HSP90 affects the expression of genetic variation and developmental stability in quantitative traits

Modulation of the activity of the molecular chaperone HSP90 has been extensively discussed as a means to alter phenotype in many traits and organisms. Such changes can be due to the exposure of cryptic genetic variation, which in some instances may also be accomplished by mild environmental alteration. Should such polymorphisms be widespread, natural selection may be more effective at producing phenotypic change in suboptimal environments. However, the frequency and identity of buffered polymorphisms in natural populations are unknown. Here, we employ quantitative genetic dissection of an Arabidopsis thaliana developmental response, hypocotyl elongation in the dark, to detail the underpinnings of genetic variation responsive to HSP90 modulation. We demonstrate that HSP90-dependent alleles occur in continuously distributed, environmentally responsive traits and are amenable to quantitative genetic mapping techniques. Furthermore, such alleles are frequent in natural populations and can have significant effects on natural phenotypic variation. We also find that HSP90 modulation has both general and allele-specific effects on developmental stability; that is, developmental stability is a phenotypic trait that can be affected by natural variation. However, effects of revealed variation on trait means outweigh effects of decreased developmental stability, and the HSP90-dependent trait alterations could be acted on by natural selection. Thus, HSP90 may centrally influence canalization, assimilation, and the rapid evolutionary alteration of phenotype through the concealment and exposure of cryptic genetic variation.     

Genetics of microenvironmental canalization in Arabidopsis thaliana

Canalization is a fundamental feature of many developmental systems, yet the genetic basis for this property remains elusive. We examine the genetic basis of microenvironmental canalization in the model plant Arabidopsis thaliana, focusing on differential developmental stability between genotypes in one fitness and four quantitative morphological traits. We measured developmental stability in genetically identical replicates of two populations of recombinant inbred (RI) lines and one population of geographically widespread accessions of A. thaliana grown in two different photoperiod-controlled environments. We were able to map quantitative trait loci associated with developmental stability. We also identified a candidate gene, ERECTA, that may contribute to microenvironmental canalization in rosette leaf number under long-day photoperiods, and analysis of mutant lines indicates that the er-105 allele results in increased canalization for this trait. ERECTA, which encodes a signaling protein, appears to act as an ecological amplifier by transducing developmental noise (e.g., microenvironmental variation) into phenotypic differentiation. We also measured genotypic selection on four plant architecture traits and find evidence for selection for both increased and decreased canalization at various traits.     

Deciphering morphology in Triatominae: The evolutionary signals

Many species of Triatominae show evidence for morphological plasticity. Frequent taxonomic questions arose from this variability leading to disputes about describing new subspecies, species or even genera. We suggest this phenotypic flexibility is primarily an intraspecific feature, but with potential for evolutionary changes. We present arguments for a selection regime leading to the separation of species having low developmental canalization into morphologically distinct ecotypes. We suggest that these ecotypes, or morphs, or forms, may have evolutionary importance even if gene flow still exists between them. Thus, although we consider the morphological plasticity of Triatominae as an intraspecific trait, we defend the idea that it might represent a common evolutionary route to new species. Speciation processes in Triatominae could result from disruptive selection regimes combined with weak developmental canalization. Added to this basic pattern, accidental events could hasten evolutionary change. We suggest the heterosis as one of them.     

High genetic variability and low local diversity in a population of arbuscular mycorrhizal fungi

Arbuscular mycorrhizal fungi (AMF) are ecologically important root symbionts of most terrestrial plants. Ecological studies of AMF have concentrated on differences between species; largely assuming little variability within AMF species. Although AMF are clonal, they have evolved to contain a surprisingly high within-species genetic variability, and genetically different nuclei can coexist within individual spores. These traits could potentially lead to within-population genetic variation, causing differences in physiology and symbiotic function in AMF populations, a consequence that has been largely neglected. We found highly significant genetic and phenotypic variation among isolates of a population of Glomus intraradices but relatively low total observed genetic diversity. Because we maintained the isolated population in a constant environment, phenotypic variation can be considered as variation in quantitative genetic traits. In view of the large genetic differences among isolates by randomly sampling two individual spores, <50% of the total observed population genetic diversity is represented. Adding an isolate from a distant population did not increase total observed genetic diversity. Genetic variation exceeded variation in quantitative genetic traits, indicating that selection acted on the population to retain similar traits, which might be because of the multigenomic nature of AMF, where considerable genetic redundancy could buffer the effects of changes in the genetic content of phenotypic traits. These results have direct implications for ecological research and for studying AMF genes, improving commercial AMF inoculum, and understanding evolutionary mechanisms in multigenomic organisms.     

