Evolution of pleiotropy: epistatic interaction pattern supports a mechanistic model underlying variation in genotype-phenotype map

The genotype-phenotype (GP) map consists of developmental and physiological mechanisms mapping genetic onto phenotypic variation. It determines the distribution of heritable phenotypic variance on which selection can act. Comparative studies of morphology as well as of gene regulatory networks show that the GP map itself evolves, yet little is known about the actual evolutionary mechanisms involved. The study of such mechanisms requires exploring the variation in GP maps at the population level, which presently is easier to quantify by statistical genetic methods rather than by regulatory network structures. We focus on the evolution of pleiotropy, a major structural aspect of the GP map. Pleiotropic genes affect multiple traits and underlie genetic covariance between traits, often causing evolutionary constraints. Previous quantitative genetic studies have demonstrated population-level variation in pleiotropy in the form of loci, at which genotypes differ in the genetic covariation between traits. This variation can potentially fuel evolution of the GP map under selection and/or drift. Here, we propose a developmental mechanism underlying population genetic variation in covariance and test its predictions. Specifically, the mechanism predicts that the loci identified as responsible for genetic variation in pleiotropy are involved in trait-specific epistatic interactions. We test this prediction for loci affecting allometric relationships between traits in an advanced intercross between inbred mouse strains. The results consistently support the prediction. We further find a high degree of sign epistasis in these interactions, which we interpret as an indication of adaptive gene complexes within the diverged parental lines.     

PERSPECTIVE: COMPLEX ADAPTATIONS AND THE EVOLUTION OF EVOLVABILITY

The problem of complex adaptations is studied in two largely disconnected research traditions: evolutionary biology and evolutionary computer science. This paper summarizes the results from both areas and compares their implications. In evolutionary computer science it was found that the Darwinian process of mutation, recombination and selection is not universally effective in improving complex systems like computer programs or chip designs. For adaptation to occur, these systems must possess “evolvability,” i.e., the ability of random variations to sometimes produce improvement. It was found that evolvability critically depends on the way genetic variation maps onto phenotypic variation, an issue known as the representation problem. The genotype-phenotype map determines the variability of characters, which is the propensity to vary. Variability needs to be distinguished from variations, which are the actually realized differences between individuals. The genotype-phenotype map is the common theme underlying such varied biological phenomena as genetic canalization, developmental constraints, biological versatility, developmental dissociability, and morphological integration. For evolutionary biology the representation problem has important implications: how is it that extant species acquired a genotype-phenotype map which allows improvement by mutation and selection? Is the genotype-phenotype map able to change in evolution? What are the selective forces, if any, that shape the genotype-phenotype map? We propose that the genotype-phenotype map can evolve by two main routes: epistatic mutations, or the creation of new genes. A common result for organismic design is modularity. By modularity we mean a genotype-phenotype map in which there are few pleiotropic effects among characters serving different functions, with pleiotropic effects falling mainly among characters that are part of a single functional complex. Such a design is expected to improve evolvability by limiting the interference between the adaptation of different functions. Several population genetic models are reviewed that are intended to explain the evolutionary origin of a modular design. While our current knowledge is insufficient to assess the plausibility of these models, they form the beginning of a framework for understanding the evolution of the genotype-phenotype map.     

Genetic variation in pleiotropy: differential epistasis as a source of variation in the allometric relationship between long bone lengths and body weight

Pleiotropy is an aspect of genetic architecture underlying the phenotypic covariance structure. The presence of genetic variation in pleiotropy is necessary for natural selection to shape patterns of covariation between traits. We examined the contribution of differential epistasis to variation in the intertrait relationship and the nature of this variation. Genetic variation in pleiotropy was revealed by mapping quantitative trait loci (QTLs) affecting the allometry of mouse limb and tail length relative to body weight in the mouse-inbred strain LG/J by SM/J intercross. These relationship QTLs (rQTLs) modify relationships between the traits affected by a common pleiotropic locus. We detected 11 rQTLs, mostly affecting allometry of multiple bones. We further identified epistatic interactions responsible for the observed allometric variation. Forty loci that interact epistatically with the detected rQTLs were identified. We demonstrate how these epistatic interactions differentially affect the body size variance and the covariance of traits with body size. We conclude that epistasis, by differentially affecting both the canalization and mean values of the traits of a pleiotropic domain, causes variation in the covariance structure. Variation in pleiotropy maintains evolvability of the genetic architecture, in particular the evolvability of its modular organization.     

