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.

Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as "integrated" with the founding wild stock, with ongoing gene flow, and as "segregated" with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F₂ -F₄ ; inbreeding F₂ ). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.

Local adaptation of phenology revealed in outcrosses between spawning segments of a salmonid population

Local adaptation has been demonstrated in spatially or temporally distant animal populations but seldom in proximate populations. To address the scale of local adaptation in Pacific salmon (Oncorhynchus spp.), two generations of hybrids between temporally separated spawning segments were made in a population of pink salmon (O. gorbuscha) and compared with controls to evaluate the genetic architecture underlying adult migration time and to test for declines in marine survival that resulted from outbreeding depression. Bayesian mixed-effects models revealed that adult migration times in hybrid lines were intermediate to those of controls and that additive sources of genetic variation were significant, thereby indicating that local adaptation has acted on additive genetic variation in shaping this trait. Similarly, a line cross analysis revealed that an additive model best described the genetic architecture of adult migration time. In contrast, marine survival was generally similar between control and hybrid lines, which suggested that the effect of outbreeding upon marine survival was minimal at such a fine scale of genetic divergence. The implications of these results are that (a) local adaptation can facilitate genetic divergence of life history traits between proximate subpopulations; (b) artificial relaxation of natural barriers to gene flow can cause maladaptive shifts in life history traits; and (c) wild populations may harbour fine-scale adaptive variation that supports productivity and sustainability.

Genomewide association analyses of fitness traits in captive-reared Chinook salmon: Applications in evaluating conservation strategies

A novel application of genomewide association analyses is to use trait-associated loci to monitor the effects of conservation strategies on potentially adaptive genetic variation. Comparisons of fitness between captive- and wild-origin individuals, for example, do not reveal how captive rearing affects genetic variation underlying fitness traits or which traits are most susceptible to domestication selection. Here, we used data collected across four generations to identify loci associated with six traits in adult Chinook salmon (Oncorhynchus tshawytscha) and then determined how two alternative management approaches for captive rearing affected variation at these loci. Loci associated with date of return to freshwater spawning grounds (return timing), length and weight at return, age at maturity, spawn timing, and daily growth coefficient were identified using 9108 restriction site-associated markers and random forest, an approach suitable for polygenic traits. Mapping of trait-associated loci, gene annotations, and integration of results across multiple studies revealed candidate regions involved in several fitness-related traits. Genotypes at trait-associated loci were then compared between two hatchery populations that were derived from the same source but are now managed as separate lines, one integrated with and one segregated from the wild population. While no broad-scale change was detected across four generations, there were numerous regions where trait-associated loci overlapped with signatures of adaptive divergence previously identified in the two lines. Many regions, primarily with loci linked to return and spawn timing, were either unique to or more divergent in the segregated line, suggesting that these traits may be responding to domestication selection. This study is one of the first to utilize genomic approaches to demonstrate the effectiveness of a conservation strategy, managed gene flow, on trait-associated-and potentially adaptive-loci. The results will promote the development of trait-specific tools to better monitor genetic change in captive and wild populations.

Human-mediated evolution in a threatened species? Juvenile life-history changes in Snake River salmon

Evaluations of human impacts on Earth's ecosystems often ignore evolutionary changes in response to altered selective regimes. Freshwater habitats for Snake River fall Chinook salmon (SRFCS), a threatened species in the US, have been dramatically changed by hydropower development and other watershed modifications. Associated biological changes include a shift in juvenile life history: Historically essentially 100% of juveniles migrated to sea as subyearlings, but a substantial fraction have migrated as yearlings in recent years. In contemplating future management actions for this species should major Snake River dams ever be removed (as many have proposed), it will be important to understand whether evolution is at least partially responsible for this life-history change. We hypothesized that if this trait is genetically based, parents who migrated to sea as subyearlings should produce faster-growing offspring that would be more likely to reach a size threshold to migrate to sea in their first year. We tested this with phenotypic data for over 2,600 juvenile SRFCS that were genetically matched to parents of hatchery and natural origin. Three lines of evidence supported our hypothesis: (i) the animal model estimated substantial heritability for juvenile growth rate for three consecutive cohorts; (ii) linear modeling showed an association between juvenile life history of parents and offspring growth rate; and (iii) faster-growing juveniles migrated at greater speeds, as expected if they were more likely to be heading to sea. Surprisingly, we also found that parents reared a full year in a hatchery produced the fastest growing offspring of all-apparently an example of cross-generational plasticity associated with artificial propagation. We suggest that SRFCS is an example of a potentially large class of species that can be considered to be "anthro-evolutionary"-signifying those whose evolutionary trajectories have been profoundly shaped by altered selective regimes in human-dominated landscapes.

