The population genetic theory of hidden variation and genetic robustness

Fisher's geometrical model of fitness landscape and variance in fitness within a changing environment

The fitness of an individual can be simply defined as the number of its offspring in the next generation. However, it is not well understood how selection on the phenotype determines fitness. In accordance with Fisher's fundamental theorem, fitness should have no or very little genetic variance, whereas empirical data suggest that is not the case. To bridge these knowledge gaps, we follow Fisher's geometrical model and assume that fitness is determined by multivariate stabilizing selection toward an optimum that may vary among generations. We assume random mating, free recombination, additive genes, and uncorrelated stabilizing selection and mutational effects on traits. In a constant environment, we find that genetic variance in fitness under mutation-selection balance is a U-shaped function of the number of traits (i.e., of the so-called "organismal complexity"). Because the variance can be high if the organism is of either low or high complexity, this suggests that complexity has little direct costs. Under a temporally varying optimum, genetic variance increases relative to a constant optimum and increasingly so when the mutation rate is small. Therefore, mutation and changing environment together can maintain high genetic variance. These results therefore lend support to Fisher's geometric model of a fitness landscape.

Current applications of models of genetic effects with interactions across the genome

Models of genetic effects integrate the action of genes, regulatory regions and interactions among alleles across the genome. Such theoretical frameworks are critical for applied studies in at least two ways. First, discovering genetic networks with specific effects underlying traits in populations requires the development of models that implement those effects as parameters-adjusting the implementation of epistasis parameters in genetic models has for instance been a requirement for properly testing for epistasis in gene-mapping studies. Second, studying the properties and implications of models of genetic effects that involve complex genetic networks has proven to be valuable, whether those networks have been revealed for particular organisms or inferred to be of interest from theoretical works and simulations. Here I review the current state of development and recent applications of models of genetic effects. I focus on general models aiming to depict complex genotype-to-phenotype maps and on applications of them to networks of interacting loci.

Hsp90 is important for fecundity, longevity, and buffering of cryptic deleterious variation in wild fly populations

BACKGROUND

In the laboratory, the Drosophila melanogaster heat shock protein Hsp90 can buffer the phenotypic effects of genetic variation. Laboratory experiments either manipulate Hsp90 activity pharmacologically, or they induce mutations with strong effects in the gene Hsp83, the single-copy fly gene encoding Hsp90. It is unknown whether observations from such laboratory experiments are relevant in the wild.

RESULTS

We here study naturally occurring mutations in Hsp83, and their effects on fitness and phenotypic buffering in flies derived from wild populations. We examined more than 4500 flies from 42 Drosophila populations distributed world-wide for insertions or deletions of mobile DNA in or near the Hsp83 gene. The insertions we observed occur at low population frequencies, and reduce Hsp83 gene expression. In competition experiments, mutant flies performed much more poorly than wild-type flies. Mutant flies were also significantly less fecund and shorter-lived than wild-type flies, as well as less well buffered against cryptic deleterious variation, as we show through inbreeding experiments. Specifically, in Hsp83 mutant flies female fecundity dropped to much lower levels after inbreeding than in wild-type flies. At even slightly elevated temperatures, inbred mutant Hsp83 populations went extinct, whereas inbred wild-type populations persisted.

CONCLUSIONS

Our work shows that Hsp90, a regulator of the stress response and of signaling, helps buffer deleterious variation in fruit flies derived from wild population, and that its buffering role becomes even more important under heat stress.

The QTN program and the alleles that matter for evolution: all that's gold does not glitter

The search for the alleles that matter, the quantitative trait nucleotides (QTNs) that underlie heritable variation within populations and divergence among them, is a popular pursuit. But what is the question to which QTNs are the answer? Although their pursuit is often invoked as a means of addressing the molecular basis of phenotypic evolution or of estimating the roles of evolutionary forces, the QTNs that are accessible to experimentalists, QTNs of relatively large effect, may be uninformative about these issues if large-effect variants are unrepresentative of the alleles that matter. Although 20th century evolutionary biology generally viewed large-effect variants as atypical, the field has recently undergone a quiet realignment toward a view of readily discoverable large-effect alleles as the primary molecular substrates for evolution. I argue that neither theory nor data justify this realignment. Models and experimental findings covering broad swaths of evolutionary phenomena suggest that evolution often acts via large numbers of small-effect polygenes, individually undetectable. Moreover, these small-effect variants are different in kind, at the molecular level, from the large-effect alleles accessible to experimentalists. Although discoverable QTNs address some fundamental evolutionary questions, they are essentially misleading about many others.

