Patterns of quantitative genetic variation in multiple dimensions

A fundamental question for both evolutionary biologists and breeders is the extent to which genetic correlations limit the ability of populations to respond to selection. Here I view this topic from three perspectives. First, I propose several nondimensional statistics to quantify the genetic variation present in a suite of traits and to describe the extent to which correlations limit their selection response. A review of five data sets suggests that the total variation differs substantially between populations. In all cases analyzed, however, the “effective number of dimensions” is less than two: more than half of the total genetic variation is explained by a single combination of traits. Second, I consider how patterns of variation affect the average evolutionary response to selection in a random direction. When genetic variation lies in a small number of dimensions but there are a large number of traits under selection, then the average selection response will be reduced substantially from its potential maximum. Third, I discuss how a low genetic correlation between male fitness and female fitness limits the ability of populations to adapt. Data from two recent studies of natural populations suggest this correlation can diminish or even erase any genetic benefit to mate choice. Together these results suggest that adaptation (in natural populations) and genetic improvement (in domesticated populations) may often be as much constrained by patterns of genetic correlation as by the overall amount of genetic variation.     

Some consideration on diversifying selection

The diversifying selection due to genotype-environment interaction can increase the genetic variation in natural populations. It is known, however, that the conditions for stable genetic polymorphism or marginal overdominance are quite restricted in this selection model. In this paper a simple model of diversifying selection was examined, and the following results were obtained: (1) Even when the conditions for marginal overdominance are not satisfied, if the diversifying selection is operating, the frequency of mutants can be higher than that in the case of simple mutation-selection balance. (2) This selection model causes a large amount of genetic load (environment load), even when the conditions for marginal overdominance are not satisfied, namely even when the equilibrium frequency of mutant is very low. From these results it can be concluded that the number of loci on which this type of diversifying selection is operating is very small, if any.     

Analysis of the Inheritance, Selection and Evolution of Growth Trajectories

We present methods for estimating the parameters of inheritance and selection that appear in a quantitative genetic model for the evolution growth trajectories and other "infinite-dimensional" traits that we recently introduced. Two methods for estimating the additive genetic covariance function are developed, a "full" model that fully fits the data and a "reduced" model that generates a smoothed estimate consistent with the sampling errors in the data. By decomposing the covariance function into its eigenvalues and eigenfunctions, it is possible to identify potential evolutionary changes in the population's mean growth trajectory for which there is (and those for which there is not) genetic variation. Algorithms for estimating these quantities, their confidence intervals, and for testing hypotheses about them are developed. These techniques are illustrated by an analysis of early growth in mice. Compatible methods for estimating the selection gradient function acting on growth trajectories in natural or domesticated populations are presented. We show how the estimates for the additive genetic covariance function and the selection gradient function can be used to predict the evolutionary change in a population's mean growth trajectory.     

Multistage Selection for Genetic Gain by Orthogonal Transformation

An exact transformed culling method for any number of traits or stages of selection with explicit solution for multistage selection is described in this paper. This procedure does not need numerical integration and is suitable for obtaining either desired genetic gains for a variable proportion selected or optimum aggregate breeding value for a fixed total proportion selected. The procedure has similar properties to multistage selection index and, as such, genetic gains from use of the procedure may exceed ordinary independent culling level selection. The relative efficiencies of transformed to conventional independent culling ranged from 87% to over 300%. These results suggest that for most situations one can chose a multistage selection scheme, either conventional or transformed culling, which will have an efficiency close to that of selection index. After considering cost savings associated with multistage selection, there are many situations in which economic returns from use of independent culling, either conventional or transformed, will exceed that of selection index.     

Age-specific genetic and maternal effects in fecundity of preindustrial Finnish women

A population's potential for evolutionary change depends on the amount of genetic variability expressed in traits under selection. Studies attempting to measure this variability typically do so over the life span of individuals, but theory suggests that the amount of additive genetic variance can change during the course of individuals' lives. Here we use pedigree data from historical Finns and a quantitative genetic framework to investigate how female fecundity, throughout an individual's reproductive life, is influenced by "maternal" versus additive genetic effects. We show that although maternal effects explain variation in female fecundity early in life, these effects wane with female age. Moreover, this decline in maternal effects is associated with a concomitant increase in additive genetic variance with age. Our results thus highlight that single over-lifetime estimates of trait heritability may give a misleading view of a trait's potential to respond to changing selection pressures.     