Is modularity necessary for evolvability? Remarks on the relationship between pleiotropy and evolvability

Evolvability is the ability to respond to a selective challenge. This requires the capacity to produce the right kind of variation for selection to act upon. To understand evolvability we therefore need to understand the variational properties of biological organisms. Modularity is a variational property, which has been linked to evolvability. If different characters are able to vary independently, selection will be able to optimize each character separately without interference. But although modularity seems like a good design principle for an evolvable organism, it does not therefore follow that it is the only design that can achieve evolvability. In this essay I analyze the effects of modularity and, more generally, pleiotropy on evolvability. Although, pleiotropy causes interference between the adaptation of different characters, it also increases the variational potential of those characters. The most evolvable genetic architectures may often be those with an intermediate level of integration among characters, and in particular those where pleiotropic effects are variable and able to compensate for each other's constraints.     

The Developmental Basis of Variational Modularity: Insights from Quantitative Genetics,Morphometrics, and Developmental Biology

Groups of correlated characters (variational modules) often are considered to be the result of dissociated local developmental factors, i.e., of a modular genotype–phenotype map. But certain sets of pleiotropic factors can equally well induce modular phenotypic variation—no local developmental factors are necessary for a modular covariance structure. It is thus not possible to infer genetic or developmental modularity from standing variation alone. Yet, only for approximately linear genotype–phenotype maps is the induced covariance structure stable over changes of the phenotypic mean. For larger genetic and phenotypic variation, such as on a macroevolutionary level, developmental effects often are nonlinear and variational modularity remains stable only when it is realized by local dissociated developmental factors with no overlap of pleiotropic ranges. The evo-devo concept of modularity concurs only at this macroevolutionary level with the quantitative notion of variational modularity. Empirical evidence on the genetic and developmental architecture underlying phenotypic variation is inconclusive and partly subject to methodological problems. Many studies seem to indicate modularized phenotypic variation and local clusters of QTL effects, whereas other studies find support for several alternative models of modularity and report continuous distributions of QTL effects. This inconsistency partly results from the neglect of spatial relationships among the measured traits. Given the complex development of higher organisms, a combination of pleiotropic factors and more local developmental effects with a hierarchical, overlapping, and more or less continuous distribution appears most likely.     

The effects of stress and sex on selection,genetic covariance,and the evolutionary response

The capacity of a population to adapt to selection (evolvability) depends on whether the structure of genetic variation permits the evolution of fitter trait combinations. Selection, genetic variance and genetic covariance can change under environmental stress, and males and females are not genetically independent, yet the combined effects of stress and dioecy on evolvability are not well understood. Here, we estimate selection, genetic (co)variance and evolvability in both sexes of Tribolium castaneum flour beetles under stressful and benign conditions, using a half‐sib breeding design. Although stress uncovered substantial latent heritability, stress also affected genetic covariance, such that evolvability remained low under stress. Sexual selection on males and natural selection on females favoured a similar phenotype, and there was positive intersex genetic covariance. Consequently, sexual selection on males augmented adaptation in females, and intralocus sexual conflict was weak or absent. This study highlights that increased heritability does not necessarily increase evolvability, suggests that selection can deplete genetic variance for multivariate trait combinations with strong effects on fitness, and tests the recent hypothesis that sexual conflict is weaker in stressful or novel environments.     

THE COVARIANCE STRUCTURE OF LIFE-HISTORY CHARACTERS IN DAPHNIA PULEX

The genetic covariance structure for life-history characters in two populations of cyclically parthenogenetic Daphnia pulex indicates considerable positive correlation among important fitness components, apparently at odds with the expectation if antagonistic pleiotropy is the dominant cause of the maintanence of genetic variation. Although there is no genetic correlation between offspring size and offspring number, present growth and present reproduction are both strongly positively correlated genetically with future reproduction, and early maturity is genetically correlated with larger clutch size. Although the ubiquity of antagonistic pleiotropy has been recently questioned, there are peculiarities of cyclical parthenogenesis that could lead to positive life-history covariance even when negative covariance would be expected in a similar sexual species. These include the influence of nonadditive gene action on evolution in clonally reproducing organisms, and the periodic release of hidden genetic variance within populations of cyclical parthenogens. Examination of matrix similarity, using the bootstrap for distribution-free hypothesis testing, reveals no evidence to suggest that the genetic covariance matrices differ between the populations. However, there is considerable evidence that the phenotypic and environmental covariance matrices differ between populations. These results indicate approximate stability of the genetic covariance matrix within species, an important assumption of many phenotypic evolution models, but should caution against the use of phenotypic in place of genetic covariance matrices.     