Inferring regulatory mechanisms from patterns of evolutionary divergence

The number of sequenced species is increasing at a staggering rate, calling for new approaches for incorporating evolutionary information in the study of biological mechanisms. Evolutionary conservation is widely used for assigning a function to new proteins and for predicting functional coding or non-coding sequences. Here, we argue for a complementary approach that focuses on the divergence of regulatory programs. Regulatory mechanisms can be learned from patterns of evolutionary divergence in regulatory properties such as gene expression, transcription factor binding or nucleosome positioning. We review examples of this concept using yeast as a model system, and highlight a hybrid-based approach that is highly instrumental in this analysis.

Cryptic genetic variation promotes rapid evolutionary adaptation in an RNA enzyme

Cryptic variation is caused by the robustness of phenotypes to mutations. Cryptic variation has no effect on phenotypes in a given genetic or environmental background, but it can have effects after mutations or environmental change. Because evolutionary adaptation by natural selection requires phenotypic variation, phenotypically revealed cryptic genetic variation may facilitate evolutionary adaptation. This is possible if the cryptic variation happens to be pre-adapted, or "exapted", to a new environment, and is thus advantageous once revealed. However, this facilitating role for cryptic variation has not been proven, partly because most pertinent work focuses on complex phenotypes of whole organisms whose genetic basis is incompletely understood. Here we show that populations of RNA enzymes with accumulated cryptic variation adapt more rapidly to a new substrate than a population without cryptic variation. A detailed analysis of our evolving RNA populations in genotype space shows that cryptic variation allows a population to explore new genotypes that become adaptive only in a new environment. Our observations show that cryptic variation contains new genotypes pre-adapted to a changed environment. Our results highlight the positive role that robustness and epistasis can have in adaptive evolution.

Origin of the fittest: link between emergent variation and evolutionary change as a critical question in evolutionary biology

In complex organisms, neutral evolution of genomic architecture, associated compensatory interactions in protein networks and emergent developmental processes can delineate the directions of evolutionary change, including the opportunity for natural selection. These effects are reflected in the evolution of developmental programmes that link genomic architecture with a corresponding functioning phenotype. Two recent findings call for closer examination of the rules by which these links are constructed. First is the realization that high dimensionality of genotypes and emergent properties of autonomous developmental processes (such as capacity for self-organization) result in the vast areas of fitness neutrality at both the phenotypic and genetic levels. Second is the ubiquity of context- and taxa-specific regulation of deeply conserved gene networks, such that exceptional phenotypic diversification coexists with remarkably conserved generative processes. Establishing the causal reciprocal links between ongoing neutral expansion of genomic architecture, emergent features of organisms' functionality, and often precisely adaptive phenotypic diversification therefore becomes an important goal of evolutionary biology and is the latest reincarnation of the search for a framework that links development, functioning and evolution of phenotypes. Here I examine, in the light of recent empirical advances, two evolutionary concepts that are central to this framework-natural selection and inheritance-the general rules by which they become associated with emergent developmental and homeostatic processes and the role that they play in descent with modification.

Phenotypic robustness can increase phenotypic variability after nongenetic perturbations in gene regulatory circuits

Nongenetic perturbations, such as environmental change or developmental noise, can induce novel phenotypes. If an induced phenotype appears recurrently and confers a fitness advantage, selection may promote its genetic stabilization. Nongenetic perturbations can thus initiate evolutionary innovation. Genetic variation that is not usually phenotypically visible may play an important role in this process. Populations under stabilizing selection on a phenotype that is robust to mutations can accumulate such variation. After nongenetic perturbations, this variation can produce new phenotypes. We here study the relationship between a phenotype's mutational robustness and a population's potential to generate novel phenotypic variation. To this end, we use a well-studied model of transcriptional regulation circuits that are important in many evolutionary innovations. We find that phenotypic robustness promotes phenotypic variability in response to nongenetic perturbations, but not in response to mutation. Our work suggests that nongenetic perturbations may initiate innovation more frequently in mutationally robust gene expression traits.