Some population genetic models combining artificial and natural selection pressures in the presence of assortative mating

Summary We have attempted quantitatively through a series of assortative mating models to gain insight into the interaction between the usually antagonistic tendencies of artificial and natural selection pressures. We summarize some of the robust conclusions. In cases where natural selection is expressed only through the phenotype and acts in the opposite direction to the culling incline, then fixation of the dominant or recessive type can be achieved and which occurs depends critically on the initial composition of the population and the magnitude of the degree of culling compared to the selection coefficients.With traits determined at two loci in the case that the double heterozygote is the desired kind, the effect of selfing can only be overcome by very strong artificial selection pressures (high culling order). The degree of culling to achieve its objective can be relaxed with weakening of linkage. The relevant comparison is r ₂ + (1 – r)₂ < (1 – c)indicating the precise extent of culling needed, to prevent fixation. The relationships are more complex when natural selection forces are also involved (see Model IV).Supported in part by NIH Grant USPHS 10452-09.     

Shyness and boldness in humans and other animals

The shy-bold continuum is a fundamental axis of behavioral variation in humans and at least some other species, but its taxonomic distribution and evolutionary implications are unknown. Models of optimal risk, density- or frequency-dependent selection, and phenotypic plasticity can provide a theoretical framework for understanding shyness and boldness as a product of natural selection. We sketch this framework and review the few empirical studies of shyness and boldness in natural populations. The study of shyness and boldness adds an interesting new dimension to behavioral ecology by focusing on the nature of continuous behavioral variation that exists within the familiar categories of age, sex and size.     

Evolution of quantitative traits in the wild: mind the ecology

Recent advances in the quantitative genetics of traits in wild animal populations have created new interest in whether natural selection, and genetic response to it, can be detected within long-term ecological studies. However, such studies have re-emphasized the fact that ecological heterogeneity can confound our ability to infer selection on genetic variation and detect a population''s response to selection by conventional quantitative genetics approaches. Here, I highlight three manifestations of this issue: counter gradient variation, environmentally induced covariance between traits and the correlated effects of a fluctuating environment. These effects are symptomatic of the oversimplifications and strong assumptions of the breeder''s equation when it is applied to natural populations. In addition, methods to assay genetic change in quantitative traits have overestimated the precision with which change can be measured. In the future, a more conservative approach to inferring quantitative genetic response to selection, or genomic approaches allowing the estimation of selection intensity and responses to selection at known quantitative trait loci, will provide a more precise view of evolution in ecological time.     

Genetic Architecture of Two Fitness-related Traits in Drosophila melanogaster: Ovariole Number and Thorax Length

In Drosophila melanogaster, ovariole number and thorax length are morphological characters thought to be associated with fitness. Maximum daily egg production in females is positively correlated with ovariole number, while thorax length is correlated with male reproductive success and female fecundity. Though both traits are related to fitness, ovariole number is likely to be under stabilizing selection, while thorax length appears to be under directional selection. Current research has focused on examining the sources of variation for ovariole number in relation to fitness, with a view towards elucidating how segregating variation is maintained in natural populations. Here, we utilize a diallel design to explore the genetic architecture of ovariole number and thorax length in nine isogenic lines derived from a natural population. The full diallel design allows the estimation of general combining ability (GCA), specific combining ability (SCA), and also describes variation due to reciprocal effects (RGCA and RSCA). Ovariole number and thorax length differed with respect to their genetic architecture, reflective of the independent selective forces acting on the traits. For ovariole number, GCA accounted for the majority (67.3%) of variation segregating between the lines, with no evidence of reciprocal effects or inbreeding depression; SCA accounted for a small percentage (3.9%) of the variance, suggesting dominance variation; no reciprocal effects were observed. In contrast, for thorax length, the majority of the non-error variance was accounted for by SCA (17.9%), with only one third as much variance (6.2%) due to GCA. Interestingly, RSCA (nuclear–extranuclear interactions) accounted for slightly more variation (7.5%) than GCA in these data. Thus, genetic variation for thorax length is largely in accord with predictions for a fitness trait under directional selection: little additive genetic variation and substantial dominance variation (including a suggestion of inbreeding depression); while the mechanisms underlying the maintenance of variation for ovariole number are more complex.     

