ESM - Material and Methods from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Fish stocking is used worldwide in conservation and management, but its effects on food-web dynamics and ecosystem stability are poorly known. To better understand these effects and predict the outcomes of stocking, we used an empirically validated network model of a well-studied lake ecosystem. We simulate two stocking scenarios with two native fish species valuable for fishing. In the first scenario, we stock planktivorous fish (whitefish) larvae in the ecosystem. This leads to a 1% increase in adult whitefish biomasses and decreases the biomasses of the top predator (perch). In the second scenario, we also stock perch larvae in the ecosystem. This decreases the planktivorous whitefish an…

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.

A modified niche model for generating food webs with stage-structured consumers : The stabilizing effects of life-history stages on complex food webs

1. Almost all organisms grow in size during their lifetime and switch diets, trophic positions, and interacting partners as they grow. Such ontogenetic development introduces life-history stages and flows of biomass between the stages through growth and reproduction. However, current research on complex food webs rarely considers life-history stages. The few previously proposed methods do not take full advantage of the existing food web structural models that can produce realistic food web topologies. 2. We extended the niche model by Williams & Martinez (2000) to generate food webs that included trophic species with a life-history stage structure. Our method aggregated trophic species …

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…

Figure S3 from Species' ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Changes in the adult perch biomasses in response to perch stocking (Wht300+Per50 [red]; Wht300+Per25 [pink]; Wht300+Per75 [orange]) compared to the increased whitefish stocking (Wht300 [black]). Dashed lines indicate the time point when fishing was introduced to the simulations.

Supplementary tables and figures from Detection of Allee effects in marine fishes: analytical biases generated by data availability and model selection

The demographic Allee effect, or depensation, implies positive association between per capita population growth rate and population size at low abundances, thereby lowering growth ability of sparse populations. This can have far-reaching consequences on population recovery ability and colonization success. In the context of marine fishes, there is a widespread perception that Allee effects are rare or non-existent. However, studies that have failed to detect Allee effects in marine fishes have suffered from several fundamental methodological and data limitations. In the present study, we challenge the prevailing perception about the rarity of Allee effects by analysing nine populations of A…

Species interactions, environmental gradients and body size shape population niche width

1. Competition for shared resources is commonly assumed to restrict population-level niche width of coexisting species. However, the identity and abundance of coexisting species, the prevailing environmental conditions, and the individual body size may shape the effects of interspecific interactions on species’ niche width. 2. Here we study the effects of interspecific and intraspecific interactions, lake area and altitude, and fish body size on the trophic niche width and resource use of a generalist predator, the littoral-dwelling large, sparsely rakered morph of European whitefish (Coregonus lavaretus; hereafter LSR whitefish). We use stable isotope, diet and survey fishing data from 14 …

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…

Supplementary tables and figures from Detection of Allee effects in marine fishes: analytical biases generated by data availability and model selection

The demographic Allee effect, or depensation, implies positive association between per capita population growth rate and population size at low abundances, thereby lowering growth ability of sparse populations. This can have far-reaching consequences on population recovery ability and colonization success. In the context of marine fishes, there is a widespread perception that Allee effects are rare or non-existent. However, studies that have failed to detect Allee effects in marine fishes have suffered from several fundamental methodological and data limitations. In the present study, we challenge the prevailing perception about the rarity of Allee effects by analysing nine populations of A…

Age is not just a number – senescence affects how fish populations respond to different fishing regimes

Abstract The presence of senescence in natural populations remains an unsolved problem in biology. Described as an age-dependent increase in natural mortality (known as actuarial senescence) and an age-dependent decrease in fecundity (known as reproductive senescence), the role of senescence in nature is still poorly understood. Based on empirical estimates of reproductive and actuarial senescence, we explored how senescence affects the population dynamics of Coregonus albula, a small, schooling salmonid fish. Using an empirically-based eco-evolutionary model, we investigated how the presence or absence of senescence affects how the fish population responds to pristine, intensive harvest, a…

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…

Atlantic cod recovery from the Allee effect zone : contrasting ecological and evolutionary rescue

The ability of a population to recover from disturbances is fundamental for its persistence. Impaired population recovery might be associated with a demographic Allee effect. Immigration from adjacent populations could accelerate the recovery not only by promoting population growth beyond the Allee effect threshold but also by bringing in advantageous genotypes. We explore the nature and role of ecological and evolutionary rescue in an Atlantic cod (Gadus morhua Gadidae) population fished below its Allee effect threshold. We utilize an eco-evolutionary model and simulate scenarios, where the target population evolves in response to selective fishing and sample immigrants from (a) a source p…

Eliciting expert knowledge to inform stock status for data-limited stock assessments

Data-limited fisheries are a major challenge for stock assessment analysts, as many traditional data-rich models cannot be implemented. Approaches based on stock reduction analysis offer simple ways to handle low data availability, but are particularly sensitive to assumptions on relative stock status (i.e., current biomass compared to unperturbed biomass). For the vast majority of data-limited stocks, stock status is unmeasured. The present study presents a method to elicit expert knowledge to inform stock status and a novel, user-friendly on-line application for expert elicitation. Expert opinions are compared to stock status derived from data-rich models. Here, it is evaluated how expert…