A gene's ability to buffer variation is predicted by its fitness contribution and genetic interactions

Background

Many single-gene knockouts result in increased phenotypic (e.g., morphological) variability among the mutant's offspring. This has been interpreted as an intrinsic ability of genes to buffer genetic and environmental variation. A phenotypic capacitor is a gene that appears to mask phenotypic variation: when knocked out, the offspring shows more variability than the wild type. Theory predicts that this phenotypic potential should be correlated with a gene's knockout fitness and its number of negative genetic interactions. Based on experimentally measured phenotypic capacity, it was suggested that knockout fitness was unimportant, but that phenotypic capacitors tend to be hubs in genetic and physical interaction networks.

Methodology/Principal Findings

We re-analyse the available experimental data in a combined model, which includes knockout fitness and network parameters as well as expression level and protein length as predictors of phenotypic potential. Contrary to previous conclusions, we find that the strongest predictor is in fact haploid knockout fitness (responsible for 9% of the variation in phenotypic potential), with an additional contribution from the genetic interaction network (5%); once these two factors are taken into account, protein-protein interactions do not make any additional contribution to the variation in phenotypic potential.

Conclusions/Significance

We conclude that phenotypic potential is not a mysterious “emergent” property of cellular networks. Instead, it is very simply determined by the overall fitness reduction of the organism (which in its compromised state can no longer compensate for multiple factors that contribute to phenotypic variation), and by the number (and presumably nature) of genetic interactions of the knocked-out gene. In this light, Hsp90, the prototypical phenotypic capacitor, may not be representative: typical phenotypic capacitors are not direct “buffers” of variation, but are simply genes encoding central cellular functions.

Chromatin regulators as capacitors of interspecies variations in gene expression

Gene expression varies widely between closely related species and strains, yet the genetic basis of most differences is still unknown. Several studies suggested that chromatin regulators have a key role in generating expression diversity, predicting a reduction in the interspecies differences on deletion of genes that influence chromatin structure or modifications. To examine this, we compared the genome-wide expression profiles of two closely related yeast species following the individual deletions of eight chromatin regulators and one transcription factor. In all cases, regulator deletions increased, rather than decreased, the expression differences between the species, revealing hidden genetic variability that was masked in the wild-type backgrounds. This effect was not observed for individual deletions of 11 enzymes involved in central metabolic pathways. The buffered variations were associated with trans differences, as revealed by allele-specific profiling of the interspecific hybrids. Our results support the idea that regulatory proteins serve as capacitors that buffer gene expression against hidden genetic variability.

Morphological variation over ontogeny and environments in resource polymorphic arctic charr (Salvelinus alpinus)

Natural selection requires genetically based phenotypic variation to facilitate its action and cause adaptive evolution. It has become increasingly recognized that morphological development can become canalized likely as a result of selection. However, it is largely unknown how selection may influence canalization over ontogeny and differing environments. Changes in environments or colonization of a novel one is expected to result in adaptive divergence from the ancestral population when selection favors a new phenotypic optimum. In turn, a novel environment may also expose variation previously hidden from natural selection. We tested for changes in phenotypic variation over ontogeny and environments among ecomorphs of Arctic charr (Salvelinus alpinus) from two Icelandic lakes. Populations represented varying degrees of ecological specialization, with one lake population possessing highly specialized ecomorphs exhibiting a large degree of phenotypic divergence, whereas the other displayed more subtle divergence with more ecological overlap. Here we show that ecomorphs hypothesized to be the most specialized in each lake possess significant reductions in shape variation over ontogeny regardless of environmental treatment suggesting canalized development. However, environments did change the amount of shape variation expressed in these ecomorphs, with novel environments slowing the rate at which variation was reduced over ontogeny. Thus, environmental conditions may play an important role in determining the type and amount of genetically based phenotypic variation exposed to natural selection.

