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Body size is a key component of individual fitness and an important factor in the structure and functioning of populations and ecosystems. Disentangling the effects of environmental change, harvest and intra- and inter-specific trophic effects on body size remains challenging for populations in the wild. Herring in the Northwest Atlantic provide a strong basis for evaluating hypotheses related to these drivers given that they have experienced significant warming and harvest over the past century, while also having been exposed to a wide range of other selective constraints across their range. Using data on mean length-at-age 4 for the sixteen principal populations over a period of 53 cohorts (1962-2014), we fitted a series of empirical models for temporal and between-population variation in the response to changes in sea surface temperature. We find evidence for a unified cross-population response in the form of a parabolic function according to which populations in naturally warmer environments have responded more negatively to increasing temperature compared with those in colder locations. Temporal variation in residuals from this function was highly coherent among populations, further suggesting a common response to a large-scale environmental driver. The synchrony observed in this study system, despite strong differences in harvest and ecological histories among populations and over time, clearly indicates a dominant role of environmental change on size-at-age in wild populations, in contrast to commonly reported effects of fishing. This finding has important implications for the management of fisheries as it indicates that a key trait associated with population productivity may be under considerably less short-term management control than currently assumed. Our study, overall, illustrates the need for a comparative approach within species for inferences concerning the many possible effects on body size of natural and anthropogenic drivers in the wild., (© 2024 His Majesty the King in Right of Canada and The Authors. Global Change Biology published by John Wiley & Sons Ltd. Reproduced with the permission of the Minister of Fisheries and Oceans Canada.)

In nature, organisms are exposed to variable environmental conditions that impact their performance and fitness. Despite the ubiquity of environmental variability, substantial knowledge gaps in our understanding of organismal responses to nonconstant thermal regimes remain. In the present study, using zebrafish (Danio rerio) as a model organism, we applied geometric morphometric methods to examine how challenging but ecologically realistic diel thermal fluctuations experienced during different life stages influence adult body shape, size, and condition. Zebrafish were exposed to either thermal fluctuations (22-32°C) or a static optimal temperature (27°C) sharing the same thermal mean during an early period spanning embryonic and larval ontogeny (days 0-30), a later period spanning juvenile and adult ontogeny (days 31-210), or a combination of both. We found that body shape, size, and condition were affected by thermal variability, but these plasticity-mediated changes were dependent on the timing of ontogenetic exposure. Notably, after experiencing fluctuating temperatures during early ontogeny, females displayed a deeper abdomen while males displayed an elongated caudal peduncle region. Moreover, males displayed beneficial acclimation of body condition under lifelong fluctuating temperature exposure, whereas females did not. The present study, using ecologically realistic thermal regimes, provides insight into the timing of environmental experiences that generate phenotypic variation in zebrafish., (© 2023 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

Temperature profoundly affects ectotherm physiology. Although differential thermal responses influence fitness, thus driving population dynamics and species distributions, our understanding of the molecular architecture underlying these responses is limited, especially during the critical larval stage. Here, using RNA-sequencing of laboratory-reared Atlantic cod (Gadus morhua) larvae of wild origin, we find changes in gene expression in thousands of transcripts consistent with a severe cellular stress response at both ambient and projected (+2°C and +4°C) temperatures. In addition, specific responses to stress, heat, and hypoxia were commonly identified in gene ontology enrichment analyses and 33 of the 44 genes comprising the minimum stress proteome of all organisms were upregulated. Earlier onset of the stress response was evident at higher temperatures; concomitant increased growth and mortality suggests a reduction in fitness. Temporal differences in gene expression levels do not correspond to differences in growing degree days, suggesting negative physiological consequences of warming beyond accelerated development. Because gene expression is costly, we infer that the upregulation of thousands of transcripts in response to warming in larval cod might act as an energetic drain. We hypothesize that the energetically costly stress response, coupled with increased growth rate at warmer temperatures, leads to faster depletion of energy reserves and increased risk of mortality in larval cod. As sea surface temperatures continue to rise over the next century, reduced fitness of Atlantic cod larvae might lead to population declines in this ecologically and socioeconomically important species. Further, our findings expand our understanding of transcriptomic responses to temperature by ectothermic vertebrate larvae beyond the critical first-feeding stage, a time when organisms begin balancing the energetic demands of growth, foraging, development, and maintenance. Linking the molecular basis of a thermal response to key fitness-related traits is fundamentally important to predicting how global warming will affect ectotherms., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.)

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

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

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., (© 2022 The Authors. Journal of Fish Biology published by John Wiley & Sons Ltd on behalf of Fisheries Society of the British Isles.)

