Fishery-induced selection on an Alpine whitefish: quantifying genetic and environmental effects on individual growth rate

Genomic variation from an extinct species is retained in the extant radiation following speciation reversal

Ecosystem degradation and biodiversity loss are major global challenges. When reproductive isolation between species is contingent on the interaction of intrinsic lineage traits with features of the environment, environmental change can weaken reproductive isolation and result in extinction through hybridization. By this process called speciation reversal, extinct species can leave traces in genomes of extant species through introgressive hybridization. Using historical and contemporary samples, we sequenced all four species of an Alpine whitefish radiation before and after anthropogenic lake eutrophication and the associated loss of one species through speciation reversal. Despite the extinction of this taxon, substantial fractions of its genome, including regions shaped by positive selection before eutrophication, persist within surviving species as a consequence of introgressive hybridization during eutrophication. Given the prevalence of environmental change, studying speciation reversal and its genomic consequences provides fundamental insights into evolutionary processes and informs biodiversity conservation.

Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest?

The extent and rate of harvest‐induced genetic changes in natural populations may impact population productivity, recovery, and persistence. While there is substantial evidence for phenotypic changes in harvested fishes, knowledge of genetic change in the wild remains limited, as phenotypic and genetic data are seldom considered in tandem, and the number of generations needed for genetic changes to occur is not well understood. We quantified changes in size‐at‐age, sex‐specific changes in body size, and genomic metrics in three harvested walleye (Sander vitreus) populations and a fourth reference population with low harvest levels over a 15‐year period in Mistassini Lake, Quebec. We also collected Indigenous knowledge (IK) surrounding concerns about these populations over time. Using ~9,000 SNPs, genomic metrics included changes in population structure, neutral genomic diversity, effective population size, and signatures of selection. Indigenous knowledge revealed overall reductions in body size and number of fish caught. Smaller body size, a small reduction in size‐at‐age, nascent changes to population structure (population differentiation within one river and homogenization between two others), and signatures of selection between historical and contemporary samples reflected coupled phenotypic and genomic change in the three harvested populations in both sexes, while no change occurred in the reference population. Sex‐specific analyses revealed differences in both body size and genomic metrics but were inconclusive about whether one sex was disproportionately affected. Although alternative explanations cannot be ruled out, our collective results are consistent with the hypothesis that genetic changes associated with harvesting may arise within 1–2.5 generations in long‐lived wild fishes. This study thus demonstrates the need to investigate concerns about harvest‐induced evolution quickly once they have been raised.

Ecological change alters the evolutionary response to harvest in a freshwater fish

Harvesting can induce rapid evolution in animal populations, yet the role of ecological change in buffering or enhancing that response is poorly understood. Here, we developed an eco-genetic model to examine how ecological changes brought about by two notorious invasive species, zebra and quagga mussels, influence harvest-induced evolution and resilience in a freshwater fish. Our study focused on lake whitefish (Coregonus clupeaformis) in the Laurentian Great Lakes, where the species supports valuable commercial and subsistence fisheries, and where the invasion of dreissenid (zebra and quagga) mussels caused drastic shifts in ecosystem productivity. Using our model system, we predicted faster rates of evolution of maturation reaction norms in lake whitefish under pre-invasion ecosystem conditions when growth and recruitment of young to the population were high. Slower growth rates that occurred under post-invasion conditions delayed when fish became vulnerable to the fishery, thus decreasing selection pressure and lessening the evolutionary response to harvest. Fishing with gill nets and traps nets generally selected for early maturation at small sizes, except when fishing at low levels with small mesh gill nets under pre-invasion conditions; in this latter case, evolution of delayed maturation was predicted. Overall, the invasion of dreissenid mussels lessened the evolutionary response to harvest, while also reducing the productivity and commercial yield potential of the stock. These results demonstrate how ecological conditions shape evolutionary outcomes and how invasive species can have a direct effect on evolutionary responses to harvest and sustainability.