Robustness and evolvability

Why isn't random variation always deleterious? Are there factors that sometimes make adaptation easier? Biological systems are extraordinarily robust to perturbation by mutations, recombination and the environment. It has been proposed that this robustness might make them more evolvable. Robustness to mutation allows genetic variation to accumulate in a cryptic state. Switching mechanisms known as evolutionary capacitors mean that the amount of heritable phenotypic variation available can be correlated to the degree of stress and hence to the novelty of the environment and remaining potential for adaptation. There have been two somewhat separate literatures relating robustness to evolvability. One has focused on molecular phenotypes and new mutations, the other on morphology and cryptic genetic variation. Here, we review both literatures, and show that the true distinction is whether recombination rates are high or low. In both cases, the evidence supports the claim that robustness promotes evolvability.

The beak of the other finch: coevolution of genetic covariance structure and developmental modularity during adaptive evolution

The link between adaptation and evolutionary change remains the most central and least understood evolutionary problem. Rapid evolution and diversification of avian beaks is a textbook example of such a link, yet the mechanisms that enable beak's precise adaptation and extensive adaptability are poorly understood. Often observed rapid evolutionary change in beaks is particularly puzzling in light of the neo-Darwinian model that necessitates coordinated changes in developmentally distinct precursors and correspondence between functional and genetic modularity, which should preclude evolutionary diversification. I show that during first 19 generations after colonization of a novel environment, house finches (Carpodacus mexicanus) express an array of distinct, but adaptively equivalent beak morphologies-a result of compensatory developmental interactions between beak length and width in accommodating microevolutionary change in beak depth. Directional selection was largely confined to the elimination of extremes formed by these developmental interactions, while long-term stabilizing selection along a single axis-beak depth-was mirrored in the structure of beak's additive genetic covariance. These results emphasize three principal points. First, additive genetic covariance structure may represent a historical record of the most recurrent developmental and functional interactions. Second, adaptive equivalence of beak configurations shields genetic and developmental variation in individual components from depletion by natural selection. Third, compensatory developmental interactions among beak components can generate rapid reorganization of beak morphology under novel conditions and thus greatly facilitate both the evolution of precise adaptation and extensive diversification, thereby linking adaptation and adaptability in this classic example of Darwinian evolution.

Epistatic interactions attenuate mutations affecting startle behaviour in Drosophila melanogaster

Epistasis is an important feature of the genetic architecture of quantitative traits. Previously, we showed that startle-induced locomotor behaviour of Drosophila melanogaster, a critical survival trait, is highly polygenic and exhibits epistasis. Here, we characterize epistatic interactions among homozygous P-element mutations affecting startle-induced locomotion in the Canton-S isogenic background and in 21 wild-derived inbred genetic backgrounds. We find pervasive epistasis for pairwise combinations of homozygous P-element insertional mutations as well as for mutations in wild-derived backgrounds. In all cases, the direction of the epistatic effects is to suppress the mutant phenotypes. The magnitude of the epistatic interactions in wild-derived backgrounds is highly correlated with the magnitude of the main effects of mutations, leading to phenotypic robustness of the startle response in the face of deleterious mutations. There is variation in the magnitude of epistasis among the wild-derived genetic backgrounds, indicating evolutionary potential for enhancing or suppressing effects of single mutations. These results provide a partial glimpse of the complex genetic network underlying the genetic architecture of startle behaviour and provide empirical support for the hypothesis that suppressing epistasis is the mechanism underlying genetic canalization of traits under strong stabilizing selection. Widespread suppressing epistasis will lead to underestimates of the main effects of quantitative trait loci (QTLs) in mapping experiments when not explicitly accounted for. In addition, suppressing epistasis could lead to underestimates of mutational variation for quantitative traits and overestimates of the strength of stabilizing selection, which has implications for maintenance of variation of complex traits by mutation-selection balance.

Change and maintenance of variation in quantitative traits in the context of the Price equation

The Price equation is a general description of evolutionary change in any character from one generation to the next due to natural selection and other forces such as mutation and recombination. Recently it has been widely utilised in many fields including quantitative genetics, but these applications have focused mainly on the response to selection in the mean of characters. Many different and, in some cases, conflicting models have been investigated by quantitative geneticists to examine the change and maintenance of both genetic and environmental variance of quantitative traits under selection and other forces. In this study, we use the Price equation to derive many such well-known results for the dynamics and equilibria of variances in a straightforward way and to develop them further.

Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation

Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.