Examining nonstationarity in the recruitment dynamics of fishes using Bayesian change point analysis

Marine ecosystems can undergo regime shifts, which result in nonstationarity in the dynamics of the fish populations inhabiting them. The assumption of time-invariant parameters in stock–recruitment models can lead to severe errors when forecasting renewal ability of stocks that experience shifts in their recruitment dynamics. We present a novel method for fitting stock–recruitment models using the Bayesian online change point detection algorithm, which is able to cope with sudden changes in the model parameters. We validate our method using simulations and apply it to empirical data of four demersal fishes in the southern Gulf of St. Lawrence. We show that all of the stocks have experience…

Attuning to a changing ocean

The ocean is a lifeline for human existence, but current practices risk severely undermining ocean sustainability. Present and future social−ecological challenges necessitate the maintenance and development of knowledge and action by stimulating collaboration among scientists and between science, policy, and practice. Here we explore not only how such collaborations have developed in the Nordic countries and adjacent seas but also how knowledge from these regions contributes to an understanding of how to obtain a sustainable ocean. Our collective experience may be summarized in three points: 1) In the absence of long-term observations, decision-making is subject to high risk arising from na…

Sustainability of Fishing Is about Abundance: A Response to Bernatchez et al.

Overfishing together with uncertainty or lack of recovery are characteristic challenges to fisheries management [1]. To realistically account for the multiple drivers of fish population abundances, ecosystem-based fisheries management has been accepted as the future avenue to assess and manage fisheries. However, practical implementations of ecosystem-based fisheries management remain rare, largely because of the lack of methodology and skills [2]. The discrepancy between the aims to conduct ecosystem-based and scientifically sound fisheries management and the prevailing practices becomes even wider when contrasting developed and developing countries [3].

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…

Generalist invasion in a complex lake food web

Invasive species constitute a threat not only to native populations but also to the structure and functioning of entire food webs. Despite being considered as a global problem, only a small number of studies have quantitatively predicted the food web-level consequences of invasions. Here, we use an allometric trophic network model parameterized using empirical data on species body masses and feeding interactions to predict the effects of a possible invasion of Amur sleeper (Perccottus glenii), on a well-studied lake ecosystem. We show that the modeled establishment of Amur sleeper decreased the biomasses o ftop predator fishes by about 10%–19%. These reductions were largely explained by inc…

Data from: The role of fish life histories in allometrically scaled food-web dynamics

1. 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. 2. 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, th…

Data from Detection of Allee effects in marine fishes: analytical biases generated by data availability and model selection

The demographic Allee effect, or depensation, implies positive association between per capita population growth rate and population size at low abundances, thereby lowering growth ability of sparse populations. This can have far-reaching consequences on population recovery ability and colonization success. In the context of marine fishes, there is a widespread perception that Allee effects are rare or non-existent. However, studies that have failed to detect Allee effects in marine fishes have suffered from several fundamental methodological and data limitations. In the present study, we challenge the prevailing perception about the rarity of Allee effects by analysing nine populations of A…

Data from: Environmentally-induced noise dampens and reddens with increasing trophic level in a complex food web

Stochastic variability of key abiotic factors including temperature, precipitation and the availability of light and nutrients greatly influences species’ ecological function and evolutionary fate. Despite such influence, ecologists have typically ignored the effect of abiotic stochasticity on the structure and dynamics of ecological networks. Here we help to fill that gap by advancing the theory of how abiotic stochasticity, in the form of environmental noise, affects the population dynamics of species within food webs. We do this by analysing an allometric trophic network model of Lake Constance subjected to positive (red), negative (blue), and non-autocorrelated (white) abiotic temporal …

Data from: Species’ ecological functionality alters the outcome of fish stocking success predicted by a food-web model

Fish stocking is used worldwide in conservation and management but its effects on food-web dynamics and ecosystem stability are poorly known. To better understand these effects and predict the outcomes of stocking, we used an empirically validated network model of a well-studied lake ecosystem. We simulate two stocking scenarios with two native fish species valuable for fishing. In the first scenario, we stock planktivorous fish (whitefish) larvae in the ecosystem. This leads to 1% increase in adult whitefish biomasses and decreases the biomasses of the top predator (perch). In the second scenario, we also stock perch larvae in the ecosystem. This decreases the planktivorous whitefish and t…

Data from: Towards a mechanistic understanding of vulnerability to hook-and-line fishing: boldness as the basic target of angling-induced selection

In passively operated fishing gear, boldness-related behaviors should fundamentally affect the vulnerability of individual fish and thus be under fisheries selection. To test this hypothesis, we used juvenile common-garden reared carp (Cyprinus carpio) within a narrow size-range to investigate the mechanistic basis of behavioral selection caused by angling. We focused on one key personality trait (i.e., boldness), measured in groups within ponds, two morphological traits (body-shape and head-shape), and one life-history trait (juvenile growth capacity) and studied mean standardized selection gradients caused by angling. Carp behavior was highly repeatable within ponds. In the short-term, ov…