Evaluating the Ryman-Laikre effect for marine stock enhancement and aquaculture

The Ryman-Laikre (R-L) effect is an increase in inbreeding and a reduction in total effective population size (NeT ) in a combined captive-wild system, which arises when a few captive parents produce large numbers of offspring. To facilitate evaluation of the R-L effect for scenarios that are relevant to marine stock enhancement and aquaculture, we extended the original R-L formula to explicitly account for several key factors that determine NeT , including the numbers of captive and wild adults, the ratio of captive to wild Ne/N (β), productivity of captive and wild breeders, and removal of individuals from the wild for captive breeding. We show how to provide quantitative answers to questions such as: What scenarios lead to no loss of effective size? What is the maximum effective size that can be achieved? and What scenarios insure that NeT will be no smaller than a specified value? Important results include the following: (1) For large marine populations, the value of β becomes increasingly important as the captive contribution increases. Captive propagation will sharply reduce NeT unless the captive contribution is very small or β is very large (∼103 or higher). (2) Very large values of β are only possible if wild Ne/N is tiny. Therefore, large wild populations undergoing captive enhancement at even modest levels will suffer major reductions in effective size unless wild Ne is a tiny fraction of the census size (about 10-4 or lower).

Effectiveness of managed gene flow in reducing genetic divergence associated with captive breeding

Captive breeding has the potential to rebuild depressed populations. However, associated genetic changes may decrease restoration success and negatively affect the adaptive potential of the entire population. Thus, approaches that minimize genetic risks should be tested in a comparative framework over multiple generations. Genetic diversity in two captive-reared lines of a species of conservation interest, Chinook salmon (Oncorhynchus tshawytscha), was surveyed across three generations using genome-wide approaches. Genetic divergence from the source population was minimal in an integrated line, which implemented managed gene flow by using only naturally-born adults as captive broodstock, but significant in a segregated line, which bred only captive-origin individuals. Estimates of effective number of breeders revealed that the rapid divergence observed in the latter was largely attributable to genetic drift. Three independent tests for signatures of adaptive divergence also identified temporal change within the segregated line, possibly indicating domestication selection. The results empirically demonstrate that using managed gene flow for propagating a captive-reared population reduces genetic divergence over the short term compared to one that relies solely on captive-origin parents. These findings complement existing studies of captive breeding, which typically focus on a single management strategy and examine the fitness of one or two generations.

Evolutionary consequences of fishing and their implications for salmon

We review the evidence for fisheries-induced evolution in anadromous salmonids. Salmon are exposed to a variety of fishing gears and intensities as immature or maturing individuals. We evaluate the evidence that fishing is causing evolutionary changes to traits including body size, migration timing and age of maturation, and we discuss the implications for fisheries and conservation. Few studies have fully evaluated the ingredients of fisheries-induced evolution: selection intensity, genetic variability, correlation among traits under selection, and response to selection. Most studies are limited in their ability to separate genetic responses from phenotypic plasticity, and environmental change complicates interpretation. However, strong evidence for selection intensity and for genetic variability in salmon fitness traits indicates that fishing can cause detectable evolution within ten or fewer generations. Evolutionary issues are therefore meaningful considerations in salmon fishery management. Evolutionary biologists have rarely been involved in the development of salmon fishing policy, yet evolutionary biology is relevant to the long-term success of fisheries. Future management might consider fishing policy to (i) allow experimental testing of evolutionary responses to exploitation and (ii) improve the long-term sustainability of the fishery by mitigating unfavorable evolutionary responses to fishing. We provide suggestions for how this might be done.