Genomic reaction norms represent the range of gene expression phenotypes (usually mRNA transcript levels) expressed by a genotype along an environmental gradient. Reaction norms derived from common-garden experiments are powerful approaches for disentangling plastic and adaptive responses to environmental change in natural populations. By treating gene expression as a phenotype in itself, genomic reaction norms represent invaluable tools for exploring causal mechanisms underlying organismal responses to climate change across multiple levels of biodiversity. Our goal is to provide the context, framework and motivation for applying genomic reaction norms to study the responses of natural populations to climate change. Here, we describe the utility of integrating genomics with common-garden-gradient experiments under a reaction norm analytical framework to answer fundamental questions about phenotypic plasticity, local adaptation, their interaction (i.e. genetic variation in plasticity) and future adaptive potential. An experimental and analytical framework for constructing and analysing genomic reaction norms is presented within the context of polygenic climate change responses of structured populations with gene flow. Intended for a broad eco-evo readership, we first briefly review adaptation with gene flow and the importance of understanding the genomic basis and spatial scale of adaptation for conservation and management of structured populations under anthropogenic change. Then, within a high-dimensional reaction norm framework, we illustrate how to distinguish plastic, differentially expressed (difference in reaction norm intercepts) and differentially plastic (difference in reaction norm slopes) genes, highlighting the areas of opportunity for applying these concepts. We conclude by discussing how genomic reaction norms can be incorporated into a holistic framework to understand the eco-evolutionary dynamics of climate change responses from molecules to ecosystems. We aim to inspire researchers to integrate gene expression measurements into common-garden experimental designs to investigate the genomics of climate change responses as sequencing costs become increasingly accessible., (© 2022 The Authors. Journal of Animal Ecology published by John Wiley & Sons Ltd on behalf of British Ecological Society.)

Gene flow shapes spatial genetic structure and the potential for local adaptation. Among marine animals with nonmigratory adults, the presence or absence of a pelagic larval stage is thought to be a key determinant in shaping gene flow and the genetic structure of populations. In addition, the spatial distribution of suitable habitats is expected to influence the distribution of biological populations and their connectivity patterns. We used whole genome sequencing to study demographic history and reduced representation (double-digest restriction associated DNA) sequencing data to analyse spatial genetic structure in broadnosed pipefish (Syngnathus typhle). Its main habitat is eelgrass beds, which are patchily distributed along the study area in southern Norway. Demographic connectivity among populations was inferred from long-term (~30-year) population counts that uncovered a rapid decline in spatial correlations in abundance with distance as short as ~2 km. These findings were contrasted with data for two other fish species that have a pelagic larval stage (corkwing wrasse, Symphodus melops; black goby, Gobius niger). For these latter species, we found wider spatial scales of connectivity and weaker genetic isolation-by-distance patterns, except where both species experienced a strong barrier to gene flow, seemingly due to lack of suitable habitat. Our findings verify expectations that a fragmented habitat and absence of a pelagic larval stage promote genetic structure, while presence of a pelagic larvae stage increases demographic connectivity and gene flow, except perhaps over extensive habitat gaps., (© 2022 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.)

Parasitic salmon lice (Lepeophtheirus salmonis) threaten the economic and ecological sustainability of salmon farming, and their evolved resistance to treatment with emamectin benzoate (EMB) has been a major problem for salmon farming in the Atlantic Ocean. In contrast, the Pacific Ocean, where wild salmon are far more abundant, has not seen widespread evolution of EMB-resistant lice. Here, we use EMB bioassays and counts of lice on farms from the Broughton Archipelago, Canada-a core region of salmon farming in the Pacific-to show that EMB sensitivity has dramatically decreased since 2010, concurrent with marked decrease in the field efficacy of EMB treatments. Notably, these bioassay data were not made available through public reporting by industry or by the federal regulator, but rather through Indigenous-led agreements that created a legal obligation for salmon-farming companies to provide data to First Nations. Our results suggest that salmon lice in the Pacific Ocean have recently evolved substantial resistance to EMB, and that salmon-louse outbreaks on Pacific farms will therefore be more difficult to control in the coming years., (© 2022. The Author(s).)

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

Stochastic environments shape life-history traits and can promote selection for risk-spreading strategies, such as bet-hedging. Although the strategy has often been hypothesized 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 parameterized an eco-evolutionary model, using empirical data on size-related reproductive and survival traits. To evaluate the fitness benefits of multiple-batch spawning (within a single breeding period), the mechanistic model separately simulated multiple-batch and single-batch spawning populations under temporally varying environments. We followed the arithmetic and geometric mean fitness associated with both strategies and quantified the mean changes in fitness under several environmental stochasticity levels. We found that, by spreading the environmental risk among batches, multiple-batch spawning increases fitness under fluctuating environmental conditions. The multiple-batch spawning trait is, thus, advantageous and acts as a bet-hedging strategy when the environment is exceptionally unpredictable. Our research identifies an analytically flexible, stochastic, life-history modelling approach to explore the fitness consequences of a risk-spreading strategy and elucidates the importance of evolutionary applications to life-history diversity., Competing Interests: We have no conflicts of interest to disclose., (© 2021 The Authors. Evolutionary Applications published by John Wiley & Sons Ltd.)

Competing Interests: The authors declare no competing interest.