Multidimensional analysis of Drosophila wing variation in Evolution Canyon

Environmental stress has been suggested to be a major evolutionary force, both through inducing strong selection and because of its direct impact on developmental buffering processes that alter the evolvability of organisms. In particular, temperature has attracted much attention because of its importance as an ecological feature and the relative ease with which it can be experimentally manipulated in the lab. Evolution Canyon, Lower Nahal Oren, Israel, is a well studied natural site where ecological parameters are suspected to drive evolutionary differentiation. In this study, using Drosophila melanogaster isofemale lines derived from wild flies collected on both slopes of the canyon, we investigated the effect of developmental temperature upon the different components of phenotypic variation of a complex trait: the wing. Combining geometric and traditional morphometrics, we find only limited evidence for a differentiation among slopes. Investigating simultaneously phenotypic plasticity, genetic variation among isofemale lines, variation among individuals and fluctuating asymmetry, we could not identify a consistent effect of the stressful conditions encountered on the south facing slope. The prevailing structuring effect is that of the experimentally manipulated temperature which clearly influences wing mean size and shape. Variability, in contrast, is not consistently affected by temperature. Finally, we investigated the specific relationship between individual variation and fluctuating asymmetry. Using metric multi-dimensional scaling we show that the related patterns of wing shape variation are not identical, supporting the view that the underlying developmental processes are to a certain extent different.

Alternative mechanisms of range expansion are associated with different changes of evolutionary potential

Human-induced and natural range expansion of species are expected to lead to different patterns of genetic diversity, which might themselves be trait dependent. Recent studies examined the molecular and quantitative genetic variation following the range expansion of three plant species. The results suggest that contrasting diversity patterns among species reflect how range expansion has occurred and the level of fragmentation of the original habitat. Unexpectedly, even introductions from a homogeneous environment do not preclude a species from adapting to a new environment and becoming invasive.

Evolution under canalization and the dual roles of microRNAs: a hypothesis

Canalization refers to the process by which phenotypes are stabilized within species. Evolution by natural selection can proceed efficiently only when phenotypes are canalized. The existence and identity of canalizing genes have thus been an important, but controversial topic. Recent evidence has increasingly hinted that microRNAs may be involved in canalizing gene expression. Their paradoxical properties (e.g., strongly conserved but functionally dispensable) suggest unconventional regulatory roles. We synthesized published and unpublished results and hypothesize that miRNAs may have dual functions -- in gene expression tuning and in expression buffering. In tuning, miRNAs modify the mean expression level of their targets, but in buffering they merely reduce the variance around a preset mean. In light of the constant emergence of new miRNAs, we further discuss the relative importance of these two functions in evolution.

A framework for evolutionary systems biology

BACKGROUND

Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects.

RESULTS

Here I propose a novel framework that brings together evolutionary theory and current systems biology approaches in order to quantify small effects of mutations and their epistatic interactions in silico. Central to this approach is the definition of fitness correlates that can be computed in some current systems biology models employing the rigorous algorithms that are at the core of much work in computational systems biology. The framework exploits synergies between the realism of such models and the need to understand real systems in evolutionary theory. This framework can address many longstanding topics in evolutionary biology by defining various 'levels' of the adaptive landscape. Addressed topics include the distribution of mutational effects on fitness, as well as the nature of advantageous mutations, epistasis and robustness. Combining corresponding parameter estimates with population genetics models raises the possibility of testing evolutionary hypotheses at a new level of realism.

CONCLUSION

EvoSysBio is expected to lead to a more detailed understanding of the fundamental principles of life by combining knowledge about well-known biological systems from several disciplines. This will benefit both evolutionary theory and current systems biology. Understanding robustness by analysing distributions of mutational effects and epistasis is pivotal for drug design, cancer research, responsible genetic engineering in synthetic biology and many other practical applications.

Effects of epistasis and the evolution of genetic architecture: exact results for a 2-locus model

We study a two-locus model of a quantitative trait with a continuum-of alleles and multilinear epistasis that evolves under mutation, selection, and genetic drift. We derive analytical results based on the so-called House of Gauss approximation for the genetic variance, the mean phenotype, and the mutational variance in the balance of the evolutionary forces. The analytical work is complemented by extensive individual-based computer simulations. We find that (1) analytical results are accurate in a large parameter space; (2) epistasis always reduces the equilibrium genetic variance, as predicted in earlier studies that exclude drift; (3) large-scale stochastic fluctuations and non-equilibrium phenomena like adaptive inertia can strongly influence the evolution of the genetic architecture of the trait.