Natural selection stops the evolution of male attractiveness

Sexual selection in natural populations acts on highly heritable traits and tends to be relatively strong, implicating sexual selection as a causal agent in many phenotypic radiations. Sexual selection appears to be ineffectual in promoting phenotypic divergence among contemporary natural populations, however, and there is little evidence from artificial selection experiments that sexual fitness can evolve. Here, we demonstrate that a multivariate male trait preferred by Drosophila serrata females can respond to selection and results in the maintenance of male mating success. The response to selection was associated with a gene of major effect increasing in frequency from 12 to 35% in seven generations. No further response to selection, or increase in frequency of the major gene, was observed between generations 7 and 11, indicating an evolutionary limit had been reached. Genetic analyses excluded both depletion of genetic variation and overdominance as causes of the evolutionary limit. Relaxing artificial selection resulted in the loss of 52% of the selection response after a further five generations, demonstrating that the response under artificial sexual selection was opposed by antagonistic natural selection. We conclude that male D. serrata sexually selected traits, and attractiveness to D. serrata females conferred by these traits, were held at an evolutionary limit by the lack of genetic variation that would allow an increase in sexual fitness while simultaneously maintaining nonsexual fitness. Our results suggest that sexual selection is unlikely to cause divergence among natural populations without a concomitant change in natural selection, a conclusion consistent with observational evidence from natural populations.     

Probing genetic overlap among complex human phenotypes

Geneticists and epidemiologists often observe that certain hereditary disorders cooccur in individual patients significantly more (or significantly less) frequently than expected, suggesting there is a genetic variation that predisposes its bearer to multiple disorders, or that protects against some disorders while predisposing to others. We suggest that, by using a large number of phenotypic observations about multiple disorders and an appropriate statistical model, we can infer genetic overlaps between phenotypes. Our proof-of-concept analysis of 1.5 million patient records and 161 disorders indicates that disease phenotypes form a highly connected network of strong pairwise correlations. Our modeling approach, under appropriate assumptions, allows us to estimate from these correlations the size of putative genetic overlaps. For example, we suggest that autism, bipolar disorder, and schizophrenia share significant genetic overlaps. Our disease network hypothesis can be immediately exploited in the design of genetic mapping approaches that involve joint linkage or association analyses of multiple seemingly disparate phenotypes.     

Gregor Johann Mendel and Modern Evolutionary Biology: Genetics of adaptation

The rediscovery of Mendel’s work showing that the heredity of phenotypes is controlled by discrete genes was followed by the reconciliation of Mendelian genetics with evolution by natural selection in the middle of the last century with the Modern Synthesis. In the past two decades, dramatic advances in genomic methods have facilitated the identification of the loci, genes, and even individual mutations that underlie phenotypic variants that are the putative targets of natural selection. Moreover, these methods have also changed how we can study adaptation by flipping the problem around, allowing us to first examine what loci show evidence of having been under selection, and then connecting these genetic variants to phenotypic variation. As a result, we now have an expanding list of actual genetic changes that underlie potentially adaptive phenotypic variation. Here, we synthesize how considering the effects of these adaptive loci in the context of cellular environments, genomes, organisms, and populations has provided new insights to the genetic architecture of adaptation.     

From the Cover: Model of genetic variation in human social networks

Social networks exhibit strikingly systematic patterns across a wide range of human contexts. Although genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric social network attributes is unknown. Here, we show that 3 of these attributes (in-degree, transitivity, and centrality) are heritable. We then develop a “mirror network” method to test extant network models and show that none account for observed genetic variation in human social networks. We propose an alternative “Attract and Introduce” model with two simple forms of heterogeneity that generates significant heritability and other important network features. We show that the model is well suited to real social networks in humans. These results suggest that natural selection may have played a role in the evolution of social networks. They also suggest that modeling intrinsic variation in network attributes may be important for understanding the way genes affect human behaviors and the way these behaviors spread from person to person.     