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 different patterns of thermally variable incubation, as well as the ontogenetic persistence of these effects. We also describe a physiological framework for contextualizing some of these effects, based on thermal performance theory. Lastly, we highlight key gaps in our understanding of thermally variable incubation and offer suggestions for future studies., (© 2020 Wiley Periodicals LLC.)

Chocolate Pots hot spring (CP) is an Fe-rich, circumneutral-pH geothermal spring in Yellowstone National Park. Relic hydrothermal systems have been identified on Mars, and modern hydrothermal environments such as CP are useful for gaining insight into potential pathways for generation of biosignatures of ancient microbial life on Earth and Mars. Fe isotope fractionation is recognized as a signature of dissimilatory microbial iron oxide reduction (DIR) in both the rock record and modern sedimentary environments. Previous studies in CP have demonstrated the presence of DIR in vent pool deposits and show aqueous-/solid-phase Fe isotope variations along the hot spring flow path that may be linked to this process. In this study, we examined the geochemistry and stable Fe isotopic composition of spring water and sediment core samples collected from the vent pool and along the flow path, with the goal of evaluating whether Fe isotopes can serve as a signature of past or present DIR activity. Bulk sediment Fe redox speciation confirmed that DIR is active within the hot spring vent pool sediments (but not in more distal deposits), and the observed Fe isotope fractionation between Fe(II) and Fe(III) is consistent with previous studies of DIR-driven Fe isotope fractionation. However, modeling of sediment Fe isotope distributions indicates that DIR does not produce a unique Fe isotopic signature of DIR in the vent pool environment. Because of rapid chemical and isotopic communication between the vent pool fluid and sediment, sorption of Fe(II) to Fe(III) oxides would produce an isotopic signature similar to DIR despite DIR-driven generation of large quantities of isotopically light solid-associated Fe(II). The possibility exists, however, for preservation of specific DIR-derived Fe(II) minerals such as siderite (which is present in the vent pool deposits), whose isotopic composition could serve as a long-term signature of DIR in relic hot spring environments.

Regime shifts are increasingly prevalent in the ecological literature. However, definitions vary and detection methods are still developing. Here, we employ a novel statistical algorithm based on the Bayesian online change-point detection framework 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 (>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-related regime shift on cod productivity are accentuated when regime shifts coincide, fishing mortality is high, and populations are small. The analyses suggest that increasing F increasingly sensitized cod in the mid 1970s and late 1990s to regime shifts in NAO, zooplankton abundance, and water temperature. Our work underscores the necessity of accounting for human-induced mortality in regime shift analyses of marine ecosystems., Competing Interests: One of the authors (JAH) received research funding from Canadian food retail company Loblaw Companies Limited. The funder provides general support for research on the recovery and sustainability of marine biodiversity. The funder played no role in the study design; collection, analysis, and interpretation of data; writing of the paper; or the decision to submit the paper for publication. The authors confirm that this funding does not alter our adherence to PLOS ONE policies on sharing data and materials.

Infectious 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-louse impacts on their hosts across a range of temperatures (10, 13, 16, 19, and 22 °C) and infestation levels (zero, 'low' (mean abundance ± SE = 1.6 ± 0.1 lice per fish), and 'high' infestation (6.8 ± 0.4 lice per fish)). We found that the effects of sea lice on the growth rate, condition, and survival of juvenile Atlantic salmon all worsen with increasing temperature. Our results provide a rare empirical example of how climate change may influence the impacts of marine disease in a key social-ecological system. These findings underscore the importance of considering climate-driven changes to disease impacts in wildlife conservation and agriculture.

Genetic 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 modeling 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 multilocus model. Single-locus control of complex traits is thought to be uncommon, yet blocks of linked genes, such as those associated with some types of structural genomic variation, have emerged as taxonomically widespread phenomena. Inheritance of linked architectures resembles that of single loci, thus enabling single-locus-like modeling of polygenic adaptation. Yet, the number of loci, their effect sizes, and the degree of linkage among them all occur along a continuum. We review how linked architectures are often associated, directly or indirectly, with traits expected to be under selection from anthropogenic stressors and are likely to play a large role in adaptation to environmental disturbance. We suggest using single-locus models to explore evolutionary extremes and uncertainties when the trait architecture is unknown, refining parameters as genomic information becomes available, and explicitly incorporating linkage among loci when possible. By overestimating the complexity (e.g., number of independent loci) of the genomic architecture of traits under selection, we risk underestimating the complexity (e.g., nonlinearity) of their evolutionary dynamics., (© The American Genetic Association 2020.)

