Simulating fishery-induced evolution in chinook salmon: the role of gear, location, and genetic correlation among traits

Assortative mating for reproductive timing affects population recruitment and resilience in a quantitative genetic model

Quantitative models that simulate the inheritance and evolution of fitness-linked traits offer a method for predicting how environmental or anthropogenic perturbations can affect the dynamics of wild populations. Random mating between individuals within populations is a key assumption of many such models used in conservation and management to predict the impacts of proposed management or conservation actions. However, recent evidence suggests that non-random mating may be underestimated in wild populations and play an important role in diversity-stability relationships. Here we introduce a novel individual-based quantitative genetic model that incorporates assortative mating for reproductive timing, a defining attribute of many aggregate breeding species. We demonstrate the utility of this framework by simulating a generalized salmonid lifecycle, varying input parameters, and comparing model outputs to theoretical expectations for several eco-evolutionary, population dynamic scenarios. Simulations with assortative mating systems resulted in more resilient and productive populations than those that were randomly mating. In accordance with established ecological and evolutionary theory, we also found that decreasing the magnitude of trait correlations, environmental variability, and strength of selection each had a positive effect on population growth. Our model is constructed in a modular framework so that future components can be easily added to address pressing issues such as the effects of supportive breeding, variable age structure, differential selection by sex or age, and fishery interactions on population growth and resilience. With code published in a public Github repository, model outputs may easily be tailored to specific study systems by parameterizing with empirically generated values from long-term ecological monitoring programs.

Resurgence of an apex marine predator and the decline in prey body size

Recent recoveries of marine mammal populations worldwide have heightened concerns for their potential impacts on global fisheries. While predator-induced reductions in prey abundance have been documented, trait-mediated changes in life-history characteristics are rarely considered. Here we provide a striking example of the impact of a resurging apex marine predator on a commercially important fish species through changes in prey life-history traits. We find that widespread declines in the body size of Chinook salmon over the past 50 y can be explained by intensified predation by growing populations of resident killer whales that selectively feed on large Chinook salmon, thus revealing a potential conflict between salmon fisheries and marine mammal conservation objectives.

In light of recent recoveries of marine mammal populations worldwide and heightened concern about their impacts on marine food webs and global fisheries, it has become increasingly important to understand the potential impacts of large marine mammal predators on prey populations and their life-history traits. In coastal waters of the northeast Pacific Ocean, marine mammals have increased in abundance over the past 40 to 50 y, including fish-eating killer whales that feed primarily on Chinook salmon. Chinook salmon, a species of high cultural and economic value, have exhibited marked declines in average size and age throughout most of their North American range. This raises the question of whether size-selective predation by marine mammals is generating these trends in life-history characteristics. Here we show that increased predation since the 1970s, but not fishery selection alone, can explain the changes in age and size structure observed for Chinook salmon populations along the west coast of North America. Simulations suggest that the decline in mean size results from the selective removal of large fish and an evolutionary shift toward faster growth and earlier maturation caused by selection. Our conclusion that intensifying predation by fish-eating killer whales contributes to the continuing decline in Chinook salmon body size points to conflicting management and conservation objectives for these two iconic species.

Conservation Genomics in a Changing Arctic

Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

Genetic architecture of age at maturity can generate divergent and disruptive harvest-induced evolution

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'.

Proteomics and the search for welfare and stress biomarkers in animal production in the one-health context

Stress and welfare are important factors in animal production in the context of growing production optimization and scrutiny by the general public.

Changes in Size and Age of Chinook Salmon Oncorhynchus tshawytscha Returning to Alaska

The average sizes of Pacific salmon have declined in some areas in the Northeast Pacific over the past few decades, but the extent and geographic distribution of these declines in Alaska is uncertain. Here, we used regression analyses to quantify decadal trends in length and age at maturity in ten datasets from commercial harvests, weirs, and spawner abundance surveys of Chinook salmon Oncorhynchus tshawytscha throughout Alaska. We found that on average these fish have become smaller over the past 30 years (~6 generations), because of a decline in the predominant age at maturity and because of a decrease in age-specific length. The proportion of older and larger 4-ocean age fish in the population declined significantly (P < 0.05) in all stocks examined by return year or brood year. Our analyses also indicated that the age-specific lengths of 4-ocean fish (9 of 10 stocks) and of 3-ocean fish (5 of 10 stocks) have declined significantly (P < 0.05). Size-selective harvest may be driving earlier maturation and declines in size, but the evidence is not conclusive, and additional factors, such as ocean conditions or competitive interactions with other species of salmon, may also be responsible. Regardless of the cause, these wide-spread phenotypic shifts influence fecundity and population abundance, and ultimately may put populations and associated fisheries at risk of decline.

How fast is fisheries-induced evolution? Quantitative analysis of modelling and empirical studies

A number of theoretical models, experimental studies and time-series studies of wild fish have explored the presence and magnitude of fisheries-induced evolution (FIE). While most studies agree that FIE is likely to be happening in many fished stocks, there are disagreements about its rates and implications for stock viability. To address these disagreements in a quantitative manner, we conducted a meta-analysis of FIE rates reported in theoretical and empirical studies. We discovered that rates of phenotypic change observed in wild fish are about four times higher than the evolutionary rates reported in modelling studies, but correlation between the rate of change and instantaneous fishing mortality (F) was very similar in the two types of studies. Mixed-model analyses showed that in the modelling studies traits associated with reproductive investment and growth evolved slower than rates related to maturation. In empirical observations age-at-maturation was changing faster than other life-history traits. We also found that, despite different assumption and modelling approaches, rates of evolution for a given F value reported in 10 of 13 modelling studies were not significantly different.

Quantifying and comparing size selectivity among Alaskan sockeye salmon fisheries

Quantifying long-term size-selective harvest patterns is necessary for understanding the potential evolutionary effects on exploited species. The comparison of fishery selection patterns on the same species subject to different gear types, in different areas, and over multi-decadal periods can reveal the factors influencing selection. In this study we quantified and compared size-selective harvest by nine Alaskan sockeye salmon (Oncorhynchus nerka) fisheries to understand overall patterns. We calculated length-specific linear selection differentials (the difference in average length of fish before vs. after fishing), which are produced by different combinations of exploitation rates and length-selectivity values, and nonlinear standardized differentials, describing disruptive selection, across all years for each fishery. Selection differentials varied among years, but larger fish were caught in 73% of years for males and 84% of years for females, leaving smaller fish to spawn. Disruptive selection was observed on female and male fish in 84% and 92% of years, respectively. Linear selection was stronger on females than males in 77% of years examined, and disruptive selection was stronger on males in 71% of years. Selection pressure was influenced by a combination of factors under and beyond management control; analyses using mixed-effects models indicated that fisheries were less size selective in years when fish were larger than average and had lower exploitation rates. The observed harvest of larger than average sockeye salmon is consistent with the hypothesis that size-selective fishing contributes to decreasing age and length at maturation trends over time, but temporal variability in selection and strong disruptive selection suggests that the overall directional pressure is weaker than is often assumed in evolutionary models.