Size-selective fishing and the potential for fisheries-induced evolution in lake whitefish

The long-term evolutionary effects of fishing on maturation schedules can depend on gear type, the shape of the gear type's size-selectivity function, and the size and age structure of a population. Our goal was to better understand how environmentally induced differences in somatic growth influence the evolutionary effects of size-selective fisheries, using lake whitefish (Coregonus clupeaformis) in Lake Huron as a case study. Using a state-dependent optimization model of energy allocation parameterized for lake whitefish, we show that fishing with gill nets (bell-shaped selectivity) and trap nets (sigmoid-shaped selectivity) can be potent agents of selection on size thresholds for maturity. Compared to trap nets and large mesh (114 mm) gill nets, small mesh (89 mm) gill nets are better able to buffer populations from fishing-induced evolution by safeguarding large, fecund fish, but only when overall fishing mortality is low and growth rates sufficiently fast such that fish can outgrow vulnerable size classes. Regardless of gear type, and all else being equal, high fishing mortality in combination with low growth rates is expected to intensify the long-term evolutionary effects of fishing.

Hormonal responsiveness to stress is negatively associated with vulnerability to angling capture in fish

Differences in behavior and physiology amongst individuals often alter relative fitness levels in the environment. However, the ideal behavioral/physiological phenotype in a given environment may be altered by human activity, leading to an evolutionary response in the affected population. One example of this process can be found in fisheries (including recreational freshwater fisheries), where selective capture and harvest of individuals with certain phenotypes can drive evolutionary change. While some life history traits and behavioral tendencies influencing capture likelihood have been studied, the physiological mechanisms driving this vulnerability remain poorly understood. To address this, we assessed how two major physiological characteristics (hormonal responsiveness to stress and metabolic phenotype) and one behavioral characteristic (boldness) impact the likelihood of an individual being captured by anglers. Largemouth bass, Micropterus salmoides, derived from a population artificially selected for differential angling vulnerability were assessed for boldness and for stress responsiveness (as indicated by plasma cortisol levels) following an air-exposure challenge. Largemouth bass were then stocked into a pond where experimental angling trials took place, and a subset of captured and uncaptured fish were afterwards assessed for metabolic phenotype. The results showed that stress responsiveness was the primary driver of angling vulnerability, with individuals that experienced lower rises in cortisol following the air-exposure challenge more likely to be captured. Neither boldness nor metabolic phenotype influenced capture probability. The results from this study indicate that fisheries-induced selective pressure may act on physiology, potentially altering stress responsiveness and its associated behaviors in populations exploited by recreational anglers.

Roles of density-dependent growth and life history evolution in accounting for fisheries-induced trait changes

The relative roles of density dependence and life history evolution in contributing to rapid fisheries-induced trait changes remain debated. In the 1930s, northeast Arctic cod (Gadus morhua), currently the world's largest cod stock, experienced a shift from a traditional spawning-ground fishery to an industrial trawl fishery with elevated exploitation in the stock's feeding grounds. Since then, age and length at maturation have declined dramatically, a trend paralleled in other exploited stocks worldwide. These trends can be explained by demographic truncation of the population's age structure, phenotypic plasticity in maturation arising through density-dependent growth, fisheries-induced evolution favoring faster-growing or earlier-maturing fish, or a combination of these processes. Here, we use a multitrait eco-evolutionary model to assess the capacity of these processes to reproduce 74 y of historical data on age and length at maturation in northeast Arctic cod, while mimicking the stock's historical harvesting regime. Our results show that model predictions critically depend on the assumed density dependence of growth: when this is weak, life history evolution might be necessary to prevent stock collapse, whereas when a stronger density dependence estimated from recent data is used, the role of evolution in explaining fisheries-induced trait changes is diminished. Our integrative analysis of density-dependent growth, multitrait evolution, and stock-specific time series data underscores the importance of jointly considering evolutionary and ecological processes, enabling a more comprehensive perspective on empirically observed stock dynamics than previous studies could provide.

Embryonic gene expression of Coregonus palaea (whitefish) under pathogen stress as analyzed by high-throughput RNA-sequencing