Genetic improvement of production while maintaining fitness

Selection for production tends to decrease fitness, in particular, major components such as reproductive performance. Under an infinitesimal genetic model restricted index selection can maintain reproductive performance while improving production. However, reproductive traits are thought to be controlled by a finite number of recessive alleles at low frequency. Culling for low reproduction may weed out the negative homozygous genotypes for reproduction in any generation, thus controlling the frequencies of alleles negative for reproduction. Restricted index selection, culling for low reproduction and a new method called empirical restricted index selection were compared for their efficiency in improving production while maintaining reproduction. Empirical restricted index selection selects animals that have on average the highest estimated breeding values for production and on average the same estimated breeding values for reproduction as the base population. An infinitesimal genetic model and models with a finite number of loci for reproduction with rare deleterious recessive alleles, which have additive, dominant or no pleiotropic effects on production, were considered. When reproduction was controlled by a finite number of loci with rare recessive alleles, restricted index selection could not maintain reproduction. The culling of 20% of the animals on reproduction maintained reproduction with all genetic models, except for the model where loci for reproduction had additive effects on production. Empirical restricted selection maintained reproduction with all models and yielded higher production responses than culling on reproduction, except when there were dominant pleiotropic effects on production.     

Population genetics of the inhabitants of the European northern RSFSR. VI. The dynamics of the genetic load

The dynamics of the lethal equivalents in two rural populations of Archangelsk regions during the periods from 1930 to 1953 and from 1954 to 1970 was investigated. The outcomes of 1617 pregnancies for 500 couples were analysed. The coefficient of inbreeding varied fo these couples from 0.001 to 0.08. For computing the genetic load, we followed the the methodology suggested by Morton, Crow and Muller in S. Smith's modification. The importance of comprehensive determination of inbreeding coefficient for reliable estimation of the genetic load was demonstrated. By comparing the two groups, it was shown that the coefficient B diminished approximately twice and the B/A ratio increased in both populations also by the factor of two. It is supposed that the diminishing of the number of lethal equivalents can be explained by a decrease in natural selection pressure. It is also supposed, that the segregational load is more sensitive to the decrease in natural selection pressure.'     

Evolutionary rescue and the limits of adaptation

Populations subject to severe stress may be rescued by natural selection, but its operation is restricted by ecological and genetic constraints. The cost of natural selection expresses the limited capacity of a population to sustain the load of mortality or sterility required for effective selection. Genostasis expresses the lack of variation that prevents many populations from adapting to stress. While the role of relative fitness in adaptation is well understood, evolutionary rescue emphasizes the need to recognize explicitly the importance of absolute fitness. Permanent adaptation requires a range of genetic variation in absolute fitness that is broad enough to provide a few extreme types capable of sustained growth under a stress that would cause extinction if they were not present. This principle implies that population size is an important determinant of rescue. The overall number of individuals exposed to selection will be greater when the population declines gradually under a constant stress, or is progressively challenged by gradually increasing stress. In gradually deteriorating environments, survival at lethal stress may be procured by prior adaptation to sublethal stress through genetic correlation. Neither the standing genetic variation of small populations nor the mutation supply of large populations, however, may be sufficient to provide evolutionary rescue for most populations.     

Reconciling strong stabilizing selection with the maintenance of genetic variation in a natural population of black field crickets (Teleogryllus commodus)

Genetic variation in single traits, including those closely related to fitness, is pervasive and generally high. By contrast, theory predicts that several forms of selection, including stabilizing selection, will eliminate genetic variation. Stabilizing selection in natural populations tends to be stronger than that assumed in theoretical models of the maintenance of genetic variation. The widespread presence of genetic variation in the presence of strong stabilizing selection is a persistent problem in evolutionary genetics that currently has no compelling explanation. The recent insight that stabilizing selection often acts most strongly on trait combinations via correlational selection may reconcile this problem. Here we show that for a set of male call properties in the cricket Teleogryllus commodus, the pattern of multivariate stabilizing sexual selection is closely associated with the degree of additive genetic variance. The multivariate trait combinations experiencing the strongest stabilizing selection harbored very little genetic variation while combinations under weak selection contained most of the genetic variation. Our experiment provides empirical support for the prediction that a small number of trait combinations experiencing strong stabilizing selection will have reduced genetic variance and that genetically independent trait combinations experiencing weak selection can simultaneously harbor much higher levels of genetic variance.     