On the adaptive accuracy of directional asymmetry in insect wing size

Subtle left-right biases are often observed in organisms with an overall bilateral symmetry. The evolutionary significance of these directional asymmetries remains uncertain, however, and scenarios of both developmental constraints and adaptation have been suggested. Reviewing the literature on asymmetry in insect wings, we analyze patterns of directional asymmetry in wing size to evaluate the possible adaptive significance of this character. We found that directional asymmetry in wing size is widespread among insects, with left- and right-biased asymmetries commonly observed. The direction of the asymmetry does not appear to be evolutionarily conserved above the species level. Overall, we argue that the very small magnitude of directional asymmetry, 0.7% of the wing size on average, associated with an extremely imprecise expression, precludes directional asymmetry from playing any major adaptive role.

Increase in quantitative variation after exposure to environmental stresses and/or introduction of a major mutation: G x E interaction and epistasis or canalization?

Why does phenotypic variation increase upon exposure of the population to environmental stresses or introduction of a major mutation? It has usually been interpreted as evidence of canalization (or robustness) of the wild-type genotype; but an alternative population genetic theory has been suggested by J. Hermisson and G. Wagner: "the release of hidden genetic variation is a generic property of models with epistasis or genotype-environment interaction." In this note we expand their model to include a pleiotropic fitness effect and a direct effect on residual variance of mutant alleles. We show that both the genetic and environmental variances increase after the genetic or environmental change, but these increases could be very limited if there is strong pleiotropic selection. On the basis of more realistic selection models, our analysis lends further support to the genetic theory of Hermisson and Wagner as an interpretation of hidden variance.

Theoretical approaches to the evolution of development and genetic architecture

Developmental evolutionary biology has, in the past decade, started to move beyond simply adapting traditional population and quantitative genetics models and has begun to develop mathematical approaches that are designed specifically to study the evolution of complex, nonadditive systems. This article first reviews some of these methods, discussing their strengths and shortcomings. The article then considers some of the principal questions to which these theoretical methods have been applied, including the evolution of canalization, modularity, and developmental associations between traits. I briefly discuss the kinds of data that could be used to test and apply the theories, as well as some consequences for other approaches to phenotypic evolution of discoveries from theoretical studies of developmental evolution.

Robustness promotes evolvability of thermotolerance in an RNA virus

BACKGROUND

The ability for an evolving population to adapt to a novel environment is achieved through a balance of robustness and evolvability. Robustness is the invariance of phenotype in the face of perturbation and evolvability is the capacity to adapt in response to selection. Genetic robustness has been posited, depending on the underlying mechanism, to either decrease the efficacy of selection, or increase the possibility of future adaptation. However, the true effect of genetic robustness on evolvability in biological systems remains uncertain.

RESULTS

Here we demonstrate that genetic robustness increases evolvability of thermotolerance in laboratory populations of the RNA virus phi6. We observed that populations founded by robust clones evolved greater resistance to heat shock, relative to populations founded by brittle (less-robust) clones. Thus, we provide empirical evidence for the idea that robustness can promote evolvability in this environment, and further suggest that evolvability can arise indirectly via selection for robustness, rather than through direct selective action.

CONCLUSION

Our data imply that greater tolerance of mutational change is associated with virus adaptability in a new niche, a finding generally relevant to evolutionary biology, and informative for elucidating how viruses might evolve to emerge in new habitats and/or overcome novel therapies.