Most fishes produce free-living embryos that are exposed to environmental stressors immediately following fertilization, including pathogenic microorganisms. Initial immune protection of embryos involves the chorion, as a protective barrier, and maternally-allocated antimicrobial compounds. At later developmental stages, host-genetic effects influence susceptibility and tolerance, suggesting a direct interaction between embryo genes and pathogens. So far, only a few host genes could be identified that correlate with embryonic survival under pathogen stress in salmonids. Here, we utilized high-throughput RNA-sequencing in order to describe the transcriptional response of a non-model fish, the Alpine whitefish Coregonus palaea, to infection, both in terms of host genes that are likely manipulated by the pathogen, and those involved in an early putative immune response. Embryos were produced in vitro, raised individually, and exposed at the late-eyed stage to a virulent strain of the opportunistic fish pathogen Pseudomonas fluorescens. The pseudomonad increased embryonic mortality and affected gene expression substantially. For example, essential, upregulated metabolic pathways in embryos under pathogen stress included ion binding pathways, aminoacyl-tRNA-biosynthesis, and the production of arginine and proline, most probably mediated by the pathogen for its proliferation. Most prominently downregulated transcripts comprised the biosynthesis of unsaturated fatty acids, the citrate cycle, and various isoforms of b-cell transcription factors. These factors have been shown to play a significant role in host blood cell differentiation and renewal. With regard to specific immune functions, differentially expressed transcripts mapped to the complement cascade, MHC class I and II, TNF-alpha, and T-cell differentiation proteins. The results of this study reveal insights into how P. fluorescens impairs the development of whitefish embryos and set a foundation for future studies investigating host pathogen interactions in fish embryos.

Rapidly shifting maturation schedules following reduced commercial harvest in a freshwater fish

Size-selective harvest of fish stocks can lead to maturation at smaller sizes and younger ages, which may depress stock productivity and recovery. Such changes in maturation may be very slow to reverse, even following complete fisheries closures. We evaluated temporal trends in maturation of five Great Lakes stocks of yellow perch (Perca flavescens Mitchill) using indices that attempt to disentangle plastic and evolutionary changes in maturation: age at 50% maturity and probabilistic maturation reaction norms (PMRNs). Four populations were fished commercially throughout the time series, while the Lake Michigan fishery was closed following a stock collapse. We documented rapid increases in PMRNs of the Lake Michigan stock coincident with the commercial fishery closure. Saginaw Bay and Lake Huron PMRNs also increased following reduced harvest, while Lake Erie populations were continuously fished and showed little change. The rapid response of maturation may have been enhanced by the short generation time of yellow perch and potential gene flow between northern and southern Lake Michigan, in addition to potential reverse adaptation following the fishing moratorium. These results suggest that some fish stocks may retain the ability to recover from fisheries-induced life history shifts following fishing moratoria.

The evolutionary legacy of size-selective harvesting extends from genes to populations

Size-selective harvesting is assumed to alter life histories of exploited fish populations, thereby negatively affecting population productivity, recovery, and yield. However, demonstrating that fisheries-induced phenotypic changes in the wild are at least partly genetically determined has proved notoriously difficult. Moreover, the population-level consequences of fisheries-induced evolution are still being controversially discussed. Using an experimental approach, we found that five generations of size-selective harvesting altered the life histories and behavior, but not the metabolic rate, of wild-origin zebrafish (Danio rerio). Fish adapted to high positively size selective fishing pressure invested more in reproduction, reached a smaller adult body size, and were less explorative and bold. Phenotypic changes seemed subtle but were accompanied by genetic changes in functional loci. Thus, our results provided unambiguous evidence for rapid, harvest-induced phenotypic and evolutionary change when harvesting is intensive and size selective. According to a life-history model, the observed life-history changes elevated population growth rate in harvested conditions, but slowed population recovery under a simulated moratorium. Hence, the evolutionary legacy of size-selective harvesting includes populations that are productive under exploited conditions, but selectively disadvantaged to cope with natural selection pressures that often favor large body size.

Toward Darwinian fisheries management

There is increasing evidence that fishing may cause rapid contemporary evolution in freshwater and marine fish populations. This has led to growing concern about the possible consequences such evolutionary change might have for aquatic ecosystems and the utility of those ecosystems to society. This special issue contains contributions from a symposium on fisheries-induced evolution held at the American Fisheries Society Annual Meeting in August 2008. Contributions include primary studies and reviews of field-based and experimental evidence, and several theoretical modeling studies advancing life-history theory and investigating potential management options. In this introduction we review the state of research in the field, discuss current controversies, and identify contributions made by the papers in this issue to the knowledge of fisheries-induced evolution. We end by suggesting directions for future research.