Change of Genetic Architecture in Response to Sex

A traditional view is that sexual reproduction increases the potential for phenotypic evolution by expanding the range of genetic variation upon which natural selection can act. However, when nonadditive genetic effects and genetic disequilibria underlie a genetic system, genetic slippage (a change in the mean genotypic value contrary to that promoted by selection) in response to sex may occur. Additionally, depending on whether natural selection is predominantly stabilizing or disruptive, recombination may either enhance or reduce the level of expressed genetic variance. Thus, the role of sexual reproduction in the dynamics of phenotypic evolution depends heavily upon the nature of natural selection and the genetic system of the study population. In the present study, on a permanent lake Daphnia pulicaria population, sexual reproduction resulted in significant genetic slippage and a significant increase in expressed genetic variance for several traits. These observations provide evidence for substantial genetic disequilibria and nonadditive genetic effects underlying the genetic system of the study population. From these results, the fitness function of the previous clonal selection phase is inferred to be directional and/or stabilizing. The data are also used to infer the effects of natural selection on the mean and the genetic variance of the population.     

Evolution in plant populations as a driver of ecological changes in arthropod communities

Heritable variation in traits can have wide-ranging impacts on species interactions, but the effects that ongoing evolution has on the temporal ecological dynamics of communities are not well understood. Here, we identify three conditions that, if experimentally satisfied, support the hypothesis that evolution by natural selection can drive ecological changes in communities. These conditions are: (i) a focal population exhibits genetic variation in a trait(s), (ii) there is measurable directional selection on the trait(s), and (iii) the trait(s) under selection affects variation in a community variable(s). When these conditions are met, we expect evolution by natural selection to cause ecological changes in the community. We tested these conditions in a field experiment examining the interactions between a native plant (Oenothera biennis) and its associated arthropod community (more than 90 spp.). Oenothera biennis exhibited genetic variation in several plant traits and there was directional selection on plant biomass, life-history strategy (annual versus biennial reproduction) and herbivore resistance. Genetically based variation in biomass and life-history strategy consistently affected the abundance of common arthropod species, total arthropod abundance and arthropod species richness. Using two modelling approaches, we show that evolution by natural selection in large O. biennis populations is predicted to cause changes in the abundance of individual arthropod species, increases in the total abundance of arthropods and a decline in the number of arthropod species. In small O. biennis populations, genetic drift is predicted to swamp out the effects of selection, making the evolution of plant populations unpredictable. In short, evolution by natural selection can play an important role in affecting the dynamics of communities, but these effects depend on several ecological factors. The framework presented here is general and can be applied to other systems to examine the community-level effects of ongoing evolution.     

The evolutionary ecology of individual phenotypic plasticity in wild populations

The ability of individual organisms to alter morphological and life-history traits in response to the conditions they experience is an example of phenotypic plasticity which is fundamental to any population's ability to deal with short-term environmental change. We currently know little about the prevalence, and evolutionary and ecological causes and consequences of variation in life history plasticity in the wild. Here we outline an analytical framework, utilizing the reaction norm concept and random regression statistical models, to assess the between-individual variation in life history plasticity that may underlie population level responses to the environment at both phenotypic and genetic levels. We discuss applications of this framework to date in wild vertebrate populations, and illustrate how natural selection and ecological constraint may alter a population's response to the environment through their effects at the individual level. Finally, we present future directions and challenges for research into individual plasticity.     