The marine phase of anadromous Atlantic salmon (Salmo salar) is the least known yet one of the most crucial with regards to population persistence. Recently, declines in many salmon populations in eastern Canada have been attributed to changes in the conditions at sea, thus reducing their survival. However, marine survival estimates are difficult to obtain given that many individuals spend multiple winters in the ocean before returning to freshwater to spawn; therefore, multiple parameters need to be estimated. We develop a model that uses an age-structured projection matrix which, coupled with yearly smolt and return abundance estimates, allows us to resample a distribution of matrices weighted by how close the resulting return estimates match the simulated returns, using a sample-importance-resampling algorithm. We test this model by simulating a simple time series of salmon abundances, and generate six different scenarios of varying salmon life histories where we simulate data for one-sea-winter (1SW)-dominated and non-1SW dominated populations, as well as scenarios where the proportion returning as 1SW is stable or highly variable. We find that our model provides reasonable estimates of marine survival for the first year at sea (S1), but highly uncertain estimates of proportion returning as 1SW (Pr) and survival in the second year at sea (S2). Our exploration of variable scenarios suggests the model is able to detect temporal trends in S1 for populations that have a considerable 1SW component in the returns; the ability of the model to detect trends in S1 diminishes as the proportion of two-sea-winter fish increases. Variability in the annual proportion of fish returning as 1SW does not seem to impact model accuracy. Our approach provides an instructive stepping-stone towards a model that can be applied to empirical abundance estimates of Atlantic salmon, and anadromous fishes in general, and therefore improve our knowledge of the marine phase of their life cycles as well as examining spatial and temporal trends in their variability., Competing Interests: The authors have declared that no competing interests exist.

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 hatched individuals were monitored under thermal variability (6 weeks) and a subsequent one-month period of thermal constancy. We found that variability can positively influence survival, relative to thermal constancy, but negatively affect growth. The observations reported here can be interpreted within the context of Jensen's Inequality (performance at average conditions is unequal to average performance across a range of conditions). Projections of future population viability in the context of climate change would be strengthened by increased experimental attention to the fitness consequences of stochastic and non-stochastic thermal variability., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

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 niche model, to produce food webs where different fish life-history stages are described as separate nodes which are connected through growth and reproduction. Then, we apply a bioenergetic model that uses the food webs and the body sizes generated by our niche model to evaluate the effect of incorporating life-history structure into food web dynamics.We show that the larger the body size of a fish species respective to the body size of its preys, the higher the biomass attained by the fish species and the greater the ecosystem stability. We also find that the larger the asymptotic body size attained by fish species the larger the total ecosystem biomass, a result that holds true for both the largest fish in the ecosystem and each fish species in the ecosystem.This work provides an expanded ATN theory that generates food webs with life-history structure for chosen species. Our work offers a systematic approach for disentangling the effects of increasing life-history complexity in food-web models.

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 accounting for phenotypic variability in several traits, reproductive success of outer-fjord cod was significantly lower than that of inner-fjord cod. This finding, given that genomically different cod ecotypes inhabit inner- and outer-fjord waters, raises the intriguing hypothesis that the populations might be diverging because of ecological speciation. Individual reproductive success, skewed within both sexes (more so among males), was positively affected by body size, which also influenced the timing of reproduction, larger individuals spawning later among females but earlier among males. Our work suggests that spatial mismatches between management and biological units exist in marine fishes and that studies of reproductive interactions between putative populations or ecotypes can provide an informative basis on which determination of the scale of local adaptation can be ascertained.

Despite the large contribution of rangeland and pasture to global soil organic carbon (SOC) stocks, there is considerable uncertainty about the impact of large herbivore grazing on SOC, especially for understudied subtropical grazing lands. It is well known that root system inputs are the source of most grassland SOC, but the impact of grazing on partitioning of carbon allocation to root tissue production compared to fine root exudation is unclear. Given that different forms of root C have differing implications for SOC synthesis and decomposition, this represents a significant gap in knowledge. Root exudates should contribute to SOC primarily after microbial assimilation, and thus promote microbial contributions to SOC based on stabilization of microbial necromass, whereas root litter deposition contributes directly as plant-derived SOC following microbial decomposition. Here, we used in situ isotope pulse-chase methodology paired with plant and soil sampling to link plant carbon allocation patterns with SOC pools in replicated long-term grazing exclosures in subtropical pasture in Florida, USA. We quantified allocation of carbon to root tissue and measured root exudation across grazed and ungrazed plots and quantified lignin phenols to assess the relative contribution of microbial vs. plant products to total SOC. We found that grazing exclusion was associated with dramatically less overall belowground allocation, with lower root biomass, fine root exudates, and microbial biomass. Concurrently, grazed pasture contained greater total SOC, and a larger fraction of SOC that originated from plant tissue deposition, suggesting that higher root litter deposition under grazing promotes greater SOC. We conclude that grazing effects on SOC depend on root system biomass, a pattern that may generalize to other C4-dominated grasslands, especially in the subtropics. Improved understanding of ecological factors underlying root system biomass may be the key to forecasting SOC and optimizing grazing management to enhance SOC accumulation., (© 2018 John Wiley & Sons Ltd.)

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 genetically divergent Atlantic cod ecotypes throughout the study area and study period. A "fjord" ecotype dominated in numbers deep inside fjords while a "North Sea" ecotype was the only type found in offshore North Sea. Both ecotypes coexisted in similar proportions throughout coastal habitats at all spatial scales. The size-at-age of the North Sea ecotype on average exceeded that of the fjord ecotype by 20% in length and 80% in weight across all habitats. Different growth and size among individuals of the two types might be one of several ecologically significant variables that allow for stable coexistence of closely related populations within the same habitat. Management plans, biodiversity initiatives and other mitigation strategies that do not account for the mixture of species ecotypes are unlikely to meet objectives related to the sustainability of fish and fisheries.