Quantifying selection differentials caused by recreational fishing: development of modeling framework and application to reproductive investment in pike (Esox lucius)

Methods for quantifying selection pressures on adaptive traits affected by size-selective fishing are still scarce, and none have as yet been developed for recreational fishing. We present an ecologically realistic age-structured model specifically tailored to recreational fishing that allows estimating selection differentials on adaptive life-history traits. The model accounts for multiple ecological feedbacks, which result in density-dependent and frequency-dependent selection. We study selection differentials on annual reproductive investment under size-selective exploitation in a highly demanded freshwater recreational fish species, northern pike (Esox lucius L.). We find that recreational angling mortality exerts positive selection differentials on annual reproductive investment, in agreement with predictions from life-history theory. The strength of selection increases with the intensity of harvesting. We also find that selection on reproductive investment can be reduced by implementing simple harvest regulations such as minimum-size limits. The general, yet computationally simple, methods introduced here allow evaluating and comparing selection pressures on adaptive traits in other fish populations and species, and thus have the potential to become a tool for evolutionary impact assessment of harvesting.

Genetic diversity of upper Lake Constance whitefish Coregonus spp. under the influence of fisheries: a DNA study based on archived scale samples from 1932, 1975 and 2006

This investigation examined changes in the genetic diversity of pelagic upper Lake Constance (ULC) whitefish Coregonus wartmanni population before and after the alteration of fishery methods and management from 1932 to 2006. The study spans a period of pronounced changes in trophic status of the lake and transitions from traditional relatively unselective pelagic seine (Klusgarn) fishing to highly size-selective nylon gillnet techniques. In addition, supportive breeding and stocking became most popular during the phase of eutrophication in the 1970s. The main hypothesis is that size-selective fisheries and breeding lead to an overall decrease in genetic variability over time. A total of 215 archived C. wartmanni scale samples from 1932, 1975 and 2006 were analysed by genotyping 11 microsatellite loci. A comparison of population genetic parameters, including allelic richness, observed and expected heterozygosities, and estimates of effective population sizes, suggests that the genetic diversity of C. wartmanni population has not decreased. The appearance of new alleles in the gene pool in 1975 and 2006 may be indicative of admixture with other forms in the lake or with stocked allochthonous forms. Overall, the fisheries management practice in ULC, including the effects of size-selective fisheries, supportive breeding and stocking, have not significantly altered the genetic diversity of Coregonus spp. over an 80 year period.

Evolutionary impact assessment: accounting for evolutionary consequences of fishing in an ecosystem approach to fisheries management

Managing fisheries resources to maintain healthy ecosystems is one of the main goals of the ecosystem approach to fisheries (EAF). While a number of international treaties call for the implementation of EAF, there are still gaps in the underlying methodology. One aspect that has received substantial scientific attention recently is fisheries-induced evolution (FIE). Increasing evidence indicates that intensive fishing has the potential to exert strong directional selection on life-history traits, behaviour, physiology, and morphology of exploited fish. Of particular concern is that reversing evolutionary responses to fishing can be much more difficult than reversing demographic or phenotypically plastic responses. Furthermore, like climate change, multiple agents cause FIE, with effects accumulating over time. Consequently, FIE may alter the utility derived from fish stocks, which in turn can modify the monetary value living aquatic resources provide to society. Quantifying and predicting the evolutionary effects of fishing is therefore important for both ecological and economic reasons. An important reason this is not happening is the lack of an appropriate assessment framework. We therefore describe the evolutionary impact assessment (EvoIA) as a structured approach for assessing the evolutionary consequences of fishing and evaluating the predicted evolutionary outcomes of alternative management options. EvoIA can contribute to EAF by clarifying how evolution may alter stock properties and ecological relations, support the precautionary approach to fisheries management by addressing a previously overlooked source of uncertainty and risk, and thus contribute to sustainable fisheries.

Genetic and life-history changes associated with fisheries-induced population collapse

Over the recent years, growing number of studies suggests that intensive size-selective fishing can cause evolutionary changes in life-history traits in the harvested population, which can have drastic negative effects on populations, ecosystems and fisheries. However, most studies to date have overlooked the potential role of immigration of fish with different phenotypes as an alternative plausible mechanism behind observed phenotypic trends. Here, we investigated the evolutionary consequences of intensive fishing simultaneously at phenotypic and molecular level in Eurasian perch (Perca fluviatilis L.) population in the Baltic Sea over a 24-year period. We detected marked changes in size- and age-distributions and increase in juvenile growth rate. We also observed reduction of age at sexual maturity in males that has frequently been considered to support the hypothesis of fisheries-induced evolution. However, combined individual-based life-history and genetic analyses indicated increased immigration of foreign individuals with different life-history patterns as an alternative mechanism behind the observed phenotypic change. This study demonstrates the value of combining genetic and phenotypic analyses and suggests that replacement or breakdown of locally adapted gene complexes may play important role in impeding the recovery of fish populations.

