EPISTASIS,PLEIOTROPY, AND THE MUTATION LOAD IN SEXUAL AND ASEXUAL POPULATIONS

Mutation may impose a substantial load on populations, which varies according to the reproductive mode of organisms. Over the past years, various authors used adaptive landscape models to predict the long‐term effect of mutation on mean fitness; however, many of these studies assumed very weak mutation rates, so that at most one mutation segregates in the population. In this article, we derive several simple approximations (confirmed by simulations) for the mutation load at high mutation rate (U), using a general model that allows us to play with the number of selected traits (n), the degree of pleiotropy of mutations, and the shape of the fitness function (which affects the average sign and magnitude of epistasis among mutations). When mutations have strong fitness effects, the equilibrium fitness of sexuals and asexuals is close to ; under weaker mutational effects, sexuals reach a different regime where is a simple function of U and of a parameter describing the shape of the fitness function. Contrarily to weak mutation results showing that is an increasing function of population size and a decreasing function of n, these parameters may have opposite effects in sexual populations at high mutation rate.     

Developmental interactions and the constituents of quantitative variation

Development is the process by which genotypes are transformed into phenotypes. Consequently, development determines the relationship between allelic and phenotypic variation in a population and, therefore, the patterns of quantitative genetic variation and covariation of traits. Understanding the developmental basis of quantitative traits may lead to insights into the origin and evolution of quantitative genetic variation, the evolutionary fate of populations, and, more generally, the relationship between development and evolution. Herein, we assume a hierarchical, modular structure of trait development and consider how epigenetic interactions among modules during ontogeny affect patterns of phenotypic and genetic variation. We explore two developmental models, one in which the epigenetic interactions between modules result in additive effects on character expression and a second model in which these epigenetic interactions produce nonadditive effects. Using a phenotype landscape approach, we show how changes in the developmental processes underlying phenotypic expression can alter the magnitude and pattern of quantitative genetic variation. Additive epigenetic effects influence genetic variances and covariances, but allow trait means to evolve independently of the genetic variances and covariances, so that phenotypic evolution can proceed without changing the genetic covariance structure that determines future evolutionary response. Nonadditive epigenetic effects, however, can lead to evolution of genetic variances and covariances as the mean phenotype evolves. Our model suggests that an understanding of multivariate evolution can be considerably enriched by knowledge of the mechanistic basis of character development.     

Evolutionary genetics of maternal effects

Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population.     

The quantitative genetics of fluctuating asymmetry

Fluctuating asymmetry (subtle departures from identical expression of a trait across an axis of symmetry) in many taxa is under stabilizing selection for reduced asymmetry. However, lack of reliable estimates of genetic parameters for asymmetry variation hampers our ability to predict the evolutionary outcome of this selection. Here we report on a study, based on analysis of variation within and between isofemale lines and of generation means (line-cross analysis), designed to dissect in detail the quantitative genetics of positional fluctuating asymmetry (PFA) in bristle number in natural populations of Drosophila falleni. PFA is defined as the difference between the two sides of the body in the placement or position of components of a meristic trait. Heritability (measured at 25 degrees C) of two related measures of PFA were 13% and 21%, both of which differed significantly from zero. In contrast, heritability estimates for fluctuating asymmetry in the total number of anterior (0.7%) and transverse (2.4%) sternopleural bristles were smaller, not significant, and in quantitative agreement with previously published estimates. Heritabilities for bristle number (trait size) were considerably greater than that for any asymmetry measure. The experimental design controlled for the potentially confounding effects of common familial environment, and repeated testing revealed that PFA differences between lines were genetically stable for up to 16 generations in the laboratory at 25 degrees C. We performed line cross analysis between strains at the extremes of the PFA distribution (highest and lowest values); parental strains, F1, F1r (reciprocal), F2, backcross, and backcross reciprocal generations were represented. The inheritance of PFA was described best by additive and dominance effects localized to the X-chromosomes, whereas autosomal dominance effects were also detected. Epistatic, maternal, and cytoplasmic effects were not detected. The inheritance of trait size was notably more complex and involved significant autosomal additive, dominance, and epistatic effects; maternal dominance effects; and additive and dominance effects localized to the X-chromosomes. The additive genetic correlation between PFA and its associated measure of trait size was negative (-0.049), but not statistically significant, indicating that the loci contributing additive genetic effects to these traits are probably different. It is suggested that PFA may be a sensitive measure of developmental instability because PFA taps the ability of an organism to integrate interconnected developmental pathways.     