Positive selection at the protein network periphery: evaluation in terms of structural constraints and cellular context

Because of recent advances in genotyping and sequencing, human genetic variation and adaptive evolution in the primate lineage have become major research foci. Here, we examine the relationship between genetic signatures of adaptive evolution and network topology. We find a striking tendency of proteins that have been under positive selection (as compared with the chimpanzee) to be located at the periphery of the interaction network. Our results are based on the analysis of two types of genome evolution, both in terms of intra- and interspecies variation. First, we looked at single-nucleotide polymorphisms and their fixed variants, single-nucleotide differences in the human genome relative to the chimpanzee. Second, we examine fixed structural variants, specifically large segmental duplications and their polymorphic precursors known as copy number variants. We propose two complementary mechanisms that lead to the observed trends. First, we can rationalize them in terms of constraints imposed by protein structure: We find that positively selected sites are preferentially located on the exposed surface of proteins. Because central network proteins (hubs) are likely to have a larger fraction of their surface involved in interactions, they tend to be constrained and under negative selection. Conversely, we show that the interaction network roughly maps to cellular organization, with the periphery of the network corresponding to the cellular periphery (i.e., extracellular space or cell membrane). This suggests that the observed positive selection at the network periphery may be due to an increase of adaptive events on the cellular periphery responding to changing environments.     

HSP90-buffered genetic variation is common in Arabidopsis thaliana

HSP90 is a protein chaperone particularly important in the maturation of a diverse set of proteins that regulate key steps in a multitude of biological processes. Alterations in HSP90 function produce altered phenotypes at low penetrance in natural populations. Previous work has shown that at least some of these phenotypes are due to genetic variation that remains phenotypically cryptic until it is revealed by the impairment of HSP90 function. Exposure of such "buffered" genetic polymorphisms can also be accomplished by environmental stress, linking the appearance of new phenotypes to defects in protein homeostasis. Should such polymorphisms be widespread, natural selection may be more effective at producing phenotypic change in suboptimal environments. In evaluating this hypothesis, a key unknown factor is the frequency with which HSP90-buffered polymorphisms occur in natural populations. Here, we present Arabidopsis thaliana populations suitable for genetic mapping that have constitutively reduced HSP90 levels. We employ quantitative genetic techniques to examine the HSP90-dependent polymorphisms affecting a host of plastic plant life-history traits. Our results demonstrate that HSP90-dependent natural variation is present at high frequencies in A. thaliana, with an expectation that at least one HSP90-dependent polymorphism will affect nearly every quantitative trait in progeny of two different wild lines. Hence, HSP90 is likely to occupy a central position in the translation of genotypic variation into phenotypic differences.     

The new mutation theory of phenotypic evolution

Recent studies of developmental biology have shown that the genes controlling phenotypic characters expressed in the early stage of development are highly conserved and that recent evolutionary changes have occurred primarily in the characters expressed in later stages of development. Even the genes controlling the latter characters are generally conserved, but there is a large component of neutral or nearly neutral genetic variation within and between closely related species. Phenotypic evolution occurs primarily by mutation of genes that interact with one another in the developmental process. The enormous amount of phenotypic diversity among different phyla or classes of organisms is a product of accumulation of novel mutations and their conservation that have facilitated adaptation to different environments. Novel mutations may be incorporated into the genome by natural selection (elimination of preexisting genotypes) or by random processes such as genetic and genomic drift. However, once the mutations are incorporated into the genome, they may generate developmental constraints that will affect the future direction of phenotypic evolution. It appears that the driving force of phenotypic evolution is mutation, and natural selection is of secondary importance.     