Integration and Evolvability in Primate Hands and Feet

Morphological integration theory predicts that sets of phenotypic traits that covary strongly due to developmental and/or functional connections between them eventually co-evolve because of a coordinated response to selection, and accordingly become less independently evolvable. This process is not irreversible, however, and phenotypic traits can become less integrated, and hence more independently evolvable, in the context of selection for divergent functions and morphologies. This study examines the reciprocal relationship between shared function, integration and evolvability by comparing integration patterns among serially homologous skeletal elements in the hands and feet of a functionally diverse sample of catarrhine primates. Two hypotheses are tested: (1) species in which the autopods are functionally more similar (e.g. quadrupedal monkeys) have more strongly integrated autopods than species in which the autopods are functionally divergent (e.g. gibbons, humans) and (2) the latter have autopods that are more evolvable, collectively and independently. Morphometric data from selected hand and foot digital rays were used to derive phenotypic variance/covariance matrices. The strength of integration among autopods was quantified using eigenanalysis and a measure of trait variational autonomy. Evolvability was estimated by subjecting phenotypic variance/covariance matrices to simulated random selection gradients, and comparing evolutionary responses among species. Results indicate that integration decreases as hands and feet become functionally divergent, and that the strongly integrated hand and foot skeletons of quadrupedal monkeys respond to selection in a highly collinear manner, even when simulated selective pressures acting on each autopod are in opposite directions in phenotypic space. Results confirm that the evolvability of morphological traits depends largely on how strongly they covary with other traits, but also with body size. The role of pleiotropy as a developmental mechanism underlying integration and evolvability is also discussed.     

Constraints on evolution and postcopulatory sexual selection: trade-offs among ejaculate characteristics

Ejaculates function as an integrated unit to ensure male fertility and paternity, can have a complex structure, and can experience multiple episodes of selection. Current studies on the evolution of ejaculates typically focus on phenotypic variation in sperm number, size, or related traits such as testes size as adaptations to postcopulatory male-male competition. However, the evolution of the integrated nature of ejaculate structure and function depends on genetic variation in and covariation between the component parts. Here we report a quantitative genetic study of the components of the ejaculate of the cockroach Nauphoeta cinerea, including those we know to experience postcopulatory sexual selection, in the context of functional integration of ejaculate characters. We use the patterns of genetic variation and covariation to infer how the integration of the functions of the ejaculate constrain and shape its evolution. Ejaculate components were highly variable, showed significant additive genetic variance, and moderate to high evolvability. The level of genetic variation in these characters, despite strong directional or truncating selection, may reflect the integration of multiple episodes of selection that occur in N. cinerea. There were few significant phenotypic correlations, but all the genetic correlations among ejaculate characters were significantly different from zero. The patterns of genetic variation and covariation suggest that there are important trade-offs among individual traits of the ejaculate and that evolution of ejaculate characteristics will not proceed unconstrained. Fully describing the genetic relationships among traits that perform as an integrated unit helps us understand how functional relationships constrain or facilitate the evolution of the complex structure that is the ejaculate.     

The pleiotropic structure of the genotype-phenotype map: the evolvability of complex organisms

It was first noticed 100 years ago that mutations tend to affect more than one phenotypic characteristic, a phenomenon that was called 'pleiotropy'. Because pleiotropy was found so frequently, the notion arose that pleiotropy is 'universal'. However, quantitative estimates of pleiotropy have not been available until recently. These estimates show that pleiotropy is highly restricted and are more in line with the notion of variational modularity than with universal pleiotropy. This finding has major implications for the evolvability of complex organisms and the mapping of disease-causing mutations.     

The evolutionary genetics of canalization

Evolutionary genetics has recently made enormous progress in understanding how genetic variation maps into phenotypic variation. However why some traits are phenotypically invariant despite apparent genetic and environmental changes has remained a major puzzle. In the 1940s, Conrad Hal Waddington coined the concept and term "canalization" to describe the robustness of phenotypes to perturbation; a similar concept was proposed by Waddington's contemporary Ivan Ivanovich Schmalhausen. This paper reviews what has been learned about canalization since Waddington. Canalization implies that a genotype's phenotype remains relatively invariant when individuals of a particular genotype are exposed to different environments (environmental canalization) or when individuals of the same single- or multilocus genotype differ in their genetic background (genetic canalization). Consequently, genetic canalization can be viewed as a particular kind of epistasis, and environmental canalization and phenotypic plasticity are two aspects of the same phenomenon. Canalization results in the accumulation of phenotypically cryptic genetic variation, which can be released after a "decanalizing" event. Thus, canalized genotypes maintain a cryptic potential for expressing particular phenotypes, which are only uncovered under particular decanalizing environmental or genetic conditions. Selection may then act on this newly released genetic variation. The accumulation of cryptic genetic variation by canalization may therefore increase evolvability at the population level by leading to phenotypic diversification under decanalizing conditions. On the other hand, under canalizing conditions, a major part of the segregating genetic variation may remain phenotypically cryptic; canalization may therefore, at least temporarily, constrain phenotypic evolution. Mechanistically, canalization can be understood in terms of transmission patterns, such as epistasis, pleiotropy, and genotype by environment interactions, and in terms of genetic redundancy, modularity, and emergent properties of gene networks and biochemical pathways. While different forms of selection can favor canalization, the requirements for its evolution are typically rather restrictive. Although there are several methods to detect canalization, there are still serious problems with unambiguously demonstrating canalization, particularly its adaptive value.     