Genetic variation in bacterial kidney disease (BKD) susceptibility in Lake Michigan Chinook Salmon and its progenitor population from the Puget Sound

Mass mortality events in wild fish due to infectious diseases are troubling, especially given the potential for long-term, population-level consequences. Evolutionary theory predicts that populations with sufficient genetic variation will adapt in response to pathogen pressure. Chinook Salmon Oncorhynchus tshawytscha were introduced into Lake Michigan in the late 1960s from a Washington State hatchery population. In the late 1980s, collapse of the forage base and nutritional stress in Lake Michigan were thought to contribute to die-offs of Chinook Salmon due to bacterial kidney disease (BKD). Previously, we demonstrated that Lake Michigan Chinook Salmon from a Wisconsin hatchery have greater survival following BKD challenge relative to their progenitor population. Here, we evaluated whether the phenotypic divergence of these populations in BKD susceptibility was due to selection rather than genetic drift. Comparison of the overall magnitude of quantitative trait to neutral marker divergence between the populations suggested selection had occurred but a direct test of quantitative trait divergence was not significant, preventing the rejection of the null hypothesis of differentiation through genetic drift. Estimates of phenotypic variation (VP ), additive genetic variation (VA ) and narrow-sense heritability (h (2)) were consistently higher in the Wisconsin relative to the Washington population. If selection had acted on the Wisconsin population there was no evidence of a concomitant loss of genetic variation in BKD susceptibility. The Renibacterium salmoninarum exposures were conducted at both 14°C and 9°C; the warmer temperature accelerated time to death in both populations and there was no evidence of phenotypic plasticity or a genotype-by-environment (G × E) interaction. High h (2) estimates for BKD susceptibility in the Wisconsin population, combined with a lack of phenotypic plasticity, predicts that future adaptive gains in BKD resistance are still possible and that these adaptive gains would be stable under the temperature range evaluated here.

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

Adaptation to human-modified ecosystems has been implicated in changing the life history of a number of wild animal populations, potentially contributing to their collapse. Fishing may be an important evolutionary force that can change the distribution of fitness-related traits; however, the magnitude and direction of the evolutionary response may be influenced by different management strategies. Most phenotypic traits subject to human-induced selection are simultaneously influenced by the environment and by genetic variation, and many traits are genetically correlated. Here, we evaluated the evolutionary outcomes of harvest activities on mean length and age at maturity in a fish population by coupling a multivariate quantitative genetic model with a Leslie life history matrix model. Lengths-at-ages were treated as genetically correlated characters parameterized from empirical data on chinook salmon (Oncorhynchus tshawytscha) populations. Using simulations, we explored the outcomes of 100 years of harvest using gill nets, which impose disruptive selection, or longlines, which impose minimum size selection, that targeted immature individuals in the high seas or maturing individuals in terminal spawning areas. Response in mean length and age depended on selection differentials imposed by harvest (which depended in turn on fishing location, gear type, and proportion of the population harvested) and on the genetic correlations between traits. Mean length was strongly influenced by the selection differential of the most abundant age class. Large differences in response were observed between the high-seas fishery, where the most abundant age was the youngest age vulnerable to harvest, compared to the terminal area fishery, where an older age class was most abundant. We observed a substantial difference in response between gill nets and longlines in the terminal fishery only. The evolution of mean age of mature individuals was less predictable, but generally increased as length decreased and decreased as length increased. The model presented here has potential for incorporating empirical data into fisheries forecasting and therefore provides a powerful means of integrating evolutionary considerations into harvest management.

Clock polymorphism in Pacific salmon: evidence for variable selection along a latitudinal gradient