Tidal wetlands contain large reservoirs of carbon in their soils and can sequester carbon dioxide (CO 2 ) at a greater rate per unit area than nearly any other ecosystem. The spatial distribution of this carbon influences climate and wetland policy. To assist with international accords such as the Paris Climate Agreement, national-level assessments such as the United States (U.S.) National Greenhouse Gas Inventory, and regional, state, local, and project-level evaluation of CO 2 sequestration credits, we developed a geodatabase (CoBluCarb) and high-resolution maps of soil organic carbon (SOC) distribution by linking National Wetlands Inventory data with the U.S. Soil Survey Geographic Database. For over 600,000 wetlands, the total carbon stock and organic carbon density was calculated at 5-cm vertical resolution from 0 to 300 cm of depth. Across the continental United States, there are 1,153-1,359 Tg of SOC in the upper 0-100 cm of soils across a total of 24 945.9 km 2 of tidal wetland area, twice as much carbon as the most recent national estimate. Approximately 75% of this carbon was found in estuarine emergent wetlands with freshwater tidal wetlands holding about 19%. The greatest pool of SOC was found within the Atchafalaya/Vermilion Bay complex in Louisiana, containing about 10% of the U.S. total. The average density across all tidal wetlands was 0.071 g cm -3 across 0-15 cm, 0.055 g cm -3 across 0-100 cm, and 0.040 g cm -3 at the 100 cm depth. There is inherent variability between and within individual wetlands; however, we conclude that it is possible to use standardized values at a range of 0-100 cm of the soil profile, to provide first-order quantification and to evaluate future changes in carbon stocks in response to environmental perturbations. This Tier 2-oriented carbon stock assessment provides a scientific method that can be copied by other nations in support of international requirements., (© 2017 John Wiley & Sons Ltd.)

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-term persistence of these inversions indicates that they are maintained by selection, possibly facilitated by coevolution of genes underlying complex traits. Our data suggest that migratory behaviour is derived from more stationary, ancestral ecotypes. Overall, we identify several large genomic regions-each containing hundreds of genes-likely involved in the maintenance of genomic divergence in Atlantic cod on both sides of the Atlantic Ocean.

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 temperate populations had fully recovered, the remainder exhibiting, on average, negligible change (impaired recovery). Singly, life-history traits did not influence recovery status. In combination, however, those that jointly reflect length-based mortality at maturity, M α , revealed that recovered populations have higher M α , which we hypothesize to reflect local adaptations associated with greater r max But, within populations, the smaller sizes at maturity generated by overfishing are predicted to increase M α , slowing recovery and increasing its uncertainty. We conclude that recovery potential is greater for populations adapted to high M but that temporal increases in M concomitant with smaller size at maturity will have the opposite effect. The recovery metric documented here ( M α ) has a sound theoretical basis, is significantly correlated with direct estimates of M that directly reflect r max , is not reliant on data-intensive time series, can be readily estimated, and offers an empirically defensible correlate of recovery, given its clear links to the positive and impaired responses to threat mitigation that have been observed in fish populations over the past three decades., (© 2017 The Author(s).)

Life-history traits are generally assumed to be inherited quantitatively. Fishing that targets large, old individuals is expected to decrease age at maturity. In Atlantic salmon (Salmo salar), it has recently been discovered that sea age at maturity is under strong control by a single locus with sexually dimorphic expression of heterozygotes, which makes it less intuitive to predict how life histories respond to selective fishing. We explore evolutionary responses to fishing in Atlantic salmon, using eco-evolutionary simulations with two alternative scenarios for the genetic architecture of age at maturity: (i) control by multiple loci with additive effects and (ii) control by one locus with sexually dimorphic expression. We show that multi-locus control leads to unidirectional evolution towards earlier maturation, whereas single-locus control causes largely divergent and disruptive evolution of age at maturity without a clear phenotypic trend but a wide range of alternative evolutionary trajectories and greater trait variability within trajectories. Our results indicate that the range of evolutionary responses to selective fishing can be wider than previously thought and that a lack of phenotypic trend need not imply that evolution has not occurred. These findings underscore the role of genetic architecture of life-history traits in understanding how human-induced selection can shape target populations.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'., (© 2016 The Author(s).)

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 reductions in abundance caused by harvest represent an upper limit to the proportional reductions in N e, and that in some cases N e can even increase with increased harvest. This result is a quite general consequence of increased adult mortality and does not depend on harvest selectivity or FIE, although both of these influence the results in a quantitative way. In scenarios that allowed evolution, N e recovered quickly after harvest ended and remained higher than in the preharvest population for well over a century, which indicates that evolution can help provide a long-term buffer against loss of genetic variability.