The Genetic Covariance between Characters Maintained by Pleiotropic Mutations

A statistical genetic model of a multivariate phenotype is derived to investigate the covariation of pleiotropic mutations with additive effects under the combined action of phenotypic selection, linkage and the mating system. Equilibrium formulas for large, randomly mating populations demonstrate that, when selection on polygenic variation is much smaller than twice the harmonic mean recombination rate between loci with interacting fitnesses, linkage disequilibrium is negligible and pleiotropy is the main cause of genetic correlations between characters. Under these conditions, approximate expressions for the dynamics of the genetic covariances due to pleiotropic mutations are obtained. Patterns of genetic covariance between characters and their evolution are discussed with reference to data on polygenic mutation, chromosomal organization and morphological integration.     

FISHER'S MODEL AND THE GENOMICS OF ADAPTATION: RESTRICTED PLEIOTROPY,HETEROGENOUS MUTATION,AND PARALLEL EVOLUTION

Genetic theories of adaptation generally overlook the genes in which beneficial substitutions occur, and the likely variation in their mutational effects. We investigate the consequences of heterogeneous mutational effects among loci on the genetics of adaptation. We use a generalization of Fisher's geometrical model, which assumes multivariate Gaussian stabilizing selection on multiple characters. In our model, mutation has a distinct variance–covariance matrix of phenotypic effects for each locus. Consequently, the distribution of selection coefficients s varies across loci. We assume each locus can only affect a limited number of independent linear combinations of phenotypic traits (restricted pleiotropy), which differ among loci, an effect we term “orientation heterogeneity.” Restricted pleiotropy can sharply reduce the overall proportion of beneficial mutations. Orientation heterogeneity has little impact on the shape of the genomic distribution, but can substantially increase the probability of parallel evolution (the repeated fixation of beneficial mutations at the same gene in independent populations), which is highest with low pleiotropy. We also consider variation in the degree of pleiotropy and in the mean s across loci. The latter impacts the genomic distribution of s, but has a much milder effect on parallel evolution. We discuss these results in the light of evolution experiments.     

Evolvability and genetic constraint in Dalechampia blossoms: components of variance and measures of evolvability

Many evolutionary arguments are based on the assumption that quantitative characters are highly evolvable entities that can be rapidly moulded by changing selection pressures. The empirical evaluation of this assumption depends on having an operational measure of evolvability that reflects the ability of a trait to respond to a given external selection pressure. We suggest short-term evolvability be measured as expected proportional response in a trait to a unit strength of directional selection, where strength of selection is defined independently of character variation and in units of the strength of selection on fitness itself. We show that the additive genetic variance scaled by the square of the trait mean, IA, is such a measure. The heritability, h2, does not measure evolvability in this sense. Based on a diallel analysis, we use IA to assess the evolvability of floral characters in a population of the neotropical vine Dalechampia scandens (Euphorbiaceae). Although we are able to demonstrate that there is additive genetic variation in a number of floral traits, we also find that most of the traits are not expected to change by more than a fraction of a percent per generation. We provide evidence that the degree of among-population divergence of traits is related to their predicted evolvabilities, but not to their heritabilities.     

On the pleiotropic structure of the genotype-phenotype map and the evolvability of complex organisms

Analyses of effects of mutants on many traits have enabled estimates to be obtained of the magnitude of pleiotropy, and in reviews of such data others have concluded that the degree of pleiotropy is highly restricted, with implications on the evolvability of complex organisms. We show that these conclusions are highly dependent on statistical assumptions, for example significance levels. We analyze models with pleiotropic effects on all traits at all loci but by variable amounts, considering distributions of numbers of traits declared significant, overall pleiotropic effects, and extent of apparent modularity of effects. We demonstrate that these highly pleiotropic models can give results similar to those obtained in analyses of experimental data and that conclusions on limits to evolvability through pleiotropy are not robust.     