Ancestral variation and the potential for genetic accommodation in larval amphibians: implications for the evolution of novel feeding strategies

Few studies provide empirical evidence for phenotypic plasticity's role in the evolution of novel traits. One way to do so is to test whether latent plasticity is present in an ancestor that can be refined, enhanced, or diminished by selection in derived taxa (through "genetic accommodation"), thereby producing novel traits. Here, we evaluated whether gut plasticity preceded and promoted the evolution of a novel feeding strategy in spadefoot toad tadpoles. We studied Scaphiopus couchii, whose tadpoles develop an elongate gut and consume only detritus, and two derived species, Spea multiplicata and Sp. bombifrons, whose tadpoles also express a novel, short-gut phenotype in response to a novel resource (anostracan shrimp). Consistent with the expectations of plasticity-mediated trait evolution, we found that shrimp induced a range of phenotypes in Scaphiopus that were not produced with detritus. This plasticity was either suppressed or exaggerated in Spea depending on whether the induced phenotypes were adaptive. Moreover, in contrast to its effects on morphology, shrimp induced little or no functional plasticity, as assessed by gut cell proliferation, in Scaphiopus. Shrimp did, however, induce substantial proliferation in Sp. bombifrons, the species that consumes the most shrimp and that produces the short-gut phenotype the most frequently. Thus, if Spea had ancestral morphological plasticity in response to a novel diet, their shrimp-induced short-gut morphology may have undergone subsequent genetic accommodation that improved its functionality. Hence, diet-induced phenotypic plasticity may have preceded and even promoted the evolution of a novel phenotype.

Rate of adaptive peak shifts with partial genetic robustness

How adaptive evolution occurs with individually deleterious but jointly beneficial mutations has been one of the major problems in population genetics theory. Adaptation in this case is commonly described as a population's escape from a local peak to a higher peak on Sewall Wright's fitness landscape. Recent molecular genetic and computational studies have suggested that genetic robustness can facilitate such peak shifts. If phenotypic expressions of new mutations are suppressed under genetic robustness, mutations that are otherwise deleterious can accumulate in the population as neutral variants. When the robustness is perturbed by an environmental change or a major mutation, these variants become exposed to natural selection. It is argued that this process promotes adaptation because allelic combinations enriched under genetic robustness can then be positively selected. Here, I propose simple two- and three-locus models of adaptation with partial genetic robustness as suggested by recent studies. The waiting time until the fixation of an adaptive haplotype was observed in stochastic simulations and compared to the expectation without robustness. It is shown that peak shifts can be delayed or accelerated depending on the conditions of genetic robustness. The evolutionary significance of these processes is discussed.

Mesosternal bristle number in a cosmopolitan drosophilid: an X-linked variable trait independent of sternopleural bristles

Mesosternal (MS) bristles in Drosophila are a pair of machrochaetae found at the sternal end of the sternopleural (STP) microchaetae, and are thought to be invariable. In a closely related drosophilid genus, Zaprionus, their number is four and, in contrast to Drosophila, they show interspecific and intraspecific variability. The genetic basis of MS bristle number variability was studied in Z. indianus, the only cosmopolitan species of the genus. The trait responded rapidly to selection and two lines were obtained, one lacking any bristles (0-0) and the other bearing the normal phenotype (2-2). Other symmetrical phenotypes, (1-1) and (3-3), could also be selected for, but with lesser success. By contrast, STP bristle number did not vary significantly between the two lines (0-0) and (2-2), revealing its genetic independence from MS bristle number. Reciprocal crosses between these two lines showed that MS bristle number is mainly influenced by a major gene on the X chromosome (i.e. F(1) males always resembled their mothers) with codominant expression (i.e. heterozygous F(1) females harboured an average phenotype of 2 bristles). However, trait penetrance was incomplete and backcrosses revealed that this variability was partly due to genetic modifiers, most likely autosomal. The canalization of MS bristle number was investigated under different temperatures, and the increased appearance of abnormal phenotypes mainly occurred at extreme temperatures. There was a bias, however, towards bristle loss, as shown by a liability (developmental map) analysis. Finally, when ancestral and introduced populations were compared, the latter were far less stable, suggesting that genetic bottlenecks may perturb the MS bristle number canalization system. MS bristle number, thus, appears to be an excellent model for investigating developmental canalization at both the quantitative and the molecular level.