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., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

The level of phenotypic plasticity displayed within a population (i.e. the slope of the reaction norm) reflects the short-term response of a population to environmental change, while variation in reaction norm slopes among populations reflects spatial variation in these responses. Thus far, studies of thermal reaction norm variation have focused on geographically driven adaptation among different latitudes, altitudes or habitats. Yet, thermal variability is a function of both space and time. For organisms that reproduce at different times of year, such variation has the potential to promote adaptive variability in thermal responses for critical early life stages. Using common-garden experiments, we examined the spatial scale of genetic variation in thermal plasticity for early life-history traits among five populations of endangered Atlantic cod (Gadus morhua) that spawn at different times of year. Patterns of plasticity for larval growth and survival suggest that population responses to climate change will differ substantially, with increasing water temperatures posing a considerably greater threat to autumn-spawning cod than to those that spawn in winter or spring. Adaptation to seasonal cooling or warming experienced during the larval stage is suggested as a possible cause. Furthermore, populations that experience relatively cold temperatures during early life might be more sensitive to changes in temperature. Substantial divergence in adaptive traits was evident at a smaller spatial scale than has previously been shown for a marine fish with no apparent physical barriers to gene flow (∼200 km). Our findings highlight the need to consider the impact of intraspecific variation in reproductive timing on thermal adaptation when forecasting the effects of climate change on animal populations.

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 thresholds at which recovery is unlikely or uncertain. Following a critique of studies on Allee effects, I quantify population-size minima and subsequent trajectories of marine fishes that have and have not recovered following threat mitigation. The data suggest that threat amelioration, albeit necessary, can be insufficient to effect recovery for populations depleted to less than 10% of maximum abundance (N(max)), especially when they remain depleted for lengthy periods of time. Comparing terrestrial and aquatic vertebrates, life-history analyses suggest that population-size thresholds for impaired recovery are likely to be comparatively low for marine fishes but high for marine mammals.Articulation of a 'recovering population paradigm' would seem warranted. It might stimulate concerted efforts to identify generic impaired recovery thresholds across species. It might also serve to reduce the confusion of terminology, and the conflation of causes and consequences with patterns currently evident in the literature on Allee effects, thus strengthening communication among researchers and enhancing the practical utility of recovery-oriented research to conservation practitioners and resource managers.

The frequently observed positive relationship between fish population abundance and spatial distribution suggests that changes in distribution can be indicative of trends in abundance. If contractions in spatial distribution precede declines in spawning stock biomass (SSB), spatial distribution reference points could complement the SSB reference points that are commonly used in marine conservation biology and fisheries management. When relevant spatial distribution information is integrated into fisheries management and recovery plans, risks and uncertainties associated with a plan based solely on the SSB criterion would be reduced. To assess the added value of spatial distribution data, we examine the relationship between SSB and four metrics of spatial distribution intended to reflect changes in population range, concentration, and density for 10 demersal populations (9 species) inhabiting the Scotian Shelf, Northwest Atlantic. Our primary purpose is to assess their potential to serve as indices of SSB, using fisheries independent survey data. We find that metrics of density offer the best correlate of spawner biomass. A decline in the frequency of encountering high density areas is associated with, and in a few cases preceded by, rapid declines in SSB in 6 of 10 populations. Density-based indices have considerable potential to serve both as an indicator of SSB and as spatially based reference points in fisheries management.

Natural environmental change has produced countless opportunities for species to disperse into and persist in habitats where they previously did not exist. Introduction and stocking programmes have facilitated similar sorts of colonization opportunities across considerably greater geographical scales and often in much shorter periods of time. Even though the mechanism of colonization differs, the result can be the same: evolutionary change in the colonizing population in response to novel selection pressures. As a consequence, some human-mediated fish transfers have unintentionally yielded novel research opportunities to study how phenotypes and genes interact with their environment and affect ecological and evolutionary change. The primary purpose here is to explore how work, directly or indirectly involved with human-mediated transfers, has unintentionally yielded novel research and research opportunities in fish ecology and evolution. Insights have produced new knowledge or altered previously held perceptions on topics such as local adaptation, rate of evolutionary change, phenotypic plasticity, alternative reproductive strategies, population structure and colonization probability. Well-documented stocking programmes, especially in terms of history, numbers and original population sources, can provide highly fertile ground for generating further insights on the ecology and evolution of fishes and of the factors likely to influence the success of conservation-based, restoration programmes., (© 2014 The Fisheries Society of the British Isles.)

The evolution of life histories over contemporary time scales will almost certainly affect population demography. One important pathway for such eco-evolutionary interactions is the density-dependent regulation of population dynamics. Here, we investigate how fisheries-induced evolution (FIE) might alter density-dependent population-productivity relationships. To this end, we simulate the eco-evolutionary dynamics of an Atlantic cod (Gadus morhua) population under fishing, followed by a period of recovery in the absence of fishing. FIE is associated with increases in juvenile production, the ratio of juveniles to mature population biomass, and the ratio of the mature population biomass relative to the total population biomass. In contrast, net reproductive rate (R 0 ) and per capita population growth rate (r) decline concomitantly with evolution. Our findings suggest that FIE can substantially modify the fundamental population-productivity relationships that underlie density-dependent population regulation and that form the primary population-dynamical basis for fisheries stock-assessment projections. From a conservation and fisheries-rebuilding perspective, we find that FIE reduces R 0 and r, the two fundamental correlates of population recovery ability and inversely extinction probability.