Seasonal timing of life-history events is often under strong natural selection. The Clock gene is a central component of an endogenous circadian clock that senses changes in photoperiod (day length) and mediates seasonal behaviours. Among Pacific salmonids (Oncorhynchus spp.), seasonal timing of migration and breeding is influenced by photoperiod. To expand a study of 42 North American Chinook salmon (Oncorhynchus tshawytscha) populations, we tested whether duplicated Clock genes contribute to population differences in reproductive timing. Specifically, we examined geographical variation along a similar latitudinal gradient in the polyglutamine domain (PolyQ) of OtsClock1a and OtsClock1b among 53 populations of three species: chum (Oncorhynchus keta), coho (Oncorhynchus kisutch) and pink salmon (Oncorhynchus gorbuscha). We found evidence for variable selection on OtsClock1b that corresponds to latitudinal variation in reproductive timing among these species. We evaluated the contribution of day length and a freshwater migration index to OtsClock1b PolyQ domain variation using regression trees and found that day length at spawning explains much of the variation in OtsClock1b allele frequency among chum and Chinook, but not coho and pink salmon populations. Our findings suggest that OtsClock1b mediates seasonal adaptation and influences geographical variation in reproductive timing in some of these highly migratory species.

Phenotypic plasticity and population viability: the importance of environmental predictability

Phenotypic plasticity plays a key role in modulating how environmental variation influences population dynamics, but we have only rudimentary understanding of how plasticity interacts with the magnitude and predictability of environmental variation to affect population dynamics and persistence. We developed a stochastic individual-based model, in which phenotypes could respond to a temporally fluctuating environmental cue and fitness depended on the match between the phenotype and a randomly fluctuating trait optimum, to assess the absolute fitness and population dynamic consequences of plasticity under different levels of environmental stochasticity and cue reliability. When cue and optimum were tightly correlated, plasticity buffered absolute fitness from environmental variability, and population size remained high and relatively invariant. In contrast, when this correlation weakened and environmental variability was high, strong plasticity reduced population size, and populations with excessively strong plasticity had substantially greater extinction probability. Given that environments might become more variable and unpredictable in the future owing to anthropogenic influences, reaction norms that evolved under historic selective regimes could imperil populations in novel or changing environmental contexts. We suggest that demographic models (e.g. population viability analyses) would benefit from a more explicit consideration of how phenotypic plasticity influences population responses to environmental change.

Quantifying six decades of fishery selection for size and age at maturity in sockeye salmon

Life history traits of wild animals can be strongly influenced, both phenotypically and evolutionarily, by hunting and fishing. However, few studies have quantified fishery selection over long time periods. We used 57 years of catch and escapement data to document the magnitude of and trends in gillnet selection on age and size at maturity of a commercially and biologically important sockeye salmon stock. Overall, the fishery has caught larger fish than have escaped to spawn, but selection has varied over time, becoming weaker and less consistent recently. Selection patterns were strongly affected by fish age and sex, in addition to extrinsic factors including fish abundance, mesh size regulations, and fish length variability. These results revealed a more complex and changing pattern of selective harvest than the 'larger is more vulnerable' model, emphasizing the need for quantified, multi-year studies before conclusions can be drawn about potential evolutionary and ecological effects of fishery selection. Furthermore, the results indicate that biologically robust escapement goals and prevention of harvest of the largest individuals may help prevent negative effects of size-selective harvest.

The genetic basis of photoperiodism and its evolutionary divergence among populations of the pitcher-plant mosquito, Wyeomyia smithii

We measured the additive genetic variance within populations and the composite additive, dominance, and epistatic effects contributing to differentiation of photoperiodic response between two southern (ancestral) and each of four progressively more northern (derived) populations of the pitcher-plant mosquito, Wyeomyia smithii. Critical photoperiod and its additive genetic variance but not its heritability increased with latitude. Directional selection on critical photoperiod during the northward divergence of W. smithii has therefore not eroded the additive genetic variance underlying this trait. Joint scaling tests of crosses between populations showed that epistatic effects, especially additive x additive and dominance x dominance interactions, overwhelm composite additive and dominance effects on critical photoperiod. The presence of substantial epistasis suggests that multiple founder events during the northward divergence of W. smithii may have been responsible for the release of progressively greater additive genetic variance in derived populations, despite directional and stabilizing selection to reduce it. If epistasis makes a similar contribution to the genetic differentiation of populations in other species, then current models of adaptive evolution that consider only additive genetic variation and covariation within populations may be of limited value in predicting how natural populations differentiate in life history.