The evolution of quantitative traits in complex environments

Species inhabit complex environments and respond to selection imposed by numerous abiotic and biotic conditions that vary in both space and time. Environmental heterogeneity strongly influences trait evolution and patterns of adaptive population differentiation. For example, heterogeneity can favor local adaptation, or can promote the evolution of plastic genotypes that alter their phenotypes based on the conditions they encounter. Different abiotic and biotic agents of selection can act synergistically to either accelerate or constrain trait evolution. The environmental context has profound effects on quantitative genetic parameters. For instance, heritabilities measured in controlled conditions often exceed those measured in the field; thus, laboratory experiments could overestimate the potential for a population to respond to selection. Nevertheless, most studies of the genetic basis of ecologically relevant traits are conducted in simplified laboratory environments, which do not reflect the complexity of nature. Here, we advocate for manipulative field experiments in the native ranges of plant species that differ in mating system, life-history strategy and growth form. Field studies are vital to evaluate the roles of disparate agents of selection, to elucidate the targets of selection and to develop a nuanced perspective on the evolution of quantitative traits. Quantitative genetics field studies will also shed light on the potential for natural populations to adapt to novel climates in highly fragmented landscapes. Drawing from our experience with the ecological model system Boechera (Brassicaceae), we discuss advancements possible through dedicated field studies, highlight future research directions and examine the challenges associated with field studies.     

Evolutionary reduction of developmental plasticity in desert spadefoot toads

Organisms vary their rates of growth and development in response to environmental inputs. Such developmental plasticity may be adaptive and positively correlate with environmental heterogeneity. However, the evolution of developmental plasticity among closely related taxa is not well understood. To determine the evolutionary pattern of plasticity, we compared plasticity in time to and size at metamorphosis in response to water desiccation in tadpoles among spadefoot species that differ in breeding pond and larval period durations. Like most tadpoles, spadefoot tadpoles possess the remarkable ability to accelerate development in response to pond drying to avoid desiccation. Here, we hypothesize that desert spadefoot tadpoles have evolved reduced plasticity to avoid desiccation in ephemeral desert pools compared to their nondesert relatives that breed in long-duration ponds. We recorded time to and size at metamorphosis following experimental manipulation of water levels and found that desert-adapted species had much less plasticity in larval period and size at metamorphosis than nondesert species, which retain the hypothetical ancestral state of plasticity. Furthermore, we observed a correlation between degree of plasticity and fat body content that may provide mechanistic insights into the evolution of developmental plasticity in amphibians.     

Bayesian approaches in evolutionary quantitative genetics

The study of evolutionary quantitative genetics has been advanced by the use of methods developed in animal and plant breeding. These methods have proved to be very useful, but they have some shortcomings when used in the study of wild populations and evolutionary questions. Problems arise from the small size of data sets typical of evolutionary studies, and the additional complexity of the questions asked by evolutionary biologists. Here, we advocate the use of Bayesian methods to overcome these and related problems. Bayesian methods naturally allow errors in parameter estimates to propagate through a model and can also be written as a graphical model, giving them an inherent flexibility. As packages for fitting Bayesian animal models are developed, we expect the application of Bayesian methods to evolutionary quantitative genetics to grow, particularly as genomic information becomes more and more associated with environmental data.     

Quantitative genetics of costly neonatal sexual size dimorphism in squirrel monkeys (Saimiri boliviensis)

Offspring size is often an intimate link between the fitness of parents and offspring. Among mammals, neonate mass is also related to adult levels of dimorphism and intrasexual competitive mating. We describe the sex‐specific genetic architecture of neonate mass in captive squirrel monkeys (Saimiri boliviensis), a small Neotropical primate. Best fitting quantitative genetic models show strong maternal genetic effects with little difference between sexes offering limited opportunity for neonatal dimorphism to respond to observed or hypothetical selection. Heritabilities that are approximately zero also imply it is unlikely that neonatal dimorphism can evolve as a correlated response to selection on adult size. However, male mass is also more dependent on maternal condition (age and parity) making dimorphism plastic. Finally, we hypothesize that large maternal genetic effects reflect income breeding and tightly synchronized seasonal reproduction in squirrel monkeys, both of which require strong maternal control of offspring growth and timing of birth.     