Negative density-dependent regulation of population dynamics promotes population growth at low abundance and is therefore vital for recovery following depletion. Inversely, any process that reduces the compensatory density-dependence of population growth can negatively affect recovery. Here, we show that increased adult mortality at low abundance can reverse compensatory population dynamics into its opposite-a demographic Allee effect. Northwest Atlantic cod (Gadus morhua) stocks collapsed dramatically in the early 1990s and have since shown little sign of recovery. Many experienced dramatic increases in natural mortality, ostensibly attributable in some populations to increased predation by seals. Our findings show that increased natural mortality of a magnitude observed for overfished cod stocks has been more than sufficient to fundamentally alter the dynamics of density-dependent population regulation. The demographic Allee effect generated by these changes can slow down or even impede the recovery of depleted populations even in the absence of fishing.

Hybrid zones provide unprecedented opportunity for the study of the evolution of reproductive isolation, and the extent of hybridization across individuals and genomes can illuminate the degree of isolation. We examine patterns of interchromosomal linkage disequilibrium (ILD) and the presence of hybridization in Atlantic cod, Gadus morhua, in previously identified hybrid zones in the North Atlantic. Here, previously identified clinal loci were mapped to the cod genome with most (∼70%) occurring in or associated with (<5 kb) coding regions representing a diverse array of possible functions and pathways. Despite the observation that clinal loci were distributed across three linkage groups, elevated ILD was observed among all groups of clinal loci and strongest in comparisons involving a region of low recombination along linkage group 7. Evidence of ILD supports a hypothesis of divergence hitchhiking transitioning to genome hitchhiking consistent with reproductive isolation. This hypothesis is supported by Bayesian characterization of hybrid classes present and we find evidence of common F1 hybrids in several regions consistent with frequent interbreeding, yet little evidence of F2 or backcrossed individuals. This work suggests that significant barriers to hybridization and introgression exist among these co-occurring groups of cod either through strong selection against hybrid individuals, or genetic incompatibility and intrinsic barriers to hybridization. In either case, the presence of strong clinal trends, and little gene flow despite extensive hybridization supports a hypothesis of reproductive isolation and cryptic speciation in Atlantic cod. Further work is required to test the degree and nature of reproductive isolation in this species.

Whether and how habitat fragmentation and population size jointly affect adaptive genetic variation and adaptive population differentiation are largely unexplored. Owing to pronounced genetic drift, small, fragmented populations are thought to exhibit reduced adaptive genetic variation relative to large populations. Yet fragmentation is known to increase variability within and among habitats as population size decreases. Such variability might instead favour the maintenance of adaptive polymorphisms and/or generate more variability in adaptive differentiation at smaller population size. We investigated these alternative hypotheses by analysing coding-gene, single-nucleotide polymorphisms associated with different biological functions in fragmented brook trout populations of variable sizes. Putative adaptive differentiation was greater between small and large populations or among small populations than among large populations. These trends were stronger for genetic population size measures than demographic ones and were present despite pronounced drift in small populations. Our results suggest that fragmentation affects natural selection and that the changes elicited in the adaptive genetic composition and differentiation of fragmented populations vary with population size. By generating more variable evolutionary responses, the alteration of selective pressures during habitat fragmentation may affect future population persistence independently of, and perhaps long before, the effects of demographic and genetic stochasticity are manifest., (© 2014 The Author(s) Published by the Royal Society. All rights reserved.)

Recovery of depleted populations is fundamentally important for conservation biology and sustainable resource harvesting. At low abundance, population growth rate, a primary determinant of population recovery, is generally assumed to be relatively fast because competition is low (i.e., negative density dependence). But population growth can be limited in small populations by an Allee effect. This is particularly relevant for collapsed populations or species that have not recovered despite large reductions in, or elimination of, threats. We investigated how an Allee effect can influence the dynamics of recovery. We used Atlantic cod (Gadus morhua) as the study organism and an empirically quantified Allee effect for the species to parameterize our simulations. We simulated recovery through an individual-based mechanistic simulation model and then compared recovery among scenarios incorporating an Allee effect, negative density dependence, and an intermediate scenario. Although an Allee effect significantly slowed recovery, such that population increase could be negligible even after 100 years or more, it also made the time required for biomass rebuilding much less predictable. Our finding that an Allee effect greatly increased the uncertainty in recovery time frames provides an empirically based explanation for why the removal of threat does not always result in the recovery of depleted populations or species., (© 2014 Society for Conservation Biology.)