Decanalization of wing development accompanied the evolution of large wings in high-altitude Drosophila

In higher organisms, the phenotypic impacts of potentially harmful or beneficial mutations are often modulated by complex developmental networks. Stabilizing selection may favor the evolution of developmental canalization—that is, robustness despite perturbation—to insulate development against environmental and genetic variability. In contrast, directional selection acts to alter the developmental process, possibly undermining the molecular mechanisms that buffer a trait’s development, but this scenario has not been shown in nature. Here, we examined the developmental consequences of size increase in highland Ethiopian Drosophila melanogaster. Ethiopian inbred strains exhibited much higher frequencies of wing abnormalities than lowland populations, consistent with an elevated susceptibility to the genetic perturbation of inbreeding. We then used mutagenesis to test whether Ethiopian wing development is, indeed, decanalized. Ethiopian strains were far more susceptible to this genetic disruption of development, yielding 26 times more novel wing abnormalities than lowland strains in F2 males. Wing size and developmental perturbability cosegregated in the offspring of between-population crosses, suggesting that genes conferring size differences had undermined developmental buffering mechanisms. Our findings represent the first observation, to our knowledge, of morphological evolution associated with decanalization in the same tissue, underscoring the sensitivity of development to adaptive change.Canalization describes the property of some biological traits to remain constant in the face of environmental and genetic changes (1–6). This phenomenon has important implications for the relationship between genetic and phenotypic variation. By masking the phenotypic effects of genetic changes, canalization may inhibit phenotypic evolution while allowing hidden genetic variation to accumulate. If canalization is overcome by environmental and/or genetic changes, this reservoir of functional variation may then be exposed. For example, Waddington (7) selected Drosophila for a missing cross-vein trait that initially only appeared in a stressful high-temperature environment but after selection, manifested under normal conditions as well. A molecular case study of canalization was provided by Rutherford and Lindquist (8), who found that Drosophila with a disabled chaperone protein (the heat shock protein Hsp90) showed a suite of developmental abnormalities. These abnormalities varied based on genetic background and environment and could be selected for Hsp90 independence. Other studies have also found that selection in the laboratory can alter developmental stability (9–12), and Hayden et al. (13) found that in vitro directional selection on ribozyme activity led to reduced genetic and environmental robustness.Canalization is difficult to disentangle from selective constraint, which complicates its study in natural populations. A rare potential example comes from the blowfly Lucilia cuprina, in which the evolution of insecticide resistance was accompanied by prolonged development and bristle asymmetry (14). Those disadvantages were subsequently reversed by the evolution of an unlinked modifier locus (15). Here, the initial cost of adaptation may have been because of pleiotropic decanalizing effects of the insecticide resistance mutation itself. Or given the contrast between the adaptive and decanalized phenotypes, a linked deleterious variant might have been fixed along with the resistance allele and later compensated by the modifier gene.Canalization might evolve because of stabilizing selection favoring the same phenotypic optimum in the face of environmental and genetic variability [as shown in the case of environmental robustness (16)], or canalization might arise from inherent properties of the biological system (17). Particularly in the former scenario, it seems possible that directional selection might undermine canalization: if selection for a new phenotypic optimum alters the developmental process, then the molecular mechanisms that had previously buffered the ancestral phenotype might fail to buffer the novel phenotype. Hence, it seems possible that recently evolved traits may show reduced canalization (until new or modified buffering mechanisms can evolve), but no such example has been reported from nature.Here, we describe a natural instance of decanalization associated with a recently evolved morphological structure, focusing on wing size and developmental stability in a high-altitude (>3,000 m) Ethiopian population of Drosophila melanogaster. Although globally distributed today, this human-commensal species probably originated in the lowlands of southern central Africa (18). The species’ arrival in Ethiopia may have roughly coincided with its crossing of the Sahara [∼10,000 y ago (19, 20)]. Highland Ethiopian flies are morphologically divergent from other D. melanogaster populations, featuring striking melanism (21), larger body size, and larger wings (Fig. 1) with distinct shape (22).Open in a separate windowFig. 1.Morphological comparisons of D. melanogaster from the Ethiopian highlands and an ancestral range Zambia population. Ethiopian strains have (A vs. B) larger body size and (C vs. D) wing size. (E) The distribution of wing widths among outbred individuals shows almost no overlap between populations. Detailed size data are given in Dataset S1.Past studies have shown that the Drosophila wing provides a convenient visible readout of development, allowing, for example, the study of variation unmasked by specific mutations (23, 24). This study repurposes mutagenesis as a generalized genetic perturbation to assess whether wing size evolution in Ethiopian D. melanogaster has undermined the stability of wing development. Initially, our observation of frequent wing abnormalities in Ethiopian inbred strains motivated the hypothesis of decanalized wing development. Mutagenesis experiments confirmed that de novo mutations were far more likely to produce wing defects in the Ethiopian strains than in the smaller-winged Zambia population (whereas a control trait showed no such difference), implying less buffered development of Ethiopian wings. A final mutagenesis experiment confirmed that wing size and decanalization were inherited together in the advanced generation offspring of an Ethiopia–Zambia cross, implying that alleles conferring larger Ethiopian wings contributed to destabilized development.     