Coevolutionary genetics of hosts and parasites with quantitative inheritance

Summary A model of host—parasite coevolution is analysed. A host resistance trait and a parasite virulence trait interact to determine the outcome of a parasitic attack, where each trait is determined by quantitative genetic variation. The resistance and virulence traits are assumed to have a fitness cost. Each host and parasite genotype is treated as a separate species in a multidimensional Lotka—Volterra system in which the numerical abundance of each genotype is free to change. Thus, the epidemiological effects of fluctuating population sizes are analysed jointly with changes in genotype frequencies. Population sizes fluctuate increasingly as the parasites' reproductive capacity increases and as resistance and virulence benefits per unit cost decline. The patterns of genetic variability depend mainly on the stability of population sizes and on the shape of the relationship between the costs and benefits of a trait.     

QUANTITATIVE GENETICS OF BRYOZOAN PHENOTYPIC EVOLUTION. II. ANALYSIS OF SELECTION AND RANDOM CHANGE IN FOSSIL SPECIES USING RECONSTRUCTED GENETIC PARAMETERS

The roles of natural selection and random genetic change in the punctuated phenotypic evolution of eight Miocene-Pliocene tropical American species of the cheilostome bryozoan Metrarabdotos are analyzed by quantitative genetic methods. Trait heritabilities and genetic covariances reconstructed by partitioning within- and among-colony phenotypic variance are similar to those previously obtained for living species of the cheilostome Stylopoma using breeding data. The hypothesis that differences in skeletal morphology between species of Metrarabdotos are entirely due to mutation and genetic drift cannot be rejected for reasonable rates of mutation maintained for periods brief enough to account for the geologically abrupt appearances of these species in the fossil record. Except for one pair of species, separated by the largest morphologic distance, directional selection acting alone would require unrealistically high rates of selective mortality to be maintained for these periods. Thus, directional selection is not strongly implicated in the divergence of Metrarabdotos species. Within species, rates of net phenotypic change are slow enough to require stabilizing selection, but mask large, relatively rapid fluctuations, all of which, however, can be attributed to chance departures from the mean phenotype by mutation and genetic drift, rather than to tracking environmental fluctuation by directional selection. The results are consistent with genetic models involving shifts between multiple adaptive peaks on which phenotypes remain more or less static through long-term stabilizing selection. Regardless of the degree to which directional selection may be involved in peak shifts, phenotypic differentiation is thus related to processes different than the pervasive stabilizing selection acting within species.     

Stabilizing selection,mutational bias,and the evolution of sex*

Stabilizing selection around a fixed phenotypic optimum is expected to disfavor sexual reproduction, since asexually reproducing organisms can maintain a higher fitness at equilibrium, while sex disrupts combinations of compensatory mutations. This conclusion rests on the assumption that mutational effects on phenotypic traits are unbiased, that is, mutation does not tend to push phenotypes in any particular direction. In this article, we consider a model of stabilizing selection acting on an arbitrary number of polygenic traits coded by bialellic loci, and show that mutational bias may greatly reduce the mean fitness of asexual populations compared with sexual ones in regimes where mutations have weak to moderate fitness effects. Indeed, mutation and drift tend to push the population mean phenotype away from the optimum, this effect being enhanced by the low effective population size of asexual populations. In a second part, we present results from individual‐based simulations showing that positive rates of sex are favored when mutational bias is present, while the population evolves toward complete asexuality in the absence of bias. We also present analytical (QLE) approximations for the selective forces acting on sex in terms of the effect of sex on the mean and variance in fitness among offspring.     

Ecological and evolutionary genetics of Arabidopsis

The crucifer Arabidopsis thaliana has been the subject of intense research into molecular and developmental genetics. One of the consequences of having this wealth of physiological and molecular data available, is that ecologists and evolutionary biologists have begun to incorporate this model system into their studies. Current research on A. thaliana and its close relatives ably illustrates the potential for synergy between mechanistic and organismal biology. On the one hand, mechanistically oriented research can be placed in an historical context, which takes into account the particular phylogenetic history and ecology of these species. This helps us to make sense of redundancies, anomalies and sub-optimalities that would otherwise be difficult to interpret. On the other hand, ecologists and evolutionary biologists now have the opportunity to investigate the physiological and molecular basis for the phenotypic changes they observe. This provides new insight into the mechanisms that influence evolutionary change.     