Harvest selection on Atlantic cod behavioral traits: implications for spatial management

Harvesting wild populations may contrast or reinforce natural agents of selection and potentially cause evolutionary changes in life-history traits such as growth and maturation. Harvest selection may also act on behavioral traits, although this field of research has so far received less attention. We used acoustic tags and a network of receivers to monitor the behavior and fate of individual Atlantic cod (Gadus morhua, N = 60) in their natural habitat on the Norwegian Skagerrak coast. Fish with a strong diel vertical migration, alternating between shallow- and deep-water habitats, had a higher risk of being captured in the fishery (traps, gillnet, hand line) as compared to fish that stayed in deeper water. There was also a significant negative correlation between fish size (30–66 cm) and the magnitude of diel vertical migration. Natural selection on behavior was less clear, but tended to favor fish with a large activity space. On a monthly time scale we found significant repeatabilities for cod behavior, meaning that individual characteristics tended to persist and therefore may be termed personality traits. We argue that an evolutionary approach to fisheries management should consider fish behavior. This would be of particular relevance for spatial management actions such as marine reserve design.

Monitoring adaptive genetic responses to environmental change

Widespread environmental changes including climate change, selective harvesting and landscape alterations now greatly affect selection regimes for most organisms. How animals and plants can adapt to these altered environments via contemporary evolution is thus of strong interest. We discuss how to use genetic monitoring to study adaptive responses via repeated analysis of the same populations over time, distinguishing between phenotypic and molecular genetics approaches. After describing monitoring designs, we develop explicit criteria for demonstrating adaptive responses, which include testing for selection and establishing clear links between genetic and environmental change. We then review a few exemplary studies that explore adaptive responses to climate change in Drosophila, selective responses to hunting and fishing, and contemporary evolution in Daphnia using resurrected resting eggs. We further review a broader set of 44 studies to assess how well they meet the proposed criteria, and conclude that only 23% fulfill all criteria. Approximately half (43%) of these studies failed to rule out the alternative hypothesis of replacement by a different, better-adapted population. Likewise, 34% of the studies based on phenotypic variation did not test for selection as opposed to drift. These shortcomings can be addressed via improved experimental designs and statistical testing. We foresee monitoring of adaptive responses as a future valuable tool in conservation biology, for identifying populations unable to evolve at sufficiently high rates and for identifying possible donor populations for genetic rescue. Technological advances will further augment the realization of this potential, especially next-generation sequencing technologies that allow for monitoring at the level of whole genomes.

Male mutation bias and possible long-term effects of human activities

The ability of a population to adapt to changing environments depends critically on the amount and kind of genetic variability it possesses. Mutations are an important source of new genetic variability and may lead to new adaptations, especially if the population size is large. Mutation rates are extremely variable between and within species, and males usually have higher mutation rates as a result of elevated rates of male germ cell division. This male bias affects the overall mutation rate. We examined the factors that influence male mutation bias, and focused on the effects of classical life-history parameters, such as the average age at reproduction and elevated rates of sperm production in response to sexual selection and sperm competition. We argue that human-induced changes in age at reproduction or in sexual selection will affect male mutation biases and hence overall mutation rates. Depending on the effective population size, these changes are likely to influence the long-term persistence of a population.

Life-history evolution and elevated natural mortality in a population of Atlantic cod (Gadus morhua)

Fisheries-induced evolution has been hypothesized to delay the recovery of collapsed fish stocks through effects on their productivity. The cod stock in the southern Gulf of St. Lawrence (SGSL) collapsed in the early 1990s and has shown no recovery since then, due mainly to high natural mortality of adult cod. Age and size at maturation of SGSL cod decreased sharply over time in cohorts produced in the 1950s and 1960s, likely reflecting an evolutionary response to intensified fishing, and have remained low since then, despite severe reductions in fishing mortality over the past 15 years. A predicted consequence of early maturation is increased natural mortality due to higher costs to reproduction. Early maturation may be a cause of increases in natural mortality of SGSL cod in the 1970s but does not appear to be related to the much larger increases since then. Instead, the current high natural mortality of SGSL cod appears to be primarily a cause, rather than a consequence, of the continued early maturation in this population, now replacing fishing mortality as the agent of selection favouring early maturity. This striking example of the failure to reverse fisheries-induced evolution by relaxing fishing pressure emphasizes the need for management strategies that minimize the chances of harvest-induced genetic change.