Environmental stress and mutational load in diploid strains of the yeast Saccharomyces cerevisiae

The negative effect of permanent contamination of populations because of spontaneous mutations does not appear to be very high if judged from the relatively good health of humans or many wild and domesticated species. This is partly explained by the fact that, in diploids, the new mutations are usually located in heterozygous loci and therefore are masked by wild-type alleles. The expression of mutations at the phenotypic level may also strongly depend on environmental factors if, for example, deleterious alleles are more easily compensated under favorable conditions. The present experiment uses diploid strains of yeast in which mutations arise at high rates because a mismatch-repair protein is missing. This mutagenesis resulted in a number of new alleles that were in heterozygous loci. They had no detectable effect on fitness when the environment was benign. A very different outcome was seen when thermal shock was applied, where fitness of the mutation-contaminated clones was lower and more diverse than that of the nonmutagenized clones. This shows that the genetic load conferred by spontaneous mutations can be underestimated or even overlooked in favorable conditions. Therefore, genetic variation can be higher and natural selection more intense when environmental conditions are getting poorer. These conclusions apply, at least, to that component of variation that directly originates from spontaneous mutations (as opposed to the variation resulting from the history of selection).     

Evolutionary optimum for male sexual traits characterized using the multivariate Robertson-Price Identity

Phenotypes tend to remain relatively constant in natural populations, suggesting a limit to trait evolution. Although stationary phenotypes suggest stabilizing selection, directional selection is more commonly reported. However, selection on phenotypes will have no evolutionary consequence if the traits do not genetically covary with fitness, a covariance known as the Robertson-Price Identity. The nature of this genetic covariance determines if phenotypes will evolve directionally or whether they reside at an evolutionary optimum. Here, we show how a set of traits can be shown to be under net stabilizing selection through an application of the multivariate Robertson-Price Identity. We characterize how a suite of male sexual displays genetically covaries with fitness in a population of Drosophila serrata. Despite strong directional sexual selection on these phenotypes directly and significant genetic variance in them, little genetic covariance was detected with overall fitness. Instead, genetic analysis of trait deviations showed substantial stabilizing selection on the genetic variance of these traits with respect to overall fitness, indicating that they reside at an evolutionary optimum. In the presence of widespread pleiotropy, stabilizing selection on focal traits will arise through the net effects of selection on other, often unmeasured, traits and will tend to be stronger on trait combinations than single traits. Such selection may be difficult to detect in phenotypic analyses if the environmental covariance between the traits and fitness obscures the underlying genetic associations. The genetic analysis of trait deviations provides a way of detecting the missing stabilizing selection inferred by recent metaanalyses.     

A general population genetic theory for the evolution of developmental interactions

The development of most phenotypic traits involves complex interactions between many underlying factors, both genetic and environmental. To study the evolution of such processes, a set of mathematical relationships is derived that describe how selection acts to change the distribution of genetic variation given arbitrarily complex developmental interactions and any distribution of genetic and environmental variation. The result is illustrated by using it to derive models for the evolution of dominance and for the evolutionary consequences of asymmetry in the distribution of genetic variation.     

Directional selection is the primary cause of phenotypic diversification

Selection is widely accepted as the principal force shaping phenotypic variation within populations. Its importance in speciation and macroevolution has been questioned, however, because phenotypic differences between species or higher taxa sometimes appear to be nonadaptive. Here, we use the quantitative trait locus (QTL) sign test to evaluate the importance of directional selection in phenotypic divergence. If a trait has a history of directional selection, QTL effects should be mostly in the same direction; otherwise QTLs with antagonistic effects should be common. Analysis of QTL effects for 572 traits from 86 studies revealed significantly fewer antagonistic QTLs than expected under neutrality, a result that validates Darwin's claim that phenotypic diversification is caused mainly by selection. Moreover, interspecific trait differences were more strongly or consistently selected than intraspecific differences, strengthening a growing consensus among students of speciation that directional selection is the primary cause of speciation. Contrary to studies of selection in contemporary populations, life history traits appear to be selected more strongly than morphological traits, but traits related to the timing of development are weakly selected relative to most other traits.     