Genome-wide association analysis reveals cryptic alleles as an important factor in heterosis for fatness in chicken F2 population

Genome-wide association studies have become possible in the chicken because of the recent availability of the complete genome sequence, a polymorphism map and high-density single nucleotide polymorphism (SNP) genotyping platforms. We used these tools to study the genetic basis of a very high level of heterosis that was previously observed for fatness in two F(2) populations established by crossing one outbred broiler (meat-type) sire with dams from two unrelated, highly inbred, light-bodied lines (Fayoumi and Leghorn). In each F(2) population, selective genotyping was carried out using phenotypically extreme males for abdominal fat percentage (AF) and about 3000 SNPs. Single-point association analysis of about 500 informative SNPs per cross showed significant association (P < 0.01) of 15 and 24 markers with AF in the Broiler x Fayoumi and Broiler x Leghorn crosses respectively. These SNPs were on 10 chromosomes (GGA1, 2, 3, 4, 7, 8, 10, 12, 15 and 27). Interestingly, of the 39 SNPs that were significantly associated with AF, there were about twice as many homozygous genotypes associated with higher AF that traced back to the inbred lines alleles, although the broiler line had on average higher AF. These SNPs are considered to be associated with QTL with cryptic alleles. This study reveals cryptic alleles as an important factor in heterosis for fatness observed in two chicken F(2) populations, and suggests epistasis as the common underlying mechanism for heterosis and cryptic allele expression. The results of this study also demonstrate the power of high marker-density SNP association studies in discovering QTL that were not detected by previous microsatellite-based genotyping studies.

Effects of population size and mutation rate on the evolution of mutational robustness

It is often assumed that the efficiency of selection for mutational robustness would be proportional to mutation rate and population size, thus being inefficient in small populations. However, Krakauer and Plotkin (2002) hypothesized that selection in small populations would favor robustness mechanisms, such as redundancy, that mask the effect of deleterious mutations. In large populations, by contrast, selection is more effective at removing deleterious mutants and fitness would be improved by eliminating mechanisms that mask the effect of deleterious mutations and thus impede their removal. Here, we test whether these predictions are supported in experiments with evolving populations of digital organisms. Digital organisms are self-replicating programs that inhabit a virtual world inside a computer. Like their organic counterparts, digital organisms mutate, compete, evolve, and adapt by natural selection to their environment. In this study, 160 populations evolved at different combinations of mutation rate and population size. After 10(4) generations, we measured the mutational robustness of the most abundant genotype in each population. Mutational robustness tended to increase with mutation rate and to decline with population size, although the dependence with population size was in part mediated by a negative relationship between fitness and robustness. These results are independent of whether genomes were constrained to their original length or allowed to change in size.

A generalized combinatorial approach for detecting gene-by-gene and gene-by-environment interactions with application to nicotine dependence

The determination of gene-by-gene and gene-by-environment interactions has long been one of the greatest challenges in genetics. The traditional methods are typically inadequate because of the problem referred to as the "curse of dimensionality." Recent combinatorial approaches, such as the multifactor dimensionality reduction (MDR) method, the combinatorial partitioning method, and the restricted partition method, have a straightforward correspondence to the concept of the phenotypic landscape that unifies biological, statistical genetics, and evolutionary theories. However, the existing approaches have several limitations, such as not allowing for covariates, that restrict their practical use. In this study, we report a generalized MDR (GMDR) method that permits adjustment for discrete and quantitative covariates and is applicable to both dichotomous and continuous phenotypes in various population-based study designs. Computer simulations indicated that the GMDR method has superior performance in its ability to identify epistatic loci, compared with current methods in the literature. We applied our proposed method to a genetics study of four genes that were reported to be associated with nicotine dependence and found significant joint action between CHRNB4 and NTRK2. Moreover, our example illustrates that the newly proposed GMDR approach can increase prediction ability, suggesting that its use is justified in practice. In summary, GMDR serves the purpose of identifying contributors to population variation better than do the other existing methods.

Selection for robustness in mutagenized RNA viruses

Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations. Whether robustness can be directly favored by natural selection remains controversial. Theory and in silico experiments predict that, at high mutation rates, slow-replicating genotypes can potentially outcompete faster counterparts if they benefit from a higher robustness. Here, we experimentally validate this hypothesis, dubbed the "survival of the flattest," using two populations of the vesicular stomatitis RNA virus. Characterization of fitness distributions and genetic variability indicated that one population showed a higher replication rate, whereas the other was more robust to mutation. The faster replicator outgrew its robust counterpart in standard competition assays, but the outcome was reversed in the presence of chemical mutagens. These results show that selection can directly favor mutational robustness and reveal a novel viral resistance mechanism against treatment by lethal mutagenesis.