Pleiotropic mutation, modularity and evolvability

The relationship between pleiotropy and the rate of evolution of a phenotypic character (evolvability) in a population is explored using computer simulations. I present results that suggest the rate of evolution of a phenotypic character may not decline when that character is pleiotropically associated to an increasing number of other characters, provided that the characters are under pure directional selection such that they are far from their optima relative to the average magnitude of a mutation. These conditions may be relevant during adaptive radiations. Adding pleiotropic associations to a set of characters in which one is under directional selection and the other is under stabilizing selection increases the rate of adaptation of the character under directional selection provided that the new characters that come to be pleiotropically associated are under directional selection. Thus, increasing the number of pleiotropic associations under these conditions increases the rate of adaptation of a character.     

A model of developmental evolution: selection, pleiotropy and compensation

Development and physiology translate genetic variation into phenotypic variation and determine the genotype-phenotype map, such as which gene affects which character (pleiotropy). Any genetic change in this mapping reflects a change in development. Here, we discuss evidence for variation in pleiotropy and propose the selection, pleiotropy and compensation model (SPC) for adaptive evolution. It predicts that adaptive change in one character is associated with deleterious pleiotropy in others and subsequent selection to compensate for these pleiotropic effects. The SPC model provides a unifying perspective for a variety of puzzling phenomena, including developmental systems drift and character homogenization. The model suggests that most adaptive signatures detected in genome scans could be the result of compensatory changes, rather than of progressive character adaptations.     

Pleiotropic Stabilizing Selection Limits the Number of Polymorphic Loci to at Most the Number of Characters

We demonstrate that, in a model incorporating weak Gaussian stabilizing selection on n additively determined characters, at most n loci are polymorphic at a stable equilibrium. The number of characters is defined to be the number of independent components in the Gaussian selection scheme. We also assume linkage equilibrium, and that either the number of loci is large enough that the phenotypic distribution in the population can be approximated as multivariate Gaussian or that selection is weak enough that the mean fitness of the population can be approximated using only the mean and the variance of the characters in the population. Our results appear to rule out antagonistic pleiotropy without epistasis as a major force in maintaining additive genetic variation in a uniform environment. However, they are consistent with the maintenance of variability by genotype-environment interaction if a trait in different environments corresponds to different characters and the number of different environments exceeds the number of polymorphic loci that affect the trait.     

Sexual Dimorphism Increases Evolvability in a Genetic Regulatory Network

The majority of work on genetic regulatory networks has focused on environmental and mutational robustness, and much less attention has been paid to the conditions under which a network may produce an evolvable phenotype. Sexually dimorphic characters often show rapid rates of change over short evolutionary time scales and while this is thought to be due to the strength of sexual selection acting on the trait, a dimorphic character with an underlying pleiotropic architecture may also influence the evolution of the regulatory network that controls the character and affect evolvability. As evolvability indicates a capacity for phenotypic change and mutational robustness refers to a capacity for phenotypic stasis, increases in evolvability may show a negative relationship with mutational robustness. I tested this with a computational model of a genetic regulatory network and found that, contrary to expectation, sexually dimorphic characters exhibited both higher mutational robustness and higher evolvability. Decomposition of the results revealed that linkage disequilibrium within sex and linkage disequilibrium between sexes, two of the three primary components of additive genetic variance and evolvability in quantitative genetics models, contributed to the differences in evolvability between sexually dimorphic and monomorphic populations. These results indicate that producing two pleiotropically linked characters did not constrain either the production of a robust phenotype or adaptive potential. Instead, the genetic system evolved to maximize both quantities.     

Effects of environmental perturbations during postnatal development on the phenotypic integration of the skull

Integration and modularity are fundamental determinants of how natural selection effects evolutionary change in complex multivariate traits. Interest in the study of the specific developmental basis of integration through experimental approaches is fairly recent and it has mainly focused on its genetic determinants. In this study, we present evidence that postnatal environmental perturbations can modify the covariance structure by influencing the variance of some developmental processes relative to the variances of other processes that contribute to such structure. We analyzed the effects of the reduction of nutrient supply in different ontogenetic stages (i.e. before and after weaning, and from birth to adulthood) in Rattus norvegicus. Our results show that this environmental perturbation alters the phenotypic variation/covariation structure of the principal modules of the skull (base, vault, and face). The covariance matrices of different treatment groups exhibit low correlations and are significantly different, indicating that the treatments influence covariance structure. Postnatal nutrient restriction also increases the variance of somatic growth. This increased variance drives an increase in overall integration of cranial morphology through the correlated allometric effects of size variation. The extent of this increase in integration depends on the time and duration of the nutritional restriction. These results support the conclusion that environmental perturbations can influence integration and thus covariance structure via developmental plasticity.