Heterozygote advantage as a natural consequence of adaptation in diploids

Molecular adaptation is typically assumed to proceed by sequential fixation of beneficial mutations. In diploids, this picture presupposes that for most adaptive mutations, the homozygotes have a higher fitness than the heterozygotes. Here, we show that contrary to this expectation, a substantial proportion of adaptive mutations should display heterozygote advantage. This feature of adaptation in diploids emerges naturally from the primary importance of the fitness of heterozygotes for the invasion of new adaptive mutations. We formalize this result in the framework of Fisher's influential geometric model of adaptation. We find that in diploids, adaptation should often proceed through a succession of short-lived balanced states that maintain substantially higher levels of phenotypic and fitness variation in the population compared with classic adaptive walks. In fast-changing environments, this variation produces a diversity advantage that allows diploids to remain better adapted compared with haploids despite the disadvantage associated with the presence of unfit homozygotes. The short-lived balanced states arising during adaptive walks should be mostly invisible to current scans for long-term balancing selection. Instead, they should leave signatures of incomplete selective sweeps, which do appear to be common in many species. Our results also raise the possibility that balancing selection, as a natural consequence of frequent adaptation, might play a more prominent role among the forces maintaining genetic variation than is commonly recognized.     

Rapid evolution of disease resistance is accompanied by functional changes in gene expression in a wild bird

Wild organisms are under increasing pressure to adapt rapidly to environmental changes. Predicting the impact of these changes on natural populations requires an understanding of the speed with which adaptive phenotypes can arise and spread, as well as of the underlying mechanisms. However, our understanding of these parameters is poor in natural populations. Here we use experimental and molecular approaches to investigate the recent emergence of resistance in eastern populations of North American house finches (Carpodacus mexicanus) to Mycoplasma galliseptum (MG), a severe conjunctivitis-causing bacterium. Two weeks following an experimental infection that took place in 2007, finches from eastern US populations with a 12-y history of exposure to MG harbored 33% lower MG loads in their conjunctivae than finches from western US populations with no prior exposure to MG. Using a cDNA microarray, we show that this phenotypic difference in resistance was associated with differences in splenic gene expression, with finches from the exposed populations up-regulating immune genes postinfection and those from the unexposed populations generally down-regulating them. The expression response of western US birds to experimental infection in 2007 was more similar to that of the eastern US birds studied in 2000, 7 y earlier in the epizootic, than to that of eastern birds in 2007. These results support the hypothesis that resistance has evolved by natural selection in the exposed populations over the 12 y of the epizootic. We hypothesize that host resistance arose and spread from standing genetic variation in the eastern US and highlight that natural selection can lead to rapid phenotypic evolution in populations when acting on such variation.     

Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce.

Controversy still exists over the adaptive nature of variation of enzyme loci. In conifers, random amplified polymorphic DNAs (RAPDs) represent a class of marker loci that is unlikely to fall within or be strongly linked to coding DNA. We have compared the genetic diversity in natural populations of black spruce [Picea mariana (Mill.) B.S.P.] using genotypic data at allozyme loci and RAPD loci as well as phenotypic data from inferred RAPD fingerprints. The genotypic data for both allozymes and RAPDs were obtained from at least six haploid megagametophytes for each of 75 sexually mature individuals distributed in five populations. Heterozygosities and population fixation indices were in complete agreement between allozyme loci and RAPD loci. In black spruce, it is more likely that the similar levels of variation detected at both enzyme and RAPD loci are due to such evolutionary forces as migration and the mating system, rather than to balancing selection and overdominance. Furthermore, we show that biased estimates of expected heterozygosity and among-population differentiation are obtained when using allele frequencies derived from dominant RAPD phenotypes.