The between-population genetic architecture for growth and maturation has not been examined in detail for many animal species despite its central importance in understanding hybrid fitness. We studied the genetic architecture of population divergence in: (i) maturation probabilities at the same age; (ii) size at age and growth, while accounting for maturity status and sex; and (iii) growth plasticity in response to environmental factors, using divergent wild and domesticated Atlantic salmon (Salmo salar). Our work examined two populations and their multigenerational hybrids in a common experimental arrangement in which salinity and quantity of suspended sediments were manipulated to mimic naturally occurring environmental variation. Average specific growth rates across environments differed among crosses, maturity groups, and cross-by-maturity groups, but a growth-rate reduction in the presence of suspended sediments was equal for all groups. Our results revealed both additive and nonadditive outbreeding effects for size at age and for growth rates that differed with life stage, as well as the presence of different sex- and size-specific maturation probabilities between populations. The major implication of our work is that estimates of the genetic architecture of growth and maturation can be biased if one does not simultaneously account for temporal changes in growth and for different maturation probabilities between populations. Namely, these correlated traits interact differently within each population and between sexes and among generations, due to nonadditive effects and a level of independence in the genetic control for traits. Our results emphasize the challenges to investigating and predicting phenotypic changes resulting from between-population outbreeding.

Captive-breeding programs can be implemented to preserve the genetic diversity of endangered populations such that the controlled release of captive-bred individuals into the wild may promote recovery. A common difficulty, however, is that programs are founded with limited wild broodstock, and inbreeding can become increasingly difficult to avoid with successive generations in captivity. Program managers must choose between maintaining the genetic purity of populations, at the risk of inbreeding depression, or interbreeding populations, at the risk of outbreeding depression. We evaluate these relative risks in a captive-breeding program for 3 endangered populations of Atlantic salmon (Salmo salar). In each of 2 years, we released juvenile F(1) and F(2) interpopulation hybrids, backcrosses, as well as inbred and noninbred within-population crosstypes into 9 wild streams. Juvenile size and survival was quantified in each year. Few crosstype effects were observed, but interestingly, the relative fitness consequences of inbreeding and outbreeding varied from year to year. Temporal variation in environmental quality might have driven some of these annual differences, by exacerbating the importance of maternal effects on juvenile fitness in a year of low environmental quality and by affecting the severity of inbreeding depression differently in different years. Nonetheless, inbreeding was more consistently associated with a negative effect on fitness, whereas the consequences of outbreeding were less predictable. Considering the challenges associated with a sound risk assessment in the wild and given that the effect of inbreeding on fitness is relatively predictable, we suggest that risk can be weighted more strongly in terms of the probable outcome of outbreeding. Factors such as genetic similarities between populations and the number of generations in isolation can sometimes be used to assess outbreeding risk, in lieu of experimentation., (© 2014 Society for Conservation Biology.)

The physical and ecological 'fingerprints' of anthropogenic climate change over the past century are now well documented in many environments and taxa. We reviewed the evidence for phenotypic responses to recent climate change in fish. Changes in the timing of migration and reproduction, age at maturity, age at juvenile migration, growth, survival and fecundity were associated primarily with changes in temperature. Although these traits can evolve rapidly, only two studies attributed phenotypic changes formally to evolutionary mechanisms. The correlation-based methods most frequently employed point largely to 'fine-grained' population responses to environmental variability (i.e. rapid phenotypic changes relative to generation time), consistent with plastic mechanisms. Ultimately, many species will likely adapt to long-term warming trends overlaid on natural climate oscillations. Considering the strong plasticity in all traits studied, we recommend development and expanded use of methods capable of detecting evolutionary change, such as the long term study of selection coefficients and temporal shifts in reaction norms, and increased attention to forecasting adaptive change in response to the synergistic interactions of the multiple selection pressures likely to be associated with climate change.

Outbreeding between segregating populations can be important from an evolutionary, conservation and economical-agricultural perspective. Whether and how outbreeding influences maternal effects in wild populations has rarely been studied, despite both the prominent maternal influence on early offspring survival and the known presence of fitness effects resulting from outbreeding in many taxa. We studied several traits during the yolk-feeding stage in multigenerational crosses between a wild and a domesticated Atlantic salmon (Salmo salar) population up to their third-generation hybrid in a common laboratory environment. Using cross-means analysis, we inferred that maternal additive outbreeding effects underlie most offspring traits but that yolk mass also underlies maternal dominant effects. As a consequence of the interplay between additive and dominant maternally controlled traits, offspring from first-generation hybrid mothers expressed an excessive proportion of residual yolk mass, relative to total mass, at the time of first feeding. Their residual yolk mass was 23-97% greater than those of other crosses and 31% more than that predicted by a purely additive model. Offspring additive, epistatic and epistatic offspring-by-maternal outbreeding effects appeared to further modify this largely maternally controlled cross-means pattern, resulting in an increase in offspring size with the percentage of domesticated alleles. Fitness implications remain elusive because of unknown phenotype-by-environment interactions. However, these results suggest how mechanistically co-adapted genetic maternal control on early offspring development can be disrupted by the effects of combining alleles from divergent populations. Complex outbreeding effects at both the maternal and offspring levels make the prediction of hybrid phenotypes difficult.