Quantification and decomposition of environment‐selection relationships

In nature, selection varies across time in most environments, but we lack an understanding of how specific ecological changes drive this variation. Ecological factors can alter phenotypic selection coefficients through changes in trait distributions or individual mean fitness, even when the trait‐absolute fitness relationship remains constant. We apply and extend a regression‐based approach in a population of Soay sheep (Ovis aries) and suggest metrics of environment‐selection relationships that can be compared across studies. We then introduce a novel method that constructs an environmentally structured fitness function. This allows calculation of full (as in existing approaches) and partial (acting separately through the absolute fitness function slope, mean fitness, and phenotype distribution) sensitivities of selection to an ecological variable. Both approaches show positive overall effects of density on viability selection of lamb mass. However, the second approach demonstrates that this relationship is largely driven by effects of density on mean fitness, rather than on the trait‐fitness relationship slope. If such mechanisms of environmental dependence of selection are common, this could have important implications regarding the frequency of fluctuating selection, and how previous selection inferences relate to longer term evolutionary dynamics.     

Introduction. Evolutionary dynamics of wild populations: the use of long-term pedigree data

Studies of populations in the wild can provide unique insights into the forces driving evolutionary dynamics. This themed issue of Proc. R. Soc. B focuses on new developments in long-term analyses of animal populations where pedigree information has been collected. These address fundamental questions in evolutionary biology concerning the genetic basis of phenotypic diversity, patterns of natural and sexual selection, the occurrence of inbreeding and inbreeding depression, and speciation. Contributions include the analysis of evolutionary responses to climate change, exploration of the genetic basis of senescence, the exploitation of advances in molecular genetic technology, and reviews of developments in quantitative genetic methodology. We discuss here common themes, specific problems and pointers for future research.     

Influence of Gene Interaction on Complex Trait Variation with Multilocus Models

Although research effort is being expended into determining the importance of epistasis and epistatic variance for complex traits, there is considerable controversy about their importance. Here we undertake an analysis for quantitative traits utilizing a range of multilocus quantitative genetic models and gene frequency distributions, focusing on the potential magnitude of the epistatic variance. All the epistatic terms involving a particular locus appear in its average effect, with the number of two-locus interaction terms increasing in proportion to the square of the number of loci and that of third order as the cube and so on. Hence multilocus epistasis makes substantial contributions to the additive variance and does not, per se, lead to large increases in the nonadditive part of the genotypic variance. Even though this proportion can be high where epistasis is antagonistic to direct effects, it reduces with multiple loci. As the magnitude of the epistatic variance depends critically on the heterozygosity, for models where frequencies are widely dispersed, such as for selectively neutral mutations, contributions of epistatic variance are always small. Epistasis may be important in understanding the genetic architecture, for example, of function or human disease, but that does not imply that loci exhibiting it will contribute much genetic variance. Overall we conclude that theoretical predictions and experimental observations of low amounts of epistatic variance in outbred populations are concordant. It is not a likely source of missing heritability, for example, or major influence on predictions of rates of evolution.     

Effects of partial selfing on the equilibrium genetic variance,mutation load,and inbreeding depression under stabilizing selection

The mating system of a species is expected to have important effects on its genetic diversity. In this article, we explore the effects of partial selfing on the equilibrium genetic variance V_g, mutation load L, and inbreeding depression δ under stabilizing selection acting on a arbitrary number n of quantitative traits coded by biallelic loci with additive effects. When the ratio is low (where U is the total haploid mutation rate on selected traits) and effective recombination rates are sufficiently high, genetic associations between loci are negligible and the genetic variance, mutation load, and inbreeding depression are well predicted by approximations based on single‐locus models. For higher values of and/or lower effective recombination, moderate genetic associations generated by epistasis tend to increase V_g, L, and δ, this regime being well predicted by approximations including the effects of pairwise associations between loci. For yet higher values of and/or lower effective recombination, a different regime is reached under which the maintenance of coadapted gene complexes reduces V_g, L, and δ. Simulations indicate that the values of V_g, L, and δ are little affected by assumptions regarding the number of possible alleles per locus.