Environmental quality and evolutionary potential: lessons from wild populations

An essential requirement to determine a population's potential for evolutionary change is to quantify the amount of genetic variability expressed for traits under selection. Early investigations in laboratory conditions showed that the magnitude of the genetic and environmental components of phenotypic variation can change with environmental conditions. However, there is no consensus as to how the expression of genetic variation is sensitive to different environmental conditions. Recently, the study of quantitative genetics in the wild has been revitalized by new pedigree analyses based on restricted maximum likelihood, resulting in a number of studies investigating these questions in wild populations. Experimental manipulation of environmental quality in the wild, as well as the use of naturally occurring favourable or stressful environments, has broadened the treatment of different taxa and traits. Here, we conduct a meta-analysis on recent studies comparing heritability in favourable versus unfavourable conditions in non-domestic and non-laboratory animals. The results provide evidence for increased heritability in more favourable conditions, significantly so for morphometric traits but not for traits more closely related to fitness. We discuss how these results are explained by underlying changes in variance components, and how they represent a major step in our understanding of evolutionary processes in wild populations. We also show how these trends contrast with the prevailing view resulting mainly from laboratory experiments on Drosophila. Finally, we underline the importance of taking into account the environmental variation in models predicting quantitative trait evolution.     

The Genetic Basis of Natural Variation in Seed Size and Seed Number and Their Trade-Off Using Arabidopsis thaliana MAGIC Lines

Offspring number and size are key traits determining an individual’s fitness and a crop’s yield. Yet, extensive natural variation within species is observed for these traits. Such variation is typically explained by trade-offs between fecundity and quality, for which an optimal solution is environmentally dependent. Understanding the genetic basis of seed size and number, as well as any possible genetic constraints preventing the maximization of both, is crucial from both an evolutionary and applied perspective. We investigated the genetic basis of natural variation in seed size and number using a set of Arabidopsis thaliana multiparent advanced generation intercross (MAGIC) lines. We also tested whether life history affects seed size, number, and their trade-off. We found that both seed size and seed number are affected by a large number of mostly nonoverlapping QTL, suggesting that seed size and seed number can evolve independently. The allele that increases seed size at most identified QTL is from the same natural accession, indicating past occurrence of directional selection for seed size. Although a significant trade-off between seed size and number is observed, its expression depends on life-history characteristics, and generally explains little variance. We conclude that the trade-off between seed size and number might have a minor role in explaining the maintenance of variation in seed size and number, and that seed size could be a valid target for selection.     

The approach to equilibrium of multilocus genotype diversity under clonal selection and cyclical parthenogenesis

Sexual generations in cyclical parthenogens are typically separated by multiple generations of clonal reproduction. In contrast to sexual reproduction, during parthenogenesis the genome of the parent is passed on to the offspring as a unit. The absence of recombination during parthenogenesis leads to differences in the action of natural selection in the two reproductive phases. In addition, since recombination is a sampling process, random genetic drift is potentially more important in sexual reproduction than in parthenogenesis. A recent development in the study of rotifer population genetics is the use of microsatellites to characterize natural populations. Microsatellites are selectively neutral, show patterns of Mendelian inheritance and tend to be much more variable than allozymes. An advantage over allozymes is that microsatellite DNA can be cloned with PCR and thus multiple loci can be assayed from a single individual. We use a new computer model in this paper to investigate the response of selectively active and selectively neutral genes to evolutionary forces during cyclical parthenogenesis. Selectively active alleles may respond differently to selection in the parthenogenetic and sexual phases of cyclical parthenogenesis. Even when strong clonal selection is acting on loci associated with adaptation, the view that emerges with microsatellites may be one of Hardy-Weinberg and linkage equilibrium. Thus studies using selectively neutral loci may fail to detect clonal selection even when it is an important feature of the rotifer population's adaptive structure.     

Reducing mutation load through sexual selection on males

Mutation load is a key parameter in evolutionary theories, but relatively little empirical information exists on the mutation load of populations, or the elimination of this load through selection. We manipulated the opportunity for sexual selection within a mutation accumulation divergence experiment to determine how sexual selection on males affected the accumulation of mutations contributing to sexual and nonsexual fitness. Sexual selection prevented the accumulation of mutations affecting male mating success, the target trait, as well as reducing mutation load on productivity, a nonsexual fitness component. Mutational correlations between mating success and productivity (estimated in the absence of sexual selection) were positive. Sexual selection significantly reduced these fitness component correlations. Male mating success significantly diverged between sexual selection treatments, consistent with the fixation of genetic differences. However, the rank of the treatments was not consistent across assays, indicating that the mutational effects on mating success were conditional on biotic and abiotic context. Our experiment suggests that greater insight into the genetic targets of natural and sexual selection can be gained by focusing on mutational rather than standing genetic variation, and on the behavior of trait variances rather than means.