Estimates of natural selection in a salmon population in captive and natural environments

Captive breeding is a commonly used strategy for species conservation. One risk of captive breeding is domestication selection--selection for traits that are advantageous in captivity but deleterious in the wild. Domestication selection is of particular concern for species that are bred in captivity for many generations and that have a high potential to interbreed with wild populations. Domestication is understood conceptually at a broad level, but relatively little is known about how natural selection differs empirically between wild and captive environments. We used genetic parentage analysis to measure natural selection on time of migration, weight, and morphology for a coho salmon (Oncorhynchus kisutch) population that was subdivided into captive and natural components. Our goal was to determine whether natural selection acting on the traits we measured differed significantly between the captive and natural environments. For males, larger individuals were favored in both the captive and natural environments in all years of the study, indicating that selection on these traits in captivity was similar to that in the wild. For females, selection on weight was significantly stronger in the natural environment than in the captive environment in 1 year and similar in the 2 environments in 2 other years. In both environments, there was evidence of selection for later time of return for both males and females. Selection on measured traits other than weight and run timing was relatively weak. Our results are a concrete example of how estimates of natural selection during captivity can be used to evaluate this common risk of captive breeding programs.

Pacific salmon extinctions: quantifying lost and remaining diversity

Widespread population extirpations and the consequent loss of ecological, genetic, and life-history diversity can lead to extinction of evolutionarily significant units (ESUs) and species. We attempted to systematically enumerate extinct Pacific salmon populations and characterize lost ecological, life history, and genetic diversity types among six species of Pacific salmon (Chinook [Oncorhynchus tshawytscha], sockeye [O. nerka], coho [O. kisutch], chum [O. keta], and pink salmon [O. gorbuscha] and steelhead trout [O. mykiss]) from the western contiguous United States. We estimated that, collectively, 29% of nearly 1400 historical populations of these six species have been lost from the Pacific Northwest and California since Euro-American contact. Across all species there was a highly significant difference in the proportion of population extinctions between coastal (0.14 extinct) and interior (0.55 extinct) regions. Sockeye salmon (which typically rely on lacustrine habitats for rearing) and stream-maturing Chinook salmon (which stay in freshwater for many months prior to spawning) had significantly higher proportional population losses than other species and maturation types. Aggregate losses of major ecological, life-history, and genetic biodiversity components across all species were estimated at 33%, 15%, and 27%, respectively. Collectively, we believe these population extirpations represent a loss of between 16% and 30% of all historical ESUs in the study area. On the other hand, over two-thirds of historical Pacific salmon populations in this area persist, and considerable diversity remains at all scales. Because over one-third of the remaining populations belong to threatened or endangered species listed under the U.S. Endangered Species Act, it is apparent that a critical juncture has been reached in efforts to preserve what remains of Pacific salmon diversity. It is also evident that persistence of existing, and evolution of future, diversity will depend on the ability of Pacific salmon to adapt to anthropogenically altered habitats.

Epistasis and the genetic divergence of photoperiodism between populations of the pitcher-plant mosquito, Wyeomyia smithii

Parallel crosses between each of two southern (ancestral) and one northern (derived) population of the pitcher-plant mosquito, Wyeomyia smithii, were made to determine the genetic components of population divergence in critical photoperiod, a phenological trait that measures adaptation to seasonality along a climatic gradient. Joint scaling tests were used to analyze means and variances of first- and second-generation hybrids in order to determine whether nonadditive genetic variance, especially epistatic variance, contributed to divergence in critical photoperiod. In both crosses, digenic epistatic effects were highly significant, indicating that genetic divergence cannot have resulted solely from differences in additively acting loci. For one cross that could be tested directly for such effects, higher order epistasis and/or linkage did not contribute to the divergence of critical photoperiod between the constituent populations.

Host acceptance and life-history traits in Drosophila busckii: tests of the hierarchy-threshold model

The hierarchy-threshold model for host-choice in insects predicts positive genetic correlations between use of different hosts, and between host use and the number of eggs carried by females. Life history theory predicts negative covariance between reproductive capacity and lifespan; hence host use and lifespan should be negatively correlated. These predictions were tested in half-sib breeding designs with the cosmopolitan Drosophila busckii. The predictions of the hierarchy-threshold model were met, supporting previous findings with other Drosophila. Predictions from life-history theory were not met for the population